From 666652151335353eef2fcd58880bcef5bc2928e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 20 Sep 2024 14:38:14 +0200 Subject: [PATCH] Batch update of modules (#6674) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Conda remove defaults channel - structural changes (#5847) * Update `branch_update_staging` (#6657) * Added nf-test for seroba/run (#6372) * Added nf-test for sequenzautils/gcwiggle (#6373) * Added nf-test for sequenzautils/gcwiggle * Added stub and locked python version as per container * Added nf-test for segemehl/index (#6375) * Added nf-test for raven (#6378) * Added nf-test for scramble/clusteridentifier (#6376) * Added nf-test for pydamage/analyze (#6379) * Added nf-test for spring/compress (#6366) * Added nf-test for survivor/merge (#6364) * Added nf-test for gatk4/splitintervals (#6302) * Added nf-test for gatk4/splitintervals * Added stub test * Added nf-test for picard/scatterintervalsbyns (#6291) * Added nf-test for picard/scatterintervalsbyns * Added stub test * Update pre-commit hook python-jsonschema/check-jsonschema to v0.29.2 (#5938) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for pureclip (#6380) * Added nf-test for pureclip * Updated power assertion * Added nf-test for snippy/run (#6368) * Added nf-test for snippy/run * Explicitly tell snippy how much RAM we have * Only snap for vcf_csi * Actually update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * remove defaults from utils_nextflow_pipeline (again) (#6382) * Swap samtools collatefastq to nf-test (#5754) * Swap to nftest * Update output channels to not snap empty ones * Add too many stubs * Update stub definition * Add nf-test to metaphlan (#6139) * add nf-test to metaphlan * add config file * Remove metaphlan/metaphlan form pytest from config * Remove ypyest files * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * update nf-test * update snapshot for metaphlan subworkflow * update metaphaln/mergemetaphlan * Update metaphlan/metaphlan assertions * Add stub and fix tests * Update subworkflow * Try adding docker.runOptions * Actually commit the second config * Try adding no-same-owner * add config to docker * remove enable docker from config * Update snapshot --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * added trio options (#6164) * added trio options * added trio options * added trio options * added trio options * added trio options * added additional optional trio output * add addtional trio output in meta * remove pytest * removed redundant channles * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal * some changes * corrected meta * removed environment.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Mahesh Binzer-Panchal * New sections for further module info (#5876) new sections for further module info * Cafe (#6209) * First commit * Complete main.nf * meta.yml * First try test * Failed nf tests * working test * working tests * Make Prettier * fix * With snapshot * sn * fix doi * Add new emitted results and snapshot a result that does not have a time stamp or random model likelihood * Not working with cafe snapshot * Working tests * Add new output variables to meta.yml * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add meta id (not working) * revert local files checks * back to s3 * Without channel of * Attempt to input data in test more verbose. Still not working * remove def * Fix version output in stub * With data on test-datasets * Fix test with variable pvalues, which was not reproducible * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add paths to new modules location data * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix input test data paths --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for dshbio/exportsegments (#6398) * Added nf-test for dshbio/filtergff3 (#6399) * Added nf-test for bioawk (#6384) * Added nf-test for snpdists (#6417) * Added nf-test for slimfastq (#6418) * Added nf-test for snpsift/split (#6416) * Updated nf-test for strelka/germline (#6415) Updated nf-test for strelka/germline * Added nf-test for svtyper/svtyper (#6414) * Added nf-test for cdhit/cdhitest (#6388) * Added nf-test for emboss/cons (#6402) * Added nf-test for eido/validate (#6401) * Added nf-test for eido/validate * Fixed assertions * Added nf-test for vg/deconstruct (#6410) * Added nf-test for wgsim (#6409) * Added nf-test for gamma/gamma (#6408) * Added nf-test for ffq (#6407) * Added nf-test for vcflib/vcfbreakmulti (#6411) * Added nf-test for cnvkit/access (#6391) * Added nf-test for cooler/digest (#6395) * Added nf-test for clonalframeml (#6390) * Added nf-test for expansionhunterdenovo/profile (#6405) * Foldmason (#6355) * Add foldmason * Add test * fix prettier * fix prettier * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/foldmason/easymsa/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update main.nf * Update main.nf.test * Update meta.yml * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add stub run tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add tbi index as an output to lofreq callparallel (#6427) Add tbi as an output to lofreq callparallel Co-authored-by: fmartinez * Update lofreq callparallel (#6429) * Add tbi as an output to lofreq callparallel * Update nf-test in lofreq callparallel * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update nf-test in lofreq callparallel * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update nf-test in lofreq callparallel --------- Co-authored-by: fmartinez Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * remove slashy strings from multiqc (#6431) * Added nf-test for cooler/makebins (#6396) * Added nf-test for seacr/callpeak (#6421) * Added nf-test for ectyper (#6400) * Added nf-test for shasum (#6419) * Fastqfilter (#6235) * First commit * Completed nf-test * Cleaned main.nf * Removed line in meta.yml * Modified meta.yml * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added snapshot for lines in log test.log * made meta.yml prettier * Simplified version extraction --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for preseq/ccurve (#6423) * Added nf-test for emmtyper (#6403) * Added nf-test for cnvpytor/importreaddepth (#6394) * Added nf-test for cnvpytor/importreaddepth * Updated tool ver and snapshot * Locked numpy version * Added nf-test for cnvpytor/callcnvs (#6393) * Added nf-test for circexplorer2/annotate (#6389) * Added nf-test for plink/bcf (#6425) * Added nf-test for biobambam/bammerge (#6385) * Added nf-test for fasttree (#6406) * Added nf-test for fasttree * Update modules/nf-core/fasttree/meta.yml * Update modules/nf-core/fasttree/meta.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for bwameth/index (#6387) * Added nf-test for bwameth/index * Updated tool ver and snapshot * Update modules/nf-core/bwameth/index/tests/main.nf.test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for epang/place (#6404) * Added nf-test for epang/place * Fixed assertion * Added stub and updated power assertion * Added nf-test for biscuit/vcf2bed (#6434) * Added nf-test for sickle (#6440) * Added nf-test for peka (#6446) * Added nf-test for gfatools/gfa2fa (#6451) * Added nf-test for panaroo/run (#6450) * Added nf-test for plasmidfinder (#6444) * Added nf-test for gffcompare (#6452) * Added nf-test for elprep/split (#6459) * Update tests and fix compression (#6463) * Update tests and fix compression * fix * Added nf-test for tbprofiler/profile (#6437) * Added nf-test for varlociraptor/estimatealignmentproperties (#6436) * Deleted pytest of filtlong (#6456) Deleted pytest files for filtlong * Added nf-test for cnvkit/genemetrics (#6392) * Added nf-test for dshbio/splitgff3 (#6461) * Added nf-test for gappa/examineassign (#6455) * Added nf-test for gappa/examineheattree (#6453) * Added nf-test for stadeniolib/scramble (#6438) * Added nf-test for plink/vcf (#6443) * Added nf-test for sequenzautils/bam2seqz (#6441) * Added nf-test for sequenzautils/bam2seqz * Locked python version * Added nf-test for pmdtools/filter (#6424) * Added nf-test for pmdtools/filter * Added stub and conda version trap * Locked samtools * Added nf-test for pindel/pindel (#6445) * Added nf-test for pindel/pindel * Fixed linting issues * Added nf-test for vt/normalize (#6435) * Added nf-test for dshbio/filterbed (#6462) * Added nf-test for dshbio/filterbed * Fixed nf-test * Added nf-test for snpeff/download (#6439) * Added nf-test for snpeff/download * Fixed linting issues * Added nf-test for plasmidid (#6433) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for entrezdirect/esummary (#6458) * Added nf-test for entrezdirect/esummary * Updated snapshot * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.3 (#6467) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Remove redundant rowname assignment (#6466) gene_info is derived from transcript_info, which only contains the columns "gene_id", "gene_name", but not "tx". Thus, the rownames assignment was not doing anything. Fortunately, the row names were not needed downstream regardless. * Update actions/setup-python digest to f677139 (#6471) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for scimap/mcmicro (#6442) * Added nf-test for scimap/mcmicro * Fixed typos * Removed module from nf-test/conda * Added nf-test for gfatools/stat (#6493) * Added nf-test for lissero (#6491) * Added nf-test for kleborate (#6492) * Added nf-test for qcat (#6422) * Added nf-test for qcat * Added stub and conda version trap * Added nf-test for maxbin2 (#6488) * Added nf-test for meningotype (#6487) * Added nf-test for methyldackel/mbias (#6485) * Added nf-test for mobsuite/recon (#6482) * Added nf-test for mobsuite/recon * Locked conda versions * Version bump * Added nf-test for purecn/normaldb (#6281) * Added nf-test for purecn/normaldb * Adjust environment * Add optparse * Try newer version from conda forge * Try adding r-utils too * Added wave containers, dynamic versioning and updated snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for msisensor2/scan (#6481) * Added nf-test for mykrobe/predict (#6479) * Added nf-test for mykrobe/predict * Fixed snapshot * Added nf-test for pasty (#6475) * Added nf-test for picard/collectinsertsizemetrics (#6473) * Added nf-test for nextgenmap (#6477) * Added nf-test for platypus (#6472) * Cleaned pytest files of porechop/abi (#6470) Cleaned pytest files for porechop/abi * Added nf-test for pbptyper (#6474) * Added nf-test for mash/dist (#6489) * Added nf-test for mtnucratio (#6480) * Added nf-test for nanolyse (#6478) * Added nf-test for nanolyse * Fixed snapshot * Added nf-test for paftools/sam2paf (#6476) * Added nf-test for snpsift/dbnsfp (#6469) * Added nf-test for eido/convert (#6460) * Added nf-test for eido/convert * Version bump and wave containers * Bump/wisecondorx (#6464) * bump wisecondorx to v1.2.9 * fix tests * Added nf-test for miniprot/index (#6483) * Added nf-test for fastawindows (#6457) * Added nf-test for fastawindows * Added stub and test * Added nf-test for gatk4/splitcram (#6303) * Added nf-test for hicap (#6495) * Added nf-test for vg/construct (#6468) * Added nf-test for paragraph/vcf2paragraph (#6448) * Added nf-test for paragraph/vcf2paragraph * Added version lock and trap --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for ngmaster (#6270) * Added nf-test for ngmaster * Added stub and version lock for python * Added nf-test for pbbam/pbmerge (#6447) * Added nf-test for pbbam/pbmerge * Updated modules, deprecation message and conda versions trap --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Added nf-test for biscuit/index (#6386) * Added nf-test for biscuit/index * Added stub and updated snapshot * Added stub and nf-test for qc * Added stub and nf-test for pileup * Added stub and nf-test for epiread --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for macrel/contigs (#6490) * Added nf-test for macrel/contigs * Version bump and snapshot update * Added nf-test for metaphlan/makedb (#6486) * Added nf-test for metaphlan/makedb * Updated power assertion * Version bump and snapshot update --------- Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> * Added nf-test for lofreq/call (#6501) * Added nf-test for miranda (#6498) * Added nf-test for snapaligner/index (#6496) * Added nf-test for transdecoder/longorf (#6413) * Migrate renovate config (#6117) * chore(config): migrate config .github/renovate.json5 * Update .github/renovate.json5 Co-authored-by: Matthias Hörtenhuber --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber * Added nf-test for mcroni (#6499) Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Bump sniffles and add missing inputs/outputs (#6503) * Bump sniffles and add missing inputs/outputs * Update modules/nf-core/sniffles/main.nf Co-authored-by: Maxime U Garcia * Update modules/nf-core/sniffles/meta.yml Co-authored-by: Maxime U Garcia --------- Co-authored-by: Maxime U Garcia * Added nf-test for vg/index (#6534) * Added nf-test for gvcftools/extractvariants (#6524) * No ".list" file is generated by this module (#6348) Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * remove "--outdir ." from fastq_screen bash command (#6247) * remove "--outdir ." from fastq_screen bash command fixes issue #6246 * adding optional fastqscreen output: fastq of nohits * fixing test.snap in fastqscreen module * fix linting fastqscreen/fastqscreen * Try pinning gdgraph, adding fastq test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia * Added nf-test for dshbio/splitbed (#6516) * updated ensemblvep modules and added nf-tests (#6538) * updating ensemblvep modules * fix tests --------- Co-authored-by: Lucpen * Add `mirTrace` module (#6507) * generate mirtrace module * fix linting * update tests and fix linting * update tests * update tests * Added nf-test for staphopiasccmec (#6535) * Added nf-test for ivar/trim (#6531) * Added nf-test for ivar/trim * Simplified version capture and added a trap * Version bump * Added nf-test for igv/js (#6529) * Added nf-test for icountmini/segment (#6528) * Added nf-test for hpsuissero (#6527) * Added nf-test for haplocheck (#6525) * Added nf-test for graphmap2/index (#6523) * Added nf-test for gappa/examinegraft (#6519) * Added nf-test for genmap/index (#6520) * Added nf-test for cnvkit/target (#6512) * Added nf-test for biobambam/bammarkduplicates2 (#6508) * Added nf-test for cooler/dump (#6514) * Added nf-test for cooler/dump * version bump * Added nf-test for goat/taxonsearch (#6522) * Added nf-test for goat/taxonsearch * Added suggested changes * Update actions/upload-artifact digest to 5076954 (#6540) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for getorganelle/config (#6521) * Added nf-test for calder2 (#6509) * Added nf-test for calder2 * Version bump * Added nf-test for mashtree (#6500) * Added nf-test for mashtree * Updated power assertions * Added nf-test for cellrangerarc/mkgtf (#6510) * Added nf-test for cellrangerarc/mkgtf * Excluded from conda profile * Added nf-test for cmseq/polymut (#6511) * Added nf-test for ismapper (#6530) * fix bug (#6541) * mcstaging/imc2mc (#6506) * create module * update meta.yml * add main.nf * add nextflow.config file * adding tests * finish tests * add conda exception in nf-test section of test.yml * change main.nf.test --------- Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * mcstaging/phenoimager2mc (#6143) * create initial module * added nextflow.config file * add test.snap * adapt main.nf to module * adapt meta.yml file * deleted env file * adapted nf.test * add test data specifications to test_data.config * added single files to test data * adapt input to file list, nor working yet * adapted to linting req, 3 warnings remain * successful tests, linting and prettier * ran test again for snapshot file * addressed minor comments in meta.yml * remove comment * remove conda test * adapt snapshot versions output and delete old snapshots * delete comment * add stub test * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> --------- Co-authored-by: Miguel A. Ibarra-Arellano Co-authored-by: Krešimir Beštak Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Add index output to bcftools reheader (#6542) * wgsim: add seed option, add stub, update test, match readsimulator pipeline (#6544) * add seed option, add stub, update test, match readsimulator * Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * change version assessment and hand seed via args * add versions md5 --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Added nf-test for estsfs (#6518) * Added nf-test for vrhyme/vrhyme (#6533) * Added nf-test for vrhyme/vrhyme * Locked dependency versions * Updated power assertions * Added nf-test for crumble (#6515) * Added nf-test for crumble * Now BAM is the default output format * Added nf-test for nanocomp (#6497) * Added nf-test for nanocomp * Updated power assertions * Fix gene table row naming in tximeta/tximport (#6551) Update tximport.r * Added nf-test for methyldackel/extract (#6549) * Added nf-test for methyldackel/extract * Version bump * Update motus/profile and add nf-test (#6212) * add nf-test to motus/profile * add stub runs to all tests * Update main.nf.test * Update main.nf.test.snap * Remove donwload db in stub run in main.nf.test * Try moving setups to just test (not stubs, as these don't need database download executed again) * update snapshot to fix conda nf-test instability --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates * Add tcoffee consensus module (#6539) * Add tcoffee consensus module * Add tcoffee consensus module * update snap * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf.test * Update main.nf * Update main.nf * test * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf.test * Update modules/nf-core/tcoffee/consensus/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update tests * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * fix typos * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Add bcftools/plugintag2tag (#6547) Add bcftools/pluginstag2tag * Added nf-test for bwameth/align (#6550) * Added nf-test for bwameth/align * Update modules/nf-core/bwameth/align/tests/main.nf.test * update single-end test assert * print version yml * ignore syntax warning during version capture * Simplified the version extraction --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Sateesh * Added nf-test for msisensorpro/scan (#6561) * nf-test + update to genotypegvcfs (#6553) * nf-test + update to genotypegvcfs * fix linting * review comments * fix old typo * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Added nf-test for pirate (#6560) * Added nf-test for minia (#6564) * Added nf-test for purecn/intervalfile (#6558) * Added nf-test for haplogrep2/classify (#6572) * Added nf-test for hmmer/hmmfetch (#6574) * Added nf-test for mapdamage2 (#6578) * Added nf-test for biobambam/bamsormadup (#6579) * Fix wrong array definition in env schema (#6585) * new tool: jvarkit/vcfpolyx (#6580) * vcfpolyx, 1st commit * vcfpolyx * vcfployx, tests ok * fix env and meta ? * remove tab * remove ws * [automated] Fix linting with Prettier * fix conda ? * remove defaults * fix meta info * I hate myslef, fix warnings * add type to meta * fix snap md5 * fix meta3/meta4 https://github.com/nf-core/modules/pull/6580#discussion_r1745494016 * fix https://github.com/nf-core/modules/pull/6580#discussion_r1745463698 * Update modules/nf-core/jvarkit/vcfpolyx/main.nf Co-authored-by: Maxime U Garcia --------- Co-authored-by: nf-core-bot Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Maxime U Garcia * Sort bcftools merge inputs, add index output and nf-test conversion (#6586) * Sort inputs and nf-test conversion * update snapshot * update mirtrace (#6593) * Orthofinder (#6288) * working with orthofinder continue feature * Working resume test * With existing data from datasets and chose stable expected outputs. * updated snap shot (sorted) * fix test to have untar-ed workdir dir input * Fix folder direction * Add new output inputs to yml * fix tag * working conda on gitpod * force diamond install to 2.1.9 * Removed defaults --------- Co-authored-by: Usman Rashid * Added nf-test for homer/annotatepeaks (#6573) * Added nf-test for homer/annotatepeaks * Removed defaults * Added nf-test for emboss/revseq (#6581) * Added nf-test for emboss/revseq * Removed defaults * Added nf-test for hapibd (#6575) * Added nf-test for hapibd * Removed defaults * Added nf-test for hypo (#6571) * Added nf-test for hypo * Removed defaults * Added nf-test for hmmer/hmmbuild (#6576) * Added nf-test for hmmer/hmmbuild * Removed defaults * Added nf-test for legsta (#6566) * Added nf-test for legsta * Removed defaults * Added nf-test for cnvkit/call (#6582) * Added nf-test for cnvkit/call * Removed defaults * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.4 (#6592) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for gubbins (#6598) * Added nf-test for gubbins * Version bump * Updated test names * Added nf-test for goleft/indexsplit (#6595) * Added nf-test for graphtyper/vcfconcatenate (#6596) * Added nf-test for geoquery/getgeo (#6594) * Added nf-test for geoquery/getgeo * Version bump and stub * Added versions trap * Locked r-base version * Updated power assertions * Fix bcftools merge for one sample (#6591) * Added nf-test for ivar/consensus (#6568) * Added nf-test for ivar/consensus * Verion bump * Added nf-test for circexplorer2/parse (#6577) * Added nf-test for circexplorer2/parse * Updated power assertion * Added nf-test for mmseqs/databases (#6563) * Added nf-test for mmseqs/databases * Updated power assertion * Removed defaults * Now sorting list * Bgzip and tabix paraphase (#6543) * Bgzip and tabix paraphase * Fixed snapshot size and added threads * remove defaults channel * fix tests * Added nf-test for ivar/variants (#6567) * Added nf-test for ivar/variants * Simplified version extraction * Version bump --------- Co-authored-by: Joon Klaps * Added nf-test for gfaffix (#6597) * Added nf-test for gfaffix * Version bump * Fixed linting * Fixed versions * version fix * Added nf-test for idr (#6570) * Added nf-test for idr * removed defaults * Added nf-test for gunc/downloaddb (#6599) * Added nf-test for metabat2/jgisummarizebamcontigdepths (#6565) * Added nf-test for metabat2/jgisummarizebamcontigdepths * Removed defaults * Added nf-test for krona/ktupdatetaxonomy (#6569) * Added nf-test for krona/ktupdatetaxonomy * Removed defaults * Updated power assertion * Mega conda environment update: Remove `name` and `defaults` (#6600) * Remove defaults channel from all modules * Remove 'name' from conda environment files * Update conda environment schema * Remove defaults from env template and GHA CI * Update Prettier in GHA test.yml workflow to match pre-commit version * Remove whitespace from environment.yml files * hmmsearch, rank and output fasta (#6601) * New subworkflow fasta_hmmsearch_rank_fastas * Add euk and mito SSU rRNA to tests * More tests * Fix trailing whitespace * Pre commit all files (#6604) * GitHub Actions: Always run pre-commit with all files. * First attempt at pre-commit on all files, automatic fixes * Ruff lint: DecryptionTimeout -> DecryptionTimeoutError * Ruff: disable block in template that uses Nextflow variables * Module meta.yml licenses - arrays in strings should not be in strings * License arrays: formatting * Add keywords to module meta files that were too short * Misc module meta.yml fixes * Wrap string licenses as arrays * Type: string instead of value * Fix more meta types * More types, keywords * Apply suggestions from code review Co-authored-by: Mahesh Binzer-Panchal * Boolean flag types --------- Co-authored-by: Mahesh Binzer-Panchal * Added nf-test for elprep/filter (#6517) * Added nf-test for elprep/filter * Updated power assertion * Now emitting logs --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for blat (#6603) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for quast (#6554) * Added nf-test for quast * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Tests for each optional input and removed pytest * Removed "ref, nogff" test --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * bcftools csq (#6605) * bcftools csq * fix lint / format * env.yml * move fun at bottom * Update modules/nf-core/bcftools/csq/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Add module and subworkflow mirtop (#6587) * add mirtop gff module * add mirtop/counts module * add mirtop/export module * add mirtop/stats module * update yml * add bam_stats_mirna_mirtop subworkflow * add required dependencies * update test * update subworkflow test * update yml and output files * fix tag linting issue? * fix linting * run prettier * try to solve conda issue * add a compatible pandas * fix linting * update failing ci mirtop/gff test * Added nf-test for angsd/contamination (#6602) * Added nf-test for angsd/contamination * Swap container version * Update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Phil Ewels * Add support for pip dependencies and force version pinning in conda (#6588) * Add support for pip dependencies and force version pinning in conda * [automated] Fix linting with Prettier --------- Co-authored-by: nf-core-bot * Add `seqcluster` module (#6614) * add seqcluster module * run prettier * Update modules/nf-core/seqcluster/collapse/environment.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/meta.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Add PREFIX to SPADES warnings log (#6615) * Update main.nf * Update main.nf.test.snap * Update actions/setup-java digest to 2dfa201 (#6617) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update GTDBTK/CLASSIFYWF: Fix bash failing if nothing to move in output directory (#6618) * Fix bash failing if nothing to move in output directory (which is a valid behaviour) * HarshilAlignmentTM * Fix fq/generate (#6610) Update snapshot, add stub * Fix `seqcluster` (#6616) * change test data with smrnaseq data and fix fastq capturing * point to nf-core repo * add pairhmm threads to haplotypecaller (#6620) * Nextclade vers bump (#6356) * Update environment.yml * Update main.nf Updated containers to 3.8.2 * Update meta.yml * Update main.nf * Create nf-test.config * Create main.nf.test nf-test module * Create main.nf.test.snap * Create nextflow.config * Update main.nf fixing biocontainer issue * Update meta.yml * nextclade version bump from 2.12 to 3.8.2 * Update meta.yml * Update test.yml regenerated test.yml * Update modules/nf-core/nextclade/datasetget/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nextclade/run/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Delete tests/modules/nf-core/nextclade/run/test.yml deleted * Delete modules/nf-core/nextclade/run/tests/nextflow.config Deleting * Delete modules/nf-core/nextclade/run/nf-test.config * Delete modules/nf-core/nextclade/datasetget/tests/nextflow.config * Delete modules/nf-core/nextclade/datasetget/nf-test.config * Update main.nf.test * Update main.nf.test making tag adhere to guidelines * Update main.nf.test add params block [this mainly because I couldn't run the test locally without it) * Update main.nf.test.snap * Update main.nf.test * Update main.nf.test add stub * Update main.nf.test * Update tests/config/pytest_modules.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update pytest_modules.yml * Delete tests/modules/nf-core/nextclade/datasetget/main.nf * Delete tests/modules/nf-core/nextclade/datasetget/test.yml * Delete tests/modules/nf-core/nextclade/run/main.nf * Update main.nf.test add stub to nextclade/datasetget test * Delete tests/modules/nf-core/nextclade/datasetget/nextflow.config * Update snapshot * Update meta.yml * Update main.nf.test updated main.nf.test * Update main.nf.test.snap * Add stubs and swap to only snapshoting part of the json * Update modules/nf-core/nextclade/datasetget/main.nf --------- Co-authored-by: shahirnm Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add optional config mode in `mirtrace/qc` (#6623) * add optional config file * update mirtrace/qc * new module gatk/variants2table (#6619) * gatk/variants2table * Update modules/nf-core/gatk4/variantstotable/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix for https://github.com/nf-core/modules/pull/6619 * add optional file arguments This is a suggestion to add additional optional file arguments per the modules guidelines: https://nf-co.re/docs/guidelines/components/modules#required-and-optional-input-files These suggestions are untested. I did not add the [gatk_config_file](https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable#--gatk-config-file) argument. My current opinion is that the type of settings this would control are best set elsewhere. * update add args, update tests * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix md5 --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Chase Mateusiak * Split deepvariant 3 (#6172) * Move DeepVariant into a subcommand module rundeepvariant, preparing for split modules The test snapshot is updated because the process name in the version file changed. * Add a split DeepVariant workflow with individual processes for each step * Remove hash unique ID and fix input structure issue * Fixes for call_variants outputing sharded file * Fix test * Remove --channels insert_size, which is only applicable for short read data The channels should be specified in the pipeline config * Replace the model type value input with ext.args config * Fix tests: should run twice for two samples in input channel * Fix linting issues and input channel description * Fix formatting of md files Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Corrections / imrpovements from @fellen31 review * Check tfrecord file names * Updating conda skipping options, because the paths have changed * Add deprecation warning for top-level process and test for the deprecated process * also skip conda for the new deprecated module --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia * 4451 add vcf2maf nf test (#4463) * add nf-test case for vcf2maf without VEP * add VEP test case for vcf2maf nf-test * update linting for vcf2maf * fix prettier for vcf2maf * remove pytest files for vcf2maf * remove vcf2maf from pytest modules yml * add modules/nf-core/vcf2maf/tests/tags.yml * add line count to vcf2maf test * add line number and versions contents yaml to vcf2maf test * remove alternate container from vcf2maf testing and use the same container for testing with or without VEP * update modules/nf-core/vcf2maf/tests/main.nf.test * update modules/nf-core/vcf2maf/tests/main.nf.test * Update and fix tests * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add conda declaration to nf-test * Remove output in snapshot * Add versions to snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update mirtop modules and subworkflow (#6635) * add arity to mirtop/gff * add prefix to mirtop output * update tests and snapshots * update yml * Add bcftools/pluginimputeinfo (#6624) * Add bcftools/pluginimputeinfo * Remove TODO * Change label * Update meta.yml --------- Co-authored-by: James A. Fellows Yates * Get HISAT2 version from CLI (#6634) fix: Get version from cli * Fix tximport summarizedexperiment (#6638) * SummarizedExperiment: don't sanitise column names * tximport: explicitly disable name sanitisation * MEGAHIT: Add support for multi-libraries, export log (#6632) * Add support for coassembly, export log * Fix formatting * teensy bit more * New module jvarkit/wgscoverageplotter (#6633) * wgscoverageplotter * Apply suggestions from code review Co-authored-by: Maxime U Garcia * fix meta * change snap * fix tags * fix env.yml * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Maxime U Garcia Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add openmsthirdparty/cometadapter (#6627) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * Update output to use type dir for compatibility with tes. (#6645) Update output to use type dir for commpatibility with tes. * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.5 (#6642) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * minor changes to fastq preprocessing (#6643) * minor changes to fastq preprocessing * Update main.nf * Update bcftools/pluginimputeinfo meta.yml (#6646) Update meta.yml * Fix GTDBTK version calling in stub test (#6649) Use the proper version calling now implemented * flye: fix nf-test, update module (#6613) * fix nf-test, update module * Update nextflow.config * Update nextflow.config * update test * small hifi dataset * remove raw tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add module openms/idmassaccuracy (#6647) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * add idmassaccuracy module * shorten version parsing --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Stop nf-test complaining about missing dependency (#6652) * Finish filepaths * Fix tags * Added nf-test for untarfiles (#6412) * Added nf-test for untarfiles * Matched conda versions with docker/singularity using wave containers * Changed test name * Added deprecation message * Remove custom params in GTDBTK/CLASSIFYWF (#6651) * Use the proper version calling now implemented * Remove custom params * Fix test * Add UPP (#6546) * Add UPP * fix lint * Update UPP * fix prettier * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * fixes * update * update tests * update * update * Update modules/nf-core/upp/align/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Usman Rashid Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: James A. Fellows Yates Co-authored-by: YSims Co-authored-by: Mahesh Binzer-Panchal Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com> Co-authored-by: Luisa Santus Co-authored-by: Francisco Martínez Co-authored-by: fmartinez Co-authored-by: FernandoDuarteF <123090819+FernandoDuarteF@users.noreply.github.com> Co-authored-by: Pieter Moris <13552343+pmoris@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Ömer An Co-authored-by: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Lucía Peña-Pérez Co-authored-by: Lucpen Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: MargotCh <55975768+MargotCh@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Chiara Schiller <94467188+chiarasch@users.noreply.github.com> Co-authored-by: Miguel A. Ibarra-Arellano Co-authored-by: Krešimir Beštak Co-authored-by: Jonathan Manning Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Eric Wei Co-authored-by: Sateesh Co-authored-by: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Co-authored-by: nf-core-bot Co-authored-by: Joon Klaps Co-authored-by: Daniel Lundin Co-authored-by: Nur M Shahir Co-authored-by: shahirnm Co-authored-by: Chase Mateusiak Co-authored-by: Marius Bjørnstad Co-authored-by: Stephen Kelly Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Venkat Malladi Co-authored-by: Júlia Mir Pedrol * update JSON schema for modules meta.yml (#5837) * update JSON schema for modules meta.yml * add identifier and ontologies to the modules meta.yml JSON schema * remove qualifier --------- Co-authored-by: Phil Ewels * Bulk update meta yml modules (#6015) * Update Abricate to include (missing) additional optional input channel and add stub (#5849) * Add missing optional input channel to abricate * Update abricate module to include missing optional input path * Update modules/nf-core/abricate/run/tests/main.nf.test Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> * Fix linting * Update modules/nf-core/abricate/run/main.nf * Get downstream module test --------- Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> * Fix custom/catadditionalfasta (#5851) * Update environment.yml * Update main.nf * update to samtools 1.20 (#5852) * update to samtools 1.20 * keep samtools 1.19.2 for now * update snapshot * [automated] Fix linting with Prettier * keep 1.20 afterall * update snapshot --------- Co-authored-by: nf-core-bot * Update input params for bwameme (#5853) * update recipe * update rthreads * update tests * Update meta.yml * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 (#5857) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * `--output-unselected` option in `samtools view` (#2674) * add unoutput option * trying to fix emit * CI fixed, tests still incorrect * Fixed the checksums * Fixed the syntax * Call this "unselected" rather than "unoutput" * Alignment rocks * bugfix: the variable needs to be visible by the output declaration * bugfix: this was not the regular file name * Updated the test case * fixup! Alignment rocks * Updated the meta.yml --------- Co-authored-by: Matthieu Muffato * stubs and test for rnaseq modules - part I (#5854) * stubs and test for bbmap_bbsplit * add test for index * add stubs for custom/catadditionalfasta * add stubs for fq/subsample * add stubs for hisat2/extractsplicesites * update fastq_align_hisat2 snapshot * add stubs for hisat2/build * add stubs for hisat2/align * more stubs bbmap/bbsplit * add stubs for preseq/lcextrap * more stubs for fq/subsample * proper stubs for hisat2/align * remove old snaps * Remove CUTUPFASTA from pytests * Revert "Remove CUTUPFASTA from pytests" This reverts commit 0fa8c1bd400ddc4c80c94cbb59f131d8a43f57b3. * Bump concoct/cutupfasta version, add stub, add nf-test (#5864) * Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting * Adding meta to multivcfanalyzer, updating test to nf-test (#5773) * Adding meta to multivcfanalyzer, updating test to nf-test * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * fix meta.yml * Add sort to vcfs * Add tab to tags * add checks for files due to failing md5 sums across docker,conda,singularity --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Concoct/concoctcoveragetable modules updates (#5868) * Bump concoct/cutupfasta version, add stub, add nf-test * Bump conda build, add stub and nf-test for CONCOT/concoctcoveragetable * Remove pytest entry --------- Co-authored-by: Aida Andrades Valtueña * Added stub logic and test to fastq_fastqc_umitools_fastp (#5858) * Added stub logic and test to fastq_fastqc_umitools_fastp * Now emitting trimmed reads * Adding input value-channel for controlling spring-decompress cmd and output (#5850) * Enable single fastq.gz-output from spring/decompress by setting meta.single_end or meta.one_strand * Controlling output with value-channel write_one_fastq_gz * Update modules/nf-core/spring/decompress/meta.yml Co-authored-by: Maxime U Garcia * nf-test for spring/decompress * Trying to please linter * Trying to please linter --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia * Update stranger (#5717) * everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * mapAD: fix `versions.yml` emission (#5874) mapAD: fix `version.yml` emission * add stub and stub test to chromap, change test names (#5872) * add stub and stub test to chromap, change test names * add stub and stub test to chromap, change test names * change setup * move setup out of test * move * produce stub files (#5875) * chore(deps): update pre-commit hook python-jsonschema/check-jsonschema to v0.28.6 (#5878) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * update peddy tests (#5880) update peddy * Update main.nf (#5870) * Update main.nf VEP html report is missing when publishing results because by default vep html file is `_summary.html` instead of `.summary.html`. This changes just adjust the module to the vep defaults to avoid the issue. * Updated html pattern in VEP to be more generic * bump MultiQC version (#5884) bump MQC * Bump shinyngs modules (#5881) * Bump shinyngs modules * Bump versions for snapshot * Update CONCOCT module(s): conda build bump, stub, and nf-test (#5869) * Version update, stub, nf-test for concoct/concoct * Bump version, add nf-test, stub to concoct/mergecutupclustering * nf-test, stub, and version conda build version bump for concoct/extrafastabins * Remove a superfluous config and specify a used one * Update modules/nf-core/concoct/extractfastabins/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Remove superfluous config file * Clean up code * Repair all stub tests that were empty --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * `fasta_binning_concoct` subworkflow: do not fail on join (#5824) * fix: do not fail on mismatch for samples not binned with concoct * Migrate to pytest * Improved Harshil alignment --------- Co-authored-by: James A. Fellows Yates * new module: datavzrd (#5883) * Generated structure for new module * Implemented module * Added semi-functional tests * Cleaned tests - test don't work yet * fix main, start nf-test * add new test data * fix linting * try to assert folders * fix tests * change output to prefix * change to prefix * update to prefix --------- Co-authored-by: vickylaram * samtools/reheader: Fix bug causing output name to be incorrectly evaluated (#5887) Fix bug causing output name to be incorrectly evaluated * nf-test for snpsites (#5284) * nf-test for snpsites * remove old pytest * Delete modules/nf-core/snpsites/tests/nextflow.config * Update modules/nf-core/snpsites/tests/main.nf.test Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * Update assert Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * renamed test Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * reverted the input * updated input...again Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * fixed typo Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * Regenerate snapshot and fix linting --------- Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added prefix to gunzip and while keeping the default name as `archive.toString() - '.gz'` (#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda * add dedicated output channel for trimmomatic stderr log (needed for multiqc) (#5501) * created new output channel capturing stderr of trimmomatic * updated output channel for trimmomatic * Add stub test and update snapshots * Add stub and update tests * Fix linting and add tee --------- Co-authored-by: John Palmer Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates * `ariba/getref` port to nf-test, add meta to tuple and stub (#5877) * port to nf-test, add meta to tuple and stub * modify meta and fix tags * change from each to tuple * Pass annotation files to last-dotplot (#5885) * Pass annotation files to last-dotplot The annotation of the target (plotted horizontally) genome is passed as a new channel. The annotation of the query (plotted vertically) genome is passed as a new component of the first channel. This is because this module typically loops on a list of alignments of various query genomes (from samplesheet) to a single target genome. The annotation files are called `annot_a` and `annot_b` because they are passed to the `-a` and `-b` arguments of `last-dotplot`. * Put arguments on separate lines. * Add meta map and reorder channels. * Test with dummy annotation files. Thanks @SPPearce for the hint. * Add meta to bowtie build (#3848) * Add meta to bowtie build * Swap fastq ngscheckmate tests * Swap to nf-test * Remove spurious changes to bowtie2 * Actually revert bowtie2 * Add the rest of bowtie2 * Again * Revert bowtie2 changes * Swap to meta.id as prefix * Swap bowtie align to nftest * Update tests * Use nft-bam * Update modules/nf-core/bowtie/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal * Swap to testdata path * Update modules/nf-core/ngscheckmate/patterngenerator/main.nf * Swap index finding to $ * Fix vafncm test * Update meta * Remove bam header md5sum * Update fastq test * Update paired bam test * Delete modules/nf-core/bowtie/align/tests/nextflow.config --------- Co-authored-by: Mahesh Binzer-Panchal * nf-test for pilon (#5293) * nf-test for pilon * linting for license * Add stub and extra test * Swap to testdata_base_path * Add missing END_VERSIONS and alignment * Add optional outputs to stub --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Bump phantompeakqualtools 1.2.2 (#5889) * Add stub section * Update yml * Add nf-test * Get rid of pytest * Make lint happy * Update tests * Update tests to make lint happy * update tests * Make lint happy * Using the same version as CI of nf-test locally might be a good idea * Use wave images * Make lint happy * Simplify tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added variance filtering to custom/matrixfilter (#5358) * Added variant filtering to matrix filter * Corrected indentation * Simplified function in single conditional block * fixed line indentation * Fixed whitespace * Fixed logic * line wrapping change * added whitespace around comments * [automated] Fix linting with Prettier * remove trailing whitespace * Update matrixfilter.R * Remove whitespace --------- Co-authored-by: Jonathan Manning Co-authored-by: nf-core-bot Co-authored-by: Jonathan Manning Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update md5sum module to be able to take multiple files (#3610) * Fix version string spurious text in singularity tests * Add config for subworkflow * Update md5sum module to work with multiple files * linting * Fix stub * Add option to generate single file * Update modules/nf-core/md5sum/main.nf Co-authored-by: Matthieu Muffato * Simplify versions processing --------- Co-authored-by: Matthieu Muffato * Add share to find path (#5899) * build: Bump deepvariant to 1.6.1 (#5801) * build: Bump deepvariant to 1.6.1 * interim dir not allowed to be a dot in 1.6 * Update modules/nf-core/deepvariant/main.nf Co-authored-by: Maxime U Garcia * hack: Hard code version https://github.com/google/deepvariant/issues/830 --------- Co-authored-by: Felix Lenner Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia * bump somalier/extract and somalier/relate version (#5894) * bump version * nf-test migratino * revert ancestry * fix linting * Update snap * fix unicode space --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added evigene/tr2aacds (#5898) * Added evigene/tr2aacds * Sorted file list and added activation script * Fixed issues raised by feedback * correct president stub (#5904) * correct president stub * Large update to module * Update prefix and meta --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix EClint errors (#5907) Fix EClint * New module: nanoq (#5896) * Add the new module nanoq * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * define the output_format * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * update the stub run with gzip * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Foldseek: createdb and easysearch modules version bump + stub nf-tests added (#5906) * foldseek/createdb version bump, added stub nf-test * foldseek/easysearch version bump, stub nf-test added * test.snap for createdb added * sourmash/compare stub, nf-test, snapshot (#4665) * sourmash/compare stub, nf-test, snapshot * Add sort * Add a sort * Update snap * Try sort inside the module * Add meta to output and change formatting on test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * adding chewbbaca/createschema module (#4512) * adding chewbbaca/createschema module * updated for handling a mix of uncompressed and compressed files * update the formatting * update the formatting * updated module to emit meta * updated test.yml * update pytest * clean the meta.yml * clean the meta.yml * clean the meta.yml * replaced conda package with environment.yml file * py-test to nf-test migration * add stub and update tests, snapshot * updated stub * update stub test * update stub test * bump the version * update * updating container version * updated test snapshot * updated nf-test snapshot * added libmamba to environment file * Fix tests and linting * Update modules/nf-core/chewbbaca/createschema/main.nf Co-authored-by: Jose Espinosa-Carrasco * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco --------- Co-authored-by: Gisela Gabernet Co-authored-by: Sateesh Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco * stubs and test for rnaseq modules - part II (#5861) * add stubs for rsem * add stubs for rseqc * add stubs for subread/featurecounts * add stubs for trimgalore * add stubs for ucsc/bedclip * add stubs and more tests for umitools/extract * update snap * update snapshot for umitools/extract * fix umitools/extract tests * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * affy/justrma add stub, nf-test and snapshot (#4651) * affy/justrma add stub, nf-test and snapshot * Update snapshot and environment * Update snap * Update modules/nf-core/affy/justrma/main.nf Co-authored-by: James A. Fellows Yates * Swap test data file paths, fix config, update snaps and stub --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates * Bump fgbio versions and swap to nftest (#5624) * Convert callduplex and callmolecular to nftest and update version * Convert zipperbams * Convert groupreadsbyumi * Convert sortbam and add stubs * Convert filterconsensusreads * Update snapshot * Update modules/nf-core/fgbio/callmolecularconsensusreads/main.nf * Add collision checks, swap test data paths * Fix conda version and linting * Apply suggestions from code review Co-authored-by: Nils Homer * Update modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml Co-authored-by: Nils Homer * Update duplex snap --------- Co-authored-by: Nils Homer Co-authored-by: Maxime U Garcia * Added pbtk/pbindex (#5901) * Added pbtk/pbindex * Removed prefix * Added agat/spfilterfeaturefromkilllist (#5771) * Added agat/spfilterfeaturefromkilllist * Added AGAT config * Included test with agat config * bump stranger to 0.9.1 (#5910) bump stranger * Update nft-bam to v0.3.0 (#5912) * Add stubs for rnaseq subworkflows - part I (#5911) * fix stub and add tests + single snapshot * add stub * fix stub * snapshot versions + better snap for stub * add versions to snapshot + add tests for stub * Add stub tests + single snapshot * Add stub tests + single snapshot * maxime sorted * Add stub tests + single snapshot * Add stub tests * Add stub tests + single snapshot * code polish + update snap * update snapshot using nft-bam * Add stubs for rnaseq subworkflows - part II (#5913) * Add stub tests + single snapshot * Add stub tests + single snapshot * fix stub and update tests for kallisto modules * Add stub tests + single snapshot * Add stub tests + single snapshot * bcftools isec input can be bcf or bcf.gz as well as vcf.gz (#5685) * bcftools isec input can be bcf or bcf.gz as well as vcf.gz * Add stub and stub test * Update tests * Update meta.yml * Add stub to name of stub test * Update meta * Update tests Changes: - exclude .tbi files from snapshot due to failing conda tests - update main.nf.test.snap - specificy path type of the output * Update tests again Changes: - include versions - sort file name list for consistent order - update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Theresa Störiko Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com> * Add stubs for rnaseq subworkflows - part III (#5921) * do not snapshot input * do not snapshot input * Add stubs for rnaseq subworkflows - part IV (#5922) do not snapshot input with stub * mulled biocontainer for vardict-java and htslib (#5920) * vardict-java bgzip mulled container * update bioconda env * code polishing Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/vardictjava/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * args3 for bgzip * args3 * Update snap * removed whitespace --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add same file clash check to bioawk (#5926) * Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 (#5893) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/upload-artifact digest to 0b2256b (#5927) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * dysgu==1.6.4_version update (#5928) * all_files_update * Update environment.yml * update_meta.yml * input==input_bam * update_snapshot * meta.yml,tags.yml update * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * update_author --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * ADD argNorm module (#5905) * ADD argnorm module * ENH correct pattern for 'hamronized' input * ENH specify hamronization command in script * ENH don't pass 'hamronized' as val * Fixed trailing whitespace * "single_end" is not relevant in this module * alignment * "db_args" to avoid any confusion with the input channel * Added a test to check $tool is provided * Implemented the stub mode * Added a test for the missing database * Reordered the arguments to match the script --------- Co-authored-by: Matthieu Muffato * Sentieon license server - testing (#5856) * test it out * ci: Add license_message script https://github.com/nf-core/sarek/issues/1380 https://github.com/DonFreed/docker-actions-test?tab=readme-ov-file * test: Add tests for sentieon bwamem Because the pytest-workflow tests are taking so long * Add scratch from meeting * Clean up sentieon secrets * ci: Fix Nextflow secrets setup * fix(sentieon): Remove encryption key because it won't get used * fix # * ci: Fix when to setup secrets * feat: Add sentieon auth mech secret * chore(sentieon): Remove bwamem pytest-workflow tests * fix: Spike in with environment variables * fix: Add SENTIEON_AUTH_DATA in env file The reason for this is because when we require it in the module it fails. That doesn't make sense for normal Sentieon users. They don't care, this is more of a GitHub actions thing. * docs(sentieon): Make this a README * test: Add local testing setup * test: Remove publishDir * style: Remove sentieon/bwamem * fix: Change comments to prints for debugging and better reporting * fix: Add a quote? * chore: Remove unnecessary variable * debug: Print variables * Fix typo Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> * chore: Clean up code * docs: Write up all the learnings from Sentieon * style: Run prettier * style: Add tags for nf-core lint * docs: Clean up notes Co-authored-by: maxulysse * chore: Add @DonFreed as maintainer --------- Co-authored-by: Edmund Miller Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: maxulysse * Fix Sentieon CI (#5934) * ci: Remove setting secrets in pytest-workflow * ci: Add a longer note about conditionals https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions#using-secrets-in-a-workflow Secrets cannot be directly referenced in if: conditionals. Instead, consider setting secrets as job-level environment variables, then referencing the environment variables to conditionally run steps in the job. For more information, see "Contexts" and jobs..steps[*].if. * ci: Check for secrets in env Because if this is coming from a fork it will fail * disable conda setup when not using a conda profile (#5935) * stubs and test for rnaseq modules - part III (#5925) * improve bbmap_split stub * update stub tests * improve stub * single snapshot * fix stub + add stub tests * fix stub + add stub tests * fix stub * restore tags * fix stub + better stub tests * fix snapshot * NARFMAP segfault (#4895) * test(narfmap): Add segfault test * fix(narfmap): Clean up log error * test(narfmap): Should segfault * chore(narfmap): Bump to 1.4.2 * test(narfmap): Mark test as passing https://github.com/edmundmiller/NARFMAP/issues/10 * style: Add extra tag for nf-core/lint * test: Update all the snapshot declarations * chore: Add a TODO for poddar's test * narfmap cleanup (#5937) * chore: Add Note about issue * test: Remove bam name Co-authored-by: maxulysse --------- Co-authored-by: maxulysse * Add CRAM/index support to NARFMAP (#5946) * feat: Add cram/index support to narfmap * chore: Remove singularity image comment * test: Update tests for CRAM * Update actions/setup-node digest to 1e60f62 (#5947) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix bcftools plugin split (#5942) * bump bclconvert (#5952) * bump bclconvert * fix snapshots * bump multiqc (#5950) * bump multiqc * update snapshot * chore: bump picard (#5948) * bump picard * fix hsmetrics test * fix markduplicates * fix extractfingerprints * fix addorreplacereadgroups * fix crosscheckfingerprints * Add prefix to output file for barrnap (#5919) * Add prefix to output file * Update barrnap to nf-test * Update tags.yml * Add missing bracket and run test * Correct format of license * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Review suggestions * Prettier * Update meta.yml * Update tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * chore(deps): update actions/setup-python digest to 39cd149 (#5961) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * LAST alignment statistics for MultiQC (#5902) * last train modified to output multiqc * Report alignment length and percent similarity, for MultiQC. * Update snapshot file. * Document the new channels * Fix indentation * Update test results. * Give a longer suffix for better MultiQC search patterns. --------- Co-authored-by: Mohammed Mahdi * Update lofreq somatic and callparallel (#5931) * update lofreq callparallel and somatic ssh * [automated] Fix linting with Prettier * suggestions * remove files tests * label lofreq somatic * Update modules/nf-core/lofreq/callparallel/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * port lofreq/callparallel to nf-test * Swap to nftest * update paths * add meta * Update main.nf * modify main * update paths * fix small errors * Update modules/nf-core/lofreq/somatic/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update main.nf.test.snap --------- Co-authored-by: AitorOP Co-authored-by: nf-core-bot Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Francisco Martínez Co-authored-by: Famke Bäuerle Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update dupradar.r according to new MultiQC (>=v1.22) config values (#5943) Update dupradar.r according to new MultiQC config values. Co-authored-by: Matthias Zepper * Update the module: nanoq (#5964) * update nanoq module * update nf-test * Update Glimpse2 phase (#5944) * Update Glimpse2 phase * Fix label * Update snapshot * Update modules/nf-core/glimpse2/phase/main.nf Co-authored-by: Maxime U Garcia * Update meta.yml --------- Co-authored-by: LouisLeNezet Co-authored-by: Maxime U Garcia Co-authored-by: Maxime U Garcia * Update dupradar test snapshot (#5966) * Update dupradar test snapshot * Dummy commit to try and trigger nf-test in ci * Revert "Dummy commit to try and trigger nf-test in ci" This reverts commit 130f9988c7041df8203aa74fb7307451c5fb0dda. * stubs and test for rnaseq modules - part IV (#5939) * fix stubs and add stub tests * fix linting * fix some linting * fix linting * better comment * change container * update snapshots * improve untar stubs * update snapshots * update snapshots * update env * better * use seqera containers * quay.io * proper usage * update snapshots * keep ubuntu for now * update tests and snap * update test and snapshot * update test and snapshot * Add new input to multiqc module for use with --rename_samples (#5973) * Add new input to multiqc module for use with --rename_samples * Update tests * update meta.yml * Add provision for sample_names * port `gridss/gridss` to nf-test (#5933) * port * remove pytest files * fix meta * Update meta.yml * fix indentation * update test with bam plugin * fix indents, try other test * remove --assembly flag for now --------- Co-authored-by: Maxime U Garcia * by remove the 2>&1 to avoid the warning message. (#5974) * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.2 (#5975) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Handle empty files (#5720) * fix: emit all fastqs, remove global log file * fix: remove rg parseing * fix(subworkflow/bcl_demultiplex): remove rg parsing, output empty fastqs, remove log file * test: update snaps * lint: traill\ing whitespace * feat: include read group parsing and empty file check in single closure * test: update snapshot * fix: lint final new line * fix: lint trailing whitespace * fix: add branch and emit empty fastq channel * tests: update snaps * lint: trailing whitespace * fix: filter bool and add test * test: update snaps * test: assert empty file exist * test: assert empty file exist * test: check file exists, update snap * Update test.yml * Update test.yml * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * lint: fix lint --------- Co-authored-by: khazen@clearnotehealth.com <--unset> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * new module: custom_gtffilter (#5965) * Add basic gtffilter implementation * Add gtffilter stub * Add gtffilter meta map * Update gtffilter meta.yml * Fix gtffilter formatting * Add first gtffilter tests * Fix problems in gtffilter module defintion * Add gtffilter nf-test snapshot * Add support for gzipped inputs to gtffilter * Add gtffilter gzip stub * Update nf-test definition for gtffilter * Add meta2 to fasta input Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add fasta meta map to gtffilter test definitions * Add gtffilter MIT license text --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Fix gtffilter output definition (#5977) * Added agat/spmergeannotations (#5772) * Added agat/spmergeannotations * Added tests with config * Rename preprocess rnaseq (#5959) * Edit content with subworkflow name * Rename subworkflow folder * Readd subworkflow with old name, with deprecation * remove rogue word * Appease eclint * Remove test suite for deprecated subworkflow * Using Seqera containers for Sentieon to avoid LD_LIBRARY errors (#5823) * Using seqera containers for sentieon * update containers for sentieon modules with quay.io registry --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: maxulysse * Swap unzip to nf-test (continuation of 5357) (#5897) * unzip stub, nf-test, snap * Revert "unzip stub, nf-test, snap" This reverts commit dec35aa305e243cb87024ab27f4f7e2b2f1c7a19. * Reapply "unzip stub, nf-test, snap" This reverts commit e0d708e51ccf89d293a583a4bd32c3a84e25949a. * added minimal required tests for process and stub * added snapshot * simplify snapshot input in stub test Co-authored-by: Matthias Hörtenhuber * remove unneeded stub files * migrate pytest for unzipfiles * add snapshot file for script block * added stub * added stub and stub test * updated stub snapshot for unzip * remove unneeded test config * Update snaps and malt * Update malt for linting * Fix linting for maltextract * Swap test-data paths for malt modules * Update modules/nf-core/maltextract/tests/main.nf.test --------- Co-authored-by: Sateesh Co-authored-by: Jenny Leopoldina Smith Co-authored-by: Matthias Hörtenhuber Co-authored-by: Maxime U Garcia * Improve strandedness derivation in rnaseq preprocessing swf (#5982) * Improve strandedness devivation * Add missing params to nf-test * RNAseq preprocessing: rrna sequences make more sense as a channel of FASTAs, port tests (#5988) * rrna sequences make more sense as a channel of FASTAs * Also update tests * Add function test to swf * Fix up subworkflow function testing * [Upgrade] Normalize input of lofreq-viterbi to match other lofreq modules (#5989) * add meta2 to input fasta channel * update snapshot; nothing new but timestamp * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Add module fgbio/collectduplexseqmetrics (#5960) * Initial commit * Rerun nf-test * Change assertion for duplex_qc output * Add ggplot2 to version.yml * Update snapshot * Correct conda packages version * Add Seqfu/derep (#5958) * add-usearch-unoise3 * add seqfu/derep * Delete modules/nf-core/usearch/unoise3/environment.yml * Delete modules/nf-core/usearch/unoise3/main.nf * remove files * update metadata * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix dataset in -stub * Clarify description * Update modules/nf-core/seqfu/derep/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * check for pre-existing output file && update test * Update main.nf --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * modify valCutoff funtion in propr.R (#5995) Co-authored-by: Cristina Araiz * liftoff: Re-added conda environment (#5981) * liftoff: Readded conda environment * Added liftoff to env file * Cleaned up env file * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.3 (#5996) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update: `CIRCULARMAPPER_CIRCULARGENERATOR` (#5997) * Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * rename elongation factor for consistency with other CM module --------- Co-authored-by: James A. Fellows Yates * Update: `CIRCULARMAPPER_REALIGNSAMFILE` (#5998) * Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * add meta to elongation factor channel for consistency with other CM module * update nf-test to include new meta * rename metas * Add stub and test to lofreq/indelqual (#5941) * Add stub and test to lofreq/indelqual * Add author * new test setup using --migrate-pytest and PR feedback * Update main.nf.test * Update meta.yml * Update main.nf * add snap; del pytest * Update meta.yml * Update main.nf.test * Update meta.yml * update test * minor fix in stub test * Update tabix and add threads (#5999) * Update tabix and add threads * fix linting * Remove problematic ifEmpty() from rnaseq preprocessing (#6000) * Refactor Sentieon (#5945) * refactor: Clean up the logic and let Sentieon figure it out * refactor: Remove Sentieon license server IP check * fix: Add a -n * Try accessing secrets in the module? * fix: Use Nextflow for if statement * update snapshot * update snapshot * extend logic to all main.nf * ci: Add Sentieon logic to pytest-workflow * test(sentieon): Add env section to every config * Revert "ci: Add Sentieon logic to pytest-workflow" This reverts commit 76884d2a3d9dc9dfbc31b788026e0ac6ee7decaf. * test: Remove pytest_modules for sentieon --------- Co-authored-by: maxulysse * ltrharvest: Added test to verify graceful handling of no ltr input (#5978) * ltrharvest: Added test to verify graceful handling of no ltr input * Updated test data paths * Fixed test data path * Removed unstable items from snapshot * Updated snapshotting logic * ltrfinder: Added test to verify graceful handling of no ltr input (#5979) * ltrretriever/ltrretriever: Added test to verify graceful handling of … (#5980) * ltrretriever/ltrretriever: Added test to verify graceful handling of no ltr input * Removed unstable items from snapshot * update nf-test t0 0.9.0 (#6010) * Fix keyword meta (#6011) * Updated mkfastq module (#5984) * Updated mkfastq module * Combined input channels * Updated main.nf.test and snap --------- Co-authored-by: zxBIB Schcolnicov Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> * bulk update of meta.yml modules structure * update meta.yml files automatically with manual curation for missing information --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: nf-core-bot Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Priyanka Surana Co-authored-by: Matthieu Muffato Co-authored-by: Aida Andrades Valtueña Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Usman Rashid Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Christian Heide <11767963+jch-13@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Raquel Manzano <36073691+RaqManzano@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning Co-authored-by: Maxime Borry Co-authored-by: vickylaram Co-authored-by: Tyler Chafin Co-authored-by: Thanh Lee Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: John Palmer <32370730+jpalmer37@users.noreply.github.com> Co-authored-by: John Palmer Co-authored-by: Charles Plessy Co-authored-by: Mahesh Binzer-Panchal Co-authored-by: Jose Espinosa-Carrasco Co-authored-by: thomgiles Co-authored-by: Jonathan Manning Co-authored-by: Matthieu Muffato Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Felix Lenner Co-authored-by: paulwolk <60699553+paulwolk@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Zohaib Anwar Co-authored-by: Gisela Gabernet Co-authored-by: Sateesh Co-authored-by: Nils Homer Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: RuthEberhardt <37174225+RuthEberhardt@users.noreply.github.com> Co-authored-by: Theresa Störiko Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com> Co-authored-by: eolaniru <149598276+eolaniru@users.noreply.github.com> Co-authored-by: poddarharsh15 <45700858+poddarharsh15@users.noreply.github.com> Co-authored-by: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Co-authored-by: Edmund Miller Co-authored-by: maxulysse Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Mohammed Mahdi Co-authored-by: AitorPeseta <119889829+AitorPeseta@users.noreply.github.com> Co-authored-by: AitorOP Co-authored-by: Francisco Martínez Co-authored-by: Famke Bäuerle Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Co-authored-by: Matthias Zepper Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet Co-authored-by: JIANHONG OU Co-authored-by: Kyle Hazen <41054023+k1sauce@users.noreply.github.com> Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Jenny Leopoldina Smith Co-authored-by: Matthias Hörtenhuber Co-authored-by: Thomas Krannich Co-authored-by: Georgia Kesisoglou <73076971+georgiakes@users.noreply.github.com> Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> Co-authored-by: caraiz2001 <105276325+caraiz2001@users.noreply.github.com> Co-authored-by: Cristina Araiz Co-authored-by: Thiseas C. Lamnidis Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com> Co-authored-by: zxBIB Schcolnicov Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> * allow identifier to be an empty string * run prettier * fixed indentation errors * fix meta.yml of missing modules --------- Co-authored-by: Phil Ewels Co-authored-by: Usman Rashid Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: James A. Fellows Yates Co-authored-by: YSims Co-authored-by: Mahesh Binzer-Panchal Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com> Co-authored-by: Luisa Santus Co-authored-by: Francisco Martínez Co-authored-by: fmartinez Co-authored-by: FernandoDuarteF <123090819+FernandoDuarteF@users.noreply.github.com> Co-authored-by: Pieter Moris <13552343+pmoris@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Ömer An Co-authored-by: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Lucía Peña-Pérez Co-authored-by: Lucpen Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: MargotCh <55975768+MargotCh@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Chiara Schiller <94467188+chiarasch@users.noreply.github.com> Co-authored-by: Miguel A. Ibarra-Arellano Co-authored-by: Krešimir Beštak Co-authored-by: Jonathan Manning Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Eric Wei Co-authored-by: Sateesh Co-authored-by: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Co-authored-by: nf-core-bot Co-authored-by: Joon Klaps Co-authored-by: Daniel Lundin Co-authored-by: Nur M Shahir Co-authored-by: shahirnm Co-authored-by: Chase Mateusiak Co-authored-by: Marius Bjørnstad Co-authored-by: Stephen Kelly Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Venkat Malladi Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Priyanka Surana Co-authored-by: Matthieu Muffato Co-authored-by: Aida Andrades Valtueña Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Christian Heide <11767963+jch-13@users.noreply.github.com> Co-authored-by: Raquel Manzano <36073691+RaqManzano@users.noreply.github.com> Co-authored-by: Maxime Borry Co-authored-by: vickylaram Co-authored-by: Tyler Chafin Co-authored-by: Thanh Lee Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: John Palmer <32370730+jpalmer37@users.noreply.github.com> Co-authored-by: John Palmer Co-authored-by: Charles Plessy Co-authored-by: Jose Espinosa-Carrasco Co-authored-by: thomgiles Co-authored-by: Jonathan Manning Co-authored-by: Matthieu Muffato Co-authored-by: Felix Lenner Co-authored-by: paulwolk <60699553+paulwolk@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Zohaib Anwar Co-authored-by: Gisela Gabernet Co-authored-by: Nils Homer Co-authored-by: RuthEberhardt <37174225+RuthEberhardt@users.noreply.github.com> Co-authored-by: Theresa Störiko Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com> Co-authored-by: eolaniru <149598276+eolaniru@users.noreply.github.com> Co-authored-by: poddarharsh15 <45700858+poddarharsh15@users.noreply.github.com> Co-authored-by: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Co-authored-by: Edmund Miller Co-authored-by: maxulysse Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Mohammed Mahdi Co-authored-by: AitorPeseta <119889829+AitorPeseta@users.noreply.github.com> Co-authored-by: AitorOP Co-authored-by: Famke Bäuerle Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Co-authored-by: Matthias Zepper Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet Co-authored-by: JIANHONG OU Co-authored-by: Kyle Hazen <41054023+k1sauce@users.noreply.github.com> Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com> Co-authored-by: Jenny Leopoldina Smith Co-authored-by: Thomas Krannich Co-authored-by: Georgia Kesisoglou <73076971+georgiakes@users.noreply.github.com> Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> Co-authored-by: caraiz2001 <105276325+caraiz2001@users.noreply.github.com> Co-authored-by: Cristina Araiz Co-authored-by: Thiseas C. Lamnidis Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com> Co-authored-by: zxBIB Schcolnicov --- modules/meta-schema.json | 127 +-- modules/nf-core/abacas/meta.yml | 63 +- modules/nf-core/abricate/run/meta.yml | 54 +- modules/nf-core/abricate/summary/meta.yml | 45 +- modules/nf-core/abritamr/run/meta.yml | 98 ++- modules/nf-core/adapterremoval/meta.yml | 155 ++-- .../nf-core/adapterremovalfixprefix/meta.yml | 51 +- modules/nf-core/admixture/meta.yml | 97 ++- modules/nf-core/affy/justrma/meta.yml | 90 +- .../nf-core/agat/convertspgff2gtf/meta.yml | 51 +- .../nf-core/agat/convertspgff2tsv/meta.yml | 40 +- .../nf-core/agat/convertspgxf2gxf/meta.yml | 51 +- modules/nf-core/agat/spaddintrons/meta.yml | 52 +- .../agat/spfilterfeaturefromkilllist/meta.yml | 69 +- .../nf-core/agat/spmergeannotations/meta.yml | 65 +- modules/nf-core/agat/spstatistics/meta.yml | 40 +- modules/nf-core/agat/sqstatbasic/meta.yml | 40 +- modules/nf-core/agrvate/meta.yml | 56 +- 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| 54 +- .../concoct/mergecutupclustering/meta.yml | 45 +- modules/nf-core/conifer/meta.yml | 51 +- .../controlfreec/assesssignificance/meta.yml | 63 +- modules/nf-core/controlfreec/freec/meta.yml | 307 +++---- .../nf-core/controlfreec/freec2bed/meta.yml | 48 +- .../controlfreec/freec2circos/meta.yml | 48 +- .../nf-core/controlfreec/makegraph/meta.yml | 86 +- .../nf-core/controlfreec/makegraph2/meta.yml | 82 +- modules/nf-core/cooler/balance/meta.yml | 51 +- modules/nf-core/cooler/cload/meta.yml | 68 +- modules/nf-core/cooler/digest/meta.yml | 39 +- modules/nf-core/cooler/dump/meta.yml | 51 +- modules/nf-core/cooler/makebins/meta.yml | 38 +- modules/nf-core/cooler/merge/meta.yml | 45 +- modules/nf-core/cooler/zoomify/meta.yml | 45 +- modules/nf-core/coreograph/meta.yml | 82 +- modules/nf-core/crabz/compress/meta.yml | 50 +- modules/nf-core/crabz/decompress/meta.yml | 50 +- .../nf-core/crisprcleanr/normalize/meta.yml | 62 +- modules/nf-core/crumble/meta.yml | 93 +- 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modules/nf-core/decoupler/decoupler/meta.yml | 96 +- modules/nf-core/dedup/meta.yml | 87 +- modules/nf-core/deeparg/downloaddata/meta.yml | 23 +- modules/nf-core/deeparg/predict/meta.yml | 106 ++- modules/nf-core/deepbgc/download/meta.yml | 20 +- modules/nf-core/deepbgc/pipeline/meta.yml | 173 ++-- modules/nf-core/deepcell/mesmer/meta.yml | 62 +- modules/nf-core/deeptmhmm/meta.yml | 100 ++- .../nf-core/deeptools/bamcoverage/meta.yml | 90 +- .../nf-core/deeptools/computematrix/meta.yml | 72 +- .../deeptools/multibamsummary/meta.yml | 64 +- .../deeptools/plotcorrelation/meta.yml | 89 +- .../deeptools/plotfingerprint/meta.yml | 84 +- .../nf-core/deeptools/plotheatmap/meta.yml | 67 +- modules/nf-core/deeptools/plotpca/meta.yml | 69 +- .../nf-core/deeptools/plotprofile/meta.yml | 68 +- .../nf-core/deepvariant/callvariants/meta.yml | 40 +- .../nf-core/deepvariant/makeexamples/meta.yml | 142 +-- modules/nf-core/deepvariant/meta.yml | 171 ++-- .../deepvariant/postprocessvariants/meta.yml | 151 ++-- .../deepvariant/rundeepvariant/meta.yml | 170 ++-- modules/nf-core/delly/call/meta.yml | 133 +-- modules/nf-core/demuxem/meta.yml | 112 +-- modules/nf-core/deseq2/differential/meta.yml | 235 +++-- modules/nf-core/diamond/blastp/meta.yml | 161 ++-- modules/nf-core/diamond/blastx/meta.yml | 173 ++-- modules/nf-core/diamond/cluster/meta.yml | 53 +- modules/nf-core/diamond/makedb/meta.yml | 68 +- modules/nf-core/dragmap/align/environment.yml | 4 +- modules/nf-core/dragmap/align/meta.yml | 128 ++- modules/nf-core/dragmap/hashtable/meta.yml | 41 +- modules/nf-core/dragonflye/meta.yml | 105 ++- .../nf-core/dshbio/exportsegments/meta.yml | 43 +- modules/nf-core/dshbio/filterbed/meta.yml | 43 +- modules/nf-core/dshbio/filtergff3/meta.yml | 43 +- modules/nf-core/dshbio/splitbed/meta.yml | 43 +- modules/nf-core/dshbio/splitgff3/meta.yml | 43 +- modules/nf-core/duphold/meta.yml | 92 +- modules/nf-core/dupradar/meta.yml | 147 ++-- modules/nf-core/dysgu/meta.yml | 94 +- modules/nf-core/ectyper/meta.yml | 69 +- modules/nf-core/eggnogmapper/meta.yml | 103 ++- modules/nf-core/eido/convert/meta.yml | 35 +- modules/nf-core/eido/validate/meta.yml | 39 +- .../eigenstratsnpcoverage/meta.yml | 79 +- modules/nf-core/eklipse/meta.yml | 85 +- modules/nf-core/elprep/filter/meta.yml | 220 +++-- modules/nf-core/elprep/merge/meta.yml | 50 +- modules/nf-core/elprep/split/meta.yml | 50 +- modules/nf-core/emboss/cons/meta.yml | 48 +- modules/nf-core/emboss/revseq/meta.yml | 46 +- modules/nf-core/emboss/seqret/meta.yml | 55 +- modules/nf-core/emmtyper/meta.yml | 45 +- modules/nf-core/endorspy/meta.yml | 65 +- modules/nf-core/ensemblvep/download/meta.yml | 56 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 52 +- modules/nf-core/ensemblvep/vep/meta.yml | 148 ++-- modules/nf-core/entrezdirect/esearch/meta.yml | 53 +- .../nf-core/entrezdirect/esummary/meta.yml | 57 +- modules/nf-core/entrezdirect/xtract/meta.yml | 61 +- modules/nf-core/epang/place/meta.yml | 95 +- modules/nf-core/epang/split/meta.yml | 61 +- modules/nf-core/estsfs/meta.yml | 84 +- modules/nf-core/evigene/tr2aacds/meta.yml | 56 +- modules/nf-core/expansionhunter/meta.yml | 133 +-- .../expansionhunterdenovo/merge/meta.yml | 90 +- .../expansionhunterdenovo/profile/meta.yml | 116 +-- modules/nf-core/falco/meta.yml | 64 +- modules/nf-core/famsa/align/meta.yml | 71 +- modules/nf-core/famsa/guidetree/meta.yml | 44 +- modules/nf-core/faqcs/meta.yml | 124 ++- modules/nf-core/fargene/meta.yml | 235 +++-- modules/nf-core/fastani/meta.yml | 54 +- modules/nf-core/fastavalidator/meta.yml | 56 +- modules/nf-core/fastawindows/meta.yml | 97 ++- modules/nf-core/fastk/fastk/meta.yml | 71 +- modules/nf-core/fastk/histex/meta.yml | 45 +- modules/nf-core/fastk/merge/meta.yml | 86 +- modules/nf-core/fastme/meta.yml | 94 +- modules/nf-core/fastp/meta.yml | 138 +-- modules/nf-core/fastqc/meta.yml | 57 +- modules/nf-core/fastqscan/meta.yml | 45 +- .../fastqscreen/buildfromindex/meta.yml | 33 +- .../nf-core/fastqscreen/fastqscreen/meta.yml | 90 +- modules/nf-core/fasttree/meta.yml | 31 +- modules/nf-core/fastx/collapser/meta.yml | 57 +- modules/nf-core/fcs/fcsadaptor/meta.yml | 91 +- modules/nf-core/fcs/fcsgx/meta.yml | 66 +- modules/nf-core/ffq/meta.yml | 29 +- .../fgbio/callduplexconsensusreads/meta.yml | 66 +- .../callmolecularconsensusreads/meta.yml | 59 +- .../fgbio/collectduplexseqmetrics/meta.yml | 135 ++- modules/nf-core/fgbio/fastqtobam/meta.yml | 55 +- .../fgbio/filterconsensusreads/meta.yml | 87 +- .../nf-core/fgbio/groupreadsbyumi/meta.yml | 74 +- modules/nf-core/fgbio/sortbam/meta.yml | 50 +- modules/nf-core/fgbio/zipperbams/meta.yml | 103 +-- modules/nf-core/filtlong/meta.yml | 70 +- modules/nf-core/flash/meta.yml | 69 +- modules/nf-core/flye/meta.yml | 117 ++- modules/nf-core/foldcomp/compress/meta.yml | 50 +- modules/nf-core/foldcomp/decompress/meta.yml | 50 +- modules/nf-core/foldmason/easymsa/meta.yml | 70 +- .../nf-core/foldseek/createdb/environment.yml | 1 + modules/nf-core/foldseek/createdb/meta.yml | 45 +- .../foldseek/easysearch/environment.yml | 1 + modules/nf-core/foldseek/easysearch/meta.yml | 72 +- modules/nf-core/fq/generate/meta.yml | 35 +- modules/nf-core/fq/lint/meta.yml | 37 +- modules/nf-core/fq/subsample/meta.yml | 48 +- modules/nf-core/fqtk/meta.yml | 80 +- modules/nf-core/freebayes/meta.yml | 178 ++-- modules/nf-core/freyja/boot/meta.yml | 98 ++- modules/nf-core/freyja/demix/meta.yml | 71 +- modules/nf-core/freyja/update/meta.yml | 38 +- modules/nf-core/freyja/variants/meta.yml | 63 +- modules/nf-core/galah/meta.yml | 87 +- modules/nf-core/gamma/gamma/meta.yml | 89 +- modules/nf-core/gangstr/meta.yml | 106 ++- modules/nf-core/ganon/buildcustom/meta.yml | 80 +- modules/nf-core/ganon/classify/meta.yml | 117 ++- modules/nf-core/ganon/report/meta.yml | 58 +- modules/nf-core/ganon/table/meta.yml | 50 +- modules/nf-core/gappa/examineassign/meta.yml | 101 ++- modules/nf-core/gappa/examinegraft/meta.yml | 46 +- .../nf-core/gappa/examineheattree/meta.yml | 106 ++- modules/nf-core/gatk/indelrealigner/meta.yml | 141 +-- .../gatk/realignertargetcreator/meta.yml | 134 +-- .../nf-core/gatk/unifiedgenotyper/meta.yml | 180 ++-- .../gatk4/addorreplacereadgroups/meta.yml | 105 ++- .../nf-core/gatk4/annotateintervals/meta.yml | 185 ++-- modules/nf-core/gatk4/applybqsr/meta.yml | 101 ++- modules/nf-core/gatk4/applyvqsr/meta.yml | 107 ++- modules/nf-core/gatk4/asereadcounter/meta.yml | 128 +-- .../nf-core/gatk4/baserecalibrator/meta.yml | 99 ++- .../nf-core/gatk4/bedtointervallist/meta.yml | 59 +- .../gatk4/calculatecontamination/meta.yml | 61 +- .../gatk4/calibratedragstrmodel/meta.yml | 95 +- .../nf-core/gatk4/cnnscorevariants/meta.yml | 119 +-- .../nf-core/gatk4/collectreadcounts/meta.yml | 136 +-- .../nf-core/gatk4/collectsvevidence/meta.yml | 163 ++-- modules/nf-core/gatk4/combinegvcfs/meta.yml | 78 +- .../gatk4/composestrtablefile/meta.yml | 45 +- .../gatk4/condensedepthevidence/meta.yml | 91 +- .../createreadcountpanelofnormals/meta.yml | 48 +- .../gatk4/createsequencedictionary/meta.yml | 37 +- .../createsomaticpanelofnormals/meta.yml | 104 ++- .../nf-core/gatk4/denoisereadcounts/meta.yml | 75 +- .../determinegermlinecontigploidy/meta.yml | 112 +-- .../gatk4/estimatelibrarycomplexity/meta.yml | 69 +- modules/nf-core/gatk4/fastqtosam/meta.yml | 50 +- .../nf-core/gatk4/filterintervals/meta.yml | 90 +- .../nf-core/gatk4/filtermutectcalls/meta.yml | 162 ++-- .../gatk4/filtervarianttranches/meta.yml | 110 ++- .../nf-core/gatk4/gatherbqsrreports/meta.yml | 43 +- .../gatk4/gatherpileupsummaries/meta.yml | 46 +- .../nf-core/gatk4/genomicsdbimport/meta.yml | 139 +-- modules/nf-core/gatk4/genotypegvcfs/meta.yml | 170 ++-- .../nf-core/gatk4/germlinecnvcaller/meta.yml | 107 ++- .../nf-core/gatk4/getpileupsummaries/meta.yml | 128 +-- .../nf-core/gatk4/haplotypecaller/meta.yml | 178 ++-- .../nf-core/gatk4/indexfeaturefile/meta.yml | 43 +- .../nf-core/gatk4/intervallisttobed/meta.yml | 42 +- .../nf-core/gatk4/intervallisttools/meta.yml | 51 +- .../gatk4/learnreadorientationmodel/meta.yml | 37 +- .../gatk4/leftalignandtrimvariants/meta.yml | 99 ++- .../gatk4/markduplicates/environment.yml | 3 +- modules/nf-core/gatk4/markduplicates/meta.yml | 121 ++- .../nf-core/gatk4/mergebamalignment/meta.yml | 77 +- .../nf-core/gatk4/mergemutectstats/meta.yml | 45 +- modules/nf-core/gatk4/mergevcfs/meta.yml | 66 +- modules/nf-core/gatk4/mutect2/meta.yml | 175 ++-- .../postprocessgermlinecnvcalls/meta.yml | 104 ++- .../gatk4/preprocessintervals/meta.yml | 128 +-- modules/nf-core/gatk4/printreads/meta.yml | 131 +-- .../nf-core/gatk4/printsvevidence/meta.yml | 108 ++- modules/nf-core/gatk4/reblockgvcf/meta.yml | 104 +-- modules/nf-core/gatk4/revertsam/meta.yml | 37 +- modules/nf-core/gatk4/samtofastq/meta.yml | 37 +- modules/nf-core/gatk4/selectvariants/meta.yml | 73 +- modules/nf-core/gatk4/shiftfasta/meta.yml | 151 ++-- modules/nf-core/gatk4/sitedepthtobaf/meta.yml | 105 ++- 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+- modules/nf-core/genmap/map/meta.yml | 97 ++- modules/nf-core/genmod/annotate/meta.yml | 45 +- modules/nf-core/genmod/compound/meta.yml | 45 +- modules/nf-core/genmod/models/meta.yml | 60 +- modules/nf-core/genmod/score/meta.yml | 60 +- modules/nf-core/genomad/download/meta.yml | 18 +- modules/nf-core/genomad/endtoend/meta.yml | 196 +++-- modules/nf-core/genomescope2/meta.yml | 136 ++- modules/nf-core/genotyphi/parse/meta.yml | 48 +- modules/nf-core/genrich/meta.yml | 133 +-- modules/nf-core/geofetch/meta.yml | 39 +- modules/nf-core/geoquery/getgeo/meta.yml | 57 +- modules/nf-core/getorganelle/config/meta.yml | 35 +- .../nf-core/getorganelle/fromreads/meta.yml | 72 +- modules/nf-core/gfaffix/meta.yml | 55 +- modules/nf-core/gfastats/meta.yml | 101 ++- modules/nf-core/gfatools/gfa2fa/meta.yml | 46 +- modules/nf-core/gfatools/stat/meta.yml | 46 +- modules/nf-core/gffcompare/meta.yml | 173 ++-- modules/nf-core/gffread/meta.yml | 84 +- modules/nf-core/gget/gget/meta.yml | 63 +- 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+- modules/nf-core/gunzip/meta.yml | 37 +- .../gvcftools/extractvariants/meta.yml | 51 +- .../nf-core/hamronization/abricate/meta.yml | 87 +- .../hamronization/amrfinderplus/meta.yml | 87 +- .../nf-core/hamronization/deeparg/meta.yml | 87 +- .../nf-core/hamronization/fargene/meta.yml | 87 +- modules/nf-core/hamronization/rgi/meta.yml | 84 +- .../nf-core/hamronization/summarize/meta.yml | 53 +- modules/nf-core/hapibd/meta.yml | 95 +- modules/nf-core/haplocheck/meta.yml | 60 +- modules/nf-core/haplogrep2/classify/meta.yml | 51 +- modules/nf-core/happy/ftxpy/meta.yml | 104 +-- modules/nf-core/happy/happy/meta.yml | 287 +++--- modules/nf-core/happy/prepy/meta.yml | 89 +- modules/nf-core/happy/sompy/meta.yml | 189 ++-- modules/nf-core/hicap/meta.yml | 88 +- modules/nf-core/hicexplorer/hicpca/meta.yml | 64 +- modules/nf-core/hifiasm/meta.yml | 198 +++-- modules/nf-core/hisat2/align/meta.yml | 107 ++- modules/nf-core/hisat2/build/meta.yml | 83 +- .../hisat2/extractsplicesites/meta.yml | 49 +- 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modules/nf-core/instrain/profile/meta.yml | 145 +-- modules/nf-core/interproscan/meta.yml | 83 +- modules/nf-core/iphop/download/meta.yml | 15 +- modules/nf-core/iphop/predict/meta.yml | 77 +- modules/nf-core/iqtree/meta.yml | 489 +++++++---- modules/nf-core/islandpath/meta.yml | 51 +- modules/nf-core/ismapper/meta.yml | 64 +- modules/nf-core/isoseq/cluster/meta.yml | 166 ++-- modules/nf-core/isoseq/refine/meta.yml | 102 ++- modules/nf-core/isoseq3/tag/meta.yml | 70 +- modules/nf-core/ivar/consensus/meta.yml | 85 +- modules/nf-core/ivar/trim/meta.yml | 71 +- modules/nf-core/ivar/variants/meta.yml | 92 +- modules/nf-core/jasminesv/environment.yml | 3 +- modules/nf-core/jasminesv/meta.yml | 110 +-- .../nf-core/jupyternotebook/environment.yml | 3 +- modules/nf-core/jupyternotebook/meta.yml | 73 +- modules/nf-core/jvarkit/vcffilterjdk/meta.yml | 178 ++-- .../nf-core/jvarkit/vcfpolyx/environment.yml | 1 - modules/nf-core/jvarkit/vcfpolyx/meta.yml | 137 +-- .../jvarkit/wgscoverageplotter/meta.yml | 106 +-- modules/nf-core/kaiju/kaiju/meta.yml | 62 +- modules/nf-core/kaiju/kaiju2krona/meta.yml | 51 +- modules/nf-core/kaiju/kaiju2table/meta.yml | 58 +- modules/nf-core/kaiju/mergeoutputs/meta.yml | 67 +- modules/nf-core/kaiju/mkfmi/meta.yml | 46 +- modules/nf-core/kalign/align/meta.yml | 52 +- modules/nf-core/kallisto/index/meta.yml | 47 +- modules/nf-core/kallisto/quant/meta.yml | 128 +-- .../nf-core/kallistobustools/count/meta.yml | 102 ++- modules/nf-core/kallistobustools/ref/meta.yml | 80 +- modules/nf-core/kat/hist/meta.yml | 110 ++- .../nf-core/khmer/normalizebymedian/meta.yml | 43 +- modules/nf-core/khmer/uniquekmers/meta.yml | 39 +- modules/nf-core/kleborate/meta.yml | 51 +- modules/nf-core/kmcp/compute/meta.yml | 62 +- modules/nf-core/kmcp/index/meta.yml | 60 +- modules/nf-core/kmcp/merge/meta.yml | 48 +- modules/nf-core/kmcp/profile/meta.yml | 55 +- modules/nf-core/kmcp/search/meta.yml | 54 +- modules/nf-core/kofamscan/meta.yml | 70 +- modules/nf-core/kraken2/add/meta.yml | 70 +- modules/nf-core/kraken2/build/meta.yml | 53 +- .../nf-core/kraken2/buildstandard/meta.yml | 26 +- modules/nf-core/kraken2/kraken2/meta.yml | 121 +-- .../krakentools/combinekreports/meta.yml | 52 +- .../krakentools/extractkrakenreads/meta.yml | 83 +- .../krakentools/kreport2krona/meta.yml | 49 +- modules/nf-core/krakenuniq/build/meta.yml | 60 +- modules/nf-core/krakenuniq/download/meta.yml | 36 +- .../krakenuniq/preloadedkrakenuniq/meta.yml | 146 ++-- modules/nf-core/krona/kronadb/meta.yml | 25 +- .../nf-core/krona/ktimporttaxonomy/meta.yml | 62 +- modules/nf-core/krona/ktimporttext/meta.yml | 53 +- .../nf-core/krona/ktupdatetaxonomy/meta.yml | 25 +- modules/nf-core/last/dotplot/meta.yml | 87 +- modules/nf-core/last/lastal/meta.yml | 74 +- modules/nf-core/last/lastdb/meta.yml | 48 +- modules/nf-core/last/mafconvert/meta.yml | 150 ++-- modules/nf-core/last/mafswap/meta.yml | 47 +- modules/nf-core/last/postmask/meta.yml | 47 +- modules/nf-core/last/split/meta.yml | 59 +- modules/nf-core/last/train/meta.yml | 66 +- modules/nf-core/learnmsa/align/meta.yml | 51 +- modules/nf-core/leehom/meta.yml | 131 ++- modules/nf-core/legsta/meta.yml | 45 +- modules/nf-core/leviosam2/index/meta.yml | 52 +- modules/nf-core/leviosam2/lift/meta.yml | 65 +- modules/nf-core/liftoff/meta.yml | 94 +- modules/nf-core/lima/meta.yml | 213 +++-- modules/nf-core/limma/differential/meta.yml | 136 +-- modules/nf-core/lissero/meta.yml | 45 +- modules/nf-core/lofreq/alnqual/meta.yml | 56 +- modules/nf-core/lofreq/call/meta.yml | 62 +- modules/nf-core/lofreq/callparallel/meta.yml | 113 +-- modules/nf-core/lofreq/filter/meta.yml | 51 +- modules/nf-core/lofreq/indelqual/meta.yml | 67 +- modules/nf-core/lofreq/somatic/meta.yml | 108 +-- modules/nf-core/lofreq/viterbi/meta.yml | 71 +- modules/nf-core/longphase/haplotag/meta.yml | 139 +-- .../nf-core/longphase/phase/environment.yml | 7 +- modules/nf-core/longphase/phase/meta.yml | 123 +-- modules/nf-core/ltrfinder/meta.yml | 60 +- modules/nf-core/ltrharvest/meta.yml | 59 +- modules/nf-core/ltrretriever/lai/meta.yml | 88 +- .../ltrretriever/ltrretriever/meta.yml | 142 +-- modules/nf-core/macrel/contigs/meta.yml | 102 ++- modules/nf-core/macs2/callpeak/meta.yml | 95 +- modules/nf-core/macs3/callpeak/meta.yml | 114 ++- modules/nf-core/mafft/meta.yml | 153 ++-- modules/nf-core/mageck/count/meta.yml | 74 +- modules/nf-core/mageck/mle/meta.yml | 84 +- modules/nf-core/mageck/test/meta.yml | 95 +- modules/nf-core/magus/align/meta.yml | 89 +- modules/nf-core/magus/guidetree/meta.yml | 51 +- modules/nf-core/malt/build/meta.yml | 52 +- modules/nf-core/malt/run/meta.yml | 73 +- modules/nf-core/maltextract/meta.yml | 58 +- .../nf-core/manta/convertinversion/meta.yml | 79 +- modules/nf-core/manta/germline/meta.yml | 175 ++-- modules/nf-core/manta/somatic/meta.yml | 215 +++-- modules/nf-core/manta/tumoronly/meta.yml | 175 ++-- modules/nf-core/mapad/index/meta.yml | 45 +- 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modules/nf-core/merquryfk/katcomp/meta.yml | 129 ++- modules/nf-core/merquryfk/katgc/meta.yml | 113 ++- modules/nf-core/merquryfk/merquryfk/meta.yml | 271 ++++-- modules/nf-core/merquryfk/ploidyplot/meta.yml | 113 ++- modules/nf-core/meryl/count/meta.yml | 53 +- modules/nf-core/meryl/histogram/meta.yml | 49 +- modules/nf-core/meryl/unionsum/meta.yml | 49 +- .../jgisummarizebamcontigdepths/meta.yml | 53 +- modules/nf-core/metabat2/metabat2/meta.yml | 107 ++- modules/nf-core/metaeuk/easypredict/meta.yml | 93 +- modules/nf-core/metamaps/classify/meta.yml | 151 ++-- modules/nf-core/metamaps/mapdirectly/meta.yml | 91 +- modules/nf-core/metaphlan/makedb/meta.yml | 18 +- .../metaphlan/mergemetaphlantables/meta.yml | 48 +- modules/nf-core/metaphlan/metaphlan/meta.yml | 93 +- .../metaphlan3/mergemetaphlantables/meta.yml | 48 +- .../nf-core/metaphlan3/metaphlan3/meta.yml | 93 +- modules/nf-core/methyldackel/extract/meta.yml | 79 +- modules/nf-core/methyldackel/mbias/meta.yml | 67 +- modules/nf-core/midas/run/meta.yml | 64 +- .../nf-core/mindagap/duplicatefinder/meta.yml | 52 +- modules/nf-core/mindagap/mindagap/meta.yml | 53 +- modules/nf-core/minia/meta.yml | 67 +- modules/nf-core/miniasm/meta.yml | 68 +- modules/nf-core/minimap2/align/meta.yml | 115 +-- modules/nf-core/minimap2/index/meta.yml | 43 +- modules/nf-core/miniprot/align/meta.yml | 67 +- modules/nf-core/miniprot/index/meta.yml | 43 +- modules/nf-core/miranda/meta.yml | 51 +- modules/nf-core/mirtop/counts/meta.yml | 83 +- modules/nf-core/mirtop/export/meta.yml | 107 ++- modules/nf-core/mirtop/gff/meta.yml | 80 +- modules/nf-core/mirtop/stats/meta.yml | 63 +- modules/nf-core/mirtrace/qc/meta.yml | 128 ++- .../mitohifi/findmitoreference/meta.yml | 46 +- modules/nf-core/mitohifi/mitohifi/meta.yml | 236 +++-- modules/nf-core/mlst/meta.yml | 45 +- modules/nf-core/mmseqs/cluster/meta.yml | 43 +- modules/nf-core/mmseqs/createdb/meta.yml | 46 +- modules/nf-core/mmseqs/createindex/meta.yml | 49 +- 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modules/nf-core/purgedups/splitfa/meta.yml | 48 +- modules/nf-core/pycoqc/meta.yml | 56 +- modules/nf-core/pydamage/analyze/meta.yml | 53 +- modules/nf-core/pydamage/filter/meta.yml | 45 +- modules/nf-core/pyrodigal/meta.yml | 98 ++- modules/nf-core/qcat/meta.yml | 46 +- modules/nf-core/qualimap/bamqc/meta.yml | 51 +- modules/nf-core/qualimap/bamqccram/meta.yml | 67 +- modules/nf-core/qualimap/rnaseq/meta.yml | 61 +- modules/nf-core/quartonotebook/meta.yml | 124 +-- modules/nf-core/quast/meta.yml | 118 ++- modules/nf-core/quilt/quilt/meta.yml | 211 +++-- modules/nf-core/racon/meta.yml | 64 +- modules/nf-core/rapidnj/meta.yml | 42 +- modules/nf-core/rasusa/meta.yml | 55 +- modules/nf-core/raven/meta.yml | 57 +- modules/nf-core/raxmlng/meta.yml | 38 +- .../repeatmodeler/builddatabase/meta.yml | 47 +- .../repeatmodeler/repeatmodeler/meta.yml | 74 +- modules/nf-core/resfinder/run/meta.yml | 266 +++--- modules/nf-core/rgi/cardannotation/meta.yml | 43 +- modules/nf-core/rgi/main/meta.yml | 109 ++- modules/nf-core/rhocall/annotate/meta.yml | 77 +- modules/nf-core/rhocall/viz/meta.yml | 72 +- modules/nf-core/ribotish/predict/meta.yml | 205 +++-- modules/nf-core/ribotish/quality/meta.yml | 113 +-- .../nf-core/ribotricer/detectorfs/meta.yml | 188 ++-- .../nf-core/ribotricer/prepareorfs/meta.yml | 58 +- modules/nf-core/ribowaltz/meta.yml | 191 ++-- modules/nf-core/rmarkdownnotebook/meta.yml | 93 +- modules/nf-core/roary/meta.yml | 57 +- modules/nf-core/rrnatranscripts/meta.yml | 25 +- .../nf-core/rsem/calculateexpression/meta.yml | 120 ++- .../nf-core/rsem/preparereference/meta.yml | 40 +- modules/nf-core/rseqc/bamstat/meta.yml | 37 +- .../nf-core/rseqc/inferexperiment/meta.yml | 45 +- modules/nf-core/rseqc/innerdistance/meta.yml | 89 +- .../nf-core/rseqc/junctionannotation/meta.yml | 117 ++- .../nf-core/rseqc/junctionsaturation/meta.yml | 56 +- .../nf-core/rseqc/readdistribution/meta.yml | 45 +- .../nf-core/rseqc/readduplication/meta.yml | 74 +- modules/nf-core/rseqc/tin/meta.yml | 64 +- modules/nf-core/rtgtools/format/meta.yml | 69 +- modules/nf-core/rtgtools/pedfilter/meta.yml | 52 +- modules/nf-core/rtgtools/rocplot/meta.yml | 63 +- modules/nf-core/rtgtools/vcfeval/meta.yml | 249 ++++-- modules/nf-core/rtn/tni/meta.yml | 76 +- modules/nf-core/sageproteomics/sage/meta.yml | 132 +-- modules/nf-core/salmon/index/meta.yml | 27 +- modules/nf-core/salmon/quant/meta.yml | 94 +- modules/nf-core/salsa2/meta.yml | 95 +- modules/nf-core/sam2lca/analyze/meta.yml | 89 +- modules/nf-core/sambamba/flagstat/meta.yml | 45 +- modules/nf-core/sambamba/markdup/meta.yml | 57 +- modules/nf-core/samblaster/meta.yml | 45 +- .../samtools/ampliconclip/environment.yml | 5 +- .../nf-core/samtools/ampliconclip/meta.yml | 89 +- .../nf-core/samtools/bam2fq/environment.yml | 5 +- modules/nf-core/samtools/bam2fq/meta.yml | 65 +- .../nf-core/samtools/calmd/environment.yml | 5 +- modules/nf-core/samtools/calmd/meta.yml | 58 +- modules/nf-core/samtools/cat/environment.yml | 5 +- modules/nf-core/samtools/cat/meta.yml | 56 +- .../nf-core/samtools/collate/environment.yml | 5 +- modules/nf-core/samtools/collate/meta.yml | 74 +- .../samtools/collatefastq/environment.yml | 4 +- .../nf-core/samtools/collatefastq/meta.yml | 125 ++- .../samtools/consensus/environment.yml | 3 +- modules/nf-core/samtools/consensus/meta.yml | 70 +- .../nf-core/samtools/convert/environment.yml | 5 +- modules/nf-core/samtools/convert/meta.yml | 111 ++- .../nf-core/samtools/coverage/environment.yml | 5 +- modules/nf-core/samtools/coverage/meta.yml | 85 +- modules/nf-core/samtools/cramsize/meta.yml | 43 +- .../nf-core/samtools/depth/environment.yml | 4 +- modules/nf-core/samtools/depth/meta.yml | 68 +- modules/nf-core/samtools/dict/environment.yml | 5 +- modules/nf-core/samtools/dict/meta.yml | 43 +- modules/nf-core/samtools/faidx/meta.yml | 85 +- .../nf-core/samtools/fasta/environment.yml | 4 +- modules/nf-core/samtools/fasta/meta.yml | 90 +- .../nf-core/samtools/fastq/environment.yml | 5 +- modules/nf-core/samtools/fastq/meta.yml | 90 +- .../nf-core/samtools/fixmate/environment.yml | 5 +- modules/nf-core/samtools/fixmate/meta.yml | 51 +- .../nf-core/samtools/flagstat/environment.yml | 5 +- modules/nf-core/samtools/flagstat/meta.yml | 54 +- .../nf-core/samtools/getrg/environment.yml | 4 +- modules/nf-core/samtools/getrg/meta.yml | 38 +- .../nf-core/samtools/idxstats/environment.yml | 5 +- modules/nf-core/samtools/idxstats/meta.yml | 51 +- .../nf-core/samtools/import/environment.yml | 4 +- modules/nf-core/samtools/import/meta.yml | 70 +- .../nf-core/samtools/index/environment.yml | 5 +- modules/nf-core/samtools/index/meta.yml | 68 +- .../nf-core/samtools/markdup/environment.yml | 5 +- modules/nf-core/samtools/markdup/meta.yml | 83 +- .../nf-core/samtools/merge/environment.yml | 5 +- modules/nf-core/samtools/merge/meta.yml | 117 ++- .../nf-core/samtools/mpileup/environment.yml | 5 +- modules/nf-core/samtools/mpileup/meta.yml | 59 +- .../nf-core/samtools/reheader/environment.yml | 5 +- modules/nf-core/samtools/reheader/meta.yml | 46 +- .../nf-core/samtools/sormadup/environment.yml | 5 +- modules/nf-core/samtools/sormadup/meta.yml | 115 ++- modules/nf-core/samtools/sort/environment.yml | 5 +- modules/nf-core/samtools/sort/meta.yml | 99 ++- .../nf-core/samtools/stats/environment.yml | 5 +- modules/nf-core/samtools/stats/meta.yml | 69 +- modules/nf-core/samtools/view/environment.yml | 5 +- modules/nf-core/samtools/view/meta.yml | 163 ++-- .../samtools/view/tests/main.nf.test.snap | 20 + modules/nf-core/scimap/mcmicro/meta.yml | 57 +- modules/nf-core/scimap/spatiallda/meta.yml | 82 +- modules/nf-core/scoary/meta.yml | 61 +- .../nf-core/scramble/clusteranalysis/meta.yml | 92 +- .../scramble/clusteridentifier/meta.yml | 61 +- modules/nf-core/seacr/callpeak/meta.yml | 59 +- modules/nf-core/segemehl/align/meta.yml | 123 +-- modules/nf-core/segemehl/index/meta.yml | 26 +- .../nf-core/semibin/singleeasybin/meta.yml | 107 ++- modules/nf-core/sentieon/applyvarcal/meta.yml | 126 +-- modules/nf-core/sentieon/bwaindex/meta.yml | 41 +- modules/nf-core/sentieon/bwamem/meta.yml | 99 ++- .../sentieon/collectvcmetrics/meta.yml | 153 ++-- .../nf-core/sentieon/coveragemetrics/meta.yml | 189 ++-- modules/nf-core/sentieon/datametrics/meta.yml | 154 ++-- modules/nf-core/sentieon/dedup/meta.yml | 164 ++-- .../nf-core/sentieon/dnamodelapply/meta.yml | 119 +-- modules/nf-core/sentieon/dnascope/meta.yml | 213 ++--- modules/nf-core/sentieon/gvcftyper/meta.yml | 130 +-- modules/nf-core/sentieon/haplotyper/meta.yml | 167 ++-- modules/nf-core/sentieon/qualcal/meta.yml | 174 ++-- modules/nf-core/sentieon/readwriter/meta.yml | 116 ++- modules/nf-core/sentieon/tnfilter/meta.yml | 140 +-- .../nf-core/sentieon/tnhaplotyper2/meta.yml | 258 +++--- modules/nf-core/sentieon/tnscope/meta.yml | 199 +++-- modules/nf-core/sentieon/varcal/meta.yml | 123 ++- modules/nf-core/sentieon/wgsmetrics/meta.yml | 107 +-- modules/nf-core/seqcluster/collapse/meta.yml | 55 +- modules/nf-core/seqfu/derep/meta.yml | 50 +- modules/nf-core/seqfu/stats/meta.yml | 67 +- modules/nf-core/seqkit/concat/meta.yml | 49 +- modules/nf-core/seqkit/fq2fa/meta.yml | 52 +- modules/nf-core/seqkit/fx2tab/meta.yml | 46 +- modules/nf-core/seqkit/grep/meta.yml | 67 +- modules/nf-core/seqkit/pair/meta.yml | 60 +- modules/nf-core/seqkit/replace/meta.yml | 48 +- modules/nf-core/seqkit/rmdup/meta.yml | 59 +- modules/nf-core/seqkit/seq/meta.yml | 47 +- modules/nf-core/seqkit/sliding/meta.yml | 46 +- modules/nf-core/seqkit/sort/meta.yml | 44 +- modules/nf-core/seqkit/split2/meta.yml | 43 +- modules/nf-core/seqkit/stats/meta.yml | 54 +- modules/nf-core/seqkit/tab2fx/meta.yml | 43 +- modules/nf-core/seqsero2/meta.yml | 69 +- modules/nf-core/seqtk/cutn/meta.yml | 47 +- modules/nf-core/seqtk/mergepe/meta.yml | 52 +- modules/nf-core/seqtk/rename/meta.yml | 49 +- modules/nf-core/seqtk/sample/meta.yml | 54 +- modules/nf-core/seqtk/seq/meta.yml | 50 +- modules/nf-core/seqtk/subseq/meta.yml | 50 +- modules/nf-core/seqtk/trim/meta.yml | 51 +- .../sequencetools/pileupcaller/meta.yml | 111 ++- .../nf-core/sequenzautils/bam2seqz/meta.yml | 78 +- .../nf-core/sequenzautils/gcwiggle/meta.yml | 53 +- modules/nf-core/seqwish/induce/meta.yml | 51 +- modules/nf-core/seroba/run/meta.yml | 63 +- modules/nf-core/severus/meta.yml | 269 ++++-- modules/nf-core/sexdeterrmine/meta.yml | 68 +- modules/nf-core/sgdemux/meta.yml | 123 ++- modules/nf-core/shapeit5/ligate/meta.yml | 61 +- modules/nf-core/shapeit5/phasecommon/meta.yml | 137 +-- modules/nf-core/shapeit5/phaserare/meta.yml | 122 +-- modules/nf-core/shapeit5/switch/meta.yml | 118 +-- modules/nf-core/shasta/meta.yml | 77 +- modules/nf-core/shasum/meta.yml | 45 +- modules/nf-core/shigatyper/meta.yml | 57 +- modules/nf-core/shigeifinder/meta.yml | 48 +- modules/nf-core/shinyngs/app/meta.yml | 107 +-- .../shinyngs/staticdifferential/meta.yml | 103 ++- .../shinyngs/staticexploratory/meta.yml | 212 +++-- .../shinyngs/validatefomcomponents/meta.yml | 136 +-- modules/nf-core/shovill/meta.yml | 92 +- modules/nf-core/sickle/meta.yml | 97 ++- modules/nf-core/simpleaf/index/meta.yml | 102 ++- modules/nf-core/simpleaf/quant/meta.yml | 123 +-- modules/nf-core/sistr/meta.yml | 86 +- modules/nf-core/slimfastq/meta.yml | 45 +- modules/nf-core/smncopynumbercaller/meta.yml | 69 +- modules/nf-core/smoothxg/meta.yml | 56 +- modules/nf-core/smoove/call/meta.yml | 95 +- modules/nf-core/snakemake/meta.yml | 78 +- modules/nf-core/snapaligner/align/meta.yml | 79 +- modules/nf-core/snapaligner/index/meta.yml | 58 +- modules/nf-core/sniffles/meta.yml | 120 ++- modules/nf-core/snippy/core/meta.yml | 112 ++- modules/nf-core/snippy/run/meta.yml | 252 ++++-- modules/nf-core/snpdists/meta.yml | 43 +- modules/nf-core/snpeff/download/meta.yml | 44 +- modules/nf-core/snpeff/snpeff/meta.yml | 96 +- modules/nf-core/snpsift/annotate/meta.yml | 81 +- modules/nf-core/snpsift/dbnsfp/meta.yml | 82 +- modules/nf-core/snpsift/split/meta.yml | 48 +- modules/nf-core/snpsites/meta.yml | 39 +- modules/nf-core/somalier/ancestry/meta.yml | 92 +- modules/nf-core/somalier/extract/meta.yml | 109 +-- modules/nf-core/somalier/relate/meta.yml | 85 +- modules/nf-core/sortmerna/meta.yml | 121 +-- modules/nf-core/sourmash/compare/meta.yml | 102 ++- modules/nf-core/sourmash/gather/meta.yml | 152 ++-- modules/nf-core/sourmash/index/meta.yml | 54 +- modules/nf-core/sourmash/sketch/meta.yml | 52 +- modules/nf-core/sourmash/taxannotate/meta.yml | 61 +- modules/nf-core/spaceranger/count/meta.yml | 132 +-- modules/nf-core/spaceranger/mkgtf/meta.yml | 27 +- modules/nf-core/spaceranger/mkref/meta.yml | 41 +- modules/nf-core/spades/meta.yml | 186 ++-- modules/nf-core/spatyper/meta.yml | 61 +- modules/nf-core/splitubam/meta.yml | 48 +- modules/nf-core/spotiflow/meta.yml | 54 +- modules/nf-core/spring/compress/meta.yml | 56 +- modules/nf-core/spring/decompress/meta.yml | 58 +- modules/nf-core/sratools/fasterqdump/meta.yml | 71 +- modules/nf-core/sratools/prefetch/meta.yml | 72 +- modules/nf-core/srst2/srst2/meta.yml | 118 ++- modules/nf-core/ssuissero/meta.yml | 45 +- modules/nf-core/stadeniolib/scramble/meta.yml | 82 +- modules/nf-core/staphopiasccmec/meta.yml | 45 +- modules/nf-core/star/align/environment.yml | 5 +- modules/nf-core/star/align/meta.yml | 246 ++++-- .../star/genomegenerate/environment.yml | 3 +- modules/nf-core/star/genomegenerate/meta.yml | 57 +- modules/nf-core/star/starsolo/meta.yml | 139 ++- modules/nf-core/staramr/search/meta.yml | 156 ++-- modules/nf-core/stardist/meta.yml | 53 +- modules/nf-core/stecfinder/meta.yml | 48 +- modules/nf-core/stitch/meta.yml | 216 +++-- modules/nf-core/stranger/meta.yml | 66 +- modules/nf-core/strelka/germline/meta.yml | 125 +-- modules/nf-core/strelka/somatic/meta.yml | 158 ++-- modules/nf-core/stringtie/merge/meta.yml | 38 +- modules/nf-core/stringtie/stringtie/meta.yml | 89 +- .../nf-core/subread/featurecounts/meta.yml | 68 +- .../summarizedexperiment/meta.yml | 112 +-- modules/nf-core/survivor/bedpetovcf/meta.yml | 43 +- modules/nf-core/survivor/filter/meta.yml | 74 +- modules/nf-core/survivor/merge/meta.yml | 89 +- modules/nf-core/survivor/simsv/meta.yml | 143 +-- modules/nf-core/survivor/stats/meta.yml | 63 +- modules/nf-core/svaba/meta.yml | 364 +++++--- .../nf-core/svanalyzer/svbenchmark/meta.yml | 166 ++-- modules/nf-core/svdb/build/meta.yml | 46 +- modules/nf-core/svdb/merge/environment.yml | 6 +- modules/nf-core/svdb/merge/meta.yml | 52 +- modules/nf-core/svdb/query/meta.yml | 88 +- modules/nf-core/svtk/baftest/meta.yml | 72 +- modules/nf-core/svtk/countsvtypes/meta.yml | 48 +- modules/nf-core/svtk/rdtest2vcf/meta.yml | 77 +- modules/nf-core/svtk/standardize/meta.yml | 69 +- modules/nf-core/svtk/vcf2bed/meta.yml | 56 +- modules/nf-core/svtyper/svtyper/meta.yml | 117 ++- modules/nf-core/svtyper/svtypersso/meta.yml | 98 ++- modules/nf-core/svync/meta.yml | 64 +- modules/nf-core/tabix/bgzip/environment.yml | 3 +- modules/nf-core/tabix/bgzip/meta.yml | 53 +- .../nf-core/tabix/bgziptabix/environment.yml | 3 +- modules/nf-core/tabix/bgziptabix/meta.yml | 70 +- modules/nf-core/tabix/tabix/meta.yml | 55 +- modules/nf-core/tailfindr/meta.yml | 51 +- modules/nf-core/taxonkit/name2taxid/meta.yml | 59 +- modules/nf-core/taxpasta/merge/meta.yml | 83 +- modules/nf-core/taxpasta/standardise/meta.yml | 68 +- modules/nf-core/tbprofiler/profile/meta.yml | 96 +- modules/nf-core/tcoffee/align/meta.yml | 113 +-- modules/nf-core/tcoffee/alncompare/meta.yml | 61 +- modules/nf-core/tcoffee/consensus/meta.yml | 80 +- modules/nf-core/tcoffee/irmsd/meta.yml | 68 +- modules/nf-core/tcoffee/seqreformat/meta.yml | 52 +- modules/nf-core/tcoffee/tcs/environment.yml | 4 +- modules/nf-core/tcoffee/tcs/meta.yml | 86 +- modules/nf-core/thermorawfileparser/meta.yml | 50 +- modules/nf-core/tiara/tiara/meta.yml | 77 +- modules/nf-core/tiddit/cov/meta.yml | 77 +- modules/nf-core/tiddit/sv/meta.yml | 99 ++- modules/nf-core/tidk/explore/meta.yml | 63 +- modules/nf-core/tidk/plot/meta.yml | 47 +- modules/nf-core/tidk/search/meta.yml | 65 +- modules/nf-core/topas/gencons/meta.yml | 140 ++- modules/nf-core/toulligqc/meta.yml | 82 +- modules/nf-core/transdecoder/longorf/meta.yml | 95 +- modules/nf-core/transdecoder/predict/meta.yml | 98 ++- modules/nf-core/trimgalore/meta.yml | 101 ++- modules/nf-core/trimmomatic/meta.yml | 93 +- modules/nf-core/trinity/meta.yml | 59 +- modules/nf-core/trust4/meta.yml | 170 +++- modules/nf-core/truvari/bench/meta.yml | 210 +++-- modules/nf-core/truvari/consistency/meta.yml | 45 +- modules/nf-core/truvari/segment/meta.yml | 45 +- modules/nf-core/trycycler/cluster/meta.yml | 58 +- modules/nf-core/trycycler/subsample/meta.yml | 53 +- modules/nf-core/tsebra/meta.yml | 93 +- modules/nf-core/tximeta/tximport/meta.yml | 198 +++-- modules/nf-core/ucsc/bedclip/meta.yml | 48 +- .../nf-core/ucsc/bedgraphtobigwig/meta.yml | 53 +- modules/nf-core/ucsc/bedtobigbed/meta.yml | 61 +- .../ucsc/bigwigaverageoverbed/meta.yml | 53 +- modules/nf-core/ucsc/gtftogenepred/meta.yml | 55 +- modules/nf-core/ucsc/liftover/meta.yml | 65 +- modules/nf-core/ucsc/wigtobigwig/meta.yml | 45 +- modules/nf-core/ultra/align/environment.yml | 3 +- modules/nf-core/ultra/align/meta.yml | 72 +- modules/nf-core/ultra/index/meta.yml | 44 +- modules/nf-core/ultra/pipeline/meta.yml | 59 +- modules/nf-core/ultraplex/meta.yml | 70 +- modules/nf-core/umicollapse/meta.yml | 94 +- modules/nf-core/umitools/dedup/meta.yml | 118 ++- modules/nf-core/umitools/extract/meta.yml | 64 +- modules/nf-core/umitools/group/meta.yml | 99 ++- .../nf-core/umitools/prepareforrsem/meta.yml | 70 +- modules/nf-core/unicycler/meta.yml | 81 +- modules/nf-core/universc/meta.yml | 46 +- modules/nf-core/untar/meta.yml | 43 +- modules/nf-core/untarfiles/meta.yml | 43 +- modules/nf-core/unzip/meta.yml | 46 +- modules/nf-core/unzipfiles/meta.yml | 46 +- modules/nf-core/upd/meta.yml | 46 +- modules/nf-core/upp/align/meta.yml | 70 +- modules/nf-core/vardictjava/meta.yml | 98 ++- modules/nf-core/variantbam/meta.yml | 48 +- .../varlociraptor/callvariants/meta.yml | 114 ++- .../estimatealignmentproperties/meta.yml | 86 +- .../nf-core/varlociraptor/preprocess/meta.yml | 147 ++-- modules/nf-core/vcf2cytosure/meta.yml | 110 +-- modules/nf-core/vcf2db/meta.yml | 53 +- modules/nf-core/vcf2maf/meta.yml | 55 +- modules/nf-core/vcfanno/meta.yml | 86 +- modules/nf-core/vcflib/vcfbreakmulti/meta.yml | 56 +- modules/nf-core/vcflib/vcffilter/meta.yml | 51 +- modules/nf-core/vcflib/vcffixup/meta.yml | 56 +- modules/nf-core/vcflib/vcfuniq/meta.yml | 56 +- modules/nf-core/vcftools/meta.yml | 822 +++++++++++++----- modules/nf-core/velocyto/meta.yml | 79 +- .../nf-core/verifybamid/verifybamid/meta.yml | 158 ++-- .../nf-core/verifybamid/verifybamid2/meta.yml | 169 ++-- modules/nf-core/vg/construct/meta.yml | 94 +- modules/nf-core/vg/deconstruct/meta.yml | 64 +- modules/nf-core/vg/index/meta.yml | 58 +- modules/nf-core/viennarna/rnacofold/meta.yml | 62 +- modules/nf-core/viennarna/rnafold/meta.yml | 55 +- modules/nf-core/viennarna/rnalfold/meta.yml | 29 +- modules/nf-core/vireo/meta.yml | 111 +-- .../nf-core/vrhyme/extractunbinned/meta.yml | 63 +- modules/nf-core/vrhyme/linkbins/meta.yml | 48 +- modules/nf-core/vrhyme/vrhyme/environment.yml | 7 +- modules/nf-core/vrhyme/vrhyme/meta.yml | 86 +- modules/nf-core/vsearch/cluster/meta.yml | 175 +++- modules/nf-core/vsearch/dereplicate/meta.yml | 58 +- modules/nf-core/vsearch/fastqfilter/meta.yml | 54 +- modules/nf-core/vsearch/sintax/meta.yml | 48 +- modules/nf-core/vsearch/sort/meta.yml | 58 +- .../nf-core/vsearch/usearchglobal/meta.yml | 169 ++-- modules/nf-core/vt/decompose/meta.yml | 54 +- modules/nf-core/vt/normalize/meta.yml | 111 +-- modules/nf-core/wfmash/meta.yml | 84 +- modules/nf-core/wgsim/meta.yml | 45 +- modules/nf-core/whamg/meta.yml | 95 +- modules/nf-core/windowmasker/convert/meta.yml | 47 +- .../nf-core/windowmasker/mkcounts/meta.yml | 45 +- modules/nf-core/windowmasker/ustat/meta.yml | 63 +- modules/nf-core/wisecondorx/convert/meta.yml | 90 +- modules/nf-core/wisecondorx/gender/meta.yml | 57 +- modules/nf-core/wisecondorx/newref/meta.yml | 45 +- modules/nf-core/wisecondorx/predict/meta.yml | 147 ++-- modules/nf-core/wittyer/meta.yml | 97 ++- modules/nf-core/xengsort/index/meta.yml | 65 +- modules/nf-core/xz/compress/meta.yml | 52 +- modules/nf-core/xz/decompress/meta.yml | 50 +- modules/nf-core/yahs/meta.yml | 87 +- modules/nf-core/yak/count/meta.yml | 47 +- modules/nf-core/yara/index/meta.yml | 40 +- modules/nf-core/yara/mapper/meta.yml | 78 +- modules/nf-core/zip/meta.yml | 44 +- 1378 files changed, 65225 insertions(+), 46375 deletions(-) diff --git a/modules/meta-schema.json b/modules/meta-schema.json index 0b855d76d07..977ee1b624d 100644 --- a/modules/meta-schema.json +++ b/modules/meta-schema.json @@ -38,40 +38,8 @@ "type": "array", "description": "Input channels for the module", "items": { - "type": "object", - "patternProperties": { - ".*": { - "type": "object", - "properties": { - "type": { - "type": "string", - "description": "Type of the input channel", - "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] - }, - "description": { - "type": "string", - "description": "Description of the input channel" - }, - "pattern": { - "type": "string", - "description": "Pattern of the input channel, given in Java glob syntax" - }, - "default": { - "type": ["string", "number", "boolean", "array", "object"], - "description": "Default value for the input channel" - }, - "enum": { - "type": "array", - "description": "List of allowed values for the input channel", - "items": { - "type": ["string", "number", "boolean", "array", "object"] - }, - "uniqueItems": true - } - }, - "required": ["type", "description"] - } - } + "type": "array", + "items": { "$ref": "#/definitions/elementProperties" } } }, "output": { @@ -79,35 +47,7 @@ "description": "Output channels for the module", "items": { "type": "object", - "patternProperties": { - ".*": { - "type": "object", - "properties": { - "type": { - "type": "string", - "description": "Type of the output channel", - "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] - }, - "description": { - "type": "string", - "description": "Description of the output channel" - }, - "pattern": { - "type": "string", - "description": "Pattern of the input channel, given in Java glob syntax" - }, - "enum": { - "type": "array", - "description": "List of allowed values for the output channel", - "items": { - "type": ["string", "number", "boolean", "array", "object"] - }, - "uniqueItems": true - } - }, - "required": ["type", "description"] - } - } + "items": { "$ref": "#/definitions/elementProperties" } } }, "tools": { @@ -160,6 +100,19 @@ "minItems": 1, "uniqueItems": true, "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]" + }, + "identifier": { + "description": "bio.tools identifier of the tool", + "anyOf": [ + { + "type": "string", + "pattern": "^biotools:.*$" + }, + { + "type": "string", + "maxLength": 0 + } + ] } }, "required": ["description"], @@ -182,5 +135,53 @@ } } }, + "definitions": { + "elementProperties": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the channel element", + "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] + }, + "description": { + "type": "string", + "description": "Description of the channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the channel, given in Java glob syntax" + }, + "enum": { + "type": "array", + "description": "List of allowed values for the channel", + "items": { + "type": ["string", "number", "boolean", "array", "object"] + }, + "uniqueItems": true + }, + "ontologies": { + "type": "array", + "description": "List of ontologies for the channel", + "uniqueItems": true, + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "string", + "pattern": "^(http|https)://.*" + } + } + } + } + }, + "required": ["type", "description"] + } + } + } + }, "required": ["name", "description", "keywords", "authors", "output", "tools"] } diff --git a/modules/nf-core/abacas/meta.yml b/modules/nf-core/abacas/meta.yml index bef9868c8bd..9cbbef0143c 100644 --- a/modules/nf-core/abacas/meta.yml +++ b/modules/nf-core/abacas/meta.yml @@ -14,40 +14,43 @@ tools: documentation: http://abacas.sourceforge.net/documentation.html doi: "10.1093/bioinformatics/btp347" licence: ["GPL v2-or-later"] + identifier: biotools:abacas input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - scaffold: - type: file - description: Fasta file containing scaffold - pattern: "*.{fasta,fa}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: Fasta file containing scaffold + pattern: "*.{fasta,fa}" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: file - description: | - List containing abacas output files - [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps', - 'test.abacas.gaps.tab', 'test.abacas.nucmer.delta', - 'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling', - 'test.abacas.tab', 'test.abacas.unused.contigs.out', - 'test.abacas.MULTIFASTA.fa' ] - pattern: "*.{abacas}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abacas*": + type: file + description: | + List containing abacas output files + [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps', + 'test.abacas.gaps.tab', 'test.abacas.nucmer.delta', + 'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling', + 'test.abacas.tab', 'test.abacas.unused.contigs.out', + 'test.abacas.MULTIFASTA.fa' ] + pattern: "*.{abacas}*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/abricate/run/meta.yml b/modules/nf-core/abricate/run/meta.yml index 927c21f60f9..dce78f3c704 100644 --- a/modules/nf-core/abricate/run/meta.yml +++ b/modules/nf-core/abricate/run/meta.yml @@ -11,34 +11,38 @@ tools: documentation: https://github.com/tseemann/abricate tool_dev_url: https://github.com/tseemann/abricate licence: ["GPL v2"] + identifier: biotools:ABRicate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: FASTA, GenBank or EMBL formatted file - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" - - databasedir: - type: directory - description: Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb` - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: FASTA, GenBank or EMBL formatted file + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + - - databasedir: + type: directory + description: Optional location of local copy of database files, possibly with + custom databases set up with `abricate --setupdb` + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Tab-delimited report of results - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab-delimited report of results + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/abricate/summary/meta.yml b/modules/nf-core/abricate/summary/meta.yml index 71f1ac27605..04153776124 100644 --- a/modules/nf-core/abricate/summary/meta.yml +++ b/modules/nf-core/abricate/summary/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/tseemann/abricate tool_dev_url: https://github.com/tseemann/abricate licence: ["GPL v2"] + identifier: biotools:ABRicate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reports: - type: file - description: FASTA, GenBank or EMBL formatted file - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reports: + type: file + description: FASTA, GenBank or EMBL formatted file + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Tab-delimited report of aggregated results - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab-delimited report of aggregated results + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/abritamr/run/meta.yml b/modules/nf-core/abritamr/run/meta.yml index a3262a9a2a6..57fefad91c6 100644 --- a/modules/nf-core/abritamr/run/meta.yml +++ b/modules/nf-core/abritamr/run/meta.yml @@ -1,54 +1,88 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "abritamr_run" -description: A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes +description: A NATA accredited tool for reporting the presence of antimicrobial resistance + genes in bacterial genomes keywords: - bacteria - fasta - antibiotic resistance tools: - "abritamr": - description: "A pipeline for running AMRfinderPlus and collating results into functional classes" + description: "A pipeline for running AMRfinderPlus and collating results into + functional classes" homepage: "https://github.com/MDU-PHL/abritamr" documentation: "https://github.com/MDU-PHL/abritamr" tool_dev_url: "https://github.com/MDU-PHL/abritamr" doi: "10.1038/s41467-022-35713-4" licence: ["GPL v3"] + identifier: biotools:abritamr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Assembled contigs in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Assembled contigs in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - matches: - type: file - description: Tab-delimited file, with a row per sequence, and columns representing functional drug classes - pattern: "*.summary_matches.txt" + - meta: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + functional drug classes + pattern: "*.summary_matches.txt" + - ${prefix}.summary_matches.txt: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + functional drug classes + pattern: "*.summary_matches.txt" - partials: - type: file - description: Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes - pattern: "*.summary_partials.txt" + - meta: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + partial hits to functional drug classes + pattern: "*.summary_partials.txt" + - ${prefix}.summary_partials.txt: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + partial hits to functional drug classes + pattern: "*.summary_partials.txt" - virulence: - type: string - description: Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification - pattern: "*.summary_virulence.txt" - - txt: - type: string - description: Tab-delimited file, combining non-empty summary files - pattern: "*.abritamr.txt" + - meta: + type: string + description: Tab-delimited file, with a row per sequence, and columns representing + AMRFinderPlus virulence gene classification + pattern: "*.summary_virulence.txt" + - ${prefix}.summary_virulence.txt: + type: string + description: Tab-delimited file, with a row per sequence, and columns representing + AMRFinderPlus virulence gene classification + pattern: "*.summary_virulence.txt" - out: - type: string - description: raw output from AMRFinder plus (per sequence) - pattern: "*.amrfinder.txt" + - meta: + type: string + description: raw output from AMRFinder plus (per sequence) + pattern: "*.amrfinder.txt" + - ${prefix}.amrfinder.out: + type: string + description: raw output from AMRFinder plus (per sequence) + pattern: "*.amrfinder.txt" + - txt: + - meta: + type: string + description: Tab-delimited file, combining non-empty summary files + pattern: "*.abritamr.txt" + - ${prefix}.abritamr.txt: + type: string + description: Tab-delimited file, combining non-empty summary files + pattern: "*.abritamr.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/adapterremoval/meta.yml b/modules/nf-core/adapterremoval/meta.yml index 2deb613b5a1..e4859571cd5 100644 --- a/modules/nf-core/adapterremoval/meta.yml +++ b/modules/nf-core/adapterremoval/meta.yml @@ -11,67 +11,120 @@ tools: homepage: https://github.com/MikkelSchubert/adapterremoval documentation: https://adapterremoval.readthedocs.io licence: ["GPL v3"] + identifier: biotools:adapterremoval input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - adapterlist: - type: file - description: Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - - adapterlist: + type: file + description: Optional text file containing list of adapters to look for for + removal with one adapter per line. Otherwise will look for default adapters + (see AdapterRemoval man page), or can be modified to remove user-specified + adapters via ext.args. output: - singles_truncated: - type: file - description: | - Adapter trimmed FastQ files of either single-end reads, or singleton - 'orphaned' reads from merging of paired-end data (i.e., one of the pair - was lost due to filtering thresholds). - pattern: "*.truncated.fastq.gz" + - meta: + type: file + description: | + Adapter trimmed FastQ files of either single-end reads, or singleton + 'orphaned' reads from merging of paired-end data (i.e., one of the pair + was lost due to filtering thresholds). + pattern: "*.truncated.fastq.gz" + - ${prefix}.truncated.fastq.gz: + type: file + description: | + Adapter trimmed FastQ files of either single-end reads, or singleton + 'orphaned' reads from merging of paired-end data (i.e., one of the pair + was lost due to filtering thresholds). + pattern: "*.truncated.fastq.gz" - discarded: - type: file - description: | - Adapter trimmed FastQ files of reads that did not pass filtering - thresholds. - pattern: "*.discarded.fastq.gz" + - meta: + type: file + description: | + Adapter trimmed FastQ files of reads that did not pass filtering + thresholds. + pattern: "*.discarded.fastq.gz" + - ${prefix}.discarded.fastq.gz: + type: file + description: | + Adapter trimmed FastQ files of reads that did not pass filtering + thresholds. + pattern: "*.discarded.fastq.gz" - paired_truncated: - type: file - description: | - Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge - with their respective R{1,2} pair due to long templates. The respective pair - is stored in 'pair{1,2}_truncated'. - pattern: "*.pair{1,2}.truncated.fastq.gz" + - meta: + type: file + description: | + Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge + with their respective R{1,2} pair due to long templates. The respective pair + is stored in 'pair{1,2}_truncated'. + pattern: "*.pair{1,2}.truncated.fastq.gz" + - ${prefix}.pair{1,2}.truncated.fastq.gz: + type: file + description: | + Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge + with their respective R{1,2} pair due to long templates. The respective pair + is stored in 'pair{1,2}_truncated'. + pattern: "*.pair{1,2}.truncated.fastq.gz" - collapsed: - type: file - description: | - Collapsed FastQ of paired-end reads that successfully merged with their - respective R1 pair but were not trimmed. - pattern: "*.collapsed.fastq.gz" + - meta: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair but were not trimmed. + pattern: "*.collapsed.fastq.gz" + - ${prefix}.collapsed.fastq.gz: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair but were not trimmed. + pattern: "*.collapsed.fastq.gz" - collapsed_truncated: - type: file - description: | - Collapsed FastQ of paired-end reads that successfully merged with their - respective R1 pair and were trimmed of adapter due to sufficient overlap. - pattern: "*.collapsed.truncated.fastq.gz" + - meta: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair and were trimmed of adapter due to sufficient overlap. + pattern: "*.collapsed.truncated.fastq.gz" + - ${prefix}.collapsed.truncated.fastq.gz: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair and were trimmed of adapter due to sufficient overlap. + pattern: "*.collapsed.truncated.fastq.gz" - paired_interleaved: - type: file - description: | - Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads - pattern: "*.paired.fastq.gz" + - meta: + type: file + description: | + Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads + pattern: "*.paired.fastq.gz" + - ${prefix}.paired.fastq.gz: + type: file + description: | + Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads + pattern: "*.paired.fastq.gz" - settings: - type: file - description: AdapterRemoval log file - pattern: "*.settings" + - meta: + type: file + description: AdapterRemoval log file + pattern: "*.settings" + - "*.settings": + type: file + description: AdapterRemoval log file + pattern: "*.settings" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/adapterremovalfixprefix/meta.yml b/modules/nf-core/adapterremovalfixprefix/meta.yml index fe3a0f7006e..f9ecdb6d699 100644 --- a/modules/nf-core/adapterremovalfixprefix/meta.yml +++ b/modules/nf-core/adapterremovalfixprefix/meta.yml @@ -1,40 +1,45 @@ name: adapterremovalfixprefix -description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup. +description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read + names are in the output. For use with DeDup. keywords: - adapterremoval - fastq - dedup tools: - adapterremovalfixprefix: - description: Fixes adapter removal prefixes to make sure no clashing read names are in the output. + description: Fixes adapter removal prefixes to make sure no clashing read names + are in the output. homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file from AdapterRemoval2 - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file from AdapterRemoval2 + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fixed_fastq: - type: file - description: FASTQ file with fixed read prefixes for DeDup - pattern: "*.{fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: FASTQ file with fixed read prefixes for DeDup + pattern: "*.{fq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/admixture/meta.yml b/modules/nf-core/admixture/meta.yml index 06aa57ff752..bbb72fef0a4 100644 --- a/modules/nf-core/admixture/meta.yml +++ b/modules/nf-core/admixture/meta.yml @@ -1,5 +1,7 @@ name: "admixture" -description: ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). +description: ADMIXTURE is a program for estimating ancestry in a model-based manner + from large autosomal SNP genotype datasets, where the individuals are unrelated + (for example, the individuals in a case-control association study). keywords: - ancestry - population genetics @@ -8,51 +10,70 @@ keywords: - gwas tools: - "admixture": - description: "ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets." + description: "ADMIXTURE is a software tool for maximum likelihood estimation of + individual ancestries from multilocus SNP genotype datasets." homepage: "https://dalexander.github.io/admixture/" documentation: "https://dalexander.github.io/admixture/admixture-manual.pdf" doi: "10.1101/gr.094052.109" licence: ["Free for Academic Use"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed_ped_geno: - type: file - description: One of PLINK ".bed" file or PLINK ".ped" or EIGENSTRAT ".geno" file. If you provide ".bed" then you need to provide ".bim" and "fam" files. If you provide ".ped" or ".geno" then you need to provide a ".map" file and an empty channel. - pattern: "*.{bed}" - - bim_map: - type: file - description: Mandatory accompanying file. One of PLINK ".bim" file or PLINK ".map" file. Provide ".bim" if ".bed" is the input. Provide ".map" if ".ped" or ".geno" is the input. - pattern: "*.{bim}" - - fam: - type: file - description: PLINK ".fam" file. Mandatory if you provide ".bed" as input. Replace with an empty channel if input is ".ped" or ".geno". - pattern: "*.{fam}" - - K: - type: integer - description: Belief of the number of ancestral populations. - pattern: "{*}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed_ped_geno: + type: file + description: One of PLINK ".bed" file or PLINK ".ped" or EIGENSTRAT ".geno" + file. If you provide ".bed" then you need to provide ".bim" and "fam" files. + If you provide ".ped" or ".geno" then you need to provide a ".map" file and + an empty channel. + pattern: "*.{bed}" + - bim_map: + type: file + description: Mandatory accompanying file. One of PLINK ".bim" file or PLINK + ".map" file. Provide ".bim" if ".bed" is the input. Provide ".map" if ".ped" + or ".geno" is the input. + pattern: "*.{bim}" + - fam: + type: file + description: PLINK ".fam" file. Mandatory if you provide ".bed" as input. Replace + with an empty channel if input is ".ped" or ".geno". + pattern: "*.{fam}" + - - K: + type: integer + description: Belief of the number of ancestral populations. + pattern: "{*}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ancestry_fractions: - type: file - description: Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis. - pattern: "*.{Q}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Q": + type: file + description: Space-delimited files containing ancestry fractions. The output + filenames have the number of populations (K) that was assumed for the analysis. + pattern: "*.{Q}" - allele_frequencies: - type: file - description: Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis. - pattern: "*.{P}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.P": + type: file + description: Space-delimited files containing the allele frequencies of the + inferred ancestral populations. The output filenames have the number of populations + (K) that was assumed for the analysis. + pattern: "*.{P}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/affy/justrma/meta.yml b/modules/nf-core/affy/justrma/meta.yml index cd9b6d6cbec..54a7beeeeef 100644 --- a/modules/nf-core/affy/justrma/meta.yml +++ b/modules/nf-core/affy/justrma/meta.yml @@ -13,46 +13,66 @@ tools: tool_dev_url: "https://github.com/Bioconductor/affy" doi: "10.1093/bioinformatics/btg405" licence: ["LGPL >=2.0"] + identifier: biotools:affy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata and CEL file names - - celfiles_dir: - type: list - description: Path to a directory containing CEL files - pattern: "*.{CEL,CEL.gz}" - - description: - type: file - description: | - Optional description file in MIAME format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata and CEL file names + - celfiles_dir: + type: list + description: Path to a directory containing CEL files + pattern: "*.{CEL,CEL.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - description: + type: file + description: | + Optional description file in MIAME format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + - rds: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.rds": + type: file + description: Serialised ExpressionSet object + pattern: "*.rds" - expression: - type: file - description: TSV-format intensity matrix - pattern: "matrix.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*matrix.tsv": + type: file + description: TSV-format intensity matrix + pattern: "matrix.tsv" - annotation: - type: file - description: TSV-format annotation table - pattern: "*.annotation.tsv" - - rds: - type: file - description: Serialised ExpressionSet object - pattern: "*.rds" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.annotation.tsv": + type: file + description: TSV-format annotation table + pattern: "*.annotation.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/agat/convertspgff2gtf/meta.yml b/modules/nf-core/agat/convertspgff2gtf/meta.yml index ab39f019b4e..5330167c08f 100644 --- a/modules/nf-core/agat/convertspgff2gtf/meta.yml +++ b/modules/nf-core/agat/convertspgff2gtf/meta.yml @@ -8,35 +8,48 @@ keywords: - conversion tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - output_gtf: - type: file - description: Annotation file in GTF format - pattern: "*.{gtf}" + - meta: + type: file + description: Annotation file in GTF format + pattern: "*.{gtf}" + - "*.agat.gtf": + type: file + description: Annotation file in GTF format + pattern: "*.{gtf}" - log: - type: file - description: Log file of the conversion process - pattern: "*.{log}" + - meta: + type: file + description: Log file of the conversion process + pattern: "*.{log}" + - "*.log": + type: file + description: Log file of the conversion process + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agat/convertspgff2tsv/meta.yml b/modules/nf-core/agat/convertspgff2tsv/meta.yml index 83078787b73..31f0986837e 100644 --- a/modules/nf-core/agat/convertspgff2tsv/meta.yml +++ b/modules/nf-core/agat/convertspgff2tsv/meta.yml @@ -9,31 +9,39 @@ keywords: - tsv tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - tsv: - type: file - description: Annotation file in TSV format - pattern: "*.{gtf}" + - meta: + type: file + description: Annotation file in TSV format + pattern: "*.{gtf}" + - "*.tsv": + type: file + description: Annotation file in TSV format + pattern: "*.{gtf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/agat/convertspgxf2gxf/meta.yml b/modules/nf-core/agat/convertspgxf2gxf/meta.yml index 0ef9881400a..d9468ec47eb 100644 --- a/modules/nf-core/agat/convertspgxf2gxf/meta.yml +++ b/modules/nf-core/agat/convertspgxf2gxf/meta.yml @@ -8,35 +8,48 @@ keywords: - conversion tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gxf: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gxf: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - output_gff: - type: file - description: Cleaned annotation file in GFF3 format - pattern: "*.{gff}" + - meta: + type: file + description: Cleaned annotation file in GFF3 format + pattern: "*.{gff}" + - "*.agat.gff": + type: file + description: Cleaned annotation file in GFF3 format + pattern: "*.{gff}" - log: - type: file - description: Log file of the conversion process - pattern: "*.{log}" + - meta: + type: file + description: Log file of the conversion process + pattern: "*.{log}" + - "*.log": + type: file + description: Log file of the conversion process + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agat/spaddintrons/meta.yml b/modules/nf-core/agat/spaddintrons/meta.yml index 666e6037622..03f17b9f9d2 100644 --- a/modules/nf-core/agat/spaddintrons/meta.yml +++ b/modules/nf-core/agat/spaddintrons/meta.yml @@ -6,37 +6,43 @@ keywords: - introns tools: - agat: - description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." + description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene + annotations in any GTF/GFF format." homepage: "https://agat.readthedocs.io/en/latest/" documentation: "https://agat.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/NBISweden/AGAT" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Input gtf/gff file - pattern: "*.{gff,gff3,gtf}" - - config: - type: file - description: Optional input agat config file - pattern: "*.{yaml,yml}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Input gtf/gff file + pattern: "*.{gff,gff3,gtf}" + - - config: + type: file + description: Optional input agat config file + pattern: "*.{yaml,yml}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: Output gff3 file with introns - pattern: "*.gff" - + - meta: + type: file + description: Output gff3 file with introns + pattern: "*.gff" + - ${output}: + type: file + description: Output gff3 file with introns + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml index d408fe7fe3b..d6c8dbb783a 100644 --- a/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml +++ b/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "agat_spfilterfeaturefromkilllist" description: | @@ -13,47 +12,49 @@ keywords: - feature tools: - "agat": - description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." + description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene + annotations in any GTF/GFF format." homepage: "https://agat.readthedocs.io/en/latest/" documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - gff: - type: file - description: Input GFF3 file that will be read - pattern: "*.{gff,gff3}" - - kill_list: - type: file - description: Kill list. One value per line. - pattern: "*.txt" - - config: - type: file - description: | - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). - pattern: "*.yaml" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gff: + type: file + description: Input GFF3 file that will be read + pattern: "*.{gff,gff3}" + - - kill_list: + type: file + description: Kill list. One value per line. + pattern: "*.txt" + - - config: + type: file + description: | + Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: Output GFF file. - pattern: "*.gff" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ] + - "*.gff": + type: file + description: Output GFF file. + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/agat/spmergeannotations/meta.yml b/modules/nf-core/agat/spmergeannotations/meta.yml index afa9ddd0e7d..fd5083b70e5 100644 --- a/modules/nf-core/agat/spmergeannotations/meta.yml +++ b/modules/nf-core/agat/spmergeannotations/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "agat_spmergeannotations" description: | @@ -10,44 +9,48 @@ keywords: - combine tools: - "agat": - description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." + description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene + annotations in any GTF/GFF format." homepage: "https://agat.readthedocs.io/en/latest/" documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gffs: - type: list - description: A list of GFFs to merge - pattern: "[ *.{gff,gff3} ]" - - config: - type: file - description: | - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, - otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml - locally type: "agat config --expose". The --config option gives you the possibility to use your - own AGAT config file (located elsewhere or named differently). - pattern: "*.yaml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gffs: + type: list + description: A list of GFFs to merge + pattern: "[ *.{gff,gff3} ]" + - - config: + type: file + description: | + Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml + locally type: "agat config --expose". The --config option gives you the possibility to use your + own AGAT config file (located elsewhere or named differently). + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: Output GFF file. - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff": + type: file + description: Output GFF file. + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/agat/spstatistics/meta.yml b/modules/nf-core/agat/spstatistics/meta.yml index c6cb21dda30..a2f897b8a64 100644 --- a/modules/nf-core/agat/spstatistics/meta.yml +++ b/modules/nf-core/agat/spstatistics/meta.yml @@ -8,31 +8,39 @@ keywords: - statistics tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - stats_txt: - type: file - description: Output of Statistics execution - pattern: "*.{txt}" + - meta: + type: file + description: Output of Statistics execution + pattern: "*.{txt}" + - "*.txt": + type: file + description: Output of Statistics execution + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agat/sqstatbasic/meta.yml b/modules/nf-core/agat/sqstatbasic/meta.yml index aba57e896ae..b813a4a8169 100644 --- a/modules/nf-core/agat/sqstatbasic/meta.yml +++ b/modules/nf-core/agat/sqstatbasic/meta.yml @@ -8,31 +8,39 @@ keywords: - statistics tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - stats_txt: - type: file - description: Output of Statistics execution - pattern: "*.{txt}" + - meta: + type: file + description: Output of Statistics execution + pattern: "*.{txt}" + - "*.txt": + type: file + description: Output of Statistics execution + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agrvate/meta.yml b/modules/nf-core/agrvate/meta.yml index 0e11d8b296a..8b45db81914 100644 --- a/modules/nf-core/agrvate/meta.yml +++ b/modules/nf-core/agrvate/meta.yml @@ -1,44 +1,50 @@ name: agrvate -description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants +description: Rapid identification of Staphylococcus aureus agr locus type and agr + operon variants keywords: - fasta - virulence - Staphylococcus aureus tools: - agrvate: - description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. + description: Rapid identification of Staphylococcus aureus agr locus type and + agr operon variants. homepage: https://github.com/VishnuRaghuram94/AgrVATE documentation: https://github.com/VishnuRaghuram94/AgrVATE tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE licence: ["MIT"] + identifier: biotools:agrvate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A Staphylococcus aureus fasta file. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A Staphylococcus aureus fasta file. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - summary: - type: file - description: A summary of the agrvate assessement - pattern: "*-summary.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${fasta.baseName}-results/${fasta.baseName}-summary.tab: + type: file + description: A summary of the agrvate assessement + pattern: "*-summary.tab" - results_dir: - type: directory - description: Results of the agrvate assessement - pattern: "*-results" + - ${fasta.baseName}-results: + type: directory + description: Results of the agrvate assessement + pattern: "*-results" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/ale/meta.yml b/modules/nf-core/ale/meta.yml index 6191741e1ea..6ada6fa314c 100644 --- a/modules/nf-core/ale/meta.yml +++ b/modules/nf-core/ale/meta.yml @@ -1,4 +1,3 @@ ---- name: "ale" description: "ALE: assembly likelihood estimator." keywords: @@ -7,44 +6,44 @@ keywords: - evaluation tools: - "ale": - description: "ALE is a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies." + description: "ALE is a generic assembly likelihood evaluation framework for assessing + the accuracy of genome and metagenome assemblies." documentation: "https://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#document-install" tool_dev_url: "https://github.com/sc932/ALE" doi: "10.1093/bioinformatics/bts723" licence: ["NCSA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - asm: - type: file - description: Assembly in FASTA format - pattern: "*.{fasta,fa}" - - - bam: - type: file - description: BAM file containing sorted read mappings - pattern: "*.{bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - asm: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fa}" + - bam: + type: file + description: BAM file containing sorted read mappings + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - ale: - type: file - description: Output TXT file containing ALE results - pattern: "*_ALEoutput.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_ALEoutput.txt": + type: file + description: Output TXT file containing ALE results + pattern: "*_ALEoutput.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rodtheo" maintainers: diff --git a/modules/nf-core/allelecounter/meta.yml b/modules/nf-core/allelecounter/meta.yml index 751b9f97b44..fce9123d704 100644 --- a/modules/nf-core/allelecounter/meta.yml +++ b/modules/nf-core/allelecounter/meta.yml @@ -6,46 +6,50 @@ keywords: - coverage tools: - allelecounter: - description: Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings) + description: Takes a file of locations and a [cr|b]am file and generates a count + of coverage of each allele at that location (given any filter settings) homepage: https://github.com/cancerit/alleleCount documentation: https://github.com/cancerit/alleleCount tool_dev_url: https://github.com/cancerit/alleleCount licence: ["GPL 3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - loci: - type: file - description: loci file - pattern: "*.{tsv}" - - fasta: - type: file - description: Input genome fasta file. Required when passing CRAM files. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - - loci: + type: file + description: loci file + pattern: "*.{tsv}" + - - fasta: + type: file + description: Input genome fasta file. Required when passing CRAM files. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - allelecount: - type: file - description: Allele count file - pattern: "*.{alleleCount}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.alleleCount": + type: file + description: Allele count file + pattern: "*.{alleleCount}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fullama" - "@fbdtemme" diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml index 21ec05e613e..1e945daa712 100644 --- a/modules/nf-core/ampcombi/environment.yml +++ b/modules/nf-core/ampcombi/environment.yml @@ -1,9 +1,8 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - bioconda::ampcombi=0.1.7 - - python=3.11 - pandas=1.5.2 + - python=3.11 diff --git a/modules/nf-core/ampcombi/meta.yml b/modules/nf-core/ampcombi/meta.yml index be104d1770b..152d0b294de 100644 --- a/modules/nf-core/ampcombi/meta.yml +++ b/modules/nf-core/ampcombi/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi" -description: A tool to parse and summarise results from antimicrobial peptides tools and present functional classification. +description: A tool to parse and summarise results from antimicrobial peptides tools + and present functional classification. keywords: - antimicrobial peptides - amps @@ -16,83 +16,164 @@ keywords: - DRAMP tools: - ampcombi: - description: "This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications." + description: "This tool parses the results of amp prediction tools into a single + table and aligns the hits against a reference database of antimicrobial peptides + for functional classifications." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - amp_input: - type: list - description: The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools. - pattern: "[*amptool.tsv, *amptool.tsv]" - - faa_input: - type: file - description: The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa - pattern: "*.faa" - - opt_amp_db: - type: directory - description: The path to the folder containing the fasta and tsv database files. - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_input: + type: list + description: The path to the directory containing the results for the AMP tools + for each sample processed or a list of files corresponding to each file generated + by AMP tools. + pattern: "[*amptool.tsv, *amptool.tsv]" + - - faa_input: + type: file + description: The path to the file corresponding to the respective protein fasta + files with '.faa' extension. File names have to contain the corresponding + sample name, i.e. sample_1.faa + pattern: "*.faa" + - - opt_amp_db: + type: directory + description: The path to the folder containing the fasta and tsv database files. + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_dir: - type: directory - description: The output directory that contains the summary output and related alignment files for one sample. - pattern: "/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/: + type: directory + description: The output directory that contains the summary output and related + alignment files for one sample. + pattern: "/*" - txt: - type: file - description: An alignment file containing the results from the DIAMOND alignment step done on all AMP hits. - pattern: "/*/*_diamond_matches.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*diamond_matches.txt: + type: file + description: An alignment file containing the results from the DIAMOND alignment + step done on all AMP hits. + pattern: "/*/*_diamond_matches.txt" - csv: - type: file - description: A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step. - pattern: "/*/*_ampcombi.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*ampcombi.csv: + type: file + description: A file containing the summary report of all predicted AMP hits + from all AMP tools given as input and the corresponding taxonomic and functional + classification from the alignment step. + pattern: "/*/*_ampcombi.csv" - faa: - type: file - description: A fasta file containing the amino acid sequences of all predicted AMP hits. - pattern: "/*/*_amp.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*amp.faa: + type: file + description: A fasta file containing the amino acid sequences of all predicted + AMP hits. + pattern: "/*/*_amp.faa" - summary_csv: - type: file - description: A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`. - pattern: "AMPcombi_summary.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - AMPcombi_summary.csv: + type: file + description: A file that concatenates all samples ampcombi summaries. This is + activated with `--complete_summary true`. + pattern: "AMPcombi_summary.csv" - summary_html: - type: file - description: A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`. - pattern: "AMPcombi_summary.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - AMPcombi_summary.html: + type: file + description: A file that concatenates all samples ampcombi summaries. This is + activated with `--complete_summary true`. + pattern: "AMPcombi_summary.html" - log: - type: file - description: A log file that captures the standard output ina log file. Can be activated by `--log`. - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: A log file that captures the standard output ina log file. Can + be activated by `--log`. + pattern: "*.log" - results_db: - type: directory - description: If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. - pattern: "/amp_ref_database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/: + type: directory + description: If the AMP reference database is not provided by the user using + the flag `--amp_database', by default the DRAMP database will be downloaded, + filtered and stored in this folder. + pattern: "/amp_ref_database" - results_db_dmnd: - type: file - description: AMP reference database converted to DIAMOND database format. - pattern: "/amp_ref_database/*.dmnd" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/*.dmnd: + type: file + description: AMP reference database converted to DIAMOND database format. + pattern: "/amp_ref_database/*.dmnd" - results_db_fasta: - type: file - description: AMP reference database fasta file, cleaned of diamond-uncompatible characters. - pattern: "/amp_ref_database/*.clean.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/*.clean.fasta: + type: file + description: AMP reference database fasta file, cleaned of diamond-uncompatible + characters. + pattern: "/amp_ref_database/*.clean.fasta" - results_db_tsv: - type: file - description: AMP reference database in tsv-format with two columns containing header and sequence. - pattern: "/amp_ref_database/*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/*.tsv: + type: file + description: AMP reference database in tsv-format with two columns containing + header and sequence. + pattern: "/amp_ref_database/*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" - "@louperelo" diff --git a/modules/nf-core/ampcombi2/cluster/meta.yml b/modules/nf-core/ampcombi2/cluster/meta.yml index 60949dc34c6..2e37a0c2fad 100644 --- a/modules/nf-core/ampcombi2/cluster/meta.yml +++ b/modules/nf-core/ampcombi2/cluster/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi2_cluster" -description: A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster. +description: A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables + and ampcombi2/complete using MMseqs2 cluster. keywords: - antimicrobial peptides - amps @@ -12,36 +12,46 @@ keywords: - mmseqs2 tools: - ampcombi2/cluster: - description: "A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools." + description: "A tool for clustering all AMP hits found across many samples and + supporting many AMP prediction tools." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - summary_file: - type: file - description: A file corresponding to the Ampcombi_summary.tsv that is generated by running 'ampcombi complete'. It is a file containing all the merged AMP results from all samples and all tools. - pattern: "*.tsv" - + - - summary_file: + type: file + description: A file corresponding to the Ampcombi_summary.tsv that is generated + by running 'ampcombi complete'. It is a file containing all the merged AMP + results from all samples and all tools. + pattern: "*.tsv" output: - cluster_tsv: - type: file - description: A file containing all the results from the merged input table 'Ampcombi_summary.tsv', but also including the cluster id number. The clustering is done using MMseqs2 cluster. - pattern: "*.tsv" + - Ampcombi_summary_cluster.tsv: + type: file + description: A file containing all the results from the merged input table 'Ampcombi_summary.tsv', + but also including the cluster id number. The clustering is done using MMseqs2 + cluster. + pattern: "*.tsv" - rep_cluster_tsv: - type: file - description: A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster. - pattern: "*.tsv" + - Ampcombi_summary_cluster_representative_seq.tsv: + type: file + description: A file containing the representative sequences of the clusters + estimated by the tool. The clustering is done using MMseqs2 cluster. + pattern: "*.tsv" - log: - type: file - description: A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. - pattern: "*.log" + - Ampcombi_cluster.log: + type: file + description: A log file that captures the standard output for the entire process + in a log file. Can be activated by `--log`. + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/ampcombi2/complete/meta.yml b/modules/nf-core/ampcombi2/complete/meta.yml index e9ae632c644..13a7468bc9b 100644 --- a/modules/nf-core/ampcombi2/complete/meta.yml +++ b/modules/nf-core/ampcombi2/complete/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi2_complete" -description: A submodule that merges all output summary tables from ampcombi/parsetables in one summary file. +description: A submodule that merges all output summary tables from ampcombi/parsetables + in one summary file. keywords: - antimicrobial peptides - amps @@ -18,32 +18,38 @@ keywords: - DRAMP tools: - ampcombi2/complete: - description: "This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'." + description: "This merges the per sample AMPcombi summaries generated by running + 'ampcombi2/parsetables'." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - summaries: - type: list - description: The path to the list of files corresponding to each sample as generated by ampcombi2/parsetables. - pattern: "[*_ampcombi.tsv, *_ampcombi.tsv]" - + - - summaries: + type: list + description: The path to the list of files corresponding to each sample as generated + by ampcombi2/parsetables. + pattern: "[*_ampcombi.tsv, *_ampcombi.tsv]" output: - tsv: - type: file - description: A file containing the complete AMPcombi summaries from all processed samples. - pattern: "*.tsv" + - Ampcombi_summary.tsv: + type: file + description: A file containing the complete AMPcombi summaries from all processed + samples. + pattern: "*.tsv" - log: - type: file - description: A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. - pattern: "*.log" + - Ampcombi_complete.log: + type: file + description: A log file that captures the standard output for the entire process + in a log file. Can be activated by `--log`. + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/ampcombi2/parsetables/meta.yml b/modules/nf-core/ampcombi2/parsetables/meta.yml index eeea5586cd1..7159b117739 100644 --- a/modules/nf-core/ampcombi2/parsetables/meta.yml +++ b/modules/nf-core/ampcombi2/parsetables/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi2_parsetables" -description: A submodule that parses and standardizes the results from various antimicrobial peptide identification tools. +description: A submodule that parses and standardizes the results from various antimicrobial + peptide identification tools. keywords: - antimicrobial peptides - amps @@ -18,89 +18,171 @@ keywords: - DRAMP tools: - ampcombi2/parsetables: - description: "A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format." + description: "A parsing tool to convert and summarise the outputs from multiple + AMP detection tools in a standardized format." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - amp_input: - type: list - description: The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools. - pattern: "[*amptool.tsv, *amptool.tsv]" - - faa_input: - type: file - description: The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa - pattern: "*.faa" - - gbk_input: - type: file - description: The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where "sample_1" is the sample name. - pattern: "*.gbk" - - opt_amp_db: - type: directory - description: The path to the folder containing the fasta and tsv database files. - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_input: + type: list + description: The path to the directory containing the results for the AMP tools + for each processed sample or a list of files corresponding to each file generated + by AMP tools. + pattern: "[*amptool.tsv, *amptool.tsv]" + - - faa_input: + type: file + description: The path to the file corresponding to the respective protein fasta + files with '.faa' extension. File names have to contain the corresponding + sample name, i.e. sample_1.faa + pattern: "*.faa" + - - gbk_input: + type: file + description: The path to the file corresponding to the respective annotated + files with either '.gbk' or '.gbff' extensions. File names must contain the + corresponding sample name, i.e. sample_1.faa where "sample_1" is the sample + name. + pattern: "*.gbk" + - - opt_amp_db: + type: directory + description: The path to the folder containing the fasta and tsv database files. + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - sample_dir: - type: directory - description: The output directory that contains the summary output and related alignment files for one sample. - pattern: "/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/: + type: directory + description: The output directory that contains the summary output and related + alignment files for one sample. + pattern: "/*" - contig_gbks: - type: directory - description: The output subdirectory that contains the gbk files containing the AMP hits for each sample. - pattern: "/*/contig_gbks" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/contig_gbks/: + type: directory + description: The output subdirectory that contains the gbk files containing + the AMP hits for each sample. + pattern: "/*/contig_gbks" - txt: - type: file - description: An alignment file containing the results from the DIAMOND alignment step done on all AMP hits. - pattern: "/*/*_diamond_matches.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_diamond_matches.txt: + type: file + description: An alignment file containing the results from the DIAMOND alignment + step done on all AMP hits. + pattern: "/*/*_diamond_matches.txt" - tsv: - type: file - description: A file containing the summary report of all predicted AMP hits from all AMP tools given as input, the corresponding taxonomic and functional classification from the alignment step and the estimated physiochemical properties. - pattern: "/*/*_ampcombi.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_ampcombi.tsv: + type: file + description: A file containing the summary report of all predicted AMP hits + from all AMP tools given as input, the corresponding taxonomic and functional + classification from the alignment step and the estimated physiochemical properties. + pattern: "/*/*_ampcombi.tsv" - faa: - type: file - description: A fasta file containing the amino acid sequences of all predicted AMP hits. - pattern: "/*/*_amp.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_amp.faa: + type: file + description: A fasta file containing the amino acid sequences of all predicted + AMP hits. + pattern: "/*/*_amp.faa" - sample_log: - type: file - description: A log file that captures the standard output per sample in a log file. Can be activated by `--log`. - pattern: "/*/*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_ampcombi.log: + type: file + description: A log file that captures the standard output per sample in a log + file. Can be activated by `--log`. + pattern: "/*/*.log" - full_log: - type: file - description: A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. - pattern: "Ampcombi_parse_tables.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - Ampcombi_parse_tables.log: + type: file + description: A log file that captures the standard output for the entire process + in a log file. Can be activated by `--log`. + pattern: "Ampcombi_parse_tables.log" - results_db: - type: directory - description: If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. - pattern: "/amp_ref_database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/: + type: directory + description: If the AMP reference database is not provided by the user using + the flag `--amp_database', by default the DRAMP database will be downloaded, + filtered and stored in this folder. + pattern: "/amp_ref_database" - results_db_dmnd: - type: file - description: AMP reference database converted to DIAMOND database format. - pattern: "/amp_ref_database/*.dmnd" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/*.dmnd: + type: file + description: AMP reference database converted to DIAMOND database format. + pattern: "/amp_ref_database/*.dmnd" - results_db_fasta: - type: file - description: AMP reference database fasta file, cleaned of diamond-uncompatible characters. - pattern: "/amp_ref_database/*.clean.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/*.clean.fasta: + type: file + description: AMP reference database fasta file, cleaned of diamond-uncompatible + characters. + pattern: "/amp_ref_database/*.clean.fasta" - results_db_tsv: - type: file - description: AMP reference database in tsv-format with two columns containing header and sequence. - pattern: "/amp_ref_database/*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/*.tsv: + type: file + description: AMP reference database in tsv-format with two columns containing + header and sequence. + pattern: "/amp_ref_database/*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/ampir/meta.yml b/modules/nf-core/ampir/meta.yml index 231cec54e2e..571ddd86a57 100644 --- a/modules/nf-core/ampir/meta.yml +++ b/modules/nf-core/ampir/meta.yml @@ -1,57 +1,69 @@ name: "ampir" -description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs. +description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) + from any given size protein dataset. ampir uses a supervised statistical machine + learning approach to predict AMPs. keywords: - ampir - amp - antimicrobial peptide prediction tools: - "ampir": - description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale." + description: "A toolkit to predict antimicrobial peptides from protein sequences + on a genome-wide scale." homepage: "https://github.com/Legana/ampir" documentation: "https://cran.r-project.org/web/packages/ampir/index.html" tool_dev_url: "https://github.com/Legana/ampir" doi: "10.1093/bioinformatics/btaa653" licence: ["GPL v2"] + identifier: biotools:ampir input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - faa: - type: file - description: FASTA file containing amino acid sequences - pattern: "*.{faa,fasta}" - - model: - type: string - description: Built-in model for AMP prediction - pattern: "{precursor,mature}" - - min_length: - type: integer - description: Minimum protein length for which predictions will be generated - pattern: "[0-9]+" - - min_probability: - type: float - description: Cut-off for AMP prediction - pattern: "[0-9].[0-9]+" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - faa: + type: file + description: FASTA file containing amino acid sequences + pattern: "*.{faa,fasta}" + - - model: + type: string + description: Built-in model for AMP prediction + pattern: "{precursor,mature}" + - - min_length: + type: integer + description: Minimum protein length for which predictions will be generated + pattern: "[0-9]+" + - - min_probability: + type: float + description: Cut-off for AMP prediction + pattern: "[0-9].[0-9]+" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - amps_faa: - type: file - description: File containing AMP predictions in amino acid FASTA format - pattern: "*.{faa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.faa": + type: file + description: File containing AMP predictions in amino acid FASTA format + pattern: "*.{faa}" - amps_tsv: - type: file - description: File containing AMP predictions in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: File containing AMP predictions in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/amplify/predict/meta.yml b/modules/nf-core/amplify/predict/meta.yml index 5ef93c83120..cbe19f3368e 100644 --- a/modules/nf-core/amplify/predict/meta.yml +++ b/modules/nf-core/amplify/predict/meta.yml @@ -1,5 +1,6 @@ name: "amplify_predict" -description: AMPlify is an attentive deep learning model for antimicrobial peptide prediction. +description: AMPlify is an attentive deep learning model for antimicrobial peptide + prediction. keywords: - antimicrobial peptides - AMPs @@ -13,33 +14,37 @@ tools: tool_dev_url: "https://github.com/bcgsc/AMPlify" doi: "10.1186/s12864-022-08310-4" licence: ["GPL v3"] + identifier: biotools:amplify input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - faa: - type: file - description: amino acid sequences fasta - pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}" - - model_dir: - type: directory - description: Directory of where models are stored (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - faa: + type: file + description: amino acid sequences fasta + pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}" + - - model_dir: + type: directory + description: Directory of where models are stored (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: amino acid sequences with prediction (AMP, non-AMP) and probability scores - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: amino acid sequences with prediction (AMP, non-AMP) and probability + scores + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/amps/meta.yml b/modules/nf-core/amps/meta.yml index de9a9da497e..61194067fb8 100644 --- a/modules/nf-core/amps/meta.yml +++ b/modules/nf-core/amps/meta.yml @@ -25,40 +25,46 @@ tools: tool_dev_url: "https://github.com/keyfm/amps" doi: "10.1186/s13059-019-1903-0" licence: ["GPL >=3"] + identifier: "" input: - - maltextract_results: - type: directory - description: MaltExtract output directory - pattern: "results/" - - taxon_list: - type: file - description: List of target taxa to evaluate used in MaltExtract - pattern: "*.txt" - - filter: - type: string - description: The filter mode used in MaltExtract - pattern: "def_anc|default|scan|ancient|crawl" + - - maltextract_results: + type: directory + description: MaltExtract output directory + pattern: "results/" + - - taxon_list: + type: file + description: List of target taxa to evaluate used in MaltExtract + pattern: "*.txt" + - - filter: + type: string + description: The filter mode used in MaltExtract + pattern: "def_anc|default|scan|ancient|crawl" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: Candidate summary heatmap in MultiQC compatible JSON format - pattern: "heatmap_overview_Wevid.json" + - results/heatmap_overview_Wevid.json: + type: file + description: Candidate summary heatmap in MultiQC compatible JSON format + pattern: "heatmap_overview_Wevid.json" - summary_pdf: - type: file - description: Candidate summary heatmap in PDF format - pattern: "heatmap_overview_Wevid.pdf" + - results/heatmap_overview_Wevid.pdf: + type: file + description: Candidate summary heatmap in PDF format + pattern: "heatmap_overview_Wevid.pdf" - tsv: - type: file - description: Candidate summary heatmap in TSV format - pattern: "heatmap_overview_Wevid.tsv" + - results/heatmap_overview_Wevid.tsv: + type: file + description: Candidate summary heatmap in TSV format + pattern: "heatmap_overview_Wevid.tsv" - candidate_pdfs: - type: directory - description: Directory of per sample output PDFs organised by reference - pattern: "pdf_candidate_profiles/" + - results/pdf_candidate_profiles/: + type: directory + description: Directory of per sample output PDFs organised by reference + pattern: "pdf_candidate_profiles/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/amrfinderplus/run/meta.yml b/modules/nf-core/amrfinderplus/run/meta.yml index 465927dffe6..d081a2bda09 100644 --- a/modules/nf-core/amrfinderplus/run/meta.yml +++ b/modules/nf-core/amrfinderplus/run/meta.yml @@ -6,50 +6,64 @@ keywords: - antibiotic resistance tools: - amrfinderplus: - description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences. + description: AMRFinderPlus finds antimicrobial resistance and other genes in protein + or nucleotide sequences. homepage: https://github.com/ncbi/amr/wiki documentation: https://github.com/ncbi/amr/wiki tool_dev_url: https://github.com/ncbi/amr doi: "10.1038/s41598-021-91456-0" licence: ["Public Domain"] + identifier: biotools:amrfinderplus input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide or protein sequences in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - - db: - type: file - description: A compressed tarball of the AMRFinderPlus database to query - pattern: "*.tar.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide or protein sequences in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - db: + type: file + description: A compressed tarball of the AMRFinderPlus database to query + pattern: "*.tar.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: AMRFinder+ final report - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: AMRFinder+ final report + pattern: "*.tsv" - mutation_report: - type: file - description: Report of organism-specific point-mutations - pattern: "*-mutations.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-mutations.tsv: + type: file + description: Report of organism-specific point-mutations + pattern: "*-mutations.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - tool_version: - type: string - description: The version of the tool in string format (useful for downstream tools such as hAMRronization) + - VER: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) - db_version: - type: string - description: The version of the used database in string format (useful for downstream tools such as hAMRronization) + - DBVER: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) authors: - "@rpetit3" - "@louperelo" diff --git a/modules/nf-core/amrfinderplus/update/meta.yml b/modules/nf-core/amrfinderplus/update/meta.yml index 7a9345d6fad..574957e10ab 100644 --- a/modules/nf-core/amrfinderplus/update/meta.yml +++ b/modules/nf-core/amrfinderplus/update/meta.yml @@ -6,27 +6,26 @@ keywords: - antibiotic resistance tools: - amrfinderplus: - description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences. + description: AMRFinderPlus finds antimicrobial resistance and other genes in protein + or nucleotide sequences. homepage: https://github.com/ncbi/amr/wiki documentation: https://github.com/ncbi/amr/wiki tool_dev_url: https://github.com/ncbi/amr doi: "10.1038/s41598-021-91456-0" licence: ["Public Domain"] + identifier: biotools:amrfinderplus # this module does have any input. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: The latest AMRFinder+ database in a compressed tarball - pattern: "*.tar.gz" + - amrfinderdb.tar.gz: + type: file + description: The latest AMRFinder+ database in a compressed tarball + pattern: "*.tar.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/angsd/contamination/meta.yml b/modules/nf-core/angsd/contamination/meta.yml index ffe6428d644..0bfb73d2a41 100644 --- a/modules/nf-core/angsd/contamination/meta.yml +++ b/modules/nf-core/angsd/contamination/meta.yml @@ -1,5 +1,6 @@ name: "angsd_contamination" -description: A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome. +description: A tool to estimate nuclear contamination in males based on heterozygosity + in the female chromosome. keywords: - angsd - population genetics @@ -12,38 +13,42 @@ tools: tool_dev_url: "https://github.com/ANGSD/angsd" doi: "10.1186/s12859-014-0356-4" licence: ["GPL v3", "MIT"] + identifier: biotools:angsd input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - icounts: - type: file - description: Internal format for dumping binary single chrs. Useful for ANGSD contamination - pattern: "*.icnts.gz" - - meta2: - type: map - description: | - Groovy Map containing information related to the hapmap_file. - e.g. [ id:'test' ] - - hapmap_file: - type: file - description: A list of variable sites to look for heterozygosity. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - icounts: + type: file + description: Internal format for dumping binary single chrs. Useful for ANGSD + contamination + pattern: "*.icnts.gz" + - - meta2: + type: map + description: | + Groovy Map containing information related to the hapmap_file. + e.g. [ id:'test' ] + - hapmap_file: + type: file + description: A list of variable sites to look for heterozygosity. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Contamination estimation output. - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Contamination estimation output. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jbv2" maintainers: diff --git a/modules/nf-core/angsd/docounts/meta.yml b/modules/nf-core/angsd/docounts/meta.yml index b1eec87da70..cbde98892f7 100644 --- a/modules/nf-core/angsd/docounts/meta.yml +++ b/modules/nf-core/angsd/docounts/meta.yml @@ -1,5 +1,6 @@ name: "angsd_docounts" -description: Calculates base frequency statistics across reference positions from BAM. +description: Calculates base frequency statistics across reference positions from + BAM. keywords: - angsd - population genetics @@ -13,58 +14,92 @@ tools: tool_dev_url: "https://github.com/ANGSD/angsd" doi: "10.1186/s12859-014-0356-4" licence: ["GPL v3, MIT"] + identifier: biotools:angsd input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A list of BAM or CRAM files - pattern: "*.{bam,cram}" - - bai: - type: file - description: List of BAM/CRAM index files - pattern: "*.{bai,csi}" - - minqfile: - type: file - description: File with individual quality score thresholds - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A list of BAM or CRAM files + pattern: "*.{bam,cram}" + - bai: + type: file + description: List of BAM/CRAM index files + pattern: "*.{bai,csi}" + - minqfile: + type: file + description: File with individual quality score thresholds + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - depth_sample: - type: file - description: Distribution of sequencing depths - pattern: "*.depthSample" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthSample": + type: file + description: Distribution of sequencing depths + pattern: "*.depthSample" - depth_global: - type: file - description: Distribution of sequencing depths - pattern: "*.depthGlobal" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthGlobal": + type: file + description: Distribution of sequencing depths + pattern: "*.depthGlobal" - qs: - type: file - description: Distribution of scores - pattern: "*.qs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.qs": + type: file + description: Distribution of scores + pattern: "*.qs" - pos: - type: file - description: Various types of depth statistics (depending on value for -dumpCounts) - pattern: "*.pos.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pos.gz": + type: file + description: Various types of depth statistics (depending on value for -dumpCounts) + pattern: "*.pos.gz" - counts: - type: file - description: Various types of statistics (related to pos.gz) - pattern: "*.counts.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.counts.gz": + type: file + description: Various types of statistics (related to pos.gz) + pattern: "*.counts.gz" - icounts: - type: file - description: Internal format for dumping binary single chrs. Useful for ANGSD contamination - pattern: "*.icnts.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.icnts.gz": + type: file + description: Internal format for dumping binary single chrs. Useful for ANGSD + contamination + pattern: "*.icnts.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/angsd/gl/meta.yml b/modules/nf-core/angsd/gl/meta.yml index 168f615d5a2..3951bbbf712 100644 --- a/modules/nf-core/angsd/gl/meta.yml +++ b/modules/nf-core/angsd/gl/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "angsd_gl" description: Calculated genotype likelihoods from BAM files. @@ -14,49 +13,51 @@ tools: tool_dev_url: "https://github.com/ANGSD/angsd" doi: "10.1186/s12859-014-0356-4" licence: ["GPL v3", "MIT"] + identifier: biotools:angsd input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A list of BAM or CRAM files - pattern: "*.{bam,cram}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: A reference genome in FASTA format - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - error_file: - type: file - description: A file containing information about type specific errors. - pattern: "*.error.chunkunordered" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A list of BAM or CRAM files + pattern: "*.{bam,cram}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: A reference genome in FASTA format + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - error_file: + type: file + description: A file containing information about type specific errors. + pattern: "*.error.chunkunordered" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - genotype_likelihood: - type: file - description: File containing genotype likelihoods per sample - pattern: "*.{glf,beagle}.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{glf,beagle}.gz": + type: file + description: File containing genotype likelihoods per sample + pattern: "*.{glf,beagle}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" - "@TCLamnidis" diff --git a/modules/nf-core/annotsv/annotsv/meta.yml b/modules/nf-core/annotsv/annotsv/meta.yml index f690f0aa123..6458f2627c8 100644 --- a/modules/nf-core/annotsv/annotsv/meta.yml +++ b/modules/nf-core/annotsv/annotsv/meta.yml @@ -14,80 +14,97 @@ tools: tool_dev_url: "https://github.com/lgmgeo/AnnotSV" doi: 10.1093/bioinformatics/bty304 licence: ["GPL-3.0"] + identifier: biotools:AnnotSV input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sv_vcf: - type: file - description: A VCF or BED file containing the structural variants to be annotated - pattern: "*.{bed,vcf,vcf.gz}" - - sv_vcf_index: - type: file - description: OPTIONAL - The index for gzipped VCF files - pattern: "*.tbi" - - candidate_small_variants: - type: file - description: OPTIONAL - A file containing candidate small variants - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing annotations information - - annotations: - type: directory - description: | - The directory containing the annotations (URL to download this will be made available soon) - For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation) - - meta3: - type: map - description: | - Groovy Map containing candidate genes information - - candidate_genes: - type: file - description: OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated) - pattern: "*.txt" - - meta4: - type: map - description: | - Groovy Map containing candidate false positive SNV information - - false_positive_snv: - type: file - description: OPTIONAL - A VCF file containing small variant candidates - pattern: "*.{vcf,vcf.gz}" - - meta5: - type: map - description: | - Groovy Map containing candidate gene transcripts information - - gene_transcripts: - type: file - description: OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated) - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sv_vcf: + type: file + description: A VCF or BED file containing the structural variants to be annotated + pattern: "*.{bed,vcf,vcf.gz}" + - sv_vcf_index: + type: file + description: OPTIONAL - The index for gzipped VCF files + pattern: "*.tbi" + - candidate_small_variants: + type: file + description: OPTIONAL - A file containing candidate small variants + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing annotations information + - annotations: + type: directory + description: | + The directory containing the annotations (URL to download this will be made available soon) + For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation) + - - meta3: + type: map + description: | + Groovy Map containing candidate genes information + - candidate_genes: + type: file + description: OPTIONAL - A file containing genes (either space-separated, tab-separated + or line-break-separated) + pattern: "*.txt" + - - meta4: + type: map + description: | + Groovy Map containing candidate false positive SNV information + - false_positive_snv: + type: file + description: OPTIONAL - A VCF file containing small variant candidates + pattern: "*.{vcf,vcf.gz}" + - - meta5: + type: map + description: | + Groovy Map containing candidate gene transcripts information + - gene_transcripts: + type: file + description: OPTIONAL - A file containing the preferred gene transcripts to + be used in priority during annotation (either space-separated or tab-separated) + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV file containing the annotated variants - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV file containing the annotated variants + pattern: "*.tsv" - unannotated_tsv: - type: file - description: OPTIONAL - TSV file containing the unannotated variants - pattern: "*.unannotated.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unannotated.tsv": + type: file + description: OPTIONAL - TSV file containing the unannotated variants + pattern: "*.unannotated.tsv" - vcf: - type: file - description: | - OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: | + OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args) + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/annotsv/installannotations/meta.yml b/modules/nf-core/annotsv/installannotations/meta.yml index a04c4f1d7fe..a7b11d7011c 100644 --- a/modules/nf-core/annotsv/installannotations/meta.yml +++ b/modules/nf-core/annotsv/installannotations/meta.yml @@ -12,15 +12,18 @@ tools: documentation: "https://lbgi.fr/AnnotSV/" tool_dev_url: "https://github.com/lgmgeo/AnnotSV" licence: ["GPL v3"] + identifier: biotools:AnnotSV output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotations: - type: file - description: A folder containing the annotations - pattern: "AnnotSV_annotations" + - AnnotSV_annotations: + type: file + description: A folder containing the annotations + pattern: "AnnotSV_annotations" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/anota2seq/anota2seqrun/meta.yml b/modules/nf-core/anota2seq/anota2seqrun/meta.yml index 67a8555b8dd..3e864634066 100644 --- a/modules/nf-core/anota2seq/anota2seqrun/meta.yml +++ b/modules/nf-core/anota2seq/anota2seqrun/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "anota2seq_anota2seqrun" -description: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq +description: Generally applicable transcriptome-wide analysis of translational efficiency + using anota2seq keywords: - riboseq - rnaseq @@ -9,152 +9,233 @@ keywords: - differential tools: - "anota2seq": - description: "Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq" + description: "Generally applicable transcriptome-wide analysis of translational + efficiency using anota2seq" homepage: "https://bioconductor.org/packages/release/bioc/html/anota2seq.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/anota2seq/inst/doc/anota2seq.pdf" doi: "10.18129/B9.bioc.anota2seq" licence: ["GPL v3"] + identifier: biotools:anota2seq input: - - meta: - type: map - description: | - Groovy Map containing contrast information. e.g. [ id:'contrast1', - blocking:'patient' ] - - sample_treatment_col: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - counts: - type: file - description: | - Raw TSV or CSV format expression matrix - + - - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - sample_treatment_col: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata + - counts: + type: file + description: | + Raw TSV or CSV format expression matrix output: - - meta: - type: map - description: | - Groovy Map containing contrast information. e.g. [ id:'contrast1', - blocking:'patient' ] - translated_mrna: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - differences in RNA levels across conditions for Ribo-seq samples. See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".translated_mRNA.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.translated_mRNA.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".translated_mRNA.anota2seq.results.tsv" - total_mrna: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - differences in RNA levels across conditions for RNA-seq samples. See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".total_mRNA.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.total_mRNA.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".total_mRNA.anota2seq.results.tsv" - translation: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - differences in translation across conditions, being differences in - translated RNA levels not explained by total RNA levels. See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".translation.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.translation.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + differences in translation across conditions, being differences in translated + RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".translation.anota2seq.results.tsv" - buffering: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - buffering across conditions, being stable levels of translated RNA - (from riboseq samples) across conditions, despite changes in total - mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html - for description of output columns. - pattern: ".buffering.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.buffering.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + buffering across conditions, being stable levels of translated RNA (from riboseq + samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".buffering.anota2seq.results.tsv" - mrna_abundance: - type: file - description: anota2seq results for the 'mRNA abunance' analysis, describing changes - across conditions consistent between total mRNA and translated RNA - (RNA-seq and Riboseq samples). See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".mRNA_abundance.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.mRNA_abundance.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'mRNA abunance' analysis, describing + changes across conditions consistent between total mRNA and translated RNA + (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".mRNA_abundance.anota2seq.results.tsv" - rdata: - type: file - description: Serialised Anota2seqDataSet object - pattern: ".Anota2seqDataSet.rds" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.Anota2seqDataSet.rds": + type: file + description: Serialised Anota2seqDataSet object + pattern: ".Anota2seqDataSet.rds" - fold_change_plot: - type: file - description: | - A fold change plot in PNG format, from anota2seq's anota2seqPlotFC() - method. - pattern: ".fold_change.png" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.fold_change.png": + type: file + description: | + A fold change plot in PNG format, from anota2seq's anota2seqPlotFC() + method. + pattern: ".fold_change.png" - interaction_p_distribution_plot: - type: file - description: | - The distribution of p-values and adjusted p-values for the omnibus - interaction (both using densities and histograms). The second page of - the pdf displays the same plots but for the RVM statistics if RVM is - used. - pattern: ".interaction_p_distribution.pdf" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.interaction_p_distribution.pdf": + type: file + description: | + The distribution of p-values and adjusted p-values for the omnibus + interaction (both using densities and histograms). The second page of + the pdf displays the same plots but for the RVM statistics if RVM is + used. + pattern: ".interaction_p_distribution.pdf" - residual_distribution_summary_plot: - type: file - description: | - Summary plot for assessing normal distribution of regression residuals. - pattern: ".residual_distribution_summary.jpeg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.residual_distribution_summary.jpeg": + type: file + description: | + Summary plot for assessing normal distribution of regression residuals. + pattern: ".residual_distribution_summary.jpeg" - residual_vs_fitted_plot: - type: file - description: | - QC plot showing residuals against fitted values. - pattern: ".residual_vs_fitted.jpeg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.residual_vs_fitted.jpeg": + type: file + description: | + QC plot showing residuals against fitted values. + pattern: ".residual_vs_fitted.jpeg" - rvm_fit_for_all_contrasts_group_plot: - type: file - description: | - QC plot showing the CDF of variance (theoretical vs empirical), all - contrasts. - pattern: ".rvm_fit_for_all_contrasts_group.jpg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.rvm_fit_for_all_contrasts_group.jpg": + type: file + description: | + QC plot showing the CDF of variance (theoretical vs empirical), all + contrasts. + pattern: ".rvm_fit_for_all_contrasts_group.jpg" - rvm_fit_for_interactions_plot: - type: file - description: | - QC plot showing the CDF of variance (theoretical vs empirical), for - interactions. - pattern: ".rvm_fit_for_interactions.jpg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.rvm_fit_for_interactions.jpg": + type: file + description: | + QC plot showing the CDF of variance (theoretical vs empirical), for + interactions. + pattern: ".rvm_fit_for_interactions.jpg" - rvm_fit_for_omnibus_group_plot: - type: file - description: | - QC plot showing the CDF of variance (theoretical vs empirical), for - omnibus group. - pattern: ".rvm_fit_for_omnibus_group.jpg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.rvm_fit_for_omnibus_group.jpg": + type: file + description: | + QC plot showing the CDF of variance (theoretical vs empirical), for + omnibus group. + pattern: ".rvm_fit_for_omnibus_group.jpg" - simulated_vs_obt_dfbetas_without_interaction_plot: - type: file - description: | - Bar graphs of the frequencies of outlier dfbetas using different - dfbetas thresholds. - pattern: ".simulated_vs_obt_dfbetas_without_interaction.pdf" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.simulated_vs_obt_dfbetas_without_interaction.pdf": + type: file + description: | + Bar graphs of the frequencies of outlier dfbetas using different + dfbetas thresholds. + pattern: ".simulated_vs_obt_dfbetas_without_interaction.pdf" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/antismash/antismashlite/meta.yml b/modules/nf-core/antismash/antismashlite/meta.yml index 21f506bd846..638283432c0 100644 --- a/modules/nf-core/antismash/antismashlite/meta.yml +++ b/modules/nf-core/antismash/antismashlite/meta.yml @@ -23,110 +23,207 @@ tools: tool_dev_url: "https://github.com/antismash/antismash" doi: "10.1093/nar/gkab335" licence: ["AGPL v3"] + identifier: biotools:antismash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequence_input: - type: file - description: nucleotide sequence file (annotated) - pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" - - databases: - type: directory - description: | - Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory - "data/databases") - pattern: "*/" - - antismash_dir: - type: directory - description: | - A local copy of an AntiSMASH installation folder. This is required when running with - docker and singularity (not required for conda), due to attempted 'modifications' of - files during database checks in the installation directory, something that cannot - be done in immutable docker/singularity containers. Therefore, a local installation - directory needs to be mounted (including all modified files from the downloading step) - to the container as a workaround. - pattern: "*/" - - gff: - type: file - description: Annotations in GFF3 format (only if sequence_input is in FASTA format) - pattern: "*.gff" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence_input: + type: file + description: nucleotide sequence file (annotated) + pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" + - - databases: + type: directory + description: | + Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory + "data/databases") + pattern: "*/" + - - antismash_dir: + type: directory + description: | + A local copy of an AntiSMASH installation folder. This is required when running with + docker and singularity (not required for conda), due to attempted 'modifications' of + files during database checks in the installation directory, something that cannot + be done in immutable docker/singularity containers. Therefore, a local installation + directory needs to be mounted (including all modified files from the downloading step) + to the container as a workaround. + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - clusterblast_file: - type: file - description: Output of ClusterBlast algorithm - pattern: "clusterblast/*_c*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/clusterblast/*_c*.txt: + type: file + description: Output of ClusterBlast algorithm + pattern: "clusterblast/*_c*.txt" - html_accessory_files: - type: directory - description: Accessory files for the HTML output - pattern: "{css/,images/,js/}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/{css,images,js}: + type: directory + description: Accessory files for the HTML output + pattern: "{css/,images/,js/}" - knownclusterblast_html: - type: file - description: Tables with MIBiG hits in HTML format - pattern: "knownclusterblast/region*/ctg*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblast/region*/ctg*.html: + type: file + description: Tables with MIBiG hits in HTML format + pattern: "knownclusterblast/region*/ctg*.html" - knownclusterblast_dir: - type: directory - description: Directory with MIBiG hits - pattern: "knownclusterblast/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblast/: + type: directory + description: Directory with MIBiG hits + pattern: "knownclusterblast/" - knownclusterblast_txt: - type: file - description: Tables with MIBiG hits - pattern: "knownclusterblast/*_c*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblast/*_c*.txt: + type: file + description: Tables with MIBiG hits + pattern: "knownclusterblast/*_c*.txt" - svg_files_clusterblast: - type: file - description: SVG images showing the % identity of the aligned hits against their queries - pattern: "svg/clusterblast*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/svg/clusterblast*.svg: + type: file + description: SVG images showing the % identity of the aligned hits against their + queries + pattern: "svg/clusterblast*.svg" - svg_files_knownclusterblast: - type: file - description: SVG images showing the % identity of the aligned hits against their queries - pattern: "svg/knownclusterblast*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/svg/knownclusterblast*.svg: + type: file + description: SVG images showing the % identity of the aligned hits against their + queries + pattern: "svg/knownclusterblast*.svg" - gbk_input: - type: file - description: Nucleotide sequence and annotations in GenBank format; converted from input file - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.gbk: + type: file + description: Nucleotide sequence and annotations in GenBank format; converted + from input file + pattern: "*.gbk" - json_results: - type: file - description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input) - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.json: + type: file + description: Nucleotide sequence and annotations in JSON format; converted from + GenBank file (gbk_input) + pattern: "*.json" - log: - type: file - description: Contains all the logging output that antiSMASH produced during its run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.log: + type: file + description: Contains all the logging output that antiSMASH produced during + its run + pattern: "*.log" - zip: - type: file - description: Contains a compressed version of the output folder in zip format - pattern: "*.zip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.zip: + type: file + description: Contains a compressed version of the output folder in zip format + pattern: "*.zip" - gbk_results: - type: file - description: Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit - pattern: "*region*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*region*.gbk: + type: file + description: Nucleotide sequence and annotations in GenBank format; one file + per antiSMASH hit + pattern: "*region*.gbk" - clusterblastoutput: - type: file - description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm - pattern: "clusterblastoutput.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/clusterblastoutput.txt: + type: file + description: Raw BLAST output of known clusters previously predicted by antiSMASH + using the built-in ClusterBlast algorithm + pattern: "clusterblastoutput.txt" - html: - type: file - description: Graphical web view of results in HTML format - patterN: "index.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/index.html: + type: file + description: Graphical web view of results in HTML format + patterN: "index.html" - knownclusterblastoutput: - type: file - description: Raw BLAST output of known clusters of the MIBiG database - pattern: "knownclusterblastoutput.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblastoutput.txt: + type: file + description: Raw BLAST output of known clusters of the MIBiG database + pattern: "knownclusterblastoutput.txt" - json_sideloading: - type: file - description: Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading") - pattern: "regions.js" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/regions.js: + type: file + description: Sideloaded annotations of protoclusters and/or subregions (see + antiSMASH documentation "Annotation sideloading") + pattern: "regions.js" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml index 010c6267815..fdca8294b6d 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml @@ -1,5 +1,7 @@ name: antismash_antismashlitedownloaddatabases -description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs. +description: antiSMASH allows the rapid genome-wide identification, annotation and + analysis of secondary metabolite biosynthesis gene clusters. This module downloads + the antiSMASH databases for conda and docker/singularity runs. keywords: - secondary metabolites - BGC @@ -22,36 +24,40 @@ tools: tool_dev_url: https://github.com/antismash/antismash doi: "10.1093/nar/gkab335" licence: ["AGPL v3"] + identifier: biotools:antismash input: - - database_css: - type: directory - description: | - antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "css" - - database_detection: - type: directory - description: | - antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "detection" - - database_modules: - type: directory - description: | - antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "modules" + - - database_css: + type: directory + description: | + antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "css" + - - database_detection: + type: directory + description: | + antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "detection" + - - database_modules: + type: directory + description: | + antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "modules" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - database: - type: directory - description: Download directory for antiSMASH databases - pattern: "antismash_db" + - antismash_db: + type: directory + description: Download directory for antiSMASH databases + pattern: "antismash_db" - antismash_dir: - type: directory - description: | - antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines. - pattern: "antismash_dir" + - antismash_dir: + type: directory + description: | + antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines. + pattern: "antismash_dir" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/arcashla/extract/meta.yml b/modules/nf-core/arcashla/extract/meta.yml index 6a85aad0f79..381381d10e7 100644 --- a/modules/nf-core/arcashla/extract/meta.yml +++ b/modules/nf-core/arcashla/extract/meta.yml @@ -1,57 +1,82 @@ name: "arcashla_extract" -description: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates. +description: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome + 6 alternates. keywords: - HLA - genotype - RNA-seq tools: - "arcashla": - description: "arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples." + description: "arcasHLA performs high resolution genotyping for HLA class I and + class II genes from RNA sequencing, supporting both paired and single-end samples." homepage: "https://github.com/RabadanLab/arcasHLA" documentation: "https://github.com/RabadanLab/arcasHLA" tool_dev_url: "https://github.com/RabadanLab/arcasHLA" doi: "10.1093/bioinformatics/btz474" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads. - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. If the BAM file is not indexed, this tool will run samtools + index before extracting reads. + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - extracted_reads_fastq: - type: file - description: FASTQ file(s) containing chromosome 6 reads and related HLA sequences - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: FASTQ file(s) containing chromosome 6 reads and related HLA sequences + pattern: "*.fq.gz" - log: - type: file - description: Log file for run summary - pattern: "*.log" + - "*.log": + type: file + description: Log file for run summary + pattern: "*.log" - intermediate_sam: - type: file - description: Optional intermediate SAM file - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp_files/**.sam: + type: file + description: Optional intermediate SAM file + pattern: "*.sam" - intermediate_bam: - type: file - description: Optional intermediate BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp_files/**.bam: + type: file + description: Optional intermediate BAM file + pattern: "*.bam" - intermediate_sorted_bam: - type: file - description: Optional intermediate sorted BAM file - pattern: "*.sorted.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp_files/**.sorted.bam: + type: file + description: Optional intermediate sorted BAM file + pattern: "*.sorted.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-mohr" maintainers: diff --git a/modules/nf-core/argnorm/meta.yml b/modules/nf-core/argnorm/meta.yml index a977e86304c..84842b9c5ca 100644 --- a/modules/nf-core/argnorm/meta.yml +++ b/modules/nf-core/argnorm/meta.yml @@ -1,5 +1,6 @@ name: "argnorm" -description: Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD). +description: Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed + by CARD). keywords: - amr - antimicrobial resistance @@ -11,49 +12,48 @@ keywords: - drug categorization tools: - "argnorm": - description: "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD)." + description: "Normalize antibiotic resistance genes (ARGs) using the ARO ontology + (developed by CARD)." homepage: "https://argnorm.readthedocs.io/en/latest/" documentation: "https://argnorm.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/BigDataBiology/argNorm" licence: ["MIT"] + identifier: biotools:argnorm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input_tsv: - type: file - description: ARG annotation output - pattern: "*.tsv" - - - tool: - type: string - description: ARG annotation tool used - pattern: "argsoap|abricate|deeparg|resfinder|amrfinderplus" - - - db: - type: string - description: Database used for ARG annotation - pattern: "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input_tsv: + type: file + description: ARG annotation output + pattern: "*.tsv" + - - tool: + type: string + description: ARG annotation tool used + pattern: "argsoap|abricate|deeparg|resfinder|amrfinderplus" + - - db: + type: string + description: Database used for ARG annotation + pattern: "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - tsv: - type: file - description: Normalized argNorm output - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Normalized argNorm output + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Vedanth-Ramji" maintainers: diff --git a/modules/nf-core/aria2/meta.yml b/modules/nf-core/aria2/meta.yml index 0908646aecd..569e043acd1 100644 --- a/modules/nf-core/aria2/meta.yml +++ b/modules/nf-core/aria2/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "aria2" description: CLI Download utility @@ -8,35 +7,40 @@ keywords: - http(s) tools: - "aria2": - description: "aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink." + description: "aria2 is a lightweight multi-protocol & multi-source, cross platform + download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, + BitTorrent and Metalink." homepage: "https://aria2.github.io/" documentation: "https://aria2.github.io/manual/en/html/index.html" tool_dev_url: "https://github.com/aria2/aria2/" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - source_url: - type: string - description: Source URL to be downloaded - pattern: "{http,https}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - source_url: + type: string + description: Source URL to be downloaded + pattern: "{http,https}*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - downloaded_file: - type: file - description: Downloaded file from source - pattern: "*.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $downloaded_file: + type: file + description: Downloaded file from source + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@leoisl" diff --git a/modules/nf-core/ariba/getref/meta.yml b/modules/nf-core/ariba/getref/meta.yml index bbdae6dec99..680126b3e0b 100644 --- a/modules/nf-core/ariba/getref/meta.yml +++ b/modules/nf-core/ariba/getref/meta.yml @@ -13,24 +13,31 @@ tools: tool_dev_url: "https://github.com/sanger-pathogens/ariba" doi: "10.1099/mgen.0.000131" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - db_name: - type: string - description: A database to setup up for Ariba + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - db_name: + type: string + description: A database to setup up for Ariba output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: An Ariba prepared database - pattern: "*.tar.gz" + - meta: + type: file + description: An Ariba prepared database + pattern: "*.tar.gz" + - ${db_name}.tar.gz: + type: file + description: An Ariba prepared database + pattern: "*.tar.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/ariba/run/meta.yml b/modules/nf-core/ariba/run/meta.yml index bcd0b9e2d47..4fa1e0d452c 100644 --- a/modules/nf-core/ariba/run/meta.yml +++ b/modules/nf-core/ariba/run/meta.yml @@ -13,29 +13,41 @@ tools: tool_dev_url: "https://github.com/sanger-pathogens/ariba" doi: "10.1099/mgen.0.000131" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Paired-end reads in FASTQ format - pattern: "*_R[1|2].{fastq.gz,fq.gz}" - - db: - type: file - description: An Ariba prepared database - pattern: "*.tar.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Paired-end reads in FASTQ format + pattern: "*_R[1|2].{fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - db: + type: file + description: An Ariba prepared database + pattern: "*.tar.gz" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: A directory of Ariba analysis outputs - pattern: "*" + - meta: + type: file + description: A directory of Ariba analysis outputs + pattern: "*" + - ${prefix}/*: + type: file + description: A directory of Ariba analysis outputs + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/arriba/arriba/meta.yml b/modules/nf-core/arriba/arriba/meta.yml index 11f744b54d6..f230dda1fbe 100644 --- a/modules/nf-core/arriba/arriba/meta.yml +++ b/modules/nf-core/arriba/arriba/meta.yml @@ -1,5 +1,6 @@ name: arriba_arriba -description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. +description: Arriba is a command-line tool for the detection of gene fusions from + RNA-Seq data. keywords: - fusion - arriba @@ -13,97 +14,107 @@ tools: tool_dev_url: https://github.com/suhrig/arriba doi: "10.1101/gr.257246.119" licence: ["MIT"] + identifier: biotools:Arriba input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Assembly FASTA file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - blacklist: - type: file - description: Blacklist file - pattern: "*.{tsv}" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - known_fusions: - type: file - description: Known fusions file - pattern: "*.{tsv}" - - meta6: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - structural_variants: - type: file - description: Structural variants file - pattern: "*.{tsv}" - - meta7: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - tags: - type: file - description: Tags file - pattern: "*.{tsv}" - - meta8: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - protein_domains: - type: file - description: Protein domains file - pattern: "*.{gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Assembly FASTA file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - blacklist: + type: file + description: Blacklist file + pattern: "*.{tsv}" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - known_fusions: + type: file + description: Known fusions file + pattern: "*.{tsv}" + - - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - structural_variants: + type: file + description: Structural variants file + pattern: "*.{tsv}" + - - meta7: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - tags: + type: file + description: Tags file + pattern: "*.{tsv}" + - - meta8: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - protein_domains: + type: file + description: Protein domains file + pattern: "*.{gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fusions: - type: file - description: File contains fusions which pass all of Arriba's filters. - pattern: "*.{fusions.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fusions.tsv": + type: file + description: File contains fusions which pass all of Arriba's filters. + pattern: "*.{fusions.tsv}" - fusions_fail: - type: file - description: File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue. - pattern: "*.{fusions.discarded.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fusions.discarded.tsv": + type: file + description: File contains fusions that Arriba classified as an artifact or + that are also observed in healthy tissue. + pattern: "*.{fusions.discarded.tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@praveenraj2018" - "@rannick" diff --git a/modules/nf-core/arriba/download/meta.yml b/modules/nf-core/arriba/download/meta.yml index d3210616321..531c66c2f77 100644 --- a/modules/nf-core/arriba/download/meta.yml +++ b/modules/nf-core/arriba/download/meta.yml @@ -1,5 +1,6 @@ name: arriba_download -description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. +description: Arriba is a command-line tool for the detection of gene fusions from + RNA-Seq data. keywords: - fusion - arriba @@ -12,16 +13,18 @@ tools: tool_dev_url: https://github.com/suhrig/arriba doi: "10.1101/gr.257246.119" licence: ["MIT"] + identifier: biotools:Arriba output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reference: - type: directory - description: Folder with arriba references - pattern: "*" - + - "*": + type: directory + description: Folder with arriba references + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@peterpru" diff --git a/modules/nf-core/art/illumina/meta.yml b/modules/nf-core/art/illumina/meta.yml index b20df1cde87..e41db4869f0 100644 --- a/modules/nf-core/art/illumina/meta.yml +++ b/modules/nf-core/art/illumina/meta.yml @@ -1,5 +1,6 @@ name: "art_illumina" -description: Simulation tool to generate synthetic Illumina next-generation sequencing reads +description: Simulation tool to generate synthetic Illumina next-generation sequencing + reads keywords: - fastq - fasta @@ -7,51 +8,74 @@ keywords: - simulate tools: - "art": - description: "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. " + description: "ART is a set of simulation tools to generate synthetic next-generation + sequencing reads. ART simulates sequencing reads by mimicking real sequencing + process with empirical error models or quality profiles summarized from large + recalibrated sequencing data. ART can also simulate reads using user own read + error model or quality profiles. " homepage: "https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm" doi: "10.1093/bioinformatics/btr708" licence: ["GPL version 3 license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file of input DNA/RNA reference - pattern: "*.{fasta,fa}" - - sequencing_system: - type: string - description: The name of Illumina sequencing system of the built-in profile used for simulation - - fold_coverage: - type: integer - description: The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon - - read_length: - type: integer - description: The length of reads to be simulated + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file of input DNA/RNA reference + pattern: "*.{fasta,fa}" + - - sequencing_system: + type: string + description: The name of Illumina sequencing system of the built-in profile + used for simulation + - - fold_coverage: + type: integer + description: The fold of read coverage to be simulated or number of reads/read + pairs generated for each amplicon + - - read_length: + type: integer + description: The length of reads to be simulated output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Simulated reads - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: Simulated reads + pattern: "*.fq.gz" - aln: - type: file - description: OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/--noALN. - pattern: "*.aln" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.aln": + type: file + description: OPTIONAL Alignment file of the simulated reads. Enabled by default, + to disable, use -na/--noALN. + pattern: "*.aln" - sam: - type: file - description: OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/--samout. - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: OPTIONAL Alignment file in SAM format of the simulated reads. Enabled + with -sam/--samout. + pattern: "*.sam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MarieLataretu" maintainers: diff --git a/modules/nf-core/artic/guppyplex/meta.yml b/modules/nf-core/artic/guppyplex/meta.yml index 80a1d99907c..de1c615010a 100644 --- a/modules/nf-core/artic/guppyplex/meta.yml +++ b/modules/nf-core/artic/guppyplex/meta.yml @@ -6,35 +6,39 @@ keywords: - demultiplexed reads tools: - artic: - description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore + description: ARTIC pipeline - a bioinformatics pipeline for working with virus + sequencing data sequenced with nanopore homepage: https://artic.readthedocs.io/en/latest/ documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics licence: ["MIT"] + identifier: biotools:artic input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq_dir: - type: directory - description: Directory containing the fastq files with demultiplexed reads - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq_dir: + type: directory + description: Directory containing the fastq files with demultiplexed reads + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Aggregated FastQ files - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Aggregated FastQ files + pattern: "*.{fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/artic/minion/meta.yml b/modules/nf-core/artic/minion/meta.yml index 26ff4ad8576..3c90d62272d 100644 --- a/modules/nf-core/artic/minion/meta.yml +++ b/modules/nf-core/artic/minion/meta.yml @@ -7,110 +7,169 @@ keywords: - demultiplexed reads tools: - artic: - description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore + description: ARTIC pipeline - a bioinformatics pipeline for working with virus + sequencing data sequenced with nanopore homepage: https://artic.readthedocs.io/en/latest/ documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics licence: ["MIT"] + identifier: biotools:artic input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FastQ file containing reads - pattern: "*.{fastq.gz}" - - fast5_dir: - type: directory - description: Directory containing MinION FAST5 files - pattern: "*" - - sequencing_summary: - type: file - description: Path to Guppy sequencing summary - pattern: "*.{txt}" - - primer_scheme_fasta: - type: file - description: | - Sequence of the reference genome used in the scheme in FASTA format - pattern: "*.{reference.fasta}" - - primer_scheme_bed: - type: file - description: | - bed files containing coordinates of each primer in the scheme, - relative to the reference genome - pattern: "*.{scheme.bed}" - - medaka_model_file: - type: file - description: | - Medaka model file to use (if option --medaka is set) - pattern: "*.hdf5" - - medaka_model_string: - type: string - description: | - Medaka model string to use (if option --medaka is set) - pattern: "*" - - scheme: - type: string - description: Name of the primer scheme - - scheme_version: - type: string - description: Version of the primer scheme + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FastQ file containing reads + pattern: "*.{fastq.gz}" + - - fast5_dir: + type: directory + description: Directory containing MinION FAST5 files + pattern: "*" + - - sequencing_summary: + type: file + description: Path to Guppy sequencing summary + pattern: "*.{txt}" + - - '"primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta"': + type: file + description: Scheme reference file + - - '"primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed"': + type: file + description: Scheme BED file + - - medaka_model_file: + type: file + description: | + Medaka model file to use (if option --medaka is set) + pattern: "*.hdf5" + - - medaka_model_string: + type: string + description: | + Medaka model string to use (if option --medaka is set) + pattern: "*" + - - scheme: + type: string + description: Name of the primer scheme + - - scheme_version: + type: string + description: Version of the primer scheme output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: file - description: Aggregated FastQ files - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*: + type: file + description: Aggregated FastQ files + pattern: "*.fastq.gz" - bam: - type: file - description: BAM file - pattern: "*.{sorted.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sorted.bam: + type: file + description: BAM file + pattern: "*.{sorted.bam}" - bai: - type: file - description: BAM index file - pattern: "*.{sorted.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sorted.bam.bai: + type: file + description: BAM index file + pattern: "*.{sorted.bai}" - bam_trimmed: - type: file - description: BAM file with the primers left on - pattern: "*.{trimmed.rg.sorted.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.trimmed.rg.sorted.bam: + type: file + description: BAM file with the primers left on + pattern: "*.{trimmed.rg.sorted.bam}" - bai_trimmed: - type: file - description: BAM index file of bam_trimmed - pattern: "*.{sorted.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.trimmed.rg.sorted.bam.bai: + type: file + description: BAM index file of bam_trimmed + pattern: "*.{sorted.bai}" - bam_primertrimmed: - type: file - description: BAM containing reads after primer-binding site trimming - pattern: "*.{trimmed.rg.sorted.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.primertrimmed.rg.sorted.bam: + type: file + description: BAM containing reads after primer-binding site trimming + pattern: "*.{trimmed.rg.sorted.bam}" - bai_primertrimmed: - type: file - description: BAM index file of bam_primertrimmed - pattern: "*.{primertrimmed.rg.sorted.bam.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.primertrimmed.rg.sorted.bam.bai: + type: file + description: BAM index file of bam_primertrimmed + pattern: "*.{primertrimmed.rg.sorted.bam.bai}" - fasta: - type: file - description: FAST file with consensus sequence - pattern: "*.{consensus.fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.consensus.fasta: + type: file + description: FAST file with consensus sequence + pattern: "*.{consensus.fasta}" - vcf: - type: file - description: VCF file containing detected variants passing quality filter - pattern: "*.{pass.vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.pass.vcf.gz: + type: file + description: VCF file containing detected variants passing quality filter + pattern: "*.{pass.vcf.gz}" - tbi: - type: file - description: VCF index - pattern: "*.{pass.vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.pass.vcf.gz.tbi: + type: file + description: VCF index + pattern: "*.{pass.vcf.gz.tbi}" - json: - type: file - description: JSON file for MultiQC - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file for MultiQC + pattern: "*.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/ascat/meta.yml b/modules/nf-core/ascat/meta.yml index 34ea2e51d99..db7c92926a7 100644 --- a/modules/nf-core/ascat/meta.yml +++ b/modules/nf-core/ascat/meta.yml @@ -6,105 +6,151 @@ keywords: - cram tools: - ascat: - description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). + description: ASCAT is a method to derive copy number profiles of tumour cells, + accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour + purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour + cell), expressed as multiples of haploid genomes from SNP array or massively + parallel sequencing data, and calculates whole-genome allele-specific copy number + profiles (the number of copies of both parental alleles for all SNP loci across + the genome). documentation: https://github.com/VanLoo-lab/ascat/tree/master/man tool_dev_url: https://github.com/VanLoo-lab/ascat doi: "10.1093/bioinformatics/btaa538" licence: ["GPL v3"] + identifier: biotools:ascat input: - - args: - type: map - description: | - Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above. - - ``` - { - [ - "gender": "XX", - "genomeVersion": "hg19" - "purity": (optional), - "ploidy": (optional), - "gc_files": (optional), - "minCounts": (optional), - "BED_file": (optional) but recommended for WES, - "chrom_names": (optional), - "min_base_qual": (optional), - "min_map_qual": (optional), - "ref_fasta": (optional), - "skip_allele_counting_tumour": (optional), - "skip_allele_counting_normal": (optional) - ] - } - ``` - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_normal: - type: file - description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/. - pattern: "*.{bam,cram}" - - index_normal: - type: file - description: index for normal_bam/cram - pattern: "*.{bai,crai}" - - input_tumor: - type: file - description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation - pattern: "*.{bam,cram}" - - index_tumor: - type: file - description: index for tumor_bam/cram - pattern: "*.{bai,crai}" - - allele_files: - type: file - description: allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS - - loci_files: - type: file - description: loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view | head -n1 | cut -f3)\" == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi` - - bed_file: - type: file - description: Bed file for ASCAT WES (optional, but recommended for WES) - - fasta: - type: file - description: Reference fasta file (optional) - - gc_file: - type: file - description: GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content - - rt_file: - type: file - description: replication timing correction file (optional, provide only in combination with gc_file) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_normal: + type: file + description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For + modifying chromosome notation in bam files please follow + https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/. + pattern: "*.{bam,cram}" + - index_normal: + type: file + description: index for normal_bam/cram + pattern: "*.{bai,crai}" + - input_tumor: + type: file + description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation + pattern: "*.{bam,cram}" + - index_tumor: + type: file + description: index for tumor_bam/cram + pattern: "*.{bai,crai}" + - - allele_files: + type: file + description: allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS + - - loci_files: + type: file + description: loci files for ASCAT WGS. Loci files without chromosome notation + can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS + Make sure the chromosome notation matches the bam/cram input files. To add + the chromosome notation to loci files (hg19/hg38) if necessary, you can run + this command `if [[ $(samtools view | head -n1 | cut -f3)\" + == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; + done; fi` + - - bed_file: + type: file + description: Bed file for ASCAT WES (optional, but recommended for WES) + - - fasta: + type: file + description: Reference fasta file (optional) + - - gc_file: + type: file + description: GC correction file (optional) - Used to do logR correction of the + tumour sample(s) with genomic GC content + - - rt_file: + type: file + description: replication timing correction file (optional, provide only in combination + with gc_file) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - allelefreqs: - type: file - description: Files containing allee frequencies per chromosome - pattern: "*{alleleFrequencies_chr*.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*alleleFrequencies_chr*.txt": + type: file + description: Files containing allee frequencies per chromosome + pattern: "*{alleleFrequencies_chr*.txt}" + - bafs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*BAF.txt": + type: file + description: BAF file + - cnvs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cnvs.txt": + type: file + description: CNV file + - logrs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*LogR.txt": + type: file + description: LogR file - metrics: - type: file - description: File containing quality metrics - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*metrics.txt": + type: file + description: File containing quality metrics + pattern: "*.{metrics.txt}" - png: - type: file - description: ASCAT plots - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*png": + type: file + description: ASCAT plots + pattern: "*.{png}" - purityploidy: - type: file - description: File with purity and ploidy data - pattern: "*.{purityploidy.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*purityploidy.txt": + type: file + description: File with purity and ploidy data + pattern: "*.{purityploidy.txt}" - segments: - type: file - description: File with segments data - pattern: "*.{segments.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*segments.txt": + type: file + description: File with segments data + pattern: "*.{segments.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aasNGC" - "@lassefolkersen" diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml index f886a3d45d8..221e2154aea 100644 --- a/modules/nf-core/ashlar/meta.yml +++ b/modules/nf-core/ashlar/meta.yml @@ -11,30 +11,39 @@ tools: documentation: "https://labsyspharm.github.io/ashlar/" doi: "10.1093/bioinformatics/btac544" licence: ["MIT"] + identifier: biotools:ASHLAR input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - images: - type: file - description: Overlapping tile image data in formats from most commercial microscopes - pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - images: + type: file + description: Overlapping tile image data in formats from most commercial microscopes + pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}" + - - opt_dfp: + type: file + description: Optional dark field image data + - - opt_ffp: + type: file + description: Optional flat field image data output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - tif: - type: file - description: A pyramidal, tiled OME-TIFF file created from input images. - pattern: "*.ome.tif" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.ome.tif": + type: file + description: A pyramidal, tiled OME-TIFF file created from input images. + pattern: "*.ome.tif" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@RobJY" - "@jmuhlich" diff --git a/modules/nf-core/assemblyscan/meta.yml b/modules/nf-core/assemblyscan/meta.yml index 4cf187798aa..d8bcf06d7b8 100644 --- a/modules/nf-core/assemblyscan/meta.yml +++ b/modules/nf-core/assemblyscan/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://github.com/rpetit3/assembly-scan tool_dev_url: https://github.com/rpetit3/assembly-scan licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: FASTA file for a given assembly - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: FASTA file for a given assembly + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: Assembly statistics in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Assembly statistics in JSON format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/ataqv/ataqv/meta.yml b/modules/nf-core/ataqv/ataqv/meta.yml index 227c9da8f51..25d56612266 100644 --- a/modules/nf-core/ataqv/ataqv/meta.yml +++ b/modules/nf-core/ataqv/ataqv/meta.yml @@ -6,64 +6,87 @@ keywords: - ataqv tools: - ataqv: - description: ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing. + description: ataqv is a toolkit for measuring and comparing ATAC-seq results. + It was written to help understand how well ATAC-seq assays have worked, and + to make it easier to spot differences that might be caused by library prep or + sequencing. homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst tool_dev_url: https://github.com/ParkerLab/ataqv doi: "10.1016/j.cels.2020.02.009" licence: ["GPL v3"] + identifier: biotools:ataqv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file with the same prefix as bam file. Required if tss_file input is provided. - pattern: "*.bam.bai" - - peak_file: - type: file - description: A BED file of peaks called for alignments in the BAM file - pattern: "*.bed" - - organism: - type: string - description: The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv). - - mito_name: - type: string - description: Name of the mitochondrial sequence. - - tss_file: - type: file - description: A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed. - pattern: "*.bed" - - excl_regs_file: - type: file - description: A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored. - pattern: "*.bed" - - autosom_ref_file: - type: file - description: A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file with the same prefix as bam file. Required if tss_file + input is provided. + pattern: "*.bam.bai" + - peak_file: + type: file + description: A BED file of peaks called for alignments in the BAM file + pattern: "*.bed" + - - organism: + type: string + description: The subject of the experiment, which determines the list of autosomes + (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv). + - - mito_name: + type: string + description: Name of the mitochondrial sequence. + - - tss_file: + type: file + description: A BED file of transcription start sites for the experiment organism. + If supplied, a TSS enrichment score will be calculated according to the ENCODE + data standards. This calculation requires that the BAM file of alignments + be indexed. + pattern: "*.bed" + - - excl_regs_file: + type: file + description: A BED file containing excluded regions. Peaks or TSS overlapping + these will be ignored. + pattern: "*.bed" + - - autosom_ref_file: + type: file + description: A file containing autosomal reference names, one per line. The + names must match the reference names in the alignment file exactly, or the + metrics based on counts of autosomal alignments will be wrong. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - json: - type: file - description: The JSON file to which metrics will be written. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ataqv.json": + type: file + description: The JSON file to which metrics will be written. - problems: - type: file - description: If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with ".problems" appended. If no read groups are found, the reads will be written to one file named after the BAM file. - pattern: "*.problems" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.problems": + type: file + description: If given, problematic reads will be logged to a file per read group, + with names derived from the read group IDs, with ".problems" appended. If + no read groups are found, the reads will be written to one file named after + the BAM file. + pattern: "*.problems" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@i-pletenev" maintainers: diff --git a/modules/nf-core/ataqv/mkarv/meta.yml b/modules/nf-core/ataqv/mkarv/meta.yml index be4ff3ed519..89576765ac4 100644 --- a/modules/nf-core/ataqv/mkarv/meta.yml +++ b/modules/nf-core/ataqv/mkarv/meta.yml @@ -8,25 +8,31 @@ keywords: - mkarv tools: - "ataqv": - description: "ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing." + description: "ataqv is a toolkit for measuring and comparing ATAC-seq results. + It was written to help understand how well ATAC-seq assays have worked, and + to make it easier to spot differences that might be caused by library prep or + sequencing." homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" tool_dev_url: "https://github.com/ParkerLab/ataqv" licence: ["GPL v3"] + identifier: biotools:ataqv input: - - json: - type: file - description: The JSON file with ataqv metrics - pattern: "*.json" + - - '"jsons/*"': + type: file + description: JSON files + pattern: "*.json" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: directory - description: Web application to visualize results in HTML format - pattern: "*.html" + - html: + type: directory + description: Web application to visualize results in HTML format + pattern: "*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjlang" maintainers: diff --git a/modules/nf-core/atlas/call/meta.yml b/modules/nf-core/atlas/call/meta.yml index a07bc6a7dd7..e5ff94d844e 100644 --- a/modules/nf-core/atlas/call/meta.yml +++ b/modules/nf-core/atlas/call/meta.yml @@ -7,64 +7,70 @@ keywords: - population genetics tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A BAM/ file - pattern: "*.bam" - - bai: - type: file - description: The BAI file for the input BAM file - pattern: "*.bai" - - fasta: - type: file - description: The reference FASTA file used to generate the BAM file - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: The index of the FASTA file used for to generate the BAM file - pattern: "*.fai" - - recal: - type: file - description: Optional recalibration file from atlas recal function in text format - pattern: "*.txt" - - pmd: - type: file - description: Optional PMD file from atlas pmd function in text format - pattern: "*.txt" - - known_alleles: - type: file - description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation. - pattern: "*.{txt.tsv}" - - method: - type: string - description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation. - pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A BAM/ file + pattern: "*.bam" + - bai: + type: file + description: The BAI file for the input BAM file + pattern: "*.bai" + - pmd: + type: file + description: Optional PMD file from atlas pmd function in text format + pattern: "*.txt" + - recal: + type: file + description: Optional recalibration file from atlas recal function in text format + pattern: "*.txt" + - - fasta: + type: file + description: The reference FASTA file used to generate the BAM file + pattern: "*.{fasta,fna,fa}" + - - fai: + type: file + description: The index of the FASTA file used for to generate the BAM file + pattern: "*.fai" + - - known_alleles: + type: file + description: Optional tab separated text file containing 1-based list of known + alleles. See atlas call documentation. + pattern: "*.{txt.tsv}" + - - method: + type: string + description: Which variant calling algorithm to use. Some may require additional + parameters supplied via ext.args. Check atlas documentation. + pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with variant calls - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file with variant calls + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/atlas/pmd/meta.yml b/modules/nf-core/atlas/pmd/meta.yml index ed2ec3691ba..e7090bd9a13 100644 --- a/modules/nf-core/atlas/pmd/meta.yml +++ b/modules/nf-core/atlas/pmd/meta.yml @@ -6,72 +6,96 @@ keywords: - bam tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Single input BAM file - pattern: "*.bam" - - bai: - type: file - description: The BAI file for the input BAM file - pattern: "*.bai" - - fasta: - type: file - description: The reference genome provided as FASTA file - pattern: "*.fasta" - - fai: - type: file - description: The FAI file for the reference genome FASTA file - pattern: "*.fai" - - pool_rg_txt: - type: file - description: | - Optional. Provide the names of read groups that should be merged for PMD estimation. - All read groups that should be pooled listed on one line, separated by any white space. - Other read groups will be recalibrated separately. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Single input BAM file + pattern: "*.bam" + - bai: + type: file + description: The BAI file for the input BAM file + pattern: "*.bai" + - pool_rg_txt: + type: file + description: | + Optional. Provide the names of read groups that should be merged for PMD estimation. + All read groups that should be pooled listed on one line, separated by any white space. + Other read groups will be recalibrated separately. + pattern: "*.txt" + - - fasta: + type: file + description: The reference genome provided as FASTA file + pattern: "*.fasta" + - - fai: + type: file + description: The FAI file for the reference genome FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - empiric: - type: file - description: A list of pmd patterns estimated with the empirical method for each readgroup - pattern: "*_PMD_input_Empiric.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_input_Empiric.txt": + type: file + description: A list of pmd patterns estimated with the empirical method for + each readgroup + pattern: "*_PMD_input_Empiric.txt" - exponential: - type: file - description: A list of pmd patterns estimated with the exponential method for each readgroup - pattern: "*_PMD_input_Exponential.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_input_Exponential.txt": + type: file + description: A list of pmd patterns estimated with the exponential method for + each readgroup + pattern: "*_PMD_input_Exponential.txt" - counts: - type: file - description: | - The counts of all possible transitions for each read position - (or up to a certain position, see specific command length) - pattern: "*_PMD_Table_counts.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_Table_counts.txt": + type: file + description: | + The counts of all possible transitions for each read position + (or up to a certain position, see specific command length) + pattern: "*_PMD_Table_counts.txt" - table: - type: file - description: | - For all possible transitions the ratio of the transition counts, - which are taken from the _counts.txt table, over the total amount - of the base that was mutated, for each position and readgroup - pattern: "*_PMD_Table.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_Table.txt": + type: file + description: | + For all possible transitions the ratio of the transition counts, + which are taken from the _counts.txt table, over the total amount + of the base that was mutated, for each position and readgroup + pattern: "*_PMD_Table.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@merszym" diff --git a/modules/nf-core/atlas/recal/meta.yml b/modules/nf-core/atlas/recal/meta.yml index 47b9c9afe6d..68f3784d197 100644 --- a/modules/nf-core/atlas/recal/meta.yml +++ b/modules/nf-core/atlas/recal/meta.yml @@ -6,51 +6,59 @@ keywords: - bias tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - empiric: - type: file - description: Optional txt file from PMD estimations (atlas/pmd) - pattern: "*.txt" - - alleles: - type: file - description: Optional bed file with known alleles - pattern: "*.bed" - - invariant_sites: - type: file - description: Optional bed file with invariant site coordinates - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - empiric: + type: file + description: Optional txt file from PMD estimations (atlas/pmd) + pattern: "*.txt" + - readgroups: + type: file + description: read groups + - - alleles: + type: file + description: Optional bed file with known alleles + pattern: "*.bed" + - - invariant_sites: + type: file + description: Optional bed file with invariant site coordinates + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - recal_patterns: - type: file - description: file containing the sequencing bias for each of the Read Group pools - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: file containing the sequencing bias for each of the Read Group + pools + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ltcrod" maintainers: diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/meta.yml index 24621b1901b..d16a41bfeb6 100644 --- a/modules/nf-core/atlas/splitmerge/meta.yml +++ b/modules/nf-core/atlas/splitmerge/meta.yml @@ -7,58 +7,69 @@ keywords: - read group tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Single input BAM file. - pattern: "*.bam" - - bai: - type: file - description: The BAI file for the input BAM file - pattern: "*.bai" - - read_group_settings: - type: file - description: | - TXT file containing the split and merge settings for - each readgroup. Each line consist of one readgroup, - single/double identifier and the maximum cycle number - of the sequencer. e.g. "RG1 single 100" - pattern: "*.txt" - - blacklist: - type: file - description: | - blacklist.txt (optional), A txt file with blacklisted read names - that should be ignored and just written to file, each on a new line - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Single input BAM file. + pattern: "*.bam" + - bai: + type: file + description: The BAI file for the input BAM file + pattern: "*.bai" + - read_group_settings: + type: file + description: | + TXT file containing the split and merge settings for + each readgroup. Each line consist of one readgroup, + single/double identifier and the maximum cycle number + of the sequencer. e.g. "RG1 single 100" + pattern: "*.txt" + - blacklist: + type: file + description: | + blacklist.txt (optional), A txt file with blacklisted read names + that should be ignored and just written to file, each on a new line + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: A BAM file with suffix_mergedReads.bam - pattern: "*_mergedReads.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_mergedReads.bam": + type: file + description: A BAM file with suffix_mergedReads.bam + pattern: "*_mergedReads.bam" - txt: - type: file - description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: A file listing all reads that were filtered out in the merging + process with suffix_ignoredReads.txt.gz + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@merszym" maintainers: diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml index 3e34244e038..d735b0707bc 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml @@ -11,44 +11,61 @@ tools: documentation: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" tool_dev_url: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on input GTF file - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing information in input FASTA file - e.g. [ id:'test' ] - - gtf: - type: file - description: gtf annotation file - pattern: "*.{gtf}" - - fasta: - type: file - description: | - An optional cDNA file for extracting meta info and/or filtering. - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing information on input GTF file + e.g. [ id:'test' ] + - gtf: + type: file + description: gtf annotation file + pattern: "*.{gtf}" + - - meta2: + type: map + description: | + Groovy Map containing information in input FASTA file + e.g. [ id:'test' ] + - fasta: + type: file + description: | + An optional cDNA file for extracting meta info and/or filtering. + pattern: "*.{gtf}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - feature_annotation: - type: file - description: TSV file with feature annotation - pattern: "*.{tsv}" + - meta: + type: file + description: TSV file with feature annotation + pattern: "*.{tsv}" + - "*.anno.tsv": + type: file + description: TSV file with feature annotation + pattern: "*.{tsv}" - filtered_cdna: - type: file - description: | - Where --parse-cdnas is specified in ext.args and an input fasta file is - provided, filtered sequences are output to the specified file. No file - will be output if this is not specified (for example for use of - --dummy-from-cdnas only). See documentation at - https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. - pattern: "*.{tsv}" + - meta: + type: file + description: | + Where --parse-cdnas is specified in ext.args and an input fasta file is + provided, filtered sequences are output to the specified file. No file + will be output if this is not specified (for example for use of + --dummy-from-cdnas only). See documentation at + https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. + pattern: "*.{tsv}" + - "*.fa.gz": + type: file + description: | + Where --parse-cdnas is specified in ext.args and an input fasta file is + provided, filtered sequences are output to the specified file. No file + will be output if this is not specified (for example for use of + --dummy-from-cdnas only). See documentation at + https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/authentict/deam2cont/meta.yml b/modules/nf-core/authentict/deam2cont/meta.yml index 0c05fbc4633..59bfb10f05f 100644 --- a/modules/nf-core/authentict/deam2cont/meta.yml +++ b/modules/nf-core/authentict/deam2cont/meta.yml @@ -1,5 +1,6 @@ name: "authentict_deam2cont" -description: Use deamination patterns to estimate contamination in single-stranded libraries +description: Use deamination patterns to estimate contamination in single-stranded + libraries keywords: - authentict - ancientDNA @@ -9,44 +10,58 @@ keywords: - damage tools: - "authentict": - description: "Estimates present-day DNA contamination in ancient DNA single-stranded libraries." + description: "Estimates present-day DNA contamination in ancient DNA single-stranded + libraries." homepage: "https://github.com/StephanePeyregne/AuthentiCT" documentation: "https://github.com/StephanePeyregne/AuthentiCT" tool_dev_url: "https://github.com/StephanePeyregne/AuthentiCT" doi: "10.1186/s13059-020-02123-y" licence: ["GPL v3"] + identifier: biotools:authentict input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file (Mandatory) - pattern: "*.{bam,cram,sam}" - - config: - type: file - description: Optional AuthentiCT configuration text file - pattern: "*" - - positions: - type: file - description: Optional text file with positions that sequences should overlap - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file (Mandatory) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - config: + type: file + description: Optional AuthentiCT configuration text file + pattern: "*" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - positions: + type: file + description: Optional text file with positions that sequences should overlap + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Maximum likelihood estimates with associated standard errors - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Maximum likelihood estimates with associated standard errors + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scarlhoff" - "@StephanePeyregne" diff --git a/modules/nf-core/backsub/meta.yml b/modules/nf-core/backsub/meta.yml index b01dce6d935..be82c9db987 100644 --- a/modules/nf-core/backsub/meta.yml +++ b/modules/nf-core/backsub/meta.yml @@ -1,5 +1,6 @@ name: "backsub" -description: Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched `tif` images. +description: Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched + `tif` images. keywords: - background - cycif @@ -9,53 +10,59 @@ keywords: - highly_multiplexed_imaging tools: - "backsub": - description: "Module for pixel-by-pixel channel subtraction scaled by exposure times" + description: "Module for pixel-by-pixel channel subtraction scaled by exposure + times" homepage: "https://github.com/SchapiroLabor/Background_subtraction" documentation: "https://github.com/SchapiroLabor/Background_subtraction/blob/master/README.md" tool_dev_url: "https://github.com/SchapiroLabor/Background_subtraction" licence: ["MIT licence"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - image: - type: file - description: Multi-channel image file - pattern: "*.{tif,tiff}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - markerfile: - type: file - description: Marker file with channel names, exposure times, and specified background to subtract (and remove to exclude channels from output) - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - image: + type: file + description: Multi-channel image file + pattern: "*.{tif,tiff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - markerfile: + type: file + description: Marker file with channel names, exposure times, and specified background + to subtract (and remove to exclude channels from output) + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - backsub_tif: - type: file - description: Background corrected pyramidal ome.tif - pattern: "*.{tif}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.ome.tif": + type: file + description: Background corrected pyramidal ome.tif + pattern: "*.{tif}" - markerout: - type: file - description: Marker file adjusted to match the background corrected image - pattern: "*.{csv}" + - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.csv": + type: file + description: Marker file adjusted to match the background corrected image + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kbestak" maintainers: diff --git a/modules/nf-core/bacphlip/meta.yml b/modules/nf-core/bacphlip/meta.yml index 1bd8f68aad0..b6f008218db 100644 --- a/modules/nf-core/bacphlip/meta.yml +++ b/modules/nf-core/bacphlip/meta.yml @@ -15,34 +15,46 @@ tools: tool_dev_url: https://github.com/adamhockenberry/bacphlip doi: 10.7717/peerj.11396 licence: ["MIT"] + identifier: biotools:bacphlip input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing phage contigs/scaffolds/chromosomes (if it is a multi-FASTA file be sure to add the `--multi_fasta` argument) - pattern: "*.{fasta,fna,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing phage contigs/scaffolds/chromosomes (if it + is a multi-FASTA file be sure to add the `--multi_fasta` argument) + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bacphlip_results: - type: file - description: TSV file containing Temperate and Virulent scores for each phage sequence - pattern: "*.bacphlip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bacphlip": + type: file + description: TSV file containing Temperate and Virulent scores for each phage + sequence + pattern: "*.bacphlip" - hmmsearch_results: - type: file - description: TSV file containing binary output indicating gene presence/absence based on hmmsearch results - pattern: "*.hmmsearch.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hmmsearch.tsv": + type: file + description: TSV file containing binary output indicating gene presence/absence + based on hmmsearch results + pattern: "*.hmmsearch.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml index c0e53e2a303..f947e61bcd1 100644 --- a/modules/nf-core/bakta/bakta/meta.yml +++ b/modules/nf-core/bakta/bakta/meta.yml @@ -12,76 +12,134 @@ tools: tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" licence: ["GPL v3"] + identifier: biotools:bakta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - FASTA file to be annotated. Has to contain at least a non-empty string dummy value. - - db: - type: file - description: | - Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/'). - - proteins: - type: file - description: FASTA/GenBank file of trusted proteins to first annotate from (optional) - - prodigal_tf: - type: file - description: Training file to use for Prodigal (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + FASTA file to be annotated. Has to contain at least a non-empty string dummy value. + - - db: + type: file + description: | + Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/'). + - - proteins: + type: file + description: FASTA/GenBank file of trusted proteins to first annotate from (optional) + - - prodigal_tf: + type: file + description: Training file to use for Prodigal (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: genome statistics and annotation summary - pattern: "*.txt" - - tsv: - type: file - description: annotations as simple human readble tab separated values - pattern: "*.tsv" - - gff: - type: file - description: annotations & sequences in GFF3 format - pattern: "*.gff3" - - gbff: - type: file - description: annotations & sequences in (multi) GenBank format - pattern: "*.gbff" - embl: - type: file - description: annotations & sequences in (multi) EMBL format - pattern: "*.embl" - - fna: - type: file - description: replicon/contig DNA sequences as FASTA - pattern: "*.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.embl: + type: file + description: annotations & sequences in (multi) EMBL format + pattern: "*.embl" - faa: - type: file - description: CDS/sORF amino acid sequences as FASTA - pattern: "*.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.faa: + type: file + description: CDS/sORF amino acid sequences as FASTA + pattern: "*.faa" - ffn: - type: file - description: feature nucleotide sequences as FASTA - pattern: "*.ffn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ffn: + type: file + description: feature nucleotide sequences as FASTA + pattern: "*.ffn" + - fna: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fna: + type: file + description: replicon/contig DNA sequences as FASTA + pattern: "*.fna" + - gbff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.gbff: + type: file + description: annotations & sequences in (multi) GenBank format + pattern: "*.gbff" + - gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.gff3: + type: file + description: annotations & sequences in GFF3 format + pattern: "*.gff3" - hypotheticals_tsv: - type: file - description: additional information on hypothetical protein CDS as simple human readble tab separated values - pattern: "*.hypotheticals.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hypotheticals.tsv: + type: file + description: additional information on hypothetical protein CDS as simple human + readble tab separated values + pattern: "*.hypotheticals.tsv" - hypotheticals_faa: - type: file - description: hypothetical protein CDS amino acid sequences as FASTA - pattern: "*.hypotheticals.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hypotheticals.faa: + type: file + description: hypothetical protein CDS amino acid sequences as FASTA + pattern: "*.hypotheticals.faa" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: annotations as simple human readble tab separated values + pattern: "*.tsv" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: genome statistics and annotation summary + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" - "@oschwengers" diff --git a/modules/nf-core/bakta/baktadbdownload/meta.yml b/modules/nf-core/bakta/baktadbdownload/meta.yml index 21acacdac1f..a0a3a4559db 100644 --- a/modules/nf-core/bakta/baktadbdownload/meta.yml +++ b/modules/nf-core/bakta/baktadbdownload/meta.yml @@ -15,15 +15,18 @@ tools: tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" licence: ["GPL v3"] + identifier: biotools:bakta output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: BAKTA database directory - pattern: "db*/" + - db*: + type: directory + description: BAKTA database directory + pattern: "db*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@jasmezz" diff --git a/modules/nf-core/bam2fastx/bam2fastq/meta.yml b/modules/nf-core/bam2fastx/bam2fastq/meta.yml index c7a884408de..328931f4178 100644 --- a/modules/nf-core/bam2fastx/bam2fastq/meta.yml +++ b/modules/nf-core/bam2fastx/bam2fastq/meta.yml @@ -1,47 +1,50 @@ name: "bam2fastx_bam2fastq" -description: Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data +description: Conversion of PacBio BAM files into gzipped fastq files, including splitting + of barcoded data keywords: - bam2fastx - bam2fastq - pacbio tools: - "bam2fastx": - description: "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files" + description: "Converting and demultiplexing of PacBio BAM files into gzipped fasta + and fastq files" homepage: "https://github.com/PacificBiosciences/bam2fastx" documentation: "https://github.com/PacificBiosciences/bam2fastx" tool_dev_url: "https://github.com/PacificBiosciences/bam2fastx" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: PacBio BAM file - pattern: "*.bam" - - index: - type: file - description: PacBio BAM file index (.pbi) - pattern: "*.pbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: PacBio BAM file + pattern: "*.bam" + - index: + type: file + description: PacBio BAM file index (.pbi) + pattern: "*.pbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Gzipped FASTQ file - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Gzipped FASTQ file + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/bamaligncleaner/meta.yml b/modules/nf-core/bamaligncleaner/meta.yml index 1278aefb433..0293aaaa3bb 100644 --- a/modules/nf-core/bamaligncleaner/meta.yml +++ b/modules/nf-core/bamaligncleaner/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/maxibor/bamAlignCleaner tool_dev_url: https://github.com/maxibor/bamAlignCleaner licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bamclipper/meta.yml b/modules/nf-core/bamclipper/meta.yml index d857845b780..0243c488008 100644 --- a/modules/nf-core/bamclipper/meta.yml +++ b/modules/nf-core/bamclipper/meta.yml @@ -8,55 +8,57 @@ keywords: - bam tools: - "bamclipper": - description: "BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing" + description: "BAMClipper: removing primers from alignments to minimize false-negative + mutations in amplicon next-generation sequencing" homepage: "https://github.com/tommyau/bamclipper" documentation: "https://github.com/tommyau/bamclipper" tool_dev_url: "https://github.com/tommyau/bamclipper" doi: "10.1038/s41598-017-01703-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information `[ id:'sample1']` - - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - - bai: - type: file - description: BAI index of the input BAM file - pattern: "*.bam.bai" - - - bedpe: - type: file - description: BEDPE file of primer pair locations - pattern: "*.bed" - + - - meta: + type: map + description: | + Groovy Map containing sample information `[ id:'sample1']` + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: BAI index of the input BAM file + pattern: "*.bam.bai" + - bedpe: + type: file + description: BEDPE file of primer pair locations + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Sorted BAM file containing clipped query sequences according to the given primer pair locations - pattern: "*.primerclipped.bam" - + - meta: + type: map + description: | + Groovy Map containing sample information `[ id:'sample1']` + - "*.primerclipped.bam": + type: file + description: Sorted BAM file containing clipped query sequences according to + the given primer pair locations + pattern: "*.primerclipped.bam" - bai: - type: file - description: "BAI index of the output BAM file" - pattern: "*.primerclipped.bam.bai" - + - meta: + type: map + description: | + Groovy Map containing sample information `[ id:'sample1']` + - "*.primerclipped.bam.bai": + type: file + description: "BAI index of the output BAM file" + pattern: "*.primerclipped.bam.bai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@krannich479" maintainers: diff --git a/modules/nf-core/bamcmp/meta.yml b/modules/nf-core/bamcmp/meta.yml index 1a83b7a57e8..021652e850b 100644 --- a/modules/nf-core/bamcmp/meta.yml +++ b/modules/nf-core/bamcmp/meta.yml @@ -1,5 +1,7 @@ name: bamcmp -description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX). +description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary + genome and a contamination genome. For instance, filtering out mouse reads from + patient derived xenograft mouse models (PDX). keywords: - filter - xenograft @@ -9,39 +11,61 @@ keywords: - mouse tools: - bamcmp: - description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else reads which multimap to the contamination genome will be spuriously kept. + description: Bamcmp is a tool for deconvolving host and graft reads, using two + bam files. Reads should be mapped to two genomes, and the mapped, sorted bam + files supplied to the tool. It is highly recommended to use the "-s as" option + not the "-s mapq" option, else reads which multimap to the contamination genome + will be spuriously kept. homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp doi: "10.1158/1541-7786.MCR-16-0431" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - primary_aligned_bam: - type: file - description: BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep) - pattern: "*.{bam,cram,sam}" - - contaminant_aligned_bam: - type: file - description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out) - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - primary_aligned_bam: + type: file + description: BAM/CRAM/SAM file with the reads aligned to the primary genome + (the one you want to keep) + pattern: "*.{bam,cram,sam}" + - contaminant_aligned_bam: + type: file + description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome + (the one you want to filter out) + pattern: "*.{bam,cram,sam}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - primary_filtered_bam: - type: file - description: Bam file containing the reads which align better to the primary genome. - pattern: "*.{bam,cram,sam}" + - meta: + type: file + description: Bam file containing the reads which align better to the primary + genome. + pattern: "*.{bam,cram,sam}" + - ${prefix}.bam: + type: file + description: Bam file containing the reads which align better to the primary + genome. + pattern: "*.{bam,cram,sam}" - contamination_bam: - type: file - description: Bam file containing the reads which align better to the contaminant genome. - pattern: "*.{bam,cram,sam}" + - meta: + type: file + description: Bam file containing the reads which align better to the contaminant + genome. + pattern: "*.{bam,cram,sam}" + - ${prefix2}.bam: + type: file + description: Bam file containing the reads which align better to the contaminant + genome. + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kmurat1" - "@sppearce" diff --git a/modules/nf-core/bamstats/generalstats/meta.yml b/modules/nf-core/bamstats/generalstats/meta.yml index a0921f4a3e3..664e2435b95 100644 --- a/modules/nf-core/bamstats/generalstats/meta.yml +++ b/modules/nf-core/bamstats/generalstats/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bamstats_generalstats" description: write your description here @@ -13,34 +12,33 @@ tools: documentation: "https://github.com/guigolab/bamstats/" tool_dev_url: "https://github.com/guigolab" licence: ["BSD-3-clause"] + identifier: biotools:bamstats-ip input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: json containing bam statistics - pattern: "*.json" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.json": + type: file + description: json containing bam statistics + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@johnoooh" diff --git a/modules/nf-core/bamtofastq10x/meta.yml b/modules/nf-core/bamtofastq10x/meta.yml index 2ac31a5cf82..ace49c25182 100644 --- a/modules/nf-core/bamtofastq10x/meta.yml +++ b/modules/nf-core/bamtofastq10x/meta.yml @@ -1,6 +1,8 @@ name: bamtofastq10x -description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis +description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell + Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used + as inputs to re-run analysis keywords: - bam @@ -10,38 +12,40 @@ keywords: tools: - bamtofastq10x: - description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis + description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, + Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that + can be used as inputs to re-run analysis homepage: https://github.com/10XGenomics/bamtofastq documentation: https://github.com/10XGenomics/bamtofastq tool_dev_url: https://github.com/10XGenomics/bamtofastq licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: fastq compressed file - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq.gz": + type: file + description: fastq compressed file + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BlueBicycleBlog" maintainers: diff --git a/modules/nf-core/bamtools/convert/meta.yml b/modules/nf-core/bamtools/convert/meta.yml index 3cc8ae6aa89..a97d0e4ae8e 100644 --- a/modules/nf-core/bamtools/convert/meta.yml +++ b/modules/nf-core/bamtools/convert/meta.yml @@ -1,5 +1,6 @@ name: bamtools_convert -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - bamtools/convert @@ -19,30 +20,33 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - data: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bed,fasta,fastq,json,pileup,sam,yaml}": + type: file + description: Output file + pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - out: - type: file - description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml) - pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/bamtools/split/meta.yml b/modules/nf-core/bamtools/split/meta.yml index e42242bbd7a..c580fbbae99 100644 --- a/modules/nf-core/bamtools/split/meta.yml +++ b/modules/nf-core/bamtools/split/meta.yml @@ -1,5 +1,6 @@ name: bamtools_split -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - bamtools/split @@ -13,30 +14,33 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A list of one or more BAM files to merge and then split - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A list of one or more BAM files to merge and then split + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Several Bam files - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Several Bam files + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" - "@matthdsm" diff --git a/modules/nf-core/bamtools/stats/meta.yml b/modules/nf-core/bamtools/stats/meta.yml index 28db686fa54..952eab3e5bf 100644 --- a/modules/nf-core/bamtools/stats/meta.yml +++ b/modules/nf-core/bamtools/stats/meta.yml @@ -1,5 +1,6 @@ name: "bamtools_stats" -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - stats @@ -11,30 +12,33 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: File containing alignment statistics - pattern: "*.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing alignment statistics + pattern: "*.stats" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/bamutil/trimbam/meta.yml b/modules/nf-core/bamutil/trimbam/meta.yml index f40a7e5d71f..ce603e76b3f 100644 --- a/modules/nf-core/bamutil/trimbam/meta.yml +++ b/modules/nf-core/bamutil/trimbam/meta.yml @@ -1,5 +1,6 @@ name: bamutil_trimbam -description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping +description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and + quality to ‘!’, or by soft clipping keywords: - bam - trim @@ -8,42 +9,48 @@ keywords: - trimBam tools: - bamutil: - description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam. + description: Programs that perform operations on SAM/BAM files, all built into + a single executable, bam. homepage: https://genome.sph.umich.edu/wiki/BamUtil documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam tool_dev_url: https://github.com/statgen/bamUtil doi: "10.1101/gr.176552.114" licence: ["GPL v3"] + identifier: biotools:bamutil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - trim_left: - type: integer - description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming. - - trim_right: - type: integer - description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - trim_left: + type: integer + description: Number of bases to trim off the right-hand side of a read. Reverse + strands are reversed before trimming. + - trim_right: + type: integer + description: Number of bases to trim off the right-hand side of a read. Reverse + strands are reversed before trimming. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Trimmed but unsorted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Trimmed but unsorted BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bandage/image/meta.yml b/modules/nf-core/bandage/image/meta.yml index 94ce8a80ed6..052780695e9 100644 --- a/modules/nf-core/bandage/image/meta.yml +++ b/modules/nf-core/bandage/image/meta.yml @@ -12,34 +12,43 @@ tools: homepage: https://github.com/rrwick/Bandage documentation: https://github.com/rrwick/Bandage licence: ["GPL-3.0-or-later"] + identifier: biotools:bandage input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly graph in GFA 1.0 format - pattern: "*.gfa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly graph in GFA 1.0 format + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - png: - type: file - description: Bandage image in PNG format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: Bandage image in PNG format + pattern: "*.png" - svg: - type: file - description: Bandage image in SVG format - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: Bandage image in SVG format + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml index a683e712383..7464c520edd 100644 --- a/modules/nf-core/barrnap/meta.yml +++ b/modules/nf-core/barrnap/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "barrnap" description: barrnap uses a hmmer profile to find rrnas in reads or contig fasta files @@ -8,38 +7,42 @@ keywords: - removal tools: - "barrnap": - description: "Barrnap predicts the location of ribosomal RNA genes in genomes (bacteria, archaea, metazoan mitochondria and eukaryotes)." + description: "Barrnap predicts the location of ribosomal RNA genes in genomes + (bacteria, archaea, metazoan mitochondria and eukaryotes)." homepage: "https://github.com/tseemann/barrnap" documentation: "https://github.com/tseemann/barrnap" tool_dev_url: "https://github.com/tseemann/barrnap" licence: ["GPL v3"] + identifier: biotools:barrnap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq or fasta file nucleotides (it can be amino acids as well) - pattern: "*.{fna,fasta,faa,fastq}" - - dbname: - type: string - description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: fasta file + pattern: "*.fasta" + - dbname: + type: string + description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: gff file containing coordinates of genes - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.gff": + type: file + description: gff file containing coordinates of genes + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@danilodileo" maintainers: diff --git a/modules/nf-core/bases2fastq/meta.yml b/modules/nf-core/bases2fastq/meta.yml index 8de98e13908..dff90c1f304 100644 --- a/modules/nf-core/bases2fastq/meta.yml +++ b/modules/nf-core/bases2fastq/meta.yml @@ -6,61 +6,102 @@ keywords: - fastq tools: - "bases2fastq": - description: "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis" + description: "Demultiplexes sequencing data and converts base calls into FASTQ + files for secondary analysis" homepage: "https://go.elementbiosciences.com/bases2fastq-download" documentation: "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq" licence: ["http://go.elembio.link/eula"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - run_manifest: - type: file - description: RunManifest file - pattern: "*.{csv}" - - run_dir: - type: directory - description: "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - run_manifest: + type: file + description: RunManifest file + pattern: "*.{csv}" + - run_dir: + type: directory + description: "Input run directory containing optionally containing a RunManifest.json + if run_manifest is not supplied" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "output/Samples/*/*_R*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/Samples/**/*_R*.fastq.gz: + type: file + description: Demultiplexed sample FASTQ files + pattern: "output/Samples/*/*_R*.fastq.gz" - sample_json: - type: file - description: Demultiplexed sample stats - pattern: "output/Samples/*/*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/Samples/**/*_stats.json: + type: file + description: Demultiplexed sample stats + pattern: "output/Samples/*/*.json" - qc_report: - type: file - description: QC HTML report - pattern: "output/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/*.html: + type: file + description: QC HTML report + pattern: "output/*.html" - run_stats: - type: file - description: QC HTML report - pattern: "output/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/RunStats.json: + type: file + description: QC HTML report + pattern: "output/*.html" - generated_run_manifest: - type: file - description: Updated Run Manifest JSON from the run_manifest csv - pattern: "output/RunManifest.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/RunManifest.json: + type: file + description: Updated Run Manifest JSON from the run_manifest csv + pattern: "output/RunManifest.json" - metrics: - type: file - description: Sample metrics - pattern: "output/Metrics.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/Metrics.csv: + type: file + description: Sample metrics + pattern: "output/Metrics.csv" - unassigned: - type: file - description: Unassigned Sequences - pattern: "output/UnassignedSequences.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/UnassignedSequences.csv: + type: file + description: Unassigned Sequences + pattern: "output/UnassignedSequences.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/basicpy/meta.yml b/modules/nf-core/basicpy/meta.yml index 61e03566697..b143f5db116 100644 --- a/modules/nf-core/basicpy/meta.yml +++ b/modules/nf-core/basicpy/meta.yml @@ -1,5 +1,7 @@ name: "basicpy" -description: BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm. +description: BaSiCPy is a python package for background and shading correction of + optical microscopy images. It is developed based on the Matlab version of BaSiC + tool with major improvements in the algorithm. keywords: - illumiation_correction - background_correction @@ -7,36 +9,41 @@ keywords: - imaging tools: - "basicpy": - description: "BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm." + description: "BaSiCPy is a python package for background and shading correction + of optical microscopy images. It is developed based on the Matlab version of + BaSiC tool with major improvements in the algorithm." homepage: "https://github.com/peng-lab/BaSiCPy" documentation: "https://basicpy.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/peng-lab/BaSiCPy" doi: 10.1038/ncomms14836 license: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - image: - type: file - description: Tiff file to be used for dark and flat field illumination correction - pattern: "*.{tiff,tif}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - image: + type: file + description: Tiff file to be used for dark and flat field illumination correction + pattern: "*.{tiff,tif}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fields: - type: file - description: Tiff fields for dark and flat field illumination correction - pattern: "*.{tiff,tif}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.tiff": + type: file + description: Tiff fields for dark and flat field illumination correction + pattern: "*.{tiff,tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/bbmap/align/meta.yml b/modules/nf-core/bbmap/align/meta.yml index a0bddba4010..38bd8e141b4 100644 --- a/modules/nf-core/bbmap/align/meta.yml +++ b/modules/nf-core/bbmap/align/meta.yml @@ -9,41 +9,55 @@ keywords: - reference tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - ref: - type: file - description: | - Either "ref" a directory containing an index, the name of another directory - with a "ref" subdirectory containing an index or the name of a fasta formatted - nucleotide file containg the reference to map to. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - ref: + type: file + description: | + Either "ref" a directory containing an index, the name of another directory + with a "ref" subdirectory containing an index or the name of a fasta formatted + nucleotide file containg the reference to map to. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.{bam}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/bbmap/bbduk/meta.yml b/modules/nf-core/bbmap/bbduk/meta.yml index 9a1f0562860..5665a268033 100644 --- a/modules/nf-core/bbmap/bbduk/meta.yml +++ b/modules/nf-core/bbmap/bbduk/meta.yml @@ -7,43 +7,53 @@ keywords: - fastq tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - contaminants: - type: file - description: | - Reference files containing adapter and/or contaminant sequences for sequence kmer matching + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - contaminants: + type: file + description: | + Reference files containing adapter and/or contaminant sequences for sequence kmer matching output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: The trimmed/modified fastq reads + pattern: "*fastq.gz" - log: - type: file - description: Bbduk log file - pattern: "*bbduk.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Bbduk log file + pattern: "*bbduk.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon09" maintainers: diff --git a/modules/nf-core/bbmap/bbmerge/meta.yml b/modules/nf-core/bbmap/bbmerge/meta.yml index 514412e8bee..240c47407e9 100644 --- a/modules/nf-core/bbmap/bbmerge/meta.yml +++ b/modules/nf-core/bbmap/bbmerge/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "bbmap_bbmerge" description: Merging overlapping paired reads into a single read. @@ -8,61 +7,69 @@ keywords: - overlap-based merging tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: | - List of input paired end fastq files - pattern: "*.{fastq,fq}.gz" - - - interleave: - type: boolean - description: | - Indicates whether the input paired reads are interleaved or not - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: | + List of input paired end fastq files + pattern: "*.{fastq,fq}.gz" + - - interleave: + type: boolean + description: | + Indicates whether the input paired reads are interleaved or not output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - merged: - type: file - description: merged reads - pattern: "*_merged.fastq" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_merged.fastq.gz": + type: file + description: merged reads + pattern: "*_merged.fastq" - unmerged: - type: file - description: unmerged reads - pattern: "*_unmerged.fastq" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_unmerged.fastq.gz": + type: file + description: unmerged reads + pattern: "*_unmerged.fastq" - ihist: - type: file - description: insert size histogram - pattern: "*_ihist.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_ihist.txt": + type: file + description: insert size histogram + pattern: "*_ihist.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log: - type: file - description: log file containing stdout and stderr from bbmerge.sh - pattern: "*.log" - + - "*.log": + type: file + description: log file containing stdout and stderr from bbmerge.sh + pattern: "*.log" authors: - "@guille0387" maintainers: diff --git a/modules/nf-core/bbmap/bbnorm/meta.yml b/modules/nf-core/bbmap/bbnorm/meta.yml index 052c5b534d6..e21f262a29a 100644 --- a/modules/nf-core/bbmap/bbnorm/meta.yml +++ b/modules/nf-core/bbmap/bbnorm/meta.yml @@ -1,40 +1,55 @@ name: bbmap_bbnorm -description: BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution. +description: BBNorm is designed to normalize coverage by down-sampling reads over + high-depth areas of a genome, to result in a flat coverage distribution. keywords: - normalization - assembly - coverage tools: - bbmap: - description: "BBMap is a short read aligner, as well as various other bioinformatic tools." + description: "BBMap is a short read aligner, as well as various other bioinformatic + tools." homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" tool_dev_url: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/" licence: ["BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: fastq file - pattern: "*.{fastq,fq}(.gz)?" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: fastq file + pattern: "*.{fastq,fq}(.gz)?" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: fastq file - pattern: "*.{fastq, fq}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: fastq file + pattern: "*.{fastq, fq}.gz" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@danilodileo" maintainers: diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml index f4e0a5ed58e..c34196e4770 100644 --- a/modules/nf-core/bbmap/bbsplit/meta.yml +++ b/modules/nf-core/bbmap/bbsplit/meta.yml @@ -8,64 +8,91 @@ keywords: - reference tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Directory to place generated index - pattern: "*" - - primary_ref: - type: file - description: Path to the primary reference - pattern: "*" - - other_ref_names: - type: list - description: List of other reference ids apart from the primary - - other_ref_paths: - type: list - description: Path to other references paths corresponding to "other_ref_names" - - only_build_index: - type: string - description: true = only build index; false = mapping + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Directory to place generated index + pattern: "*" + - - primary_ref: + type: file + description: Path to the primary reference + pattern: "*" + - - other_ref_names: + type: list + description: List of other reference ids apart from the primary + - other_ref_paths: + type: list + description: Path to other references paths corresponding to "other_ref_names" + - - only_build_index: + type: string + description: true = only build index; false = mapping output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Directory with index files - pattern: "bbsplit" + - bbsplit: + type: directory + description: Directory with index files + pattern: "bbsplit" - primary_fastq: - type: file - description: Output reads that map to the primary reference - pattern: "*primary*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*primary*fastq.gz": + type: file + description: Output reads that map to the primary reference + pattern: "*primary*fastq.gz" - all_fastq: - type: file - description: All reads mapping to any of the references - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: All reads mapping to any of the references + pattern: "*fastq.gz" - stats: - type: file - description: Tab-delimited text file containing mapping statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*txt": + type: file + description: Tab-delimited text file containing mapping statistics + pattern: "*.txt" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bbmap/clumpify/meta.yml b/modules/nf-core/bbmap/clumpify/meta.yml index ed333971d42..7db435cd633 100644 --- a/modules/nf-core/bbmap/clumpify/meta.yml +++ b/modules/nf-core/bbmap/clumpify/meta.yml @@ -7,39 +7,49 @@ keywords: - fastq tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/ documentation: https://www.biostars.org/p/225338/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The reordered/clumped (and if necessary deduped) fastq reads - pattern: "*.clumped.fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: The reordered/clumped (and if necessary deduped) fastq reads + pattern: "*.clumped.fastq.gz" - log: - type: file - description: Clumpify log file - pattern: "*clumpify.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Clumpify log file + pattern: "*clumpify.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamuanand" maintainers: diff --git a/modules/nf-core/bbmap/filterbyname/meta.yml b/modules/nf-core/bbmap/filterbyname/meta.yml index b99f4674906..b7b86419d98 100644 --- a/modules/nf-core/bbmap/filterbyname/meta.yml +++ b/modules/nf-core/bbmap/filterbyname/meta.yml @@ -6,54 +6,62 @@ keywords: - filter tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/ documentation: https://www.biostars.org/p/225338/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and - paired-end data, respectively. - - names_to_filter: - type: string - description: | - String containing names of reads to filter out of the fastq files. - - output_format: - type: string - description: | - String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2 - - interleaved_output: - type: boolean - description: | - Whether to produce an interleaved fastq output file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and + paired-end data, respectively. + - - names_to_filter: + type: string + description: | + String containing names of reads to filter out of the fastq files. + - - output_format: + type: string + description: | + String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2 + - - interleaved_output: + type: boolean + description: | + Whether to produce an interleaved fastq output file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*${output_format}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${output_format}": + type: file + description: The trimmed/modified fastq reads + pattern: "*${output_format}" - log: - type: file - description: filterbyname.sh log file - pattern: "*.filterbyname.log" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: filterbyname.sh log file + pattern: "*.filterbyname.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tokarevvasily" - "@sppearce" diff --git a/modules/nf-core/bbmap/index/meta.yml b/modules/nf-core/bbmap/index/meta.yml index c2dd342f562..ab852b4196e 100644 --- a/modules/nf-core/bbmap/index/meta.yml +++ b/modules/nf-core/bbmap/index/meta.yml @@ -1,29 +1,33 @@ name: bbmap_index -description: Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode. +description: Creates an index from a fasta file, ready to be used by bbmap.sh in mapping + mode. keywords: - map - index - fasta tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - fasta: - type: file - description: fasta formatted file with nucleotide sequences - pattern: "*.{fna,fa,fasta}" + - - fasta: + type: file + description: fasta formatted file with nucleotide sequences + pattern: "*.{fna,fa,fasta}" output: + - index: + - ref: + type: directory + description: Directory containing the index files - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - db: - type: directory - description: Directory with index files - pattern: "ref" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@daniellundin" maintainers: diff --git a/modules/nf-core/bbmap/pileup/meta.yml b/modules/nf-core/bbmap/pileup/meta.yml index 5620fd803a8..1ad776aed30 100644 --- a/modules/nf-core/bbmap/pileup/meta.yml +++ b/modules/nf-core/bbmap/pileup/meta.yml @@ -1,44 +1,55 @@ name: "bbmap_pileup" -description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file. +description: Calculates per-scaffold or per-base coverage information from an unsorted + sam or bam file. keywords: - fasta - genome - coverage tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh" licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: Per-scaffold coverage info - pattern: "*.stats.txt" + - covstats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats.txt": + type: file + description: Coverage statistics + pattern: "*.stats.txt" - hist: - type: file - description: "Histogram of # occurrences of each depth level" - pattern: "*.hist.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.txt": + type: file + description: "Histogram of # occurrences of each depth level" + pattern: "*.hist.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/bbmap/sendsketch/meta.yml b/modules/nf-core/bbmap/sendsketch/meta.yml index 76f3e9472ba..fc27db517ef 100644 --- a/modules/nf-core/bbmap/sendsketch/meta.yml +++ b/modules/nf-core/bbmap/sendsketch/meta.yml @@ -1,5 +1,6 @@ name: "bbmap_sendsketch" -description: Compares query sketches to reference sketches hosted on a remote server via the Internet. +description: Compares query sketches to reference sketches hosted on a remote server + via the Internet. keywords: - taxonomy - classification @@ -9,34 +10,40 @@ keywords: - fasta tools: - "bbmap": - description: "BBMap is a short read aligner, as well as various other bioinformatic tools." + description: "BBMap is a short read aligner, as well as various other bioinformatic + tools." homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: file with nucleotide sequences - pattern: "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: file with nucleotide sequences + pattern: "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, + fq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hits: - type: file - description: .txt file containing hits from a query seuqnce to various reference sequences output - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: .txt file containing hits from a query seuqnce to various reference + sequences output + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phanhung2" maintainers: diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index 248eee0cefe..5bfccd2bd8f 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -13,49 +13,64 @@ tools: documentation: https://samtools.github.io/bcftools/bcftools.html#annotate doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Query VCF or BCF file, can be either uncompressed or compressed - - index: - type: file - description: Index of the query VCF or BCF file - - annotations: - type: file - description: Bgzip-compressed file with annotations - - annotations_index: - type: file - description: Index of the annotations file - - header_lines: - type: file - description: Contains lines to append to the output VCF header + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Query VCF or BCF file, can be either uncompressed or compressed + - index: + type: file + description: Index of the query VCF or BCF file + - annotations: + type: file + description: Bgzip-compressed file with annotations + - annotations_index: + type: file + description: Index of the annotations file + - - header_lines: + type: file + description: Contains lines to append to the output VCF header output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed annotated VCF file - pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Compressed annotated VCF file + pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/call/meta.yml b/modules/nf-core/bcftools/call/meta.yml index b5b46ac5833..840a6355edf 100644 --- a/modules/nf-core/bcftools/call/meta.yml +++ b/modules/nf-core/bcftools/call/meta.yml @@ -16,59 +16,74 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@LouisLeNezet" diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index eeeb20714eb..b5d1f5b2cef 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -13,44 +13,59 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbi: - type: list - description: | - List containing 2 or more index files (optional) - e.g. [ 'file1.tbi', 'file2.tbi' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbi: + type: list + description: | + List containing 2 or more index files (optional) + e.g. [ 'file1.tbi', 'file2.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF concatenated output file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: VCF concatenated output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/consensus/meta.yml b/modules/nf-core/bcftools/consensus/meta.yml index 5fd8567171f..e9fa781517d 100644 --- a/modules/nf-core/bcftools/consensus/meta.yml +++ b/modules/nf-core/bcftools/consensus/meta.yml @@ -12,42 +12,45 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf}" - - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - mask: - type: file - description: BED file used for masking - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - mask: + type: file + description: BED file used for masking + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: FASTA reference consensus file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: FASTA reference consensus file + pattern: "*.{fasta,fa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/convert/meta.yml b/modules/nf-core/bcftools/convert/meta.yml index 2c89112fff0..4f2a9f3fb3d 100644 --- a/modules/nf-core/bcftools/convert/meta.yml +++ b/modules/nf-core/bcftools/convert/meta.yml @@ -7,83 +7,129 @@ keywords: - gvcf tools: - "bcftools": - description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." + description: "BCFtools is a set of utilities that manipulate variant calls in + the Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\ + \ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations." homepage: "https://samtools.github.io/bcftools/bcftools.html" documentation: "https://samtools.github.io/bcftools/bcftools.html#convert" tool_dev_url: "https://github.com/samtools/bcftools" doi: "10.1093/gigascience/giab008" licence: ["GPL"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - The input format. Each format needs a seperate parameter to be specified in the `args`: - - GEN/SAMPLE file: `--gensample2vcf` - - gVCF file: `--gvcf2vcf` - - HAP/SAMPLE file: `--hapsample2vcf` - - HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf` - - TSV file: `--tsv2vcf` - pattern: "*.{gen,sample,g.vcf,hap,legend}{.gz,}" - - input_index: - type: file - description: (Optional) The index for the input files, if needed - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: (Optional) The reference fasta, only needed for gVCF conversion - pattern: "*.{fa,fasta}" - - bed: - type: file - description: (Optional) The BED file containing the regions for the VCF file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + The input format. Each format needs a seperate parameter to be specified in the `args`: + - GEN/SAMPLE file: `--gensample2vcf` + - gVCF file: `--gvcf2vcf` + - HAP/SAMPLE file: `--hapsample2vcf` + - HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf` + - TSV file: `--tsv2vcf` + pattern: "*.{gen,sample,g.vcf,hap,legend}{.gz,}" + - input_index: + type: file + description: (Optional) The index for the input files, if needed + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: (Optional) The reference fasta, only needed for gVCF conversion + pattern: "*.{fa,fasta}" + - - bed: + type: file + description: (Optional) The BED file containing the regions for the VCF file + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf_gz: - type: file - description: VCF merged output file (bgzipped) => when `--output-type z` is used - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF merged output file (bgzipped) => when `--output-type z` is + used + pattern: "*.vcf.gz" - vcf: - type: file - description: VCF merged output file => when `--output-type v` is used - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: VCF merged output file => when `--output-type v` is used + pattern: "*.vcf" - bcf_gz: - type: file - description: BCF merged output file (bgzipped) => when `--output-type b` is used - pattern: "*.bcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf.gz": + type: file + description: BCF merged output file (bgzipped) => when `--output-type b` is + used + pattern: "*.bcf.gz" - bcf: - type: file - description: BCF merged output file => when `--output-type u` is used - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: BCF merged output file => when `--output-type u` is used + pattern: "*.bcf" - hap: - type: file - description: hap format used by IMPUTE2 and SHAPEIT - pattern: "*.hap.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap.gz": + type: file + description: hap format used by IMPUTE2 and SHAPEIT + pattern: "*.hap.gz" - legend: - type: file - description: legend format used by IMPUTE2 and SHAPEIT - pattern: "*.legend.gz" - - sample: - type: file - description: sample format used by IMPUTE2 and SHAPEIT - pattern: "*.samples" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.legend.gz": + type: file + description: legend format used by IMPUTE2 and SHAPEIT + pattern: "*.legend.gz" + - samples: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.samples": + type: file + description: samples format used by IMPUTE2 and SHAPEIT + pattern: "*.samples" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/csq/meta.yml b/modules/nf-core/bcftools/csq/meta.yml index a45d007c300..7fb85ba020e 100644 --- a/modules/nf-core/bcftools/csq/meta.yml +++ b/modules/nf-core/bcftools/csq/meta.yml @@ -17,63 +17,77 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#csq doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF/BCF file - pattern: "*.{vcf.gz,vcf,bcf}" - - meta2: - type: map - description: | - Groovy Map containing fasta information - - fasta: - type: file - description: Fasta reference - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing fai information - - fai: - type: file - description: Fasta index - pattern: "*.{fai}" - - meta4: - type: map - description: | - Groovy Map containing gff3 information - - gff3: - type: file - description: GFF3 file - pattern: "*.{gff,gff.gz,gff3,gff3.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: Fasta reference + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing fai information + - fai: + type: file + description: Fasta index + pattern: "*.{fai}" + - - meta4: + type: map + description: | + Groovy Map containing gff3 information + - gff3: + type: file + description: GFF3 file + pattern: "*.{gff,gff.gz,gff3,gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF with annotation, bgzipped per default - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF with annotation, bgzipped per default + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml index d67c0257a1c..8ac594fc222 100644 --- a/modules/nf-core/bcftools/filter/meta.yml +++ b/modules/nf-core/bcftools/filter/meta.yml @@ -12,38 +12,53 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/index/meta.yml b/modules/nf-core/bcftools/index/meta.yml index 0207d057f3f..6897d1bd121 100644 --- a/modules/nf-core/bcftools/index/meta.yml +++ b/modules/nf-core/bcftools/index/meta.yml @@ -8,40 +8,55 @@ keywords: - tbi tools: - bcftools: - description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. + description: BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most + commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations. homepage: https://samtools.github.io/bcftools/ documentation: https://samtools.github.io/bcftools/howtos/index.html tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/gigascience/giab008" licence: ["MIT", "GPL-3.0-or-later"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file (optionally GZIPPED) - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file (optionally GZIPPED) + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - csi: - type: file - description: Default VCF file index file - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index file + pattern: "*.csi" - tbi: - type: file - description: Alternative VCF file index file for larger files (activated with -t parameter) - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index file for larger files (activated with + -t parameter) + pattern: "*.tbi" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bcftools/isec/meta.yml b/modules/nf-core/bcftools/isec/meta.yml index 7da88e19b7b..9064a33323a 100644 --- a/modules/nf-core/bcftools/isec/meta.yml +++ b/modules/nf-core/bcftools/isec/meta.yml @@ -15,36 +15,40 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - List containing 2 or more vcf/bcf files. These must be compressed and have an associated index. - e.g. [ 'file1.vcf.gz', 'file2.vcf' ] - - tbis: - type: list - description: | - List containing the tbi index files corresponding to the vcf/bcf input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf/bcf files. These must be compressed and have an associated index. + e.g. [ 'file1.vcf.gz', 'file2.vcf' ] + - tbis: + type: list + description: | + List containing the tbi index files corresponding to the vcf/bcf input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Folder containing the set operations results perform on the vcf files - pattern: "${prefix}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '${prefix}", type: "dir': + type: directory + description: Folder containing the set operations results perform on the vcf + files + pattern: "${prefix}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml index 2caf644e3a3..2cf09a1d491 100644 --- a/modules/nf-core/bcftools/merge/meta.yml +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -12,67 +12,78 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: file - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbis: - type: file - description: | - List containing the tbi index files corresponding to the vcfs input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)" - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)" - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'genome' ] - - bed: - type: file - description: "(Optional) The bed regions to merge on" - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: file + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: "(Optional) The fasta reference file (only necessary for the `--gvcf + FILE` parameter)" + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: "(Optional) The fasta reference file index (only necessary for + the `--gvcf FILE` parameter)" + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] + - bed: + type: file + description: "(Optional) The bed regions to merge on" + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: merged output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf}{,.gz}": + type: file + description: merged output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - index: - type: file - description: index of merged output - pattern: "*.{csi,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: index of merged output + pattern: "*.{csi,tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/mpileup/meta.yml b/modules/nf-core/bcftools/mpileup/meta.yml index 65410ddd661..febcb33f608 100644 --- a/modules/nf-core/bcftools/mpileup/meta.yml +++ b/modules/nf-core/bcftools/mpileup/meta.yml @@ -12,56 +12,79 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - intervals: - type: file - description: Input intervals file. A file (commonly '.bed') containing regions to subset - - meta: - type: map - description: | - Groovy Map containing information about the genome fasta, e.g. [ id: 'sarscov2' ] - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - save_mpileup: - type: boolean - description: Save mpileup file generated by bcftools mpileup + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - intervals: + type: file + description: Input intervals file. A file (commonly '.bed') containing regions + to subset + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - - save_mpileup: + type: boolean + description: Save mpileup file generated by bcftools mpileup output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF gzipped output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*vcf.gz": + type: file + description: VCF gzipped output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: tabix index file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*vcf.gz.tbi": + type: file + description: tabix index file + pattern: "*.{vcf.gz.tbi}" - stats: - type: file - description: Text output file containing stats - pattern: "*{stats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*stats.txt": + type: file + description: Text output file containing stats + pattern: "*{stats.txt}" - mpileup: - type: file - description: mpileup gzipped output for all positions - pattern: "{*.mpileup.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup.gz": + type: file + description: mpileup gzipped output for all positions + pattern: "{*.mpileup.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index a0cdeaf102e..b6edeb4aae2 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -13,54 +13,70 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be normalized - e.g. 'file1.vcf' - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: | - An optional index of the VCF file (for when the VCF is compressed) - pattern: "*.vcf.gz.tbi" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf' + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: | + An optional index of the VCF file (for when the VCF is compressed) + pattern: "*.vcf.gz.tbi" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed + BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml index d944dae7817..8898ccd204b 100644 --- a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml +++ b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml @@ -1,6 +1,6 @@ ---- name: "bcftools_pluginimputeinfo" -description: Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. +description: Adds imputation information metrics to the INFO field based on selected + FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. keywords: - impute-info - bcftools @@ -10,15 +10,24 @@ keywords: - vcf tools: - "bcftools": - description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." + description: "BCFtools is a set of utilities that manipulate variant calls in + the Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\ + \ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations." homepage: "https://samtools.github.io/bcftools/howtos/index.html" documentation: "https://samtools.github.io/bcftools/bcftools.html" tool_dev_url: "https://github.com/samtools/bcftools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] args_id: "$args" + identifier: biotools:bcftools - "bcftools plugin impute-info": - description: "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available" + description: "Bcftools plugins are tools that can be used with bcftools to manipulate + variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds + imputation information metrics to the INFO field based on selected FORMAT tags. + Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available" homepage: "https://samtools.github.io/bcftools/howtos/plugins.html" documentation: "https://samtools.github.io/bcftools/bcftools.html#plugin" tool_dev_url: "https://github.com/samtools/bcftools" @@ -26,55 +35,69 @@ tools: licence: ["MIT"] args_id: "$args2" + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF output file containing added INFO/INFO field - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF output file containing added INFO/INFO field + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@eweizy" maintainers: diff --git a/modules/nf-core/bcftools/pluginscatter/meta.yml b/modules/nf-core/bcftools/pluginscatter/meta.yml index 71805c0342d..5a31dacc0c4 100644 --- a/modules/nf-core/bcftools/pluginscatter/meta.yml +++ b/modules/nf-core/bcftools/pluginscatter/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bcftools_pluginscatter" description: Split VCF by chunks or regions, creating multiple VCFs. @@ -15,65 +14,81 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The input VCF to scatter - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - type: file - description: Optional index of the input VCF - pattern: "*.tbi" - - sites_per_chunk: - type: integer - description: | - How many variants should be in each output file - Either this or `scatter` or `scatter_file` have to be given - - scatter: - type: string - description: | - A comma delimited list of regions to scatter into - Either this or `sites_per_chunk` or `scatter_file` have to be given - - scatter_file: - type: file - description: | - A file containing a region on each line with an optional second column containing the filename - Either this or `sites_per_chunk` or `scatter` have to be given - - regions: - type: file - description: Optional file containing the regions to work on - pattern: "*.bed" - - targets: - type: file - description: Optional file containing the regions to work on (but streams instead of index-jumping) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The input VCF to scatter + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: Optional index of the input VCF + pattern: "*.tbi" + - - sites_per_chunk: + type: integer + description: | + How many variants should be in each output file + Either this or `scatter` or `scatter_file` have to be given + - - scatter: + type: string + description: | + A comma delimited list of regions to scatter into + Either this or `sites_per_chunk` or `scatter_file` have to be given + - - scatter_file: + type: file + description: | + A file containing a region on each line with an optional second column containing the filename + Either this or `sites_per_chunk` or `scatter` have to be given + - - regions: + type: file + description: Optional file containing the regions to work on + pattern: "*.bed" + - - targets: + type: file + description: Optional file containing the regions to work on (but streams instead + of index-jumping) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scatter: - type: file - description: The resulting files of the scattering - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: The resulting files of the scattering + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml index 64bfce0a89d..41f766584fb 100644 --- a/modules/nf-core/bcftools/pluginsplit/meta.yml +++ b/modules/nf-core/bcftools/pluginsplit/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bcftools_pluginsplit" description: Split VCF by sample, creating single- or multi-sample VCFs. @@ -14,60 +13,83 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF file to split + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: OPTIONAL - The index of the input VCF/BCF + pattern: "*.tbi" + - - samples: + type: file + description: | + A tab-separated file determining which samples should be in which output file + column 1: The sample name(s) in the input file + column 2: The sample name(s) to use in the output file (use `-` to keep the original name) + column 3: The name of the output file + Either this or a groups file should be given + pattern: "*" + - - groups: + type: file + description: | + A tab-separated file determining which samples should be in which output file(s) + column 1: The sample name(s) in the input file + column 2: The sample name(s) to use in the output file (use `-` to keep the original name) + column 3: The name of the output file(s) + Either this or a samples file should be given + pattern: "*" + - - regions: + type: file + description: A BED file containing regions to use + pattern: "*.bed" + - - targets: + type: file + description: A BED file containing regions to use (but streams rather than index-jumps) + pattern: "*.bed" +output: - vcf: - type: file - description: The VCF file to split - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: The resulting VCF files from the split + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: OPTIONAL - The index of the input VCF/BCF - pattern: "*.tbi" - - samples: - type: file - description: | - A tab-separated file determining which samples should be in which output file - column 1: The sample name(s) in the input file - column 2: The sample name(s) to use in the output file (use `-` to keep the original name) - column 3: The name of the output file - Either this or a groups file should be given - pattern: "*" - - groups: - type: file - description: | - A tab-separated file determining which samples should be in which output file(s) - column 1: The sample name(s) in the input file - column 2: The sample name(s) to use in the output file (use `-` to keep the original name) - column 3: The name of the output file(s) - Either this or a samples file should be given - pattern: "*" - - regions: - type: file - description: A BED file containing regions to use - pattern: "*.bed" - - targets: - type: file - description: A BED file containing regions to use (but streams rather than index-jumps) - pattern: "*.bed" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: TBI file + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf: - type: file - description: The resulting VCF files from the split - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/plugintag2tag/meta.yml b/modules/nf-core/bcftools/plugintag2tag/meta.yml index 5cbc772ce59..ad67d0cbdda 100644 --- a/modules/nf-core/bcftools/plugintag2tag/meta.yml +++ b/modules/nf-core/bcftools/plugintag2tag/meta.yml @@ -1,6 +1,6 @@ ---- name: "bcftools_plugintag2tag" -description: Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD. +description: Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized + alleles, eg LPL,LAD. keywords: - tag2tag - bcftools @@ -13,55 +13,69 @@ tools: documentation: https://samtools.github.io/bcftools/howtos/plugin.tag2tag.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@eweizy" maintainers: diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml index 303ef61024c..279b3205d6f 100644 --- a/modules/nf-core/bcftools/query/meta.yml +++ b/modules/nf-core/bcftools/query/meta.yml @@ -1,5 +1,6 @@ name: bcftools_query -description: Extracts fields from VCF or BCF files and outputs them in user-defined format. +description: Extracts fields from VCF or BCF files and outputs them in user-defined + format. keywords: - query - variant calling @@ -13,48 +14,51 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be qeuried. - pattern: "*.{vcf.gz, vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be qeuried. + pattern: "*.{vcf.gz, vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. + pattern: "*.tbi" + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: BCFTools query output file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: BCFTools query output file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@drpatelh" diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index d903cc0f136..47e5344cd5b 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -12,51 +12,60 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF/BCF file - pattern: "*.{vcf.gz,vcf,bcf}" - - header: - type: file - description: New header to add to the VCF - pattern: "*.{header.txt}" - - samples: - type: file - description: File containing sample names to update (one sample per line) - pattern: "*.{samples.txt}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Fasta index to update header sequences with - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - header: + type: file + description: New header to add to the VCF + pattern: "*.{header.txt}" + - samples: + type: file + description: File containing sample names to update (one sample per line) + pattern: "*.{samples.txt}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Fasta index to update header sequences with + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF with updated header, bgzipped per default - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF with updated header, bgzipped per default + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - index: - type: file - description: Index of VCF with updated header - pattern: "*.{csi,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: Index of VCF with updated header + pattern: "*.{csi,tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/roh/meta.yml b/modules/nf-core/bcftools/roh/meta.yml index ee928a8fa5e..032148fa4af 100644 --- a/modules/nf-core/bcftools/roh/meta.yml +++ b/modules/nf-core/bcftools/roh/meta.yml @@ -1,5 +1,6 @@ name: "bcftools_roh" -description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered. +description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites + are considered. keywords: - roh - biallelic @@ -7,53 +8,65 @@ keywords: - autozygosity tools: - "roh": - description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered." + description: "A program for detecting runs of homo/autozygosity. Only bi-allelic + sites are considered." homepage: https://www.htslib.org/ documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,.vcf.gz}" - - af_file: - type: file - description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF." - - af_file_tbi: - type: file - description: "tbi index of af_file." - - genetic_map: - type: file - description: "Genetic map in the format required also by IMPUTE2." - - regions_file: - type: file - description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." - - samples_file: - type: file - description: "File of sample names to include or exclude if prefixed with '^'." - - targets_file: - type: file - description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,.vcf.gz}" + - tbi: + type: file + description: TBI file + patthern: "*.tbi" + - - af_file: + type: file + description: "Read allele frequencies from a tab-delimited file containing the + columns: CHROM\tPOS\tREF,ALT\tAF." + - af_file_tbi: + type: file + description: "tbi index of af_file." + - - genetic_map: + type: file + description: "Genetic map in the format required also by IMPUTE2." + - - regions_file: + type: file + description: "Regions can be specified either on command line or in a VCF, BED, + or tab-delimited file (the default)." + - - samples_file: + type: file + description: "File of sample names to include or exclude if prefixed with '^'." + - - targets_file: + type: file + description: "Targets can be specified either on command line or in a VCF, BED, + or tab-delimited file (the default)." output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - roh: - type: file - description: Contains site-specific and/or per-region runs of homo/autozygosity calls. - pattern: "*.{roh}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roh": + type: file + description: Contains site-specific and/or per-region runs of homo/autozygosity + calls. + pattern: "*.{roh}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index dfbddcbac52..f7a6eff17d9 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF/BCF file to be sorted - pattern: "*.{vcf.gz,vcf,bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file to be sorted + pattern: "*.{vcf.gz,vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Sorted VCF file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Sorted VCF file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/split/meta.yml b/modules/nf-core/bcftools/split/meta.yml index 578b850f634..4526696edba 100644 --- a/modules/nf-core/bcftools/split/meta.yml +++ b/modules/nf-core/bcftools/split/meta.yml @@ -12,34 +12,37 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed vcf file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Compressed vcf file index - pattern: "*.{tbi,csi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed vcf file + pattern: "*.vcf.gz" + - tbi: + type: file + description: Compressed vcf file index + pattern: "*.{tbi,csi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - split_vcf: - type: file - description: Compressed vcf files per chromosome - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed vcf files per chromosome + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" - "@atrigila" diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml index 7ea2103e3bd..655a61c5f4f 100644 --- a/modules/nf-core/bcftools/stats/meta.yml +++ b/modules/nf-core/bcftools/stats/meta.yml @@ -13,58 +13,86 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' - - exons: - type: file - description: | - Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). - e.g. 'exons.tsv.gz' - - fasta: - type: file - description: | - Faidx indexed reference sequence file to determine INDEL context. - e.g. 'reference.fa' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. + pattern: "*.tbi" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exons: + type: file + description: | + Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). + e.g. 'exons.tsv.gz' + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Faidx indexed reference sequence file to determine INDEL context. + e.g. 'reference.fa' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: Text output file containing stats - pattern: "*_{stats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*stats.txt": + type: file + description: Text output file containing stats + pattern: "*_{stats.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml index 5eb1b196c0b..aa7785f1222 100644 --- a/modules/nf-core/bcftools/view/meta.yml +++ b/modules/nf-core/bcftools/view/meta.yml @@ -1,5 +1,6 @@ name: bcftools_view -description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF +description: View, subset and filter VCF or BCF files by position and filtering expression. + Convert between VCF and BCF keywords: - variant calling - view @@ -13,59 +14,74 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/bcl2fastq/meta.yml b/modules/nf-core/bcl2fastq/meta.yml index a8c8efd85f7..a30a33efce0 100644 --- a/modules/nf-core/bcl2fastq/meta.yml +++ b/modules/nf-core/bcl2fastq/meta.yml @@ -10,54 +10,91 @@ tools: homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software" documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf" licence: ["ILLUMINA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - samplesheet: - type: file - description: "Input samplesheet" - pattern: "*.{csv}" - - run_dir: - type: file - description: | - Input run directory containing RunInfo.xml and BCL data - Could be a directory or a tar of the directory + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samplesheet: + type: file + description: "Input samplesheet" + pattern: "*.{csv}" + - run_dir: + type: file + description: | + Input run directory containing RunInfo.xml and BCL data + Could be a directory or a tar of the directory output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "**_S*_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" + - output/**_S[1-9]*_R?_00?.fastq.gz: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" - fastq_idx: - type: file - description: Optional demultiplexed index FASTQ files - pattern: "**_S*_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" + - output/**_S[1-9]*_I?_00?.fastq.gz: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" - undetermined: - type: file - description: Optional undetermined sample FASTQ files - pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - output/**Undetermined_S0*_R?_00?.fastq.gz: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" - undetermined_idx: - type: file - description: Optional undetermined index FASTQ files - pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - output/**Undetermined_S0*_I?_00?.fastq.gz: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" - reports: - type: file - description: Demultiplexing Reports - pattern: "Reports/*" + - meta: + type: file + description: Demultiplexing Reports + pattern: "Reports/*" + - output/Reports: + type: file + description: Demultiplexing Reports + pattern: "Reports/*" - stats: - type: file - description: Statistics files - pattern: "Stats/*" + - meta: + type: file + description: Statistics files + pattern: "Stats/*" + - output/Stats: + type: file + description: Statistics files + pattern: "Stats/*" - interop: - type: file - description: Interop files - pattern: "*.{bin}" + - meta: + type: file + description: Interop files + pattern: "*.{bin}" + - InterOp/*.bin: + type: file + description: Interop files + pattern: "*.{bin}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/bclconvert/meta.yml b/modules/nf-core/bclconvert/meta.yml index c4acdb51c9a..8687d7f62e5 100644 --- a/modules/nf-core/bclconvert/meta.yml +++ b/modules/nf-core/bclconvert/meta.yml @@ -10,54 +10,91 @@ tools: homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html" documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm" licence: ["ILLUMINA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - samplesheet: - type: file - description: "Input samplesheet" - pattern: "*.{csv}" - - run_dir: - type: file - description: | - Input run directory containing RunInfo.xml and BCL data - Could be a directory or a tar of the directory + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samplesheet: + type: file + description: "Input samplesheet" + pattern: "*.{csv}" + - run_dir: + type: file + description: | + Input run directory containing RunInfo.xml and BCL data + Could be a directory or a tar of the directory output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "**_S*_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" + - output/**_S[1-9]*_R?_00?.fastq.gz: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" - fastq_idx: - type: file - description: Optional demultiplexed index FASTQ files - pattern: "**_S*_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" + - output/**_S[1-9]*_I?_00?.fastq.gz: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" - undetermined: - type: file - description: Optional undetermined sample FASTQ files - pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - output/**Undetermined_S0*_R?_00?.fastq.gz: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" - undetermined_idx: - type: file - description: Optional undetermined index FASTQ files - pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - output/**Undetermined_S0*_I?_00?.fastq.gz: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" - reports: - type: file - description: Demultiplexing Reports - pattern: "Reports/*.{csv,xml}" + - meta: + type: file + description: Demultiplexing Reports + pattern: "Reports/*.{csv,xml}" + - output/Reports: + type: file + description: Demultiplexing Reports + pattern: "Reports/*.{csv,xml}" - logs: - type: file - description: Log files - pattern: "Logs/*.{log,txt}" + - meta: + type: file + description: Log files + pattern: "Logs/*.{log,txt}" + - output/Logs: + type: file + description: Log files + pattern: "Logs/*.{log,txt}" - interop: - type: file - description: Interop files - pattern: "*.{bin}" + - meta: + type: file + description: Interop files + pattern: "*.{bin}" + - '**/InterOp/*.bin", includeInputs: true': + type: file + description: Interop files + pattern: "*.{bin}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/beagle5/beagle/meta.yml b/modules/nf-core/beagle5/beagle/meta.yml index 51b9c6b6997..56793d1e707 100644 --- a/modules/nf-core/beagle5/beagle/meta.yml +++ b/modules/nf-core/beagle5/beagle/meta.yml @@ -1,60 +1,74 @@ name: "beagle5_beagle" -description: Beagle v5.2 is a software package for phasing genotypes and for imputing ungenotyped markers. +description: Beagle v5.2 is a software package for phasing genotypes and for imputing + ungenotyped markers. keywords: - phasing - imputation - genotype tools: - "beagle5": - description: "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers." + description: "Beagle is a software package for phasing genotypes and for imputing + ungenotyped markers." homepage: "https://faculty.washington.edu/browning/beagle/b5_2.html" documentation: "https://faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf" doi: "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: target VCF input file to be imputed and or phased - pattern: "*.{vcf,vcf.gz}" - - ref: - type: file - description: reference panel in bref3 or VCF format - pattern: "*.{vcf,vcf.gz,bref3}" - - genmap: - type: file - description: a PLINK format genetic map with cM units - pattern: "*.{map,map.gz,map.zip}" - - exclsamples: - type: file - description: text file containing samples one sample per line to be excluded from the analysis - pattern: "*.*" - - exclmarkers: - type: file - description: text file containing markers one marker per line to be excluded from the analysis - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: target VCF input file to be imputed and or phased + pattern: "*.{vcf,vcf.gz}" + - - refpanel: + type: file + description: target reference panel + - - genmap: + type: file + description: a PLINK format genetic map with cM units + pattern: "*.{map,map.gz,map.zip}" + - - exclsamples: + type: file + description: text file containing samples one sample per line to be excluded + from the analysis + pattern: "*.*" + - - exclmarkers: + type: file + description: text file containing markers one marker per line to be excluded + from the analysis + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: bgzip compressed VCF file that contains phased non missing genotypes + for all non reference samples + pattern: "*.vcf.gz" - log: - type: file - description: a summary of the analysis that includes the Beagle version, the command line arguments, and compute time. - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: a summary of the analysis that includes the Beagle version, the + command line arguments, and compute time. + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" maintainers: diff --git a/modules/nf-core/bedgovcf/meta.yml b/modules/nf-core/bedgovcf/meta.yml index 406935eba50..6acbd65c14a 100644 --- a/modules/nf-core/bedgovcf/meta.yml +++ b/modules/nf-core/bedgovcf/meta.yml @@ -1,4 +1,3 @@ ---- name: "bedgovcf" description: Convert a BED file to a VCF file according to a YAML config keywords: @@ -13,45 +12,46 @@ tools: documentation: "https://github.com/nvnieuwk/bedgovcf" tool_dev_url: "https://github.com/nvnieuwk/bedgovcf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bed: - type: file - description: The BED file to convert to VCF - pattern: "*.bed" - - config: - type: file - description: The config file to use for the conversion - pattern: "*.{yml,yaml}" - - meta2: - type: map - description: | - Groovy Map containing fasta index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: The fasta index file - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: The BED file to convert to VCF + pattern: "*.bed" + - config: + type: file + description: The config file to use for the conversion + pattern: "*.{yml,yaml}" + - - meta2: + type: map + description: | + Groovy Map containing fasta index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: The fasta index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The converted VCF file - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: The converted VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" diff --git a/modules/nf-core/bedops/convert2bed/meta.yml b/modules/nf-core/bedops/convert2bed/meta.yml index eea91965074..6d84c031601 100644 --- a/modules/nf-core/bedops/convert2bed/meta.yml +++ b/modules/nf-core/bedops/convert2bed/meta.yml @@ -12,36 +12,33 @@ tools: tool_dev_url: "https://github.com/bedops" doi: "10.1093/bioinformatics/bts277" licence: ["GNU v2"] + identifier: biotools:bedops input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: Sorted BAM/GFF/GTF/GVF/PSL file - pattern: "*.{bam,gff,gtf,gvf,psl}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - in_file: + type: file + description: Input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bed: - type: file - description: Sorted BED file - pattern: "*.{bed}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bed": + type: file + description: Sorted BED file + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/bedops/gtf2bed/meta.yml b/modules/nf-core/bedops/gtf2bed/meta.yml index 2646b74a2f8..5fe3ad8bc4c 100644 --- a/modules/nf-core/bedops/gtf2bed/meta.yml +++ b/modules/nf-core/bedops/gtf2bed/meta.yml @@ -6,33 +6,40 @@ keywords: - conversion tools: - gtf2bed: - description: The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data. + description: The gtf2bed script converts 1-based, closed [start, end] Gene Transfer + Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted + data. homepage: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html documentation: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html tool_dev_url: https://github.com/bedops/bedops doi: 10.1093/bioinformatics/bts277 licence: ["GPL v2"] + identifier: biotools:bedops input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - gtf: - type: file - description: A reference file in GTF format - pattern: "*.{gtf,gtf.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: A reference file in GTF format + pattern: "*.{gtf,gtf.gz}" output: - bed: - type: file - description: A reference file in BED format - pattern: "*.{bed}" + - meta: + type: file + description: A reference file in BED format + pattern: "*.{bed}" + - "*.bed": + type: file + description: A reference file in BED format + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidecarlson" diff --git a/modules/nf-core/bedtools/bamtobed/meta.yml b/modules/nf-core/bedtools/bamtobed/meta.yml index b6d149296df..201718855d9 100644 --- a/modules/nf-core/bedtools/bamtobed/meta.yml +++ b/modules/nf-core/bedtools/bamtobed/meta.yml @@ -12,30 +12,33 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file containing genomic intervals. - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file containing genomic intervals. + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/bedtools/closest/meta.yml b/modules/nf-core/bedtools/closest/meta.yml index 4a9b390b153..8b899899160 100644 --- a/modules/nf-core/bedtools/closest/meta.yml +++ b/modules/nf-core/bedtools/closest/meta.yml @@ -1,5 +1,6 @@ name: "bedtools_closest" -description: For each feature in A, finds the closest feature (upstream or downstream) in B. +description: For each feature in A, finds the closest feature (upstream or downstream) + in B. keywords: - bedtools - closest @@ -12,38 +13,42 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/closest.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_1: - type: file - description: The file to find the closest features of - pattern: "*.{bed,vcf,gff}(.gz)?" - - input_2: - type: list - description: The input file(s) to find the closest features from - pattern: "*.{bed,vcf,gff}(.gz)?" - - fasta_fai: - type: file - description: The index of the FASTA reference. Needed when the argument `--sorted` is used - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_1: + type: file + description: The file to find the closest features of + pattern: "*.{bed,vcf,gff}(.gz)?" + - input_2: + type: list + description: The input file(s) to find the closest features from + pattern: "*.{bed,vcf,gff}(.gz)?" + - - fasta_fai: + type: file + description: The index of the FASTA reference. Needed when the argument `--sorted` + is used + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: The resulting BED file containing the closest features - pattern: "*.{bed,vcf,gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: The resulting BED file containing the closest features + pattern: "*.{bed,vcf,gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bedtools/complement/meta.yml b/modules/nf-core/bedtools/complement/meta.yml index ee84bd79a41..b74cb95d74e 100644 --- a/modules/nf-core/bedtools/complement/meta.yml +++ b/modules/nf-core/bedtools/complement/meta.yml @@ -1,5 +1,6 @@ name: bedtools_complement -description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. +description: Returns all intervals in a genome that are not covered by at least one + interval in the input BED/GFF/VCF file. keywords: - bed - gff @@ -13,34 +14,38 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - sizes: - type: file - description: File which defines the chromosome lengths for a given genome - pattern: "*.{sizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - sizes: + type: file + description: File which defines the chromosome lengths for a given genome + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file with all genomic intervals that are not covered by at least one record from the input file. - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file with all genomic intervals that are not covered by at + least one record from the input file. + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/coverage/meta.yml b/modules/nf-core/bedtools/coverage/meta.yml index 7c5648566a4..ea4d0ef4b5e 100644 --- a/modules/nf-core/bedtools/coverage/meta.yml +++ b/modules/nf-core/bedtools/coverage/meta.yml @@ -1,5 +1,6 @@ name: "bedtools_coverage" -description: computes both the depth and breadth of coverage of features in file B on the features in file A +description: computes both the depth and breadth of coverage of features in file B + on the features in file A keywords: - bedtools - coverage @@ -16,41 +17,44 @@ tools: tool_dev_url: "https://github.com/arq5x/bedtools2" doi: "10.1093/bioinformatics/btq033" licence: ["GPL v2", "MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_A: - type: file - description: BAM/BED/GFF/VCF file - pattern: "*.{bam,bed,gff,vcf}" - - input_B: - type: file - description: One or more BAM/BED/GFF/VCF file - pattern: "*.{bam,bed,gff,vcf}" - - genome_file: - type: file - description: | - Optional reference genome 2 column file that defines the expected chromosome order - in the input files for use with the -sorted option. - When `genome_file` is provided, `-sorted` option is added to the command. - pattern: "*.{fai,txt,chromsizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_A: + type: file + description: BAM/BED/GFF/VCF file + pattern: "*.{bam,bed,gff,vcf}" + - input_B: + type: file + description: One or more BAM/BED/GFF/VCF file + pattern: "*.{bam,bed,gff,vcf}" + - - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order + in the input files for use with the -sorted option. + When `genome_file` is provided, `-sorted` option is added to the command. + pattern: "*.{fai,txt,chromsizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing coverage of sequence alignments - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing coverage of sequence alignments + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml index 2b2385e3ea8..41b1f8f491a 100644 --- a/modules/nf-core/bedtools/genomecov/meta.yml +++ b/modules/nf-core/bedtools/genomecov/meta.yml @@ -1,5 +1,6 @@ name: bedtools_genomecov -description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. +description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) + summaries of feature coverage (e.g., aligned sequences) for a given genome. keywords: - bed - bam @@ -12,39 +13,50 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - scale: - type: integer - description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - - sizes: - type: file - description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - scale: + type: integer + description: Number containing the scale factor for the output. Set to 1 to + disable. Setting to a value other than 1 will also get the -bg bedgraph output + format as this is required for this command switch + - - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and + chromosome sizes in the second column + - - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", + ".tab", etc.) It is set arbitrarily by the user and corresponds to the file + format which depends on arguments. + - - sort: + type: boolean + description: Sort the output output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - genomecov: - type: file - description: Computed genome coverage file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Computed genome coverage file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/getfasta/meta.yml b/modules/nf-core/bedtools/getfasta/meta.yml index 41917fe3ffb..bb38fa2591d 100644 --- a/modules/nf-core/bedtools/getfasta/meta.yml +++ b/modules/nf-core/bedtools/getfasta/meta.yml @@ -1,5 +1,6 @@ name: bedtools_getfasta -description: extract sequences in a FASTA file based on intervals defined in a feature file. +description: extract sequences in a FASTA file based on intervals defined in a feature + file. keywords: - bed - fasta @@ -10,34 +11,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Output fasta file with extracted sequences - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: Output fasta file with extracted sequences + pattern: "*.{fa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bedtools/groupby/meta.yml b/modules/nf-core/bedtools/groupby/meta.yml index bcbc561a094..3be92b0778f 100644 --- a/modules/nf-core/bedtools/groupby/meta.yml +++ b/modules/nf-core/bedtools/groupby/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: bedtools_groupby -description: Groups features in a BED file by given column(s) and computes summary statistics for each group to another column. +description: Groups features in a BED file by given column(s) and computes summary + statistics for each group to another column. keywords: - bed - groupby @@ -14,33 +14,36 @@ tools: homepage: https://bedtools.readthedocs.io/en/latest/ doi: 10.1093/bioinformatics/btq033 licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - summary_column: - type: integer - description: Column to be summarized (1-based) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - summary_col: + type: string + description: Column to summarize output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - bed: - type: file - description: Grouped by bed file with combined features - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: Grouped by bed file with combined features + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mashehu" maintainers: diff --git a/modules/nf-core/bedtools/intersect/meta.yml b/modules/nf-core/bedtools/intersect/meta.yml index 0939cb54a09..45ecf377a1a 100644 --- a/modules/nf-core/bedtools/intersect/meta.yml +++ b/modules/nf-core/bedtools/intersect/meta.yml @@ -10,43 +10,47 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals1: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - intervals2: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference chromosome sizes - e.g. [ id:'test' ] - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - intervals2: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference chromosome sizes + e.g. [ id:'test' ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - intersect: - type: file - description: File containing the description of overlaps found between the two features - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: File containing the description of overlaps found between the two + features + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/jaccard/meta.yml b/modules/nf-core/bedtools/jaccard/meta.yml index 2b5422841ff..3ae68e58a96 100644 --- a/modules/nf-core/bedtools/jaccard/meta.yml +++ b/modules/nf-core/bedtools/jaccard/meta.yml @@ -14,43 +14,47 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_a: - type: file - description: VCF,GFF or BED file to use with the `-a` option - pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" - - input_b: - type: file - description: VCF,GFF or BED file to use with the `-b` option - pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" - - meta2: - type: map - description: | - Groovy Map containing genome file information - e.g. [ id:'test', single_end:false ] - - genome_file: - type: file - description: A file containing all the contigs of the genome used to create the input files - pattern: "*.{txt,sizes,fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_a: + type: file + description: VCF,GFF or BED file to use with the `-a` option + pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" + - input_b: + type: file + description: VCF,GFF or BED file to use with the `-b` option + pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" + - - meta2: + type: map + description: | + Groovy Map containing genome file information + e.g. [ id:'test', single_end:false ] + - genome_file: + type: file + description: A file containing all the contigs of the genome used to create + the input files + pattern: "*.{txt,sizes,fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file containing the results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file containing the results + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bedtools/makewindows/meta.yml b/modules/nf-core/bedtools/makewindows/meta.yml index f89d71753df..df047f66315 100644 --- a/modules/nf-core/bedtools/makewindows/meta.yml +++ b/modules/nf-core/bedtools/makewindows/meta.yml @@ -7,35 +7,39 @@ keywords: - chunking tools: - bedtools: - description: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + description: A set of tools for genomic analysis tasks, specifically enabling + genome arithmetic (merge, count, complement) on various file types. homepage: https://bedtools.readthedocs.io documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html doi: "10.1093/bioinformatics/btq033" licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - regions: - type: file - description: BED file OR Genome details file () - pattern: "*.{bed,tab,fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: BED file OR Genome details file () + pattern: "*.{bed,tab,fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: BED file containing the windows - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file containing the windows + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevbrick" - "@nvnieuwk" diff --git a/modules/nf-core/bedtools/map/meta.yml b/modules/nf-core/bedtools/map/meta.yml index 0267f6ffecd..4e56bb94cf1 100644 --- a/modules/nf-core/bedtools/map/meta.yml +++ b/modules/nf-core/bedtools/map/meta.yml @@ -12,43 +12,47 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/map.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals1: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" - - intervals2: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference chromosome sizes - e.g. [ id:'test' ] - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - intervals2: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference chromosome sizes + e.g. [ id:'test' ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mapped: - type: file - description: File containing the description of overlaps found between the features in A and the features in B, with statistics - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: File containing the description of overlaps found between the features + in A and the features in B, with statistics + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ekushele" maintainers: diff --git a/modules/nf-core/bedtools/maskfasta/meta.yml b/modules/nf-core/bedtools/maskfasta/meta.yml index 94f81aba7f4..2d976645fcd 100644 --- a/modules/nf-core/bedtools/maskfasta/meta.yml +++ b/modules/nf-core/bedtools/maskfasta/meta.yml @@ -1,5 +1,6 @@ name: bedtools_maskfasta -description: masks sequences in a FASTA file based on intervals defined in a feature file. +description: masks sequences in a FASTA file based on intervals defined in a feature + file. keywords: - bed - fasta @@ -10,34 +11,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Output masked fasta file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: Output masked fasta file + pattern: "*.{fa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index d7463e3dbc0..6da542052b0 100644 --- a/modules/nf-core/bedtools/merge/meta.yml +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -1,5 +1,6 @@ name: bedtools_merge -description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +description: combines overlapping or “book-ended” features in an interval file into + a single feature which spans all of the combined features. keywords: - bed - merge @@ -11,30 +12,33 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Overlapped bed file with combined features - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/multiinter/meta.yml b/modules/nf-core/bedtools/multiinter/meta.yml index e9a69cf3bab..23d052da792 100644 --- a/modules/nf-core/bedtools/multiinter/meta.yml +++ b/modules/nf-core/bedtools/multiinter/meta.yml @@ -1,5 +1,6 @@ name: "bedtools_multiinter" -description: Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files. +description: Identifies common intervals among multiple (and subsets thereof) sorted + BED/GFF/VCF files. keywords: - bedtools - multinterval @@ -12,34 +13,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/multiinter.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - beds: - type: list - description: List of files to be merged - pattern: "*.{bed,vcf,gff}" - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - beds: + type: list + description: List of files to be merged + pattern: "*.{bed,vcf,gff}" + - - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Common interval bed - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Common interval bed + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/bedtools/shift/meta.yml b/modules/nf-core/bedtools/shift/meta.yml index 57c8994ae80..cf0719e898b 100644 --- a/modules/nf-core/bedtools/shift/meta.yml +++ b/modules/nf-core/bedtools/shift/meta.yml @@ -14,34 +14,42 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt,.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt,.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Shift BED file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Shift BED file + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ekushele" maintainers: diff --git a/modules/nf-core/bedtools/slop/meta.yml b/modules/nf-core/bedtools/slop/meta.yml index 69116715bd8..762db534a5a 100644 --- a/modules/nf-core/bedtools/slop/meta.yml +++ b/modules/nf-core/bedtools/slop/meta.yml @@ -1,5 +1,6 @@ name: bedtools_slop -description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r) +description: Adds a specified number of bases in each direction (unique values may + be specified for either -l or -r) keywords: - bed - slopBed @@ -10,30 +11,36 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - sizes: + type: file + description: Chromosome sizes file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Slopped BED file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Slopped BED file + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 7c915f5f9e8..313698f1604 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -11,35 +11,38 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BED/BEDGRAPH - pattern: "*.{bed|bedGraph}" - - genome_file: - type: file - description: | - Optional reference genome 2 column file that defines the expected chromosome order. - pattern: "*.{fai,txt,chromsizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" + - - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order. + pattern: "*.{fai,txt,chromsizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: Sorted output file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Sorted output file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/split/meta.yml b/modules/nf-core/bedtools/split/meta.yml index 725bb9a2007..7e126d22e6b 100644 --- a/modules/nf-core/bedtools/split/meta.yml +++ b/modules/nf-core/bedtools/split/meta.yml @@ -9,30 +9,36 @@ tools: description: "A powerful toolset for genome arithmetic" documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/sort.html" licence: ["MIT", "GPL v2"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file + pattern: "*.bed" + - count: + type: integer + description: Number of lines per split file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - beds: - type: list - description: list of split BED files - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: list + description: list of split BED files + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bedtools/subtract/meta.yml b/modules/nf-core/bedtools/subtract/meta.yml index 0226ff18846..ddf7d92db2d 100644 --- a/modules/nf-core/bedtools/subtract/meta.yml +++ b/modules/nf-core/bedtools/subtract/meta.yml @@ -1,5 +1,6 @@ name: bedtools_subtract -description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A. +description: Finds overlaps between two sets of regions (A and B), removes the overlaps + from A and reports the remaining portion of A. keywords: - bed - gff @@ -11,34 +12,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals1: - type: file - description: BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" - - intervals2: - type: file - description: BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - intervals2: + type: file + description: BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing the difference between the two sets of features - patters: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing the difference between the two sets of features + patters: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sidorov-si" maintainers: diff --git a/modules/nf-core/bedtools/unionbedg/meta.yml b/modules/nf-core/bedtools/unionbedg/meta.yml index ee73e8b5159..9fefd920311 100644 --- a/modules/nf-core/bedtools/unionbedg/meta.yml +++ b/modules/nf-core/bedtools/unionbedg/meta.yml @@ -12,40 +12,43 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: | - Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative - pattern: "*.{bedGraph,bedgraph}" - - meta2: - type: map - description: | - Groovy Map containing meta information for the reference chromosome sizes - e.g. [ id:'test' ] - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: | + Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative + pattern: "*.{bedGraph,bedgraph}" + - - meta2: + type: map + description: | + Groovy Map containing meta information for the reference chromosome sizes + e.g. [ id:'test' ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Combined BED file with values from all bedGraph files - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Combined BED file with values from all bedGraph files + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ekushele" maintainers: diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml index 7af01582195..c691ac0c2a4 100644 --- a/modules/nf-core/bioawk/meta.yml +++ b/modules/nf-core/bioawk/meta.yml @@ -1,5 +1,6 @@ name: "bioawk" -description: Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats. +description: Bioawk is an extension to Brian Kernighan's awk, adding the support of + several common biological data formats. keywords: - bioawk - fastq @@ -14,32 +15,36 @@ tools: documentation: "https://github.com/lh3/bioawk" tool_dev_url: "https://github.com/lh3/bioawk" licence: ["Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`. - pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input sequence biological sequence file (optionally gzipped) to + be manipulated via program specified in `$args`. + pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: | - Manipulated and gzipped version of input sequence file following program specified in `args`. - File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you! - pattern: "*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: | + Manipulated and gzipped version of input sequence file following program specified in `args`. + File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you! + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/biobambam/bammarkduplicates2/meta.yml b/modules/nf-core/biobambam/bammarkduplicates2/meta.yml index 567a0c7a12b..60b26305840 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/meta.yml +++ b/modules/nf-core/biobambam/bammarkduplicates2/meta.yml @@ -12,34 +12,43 @@ tools: documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md doi: 10.1186/1751-0473-9-13 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" - metrics: - type: file - description: Duplicate metrics file generated by biobambam - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by biobambam + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" maintainers: diff --git a/modules/nf-core/biobambam/bammerge/meta.yml b/modules/nf-core/biobambam/bammerge/meta.yml index 14433591300..f9cdc248667 100644 --- a/modules/nf-core/biobambam/bammerge/meta.yml +++ b/modules/nf-core/biobambam/bammerge/meta.yml @@ -12,37 +12,52 @@ tools: documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md doi: 10.1186/1751-0473-9-13 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List containing 1 or more bam files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List containing 1 or more bam files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Merged BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Merged BAM file + pattern: "*.bam" - bam_index: - type: file - description: BAM index file - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM index file + pattern: "*" - checksum: - type: file - description: Checksum file - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.md5": + type: file + description: Checksum file + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/biobambam/bamsormadup/meta.yml b/modules/nf-core/biobambam/bamsormadup/meta.yml index 88c95d651a4..cfd09d87560 100644 --- a/modules/nf-core/biobambam/bamsormadup/meta.yml +++ b/modules/nf-core/biobambam/bamsormadup/meta.yml @@ -13,50 +13,71 @@ tools: documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md doi: 10.1186/1751-0473-9-13 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: List containing 1 or more bam files - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in FASTA format (optional) - pattern: "*.{fa,fasta,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: List containing 1 or more bam files + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format (optional) + pattern: "*.{fa,fasta,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.bam" - bam_index: - type: file - description: BAM index file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.bai": + type: file + description: BAM index file + pattern: "*.bai" - cram: - type: file - description: CRAM file with duplicate reads marked/removed - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: CRAM file with duplicate reads marked/removed + pattern: "*.cram" - metrics: - type: file - description: Duplicate metrics file generated by biobambam - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by biobambam + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/biohansel/meta.yml b/modules/nf-core/biohansel/meta.yml index 41aa8b6ee8e..802cf8a1094 100644 --- a/modules/nf-core/biohansel/meta.yml +++ b/modules/nf-core/biohansel/meta.yml @@ -12,42 +12,57 @@ tools: tool_dev_url: "https://github.com/phac-nml/biohansel" doi: "10.1101/2020.01.10.902056" licence: ["Apache-2.0 license"] + identifier: biotools:biohansel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTA or FASTQ - pattern: "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}" - - scheme_metadata: - type: file - description: Scheme subtype metadata table - pattern: "*.{tab,tsv,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTA or FASTQ + pattern: "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}" + - - scheme_metadata: + type: file + description: Scheme subtype metadata table + pattern: "*.{tab,tsv,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - summary: - type: file - description: Tab-delimited subtyping summary output - pattern: "*summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-summary.txt: + type: file + description: Tab-delimited subtyping summary output + pattern: "*summary.txt" - kmer_results: - type: file - description: Tab-delimited subtyping kmer matching output - pattern: "*kmer-results.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-kmer-results.txt: + type: file + description: Tab-delimited subtyping kmer matching output + pattern: "*kmer-results.txt" - simple_summary: - type: file - description: A simple version of summary output - pattern: "*simple-summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-simple-summary.txt: + type: file + description: A simple version of summary output + pattern: "*simple-summary.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/biscuit/align/meta.yml b/modules/nf-core/biscuit/align/meta.yml index ba75da1c8ce..645fc2c98a3 100644 --- a/modules/nf-core/biscuit/align/meta.yml +++ b/modules/nf-core/biscuit/align/meta.yml @@ -1,5 +1,6 @@ name: biscuit_align -description: Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit. +description: Aligns single- or paired-end reads from bisulfite-converted libraries + to a reference genome using Biscuit. keywords: - biscuit - DNA methylation @@ -10,44 +11,54 @@ keywords: - bam tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/alignment tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bai: - type: file - description: Output BAM index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: Output BAM index + pattern: "*.{bai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/biscuitblaster/meta.yml b/modules/nf-core/biscuit/biscuitblaster/meta.yml index 1aa16365f95..d64cc1c2694 100644 --- a/modules/nf-core/biscuit/biscuitblaster/meta.yml +++ b/modules/nf-core/biscuit/biscuitblaster/meta.yml @@ -1,5 +1,6 @@ name: biscuit_blaster -description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit +description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed + BAM files using Biscuit keywords: - biscuit - DNA methylation @@ -10,11 +11,13 @@ keywords: - bam tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/biscuitblaster/ tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit - samblaster: description: | samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. @@ -25,6 +28,7 @@ tools: tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" licence: ["MIT"] + identifier: biotools:biscuit - samtools: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -34,39 +38,48 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bai: - type: file - description: Output BAM index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: Output BAM index + pattern: "*.{bai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/bsconv/meta.yml b/modules/nf-core/biscuit/bsconv/meta.yml index 0db30255dfc..75d9b2b7939 100644 --- a/modules/nf-core/biscuit/bsconv/meta.yml +++ b/modules/nf-core/biscuit/bsconv/meta.yml @@ -11,41 +11,45 @@ keywords: - filter tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-bsconv tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file contained mapped reads - - bai: - type: file - description: BAM file index - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file contained mapped reads + - bai: + type: file + description: BAM file index + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bsconv_bam: - type: file - description: Output BAM file containing filtered read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing filtered read alignments + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/epiread/meta.yml b/modules/nf-core/biscuit/epiread/meta.yml index e647957ceda..8974f1d952a 100644 --- a/modules/nf-core/biscuit/epiread/meta.yml +++ b/modules/nf-core/biscuit/epiread/meta.yml @@ -12,44 +12,48 @@ keywords: - bam tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/epiread_format/ tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Biscuit BAM file - - bai: - type: file - description: BAM index - - snp_bed: - type: file - description: BED file containing SNP information (optional) - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Biscuit BAM file + - bai: + type: file + description: BAM index + - snp_bed: + type: file + description: BED file containing SNP information (optional) + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - epiread_bed: - type: file - description: Gzipped BED file with methylation (and optionally SNV) information - pattern: "*.{epiread.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Gzipped BED file with methylation (and optionally SNV) information + pattern: "*.{epiread.bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/index/meta.yml b/modules/nf-core/biscuit/index/meta.yml index 549857e6d14..39a0bcf8d94 100644 --- a/modules/nf-core/biscuit/index/meta.yml +++ b/modules/nf-core/biscuit/index/meta.yml @@ -11,24 +11,28 @@ keywords: - fasta tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/alignment tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - fasta: - type: file - description: Input genome fasta file + - - fasta: + type: file + description: Input genome fasta file output: - index: - type: directory - description: Biscuit genome index directory - pattern: "BiscuitIndex" + - BiscuitIndex/*.fa*: + type: directory + description: Biscuit genome index directory + pattern: "BiscuitIndex" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/mergecg/meta.yml b/modules/nf-core/biscuit/mergecg/meta.yml index 99570c81bf2..2084f43b9d6 100644 --- a/modules/nf-core/biscuit/mergecg/meta.yml +++ b/modules/nf-core/biscuit/mergecg/meta.yml @@ -10,39 +10,43 @@ keywords: - bed tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: | - Biscuit BED file (output of biscuit vcf2bed) - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: | + Biscuit BED file (output of biscuit vcf2bed) + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mergecg_bed: - type: file - description: Gzipped BED file with merged methylation information - pattern: "*.bed.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Gzipped BED file with merged methylation information + pattern: "*.bed.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/pileup/meta.yml b/modules/nf-core/biscuit/pileup/meta.yml index b32d564e6ac..9f532797e43 100644 --- a/modules/nf-core/biscuit/pileup/meta.yml +++ b/modules/nf-core/biscuit/pileup/meta.yml @@ -1,5 +1,6 @@ name: biscuit_pileup -description: Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants +description: Computes cytosine methylation and callable SNV mutations, optionally + in reference to a germline BAM to call somatic variants keywords: - bisulfite - DNA methylation @@ -11,57 +12,61 @@ keywords: - vcf tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/pileup.html tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal_bams: - type: file - description: | - BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided - ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a - tumor BAM file is provided, exactly one normal (germline) BAM must be provided. - pattern: "*.{bam}" - - normal_bais: - type: file - description: BAM index file or files corresponding to the provided normal_bams - pattern: "*.{bai}" - - tumor_bam: - type: file - description: | - Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with - their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a - tumor BAM file is provided, exactly one normal BAM must be provided. - pattern: "*.{bam}" - - tumor_bai: - type: file - description: Optional. BAM index file corresponding to provided tumor_bam - pattern: "*.{bai}" - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal_bams: + type: file + description: | + BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided + ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a + tumor BAM file is provided, exactly one normal (germline) BAM must be provided. + pattern: "*.{bam}" + - normal_bais: + type: file + description: BAM index file or files corresponding to the provided normal_bams + pattern: "*.{bai}" + - tumor_bam: + type: file + description: | + Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with + their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a + tumor BAM file is provided, exactly one normal BAM must be provided. + pattern: "*.{bam}" + - tumor_bai: + type: file + description: Optional. BAM index file corresponding to provided tumor_bam + pattern: "*.{bai}" + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: vcf file with methylation information - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: vcf file with methylation information + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/qc/meta.yml b/modules/nf-core/biscuit/qc/meta.yml index 92199338c02..ab7500ba823 100644 --- a/modules/nf-core/biscuit/qc/meta.yml +++ b/modules/nf-core/biscuit/qc/meta.yml @@ -11,37 +11,56 @@ keywords: - quality control tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-qc tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file produced using Biscuit + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file produced using Biscuit + - - index: + type: file + description: index file output: - biscuit_qc_reports: - type: file - description: | - Summary files containing the following information: - - CpG retention by position in read - - CpH retention by position in read - - Read duplication statistics - - Insert size distribution - - Distribution of mapping qualities - - Proportion of reads mapping to each strand - - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT - pattern: "*.txt" + - meta: + type: file + description: | + Summary files containing the following information: + - CpG retention by position in read + - CpH retention by position in read + - Read duplication statistics + - Insert size distribution + - Distribution of mapping qualities + - Proportion of reads mapping to each strand + - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT + pattern: "*.txt" + - "*.txt": + type: file + description: | + Summary files containing the following information: + - CpG retention by position in read + - CpH retention by position in read + - Read duplication statistics + - Insert size distribution + - Distribution of mapping qualities + - Proportion of reads mapping to each strand + - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/vcf2bed/meta.yml b/modules/nf-core/biscuit/vcf2bed/meta.yml index f03e62c3393..76ee1cad11c 100644 --- a/modules/nf-core/biscuit/vcf2bed/meta.yml +++ b/modules/nf-core/biscuit/vcf2bed/meta.yml @@ -12,34 +12,38 @@ keywords: - vcf tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Biscuit vcf file (output of biscuit pileup) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Biscuit vcf file (output of biscuit pileup) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Gzipped BED file with methylation or SNV information - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Gzipped BED file with methylation or SNV information + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/bismark/align/meta.yml b/modules/nf-core/bismark/align/meta.yml index 69fe455a4af..e0a979b39e1 100644 --- a/modules/nf-core/bismark/align/meta.yml +++ b/modules/nf-core/bismark/align/meta.yml @@ -19,43 +19,58 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - unmapped: - type: file - description: Output FastQ file(s) containing unmapped reads - pattern: "*.{fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - unmapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fq.gz": + type: file + description: Output FastQ file(s) containing unmapped reads + pattern: "*.{fq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/coverage2cytosine/meta.yml b/modules/nf-core/bismark/coverage2cytosine/meta.yml index db05862ca01..f35117f4f27 100644 --- a/modules/nf-core/bismark/coverage2cytosine/meta.yml +++ b/modules/nf-core/bismark/coverage2cytosine/meta.yml @@ -20,42 +20,57 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_file: - type: file - description: | - A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. - - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_file: + type: file + description: | + A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. + - - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - coverage: - type: file - description: A file containing methylation calls per position. - pattern: "*.cov.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cov.gz": + type: file + description: A file containing methylation calls per position. + pattern: "*.cov.gz" - report: - type: file - description: Genomic cytosine context results. - pattern: "*report.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt.gz": + type: file + description: Genomic cytosine context results. + pattern: "*report.txt.gz" - summary: - type: file - description: Cyotosine context summary report. - pattern: "*cytosine_context_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cytosine_context_summary.txt": + type: file + description: Cyotosine context summary report. + pattern: "*cytosine_context_summary.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ewels" maintainers: diff --git a/modules/nf-core/bismark/deduplicate/meta.yml b/modules/nf-core/bismark/deduplicate/meta.yml index cb48f6b1e9a..31ffeb945b1 100644 --- a/modules/nf-core/bismark/deduplicate/meta.yml +++ b/modules/nf-core/bismark/deduplicate/meta.yml @@ -21,34 +21,43 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Deduplicated output BAM file containing read alignments - pattern: "*.{deduplicated.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.deduplicated.bam": + type: file + description: Deduplicated output BAM file containing read alignments + pattern: "*.{deduplicated.bam}" - report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.deduplication_report.txt": + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/genomepreparation/meta.yml b/modules/nf-core/bismark/genomepreparation/meta.yml index e7aa5529057..18ca34a9f8d 100644 --- a/modules/nf-core/bismark/genomepreparation/meta.yml +++ b/modules/nf-core/bismark/genomepreparation/meta.yml @@ -21,19 +21,22 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - fasta: - type: file - description: Input genome fasta file + - - fasta: + type: file + description: Input genome fasta file output: - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - BismarkIndex: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/methylationextractor/meta.yml b/modules/nf-core/bismark/methylationextractor/meta.yml index ea13ae3a3fc..673cb1ca557 100644 --- a/modules/nf-core/bismark/methylationextractor/meta.yml +++ b/modules/nf-core/bismark/methylationextractor/meta.yml @@ -20,50 +20,77 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" - - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" + - - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedgraph: - type: file - description: Bismark output file containing coverage and methylation metrics - pattern: "*.{bedGraph.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph.gz": + type: file + description: Bismark output file containing coverage and methylation metrics + pattern: "*.{bedGraph.gz}" - methylation_calls: - type: file - description: Bismark output file containing strand-specific methylation calls - pattern: "*.{txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Bismark output file containing strand-specific methylation calls + pattern: "*.{txt.gz}" - coverage: - type: file - description: Bismark output file containing coverage metrics - pattern: "*.{cov.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cov.gz": + type: file + description: Bismark output file containing coverage metrics + pattern: "*.{cov.gz}" - report: - type: file - description: Bismark splitting reports - pattern: "*_{splitting_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_splitting_report.txt": + type: file + description: Bismark splitting reports + pattern: "*_{splitting_report.txt}" - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{M-bias.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.M-bias.txt": + type: file + description: Text file containing methylation bias information + pattern: "*.{M-bias.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/report/meta.yml b/modules/nf-core/bismark/report/meta.yml index 8c57a09eb32..52fece5aeeb 100644 --- a/modules/nf-core/bismark/report/meta.yml +++ b/modules/nf-core/bismark/report/meta.yml @@ -18,42 +18,45 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - align_report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*{splitting_report.txt}" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - align_report: + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" + - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*{splitting_report.txt}" + - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: Bismark reports - pattern: "*.{html,txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.{html,txt}": + type: file + description: Bismark reports + pattern: "*.{html,txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/summary/meta.yml b/modules/nf-core/bismark/summary/meta.yml index 6acf44e6cad..907a2d706b6 100644 --- a/modules/nf-core/bismark/summary/meta.yml +++ b/modules/nf-core/bismark/summary/meta.yml @@ -21,36 +21,39 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - bam: - type: list - description: List of Bismark alignment BAM filenames - pattern: "*.bam" - - align_report: - type: file - description: Bismark alignment reports - pattern: "*report.txt" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.deduplication_report.txt" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*splitting_report.txt" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.txt" + - - bam: + type: list + description: List of Bismark alignment BAM filenames + pattern: "*.bam" + - - align_report: + type: file + description: Bismark alignment reports + pattern: "*report.txt" + - - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.deduplication_report.txt" + - - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*splitting_report.txt" + - - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.txt" output: - summary: - type: file - description: Bismark summary - pattern: "*.{html,txt}" + - "*report.{html": + type: file + description: Bismark summary + pattern: "*.{html,txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/blast/blastdbcmd/meta.yml b/modules/nf-core/blast/blastdbcmd/meta.yml index 1c2f90e1ab8..4518833cc91 100644 --- a/modules/nf-core/blast/blastdbcmd/meta.yml +++ b/modules/nf-core/blast/blastdbcmd/meta.yml @@ -14,47 +14,57 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - entry: - type: string - description: Entry identifier of sequence in database. It cannot be used along with entry_batch - - entry_batch: - type: file - description: | - File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: file - description: Input BLAST-indexed database - pattern: "*.{fa.*,fasta.*}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - entry: + type: string + description: Entry identifier of sequence in database. It cannot be used along + with entry_batch + - entry_batch: + type: file + description: | + File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: file + description: Input BLAST-indexed database + pattern: "*.{fa.*,fasta.*}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Output fasta file (default format) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Output fasta file (default format) + pattern: "*.{fasta}" - text: - type: file - description: | - Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`) - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: | + Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`) + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/blast/blastn/meta.yml b/modules/nf-core/blast/blastn/meta.yml index a0d64dd6b4b..0f5e41bb7cc 100644 --- a/modules/nf-core/blast/blastn/meta.yml +++ b/modules/nf-core/blast/blastn/meta.yml @@ -13,39 +13,42 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: directory - description: Directory containing the blast database - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: directory + description: Directory containing the blast database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: File containing blastn hits - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing blastn hits + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/blast/blastp/meta.yml b/modules/nf-core/blast/blastp/meta.yml index 5fe7c5de5cd..27052a2d098 100644 --- a/modules/nf-core/blast/blastp/meta.yml +++ b/modules/nf-core/blast/blastp/meta.yml @@ -1,5 +1,6 @@ name: blast_blastp -description: BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database +description: BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino + acid (protein) query sequence against a protein database keywords: - fasta - blast @@ -13,53 +14,68 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: directory - description: Directory containing the blast database - pattern: "*" - - out_ext: - type: string - description: | - Specify the type of output file to be generated. `xml` corresponds to BLAST xml format. - `tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format. - pattern: "xml|tsv|csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: directory + description: Directory containing the blast database + pattern: "*" + - - out_ext: + type: string + description: | + Specify the type of output file to be generated. `xml` corresponds to BLAST xml format. + `tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format. + pattern: "xml|tsv|csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - xml: - type: file - description: File containing blastp hits in XML format - pattern: "*.{xml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.xml": + type: file + description: File containing blastp hits in XML format + pattern: "*.{xml}" - tsv: - type: file - description: File containing blastp hits in tabular format - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tsv": + type: file + description: File containing blastp hits in tabular format + pattern: "*.{tsv}" - csv: - type: file - description: File containing blastp hits in comma separated format - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.csv": + type: file + description: File containing blastp hits in comma separated format + pattern: "*.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/blast/makeblastdb/meta.yml b/modules/nf-core/blast/makeblastdb/meta.yml index 9ed63901bf0..826e62e1501 100644 --- a/modules/nf-core/blast/makeblastdb/meta.yml +++ b/modules/nf-core/blast/makeblastdb/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - db: - type: directory - description: Output directory containing blast database files - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}: + type: directory + description: Output directory containing blast database files + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/blast/tblastn/meta.yml b/modules/nf-core/blast/tblastn/meta.yml index 7dff4fff093..6055742c055 100644 --- a/modules/nf-core/blast/tblastn/meta.yml +++ b/modules/nf-core/blast/tblastn/meta.yml @@ -13,39 +13,42 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: directory - description: Directory containing the blast database - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: directory + description: Directory containing the blast database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: File containing blastn hits - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing blastn hits + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" - "@gq2" diff --git a/modules/nf-core/blast/updateblastdb/meta.yml b/modules/nf-core/blast/updateblastdb/meta.yml index 4b836b48ecb..b5dc782b94a 100644 --- a/modules/nf-core/blast/updateblastdb/meta.yml +++ b/modules/nf-core/blast/updateblastdb/meta.yml @@ -13,29 +13,32 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'mito', single_end:false ] - - name: - type: string - description: Name of the NCBI BLAST database to be downloaded + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'mito', single_end:false ] + - name: + type: string + description: Name of the NCBI BLAST database to be downloaded output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'mito', single_end:false ] - db: - type: directory - description: Output directory containing blast database files - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'mito', single_end:false ] + - prefix: + type: directory + description: Output directory containing blast database files + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/blat/meta.yml b/modules/nf-core/blat/meta.yml index 25deca1aea3..70a92c9b4b7 100644 --- a/modules/nf-core/blat/meta.yml +++ b/modules/nf-core/blat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "blat" description: Queries a sequence subject @@ -8,44 +7,48 @@ keywords: - search tools: - "blat": - description: "BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments." + description: "BLAT is a bioinformatics software tool which performs rapid mRNA/DNA + and cross-species protein alignments." homepage: "https://kentinformatics.com/" documentation: "https://kentinformatics.com/documentation" doi: "10.1101/gr.229202" licence: ["Free for academic, nonprofit and personal use"] + identifier: biotools:blat input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - query: - type: file - description: Sequence file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}" - - meta2: - type: map - description: | - Groovy Map containing subject information - e.g. `[ id:'test', single_end:false ]` - - subject: - type: file - description: Sequence file - pattern: "*.{fa,nib,2bit}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - query: + type: file + description: Sequence file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}" + - - meta2: + type: map + description: | + Groovy Map containing subject information + e.g. `[ id:'test', single_end:false ]` + - subject: + type: file + description: Sequence file + pattern: "*.{fa,nib,2bit}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - psl: - type: file - description: Search results - pattern: "*.{psl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.psl": + type: file + description: Search results + pattern: "*.{psl}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d-jch" maintainers: diff --git a/modules/nf-core/bowtie/align/meta.yml b/modules/nf-core/bowtie/align/meta.yml index 7c7e8237476..7b346802370 100644 --- a/modules/nf-core/bowtie/align/meta.yml +++ b/modules/nf-core/bowtie/align/meta.yml @@ -16,47 +16,64 @@ tools: documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 licence: ["Artistic-2.0"] + identifier: biotools:bowtie input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'sarscov2' ] - - index: - type: file - description: Bowtie genome index files - pattern: "*.ebwt" - - save_unaligned: - type: boolean - description: Whether to save fastq files containing the reads which did not align. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'sarscov2' ] + - index: + type: file + description: Bowtie genome index files + pattern: "*.ebwt" + - - save_unaligned: + type: boolean + description: Whether to save fastq files containing the reads which did not + align. output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - log: - type: file - description: Log file - pattern: "*.log" + - meta: + type: file + description: Log file + pattern: "*.log" + - "*.out": + type: file + description: Log file + pattern: "*.log" + - fastq: + - meta: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - "*fastq.gz": + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/bowtie/build/meta.yml b/modules/nf-core/bowtie/build/meta.yml index dd48004f294..a878a5b7038 100644 --- a/modules/nf-core/bowtie/build/meta.yml +++ b/modules/nf-core/bowtie/build/meta.yml @@ -14,29 +14,32 @@ tools: documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 licence: ["Artistic-2.0"] + identifier: biotools:bowtie input: - - meta: - type: map - description: | - Groovy Map containing information about the genome fasta - e.g. [ id:'test' ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing information about the genome fasta + e.g. [ id:'test' ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing nformation about the genome fasta - e.g. [ id:'test' ] - index: - type: file - description: Folder containing bowtie genome index files - pattern: "*.ebwt" + - meta: + type: map + description: | + Groovy Map containing nformation about the genome fasta + e.g. [ id:'test' ] + - bowtie: + type: file + description: Folder containing bowtie genome index files + pattern: "*.ebwt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml index 38610e0ed59..f841f781285 100644 --- a/modules/nf-core/bowtie2/align/meta.yml +++ b/modules/nf-core/bowtie2/align/meta.yml @@ -16,77 +16,114 @@ tools: documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.ebwt" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Bowtie2 genome fasta file - pattern: "*.fasta" - - save_unaligned: - type: boolean - description: | - Save reads that do not map to the reference (true) or discard them (false) - (default: false) - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.ebwt" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Bowtie2 genome fasta file + pattern: "*.fasta" + - - save_unaligned: + type: boolean + description: | + Save reads that do not map to the reference (true) or discard them (false) + (default: false) + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - sam: - type: file - description: Output SAM file containing read alignments - pattern: "*.sam" + - meta: + type: file + description: Output SAM file containing read alignments + pattern: "*.sam" + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.sam" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.bam" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.bam" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.bam" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.cram" + - meta: + type: file + description: Output CRAM file containing read alignments + pattern: "*.cram" + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.cram" - csi: - type: file - description: Output SAM/BAM index for large inputs - pattern: "*.csi" + - meta: + type: file + description: Output SAM/BAM index for large inputs + pattern: "*.csi" + - "*.csi": + type: file + description: Output SAM/BAM index for large inputs + pattern: "*.csi" - crai: - type: file - description: Output CRAM index - pattern: "*.crai" + - meta: + type: file + description: Output CRAM index + pattern: "*.crai" + - "*.crai": + type: file + description: Output CRAM index + pattern: "*.crai" - log: - type: file - description: Aligment log - pattern: "*.log" + - meta: + type: file + description: Aligment log + pattern: "*.log" + - "*.log": + type: file + description: Aligment log + pattern: "*.log" - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - "*fastq.gz": + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml index 2d687991907..2729a92ec67 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -15,29 +15,32 @@ tools: documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Bowtie2 genome index files - pattern: "*.bt2" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - bowtie2: + type: file + description: Bowtie2 genome index files + pattern: "*.bt2" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml index b7ff4489f56..85a267efc65 100644 --- a/modules/nf-core/bracken/bracken/meta.yml +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -7,44 +7,61 @@ keywords: - kraken2 tools: - bracken: - description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. homepage: https://ccb.jhu.edu/software/bracken/ documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual tool_dev_url: https://github.com/jenniferlu717/Bracken doi: "10.7717/peerj-cs.104" licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kraken_report: - type: file - description: TSV file with six columns coming from kraken2 output - pattern: "*.{tsv}" - - database: - type: file - description: Directory containing the kraken2/Bracken files for analysis - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_report: + type: file + description: TSV file with six columns coming from kraken2 output + pattern: "*.{tsv}" + - - database: + type: file + description: Directory containing the kraken2/Bracken files for analysis + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reports: - type: file - description: TSV output report of the re-estimated abundances - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" + - bracken_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" - txt: - type: file - description: TXT file of bracken corrected results of Kraken2 report output - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - bracken_kraken_style_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/bracken/build/meta.yml b/modules/nf-core/bracken/build/meta.yml index 2bce245a27f..b921941e7f2 100644 --- a/modules/nf-core/bracken/build/meta.yml +++ b/modules/nf-core/bracken/build/meta.yml @@ -1,4 +1,3 @@ ---- name: "bracken_build" description: Extends a Kraken2 database to be compatible with Bracken keywords: @@ -8,39 +7,51 @@ keywords: - build tools: - "bracken": - description: "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample." + description: "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample." homepage: "https://ccb.jhu.edu/software/bracken/" documentation: "https://ccb.jhu.edu/software/bracken/" tool_dev_url: "https://github.com/jenniferlu717/Bracken/" doi: "10.7717/peerj-cs.104 " licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - kraken2db: - type: directory - description: A Kraken2 database directory - pattern: "*/" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - kraken2db: + type: directory + description: A Kraken2 database directory + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: A Kraken2 database directory with required bracken files in side - pattern: "*/" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "kraken2db , includeInputs: true": + type: directory + description: A Kraken2 database directory with required bracken files in side + pattern: "*/" + - bracken_files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '${kraken2db}/database*", includeInputs: true': + type: directory + description: Bracken files required to extend the Kraken2 database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bracken/combinebrackenoutputs/meta.yml b/modules/nf-core/bracken/combinebrackenoutputs/meta.yml index 426d0099218..9dba2e43c23 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/meta.yml +++ b/modules/nf-core/bracken/combinebrackenoutputs/meta.yml @@ -7,36 +7,41 @@ keywords: - reporting tools: - "bracken": - description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. homepage: https://ccb.jhu.edu/software/bracken/ documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual tool_dev_url: https://github.com/jenniferlu717/Bracken doi: "10.7717/peerj-cs.104" licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: List of output files from bracken - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: List of output files from bracken + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined output in table format - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Combined output in table format + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml index 29745d2c1d2..7cb6d69c184 100644 --- a/modules/nf-core/busco/busco/meta.yml +++ b/modules/nf-core/busco/busco/meta.yml @@ -7,81 +7,135 @@ keywords: - proteome tools: - busco: - description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + description: BUSCO provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs selected from OrthoDB. homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html tool_dev_url: https://gitlab.com/ezlab/busco doi: "10.1007/978-1-4939-9173-0_14" licence: ["MIT"] + identifier: biotools:busco input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleic or amino acid sequence file in FASTA format. - pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" - - mode: - type: string - description: The mode to run Busco in. One of genome, proteins, or transcriptome - pattern: "{genome,proteins,transcriptome}" - - lineage: - type: string - description: The BUSCO lineage to use, or "auto" to automatically select lineage - - busco_lineages_path: - type: directory - description: Path to local BUSCO lineages directory. - - config_file: - type: file - description: Path to BUSCO config file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleic or amino acid sequence file in FASTA format. + pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" + - - mode: + type: string + description: The mode to run Busco in. One of genome, proteins, or transcriptome + pattern: "{genome,proteins,transcriptome}" + - - lineage: + type: string + description: The BUSCO lineage to use, or "auto" to automatically select lineage + - - busco_lineages_path: + type: directory + description: Path to local BUSCO lineages directory. + - - config_file: + type: file + description: Path to BUSCO config file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - batch_summary: - type: file - description: Summary of all sequence files analyzed - pattern: "*-busco.batch_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco.batch_summary.txt": + type: file + description: Summary of all sequence files analyzed + pattern: "*-busco.batch_summary.txt" - short_summaries_txt: - type: file - description: Short Busco summary in plain text format - pattern: "short_summary.*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - short_summary.*.txt: + type: file + description: Short Busco summary in plain text format + pattern: "short_summary.*.txt" - short_summaries_json: - type: file - description: Short Busco summary in JSON format - pattern: "short_summary.*.json" - - busco_dir: - type: directory - description: BUSCO lineage specific output - pattern: "*-busco" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - short_summary.*.json: + type: file + description: Short Busco summary in JSON format + pattern: "short_summary.*.json" - full_table: - type: file - description: Full BUSCO results table - pattern: "full_table.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/full_table.tsv": + type: file + description: Full BUSCO results table + pattern: "full_table.tsv" - missing_busco_list: - type: file - description: List of missing BUSCOs - pattern: "missing_busco_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/missing_busco_list.tsv": + type: file + description: List of missing BUSCOs + pattern: "missing_busco_list.tsv" - single_copy_proteins: - type: file - description: Fasta file of single copy proteins (transcriptome mode) - pattern: "single_copy_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/single_copy_proteins.faa": + type: file + description: Fasta file of single copy proteins (transcriptome mode) + pattern: "single_copy_proteins.faa" - seq_dir: - type: directory - description: BUSCO sequence directory - pattern: "busco_sequences" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/busco_sequences": + type: directory + description: BUSCO sequence directory + pattern: "busco_sequences" - translated_dir: - type: directory - description: Six frame translations of each transcript made by the transcriptome mode - pattern: "translated_dir" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/translated_proteins": + type: directory + description: Six frame translations of each transcript made by the transcriptome + mode + pattern: "translated_dir" + - busco_dir: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco": + type: directory + description: BUSCO lineage specific output + pattern: "*-busco" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" - "@charles-plessy" diff --git a/modules/nf-core/busco/generateplot/meta.yml b/modules/nf-core/busco/generateplot/meta.yml index 796f32b43cb..72ad2c92252 100644 --- a/modules/nf-core/busco/generateplot/meta.yml +++ b/modules/nf-core/busco/generateplot/meta.yml @@ -9,26 +9,31 @@ keywords: - quality control tools: - busco: - description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + description: BUSCO provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs selected from OrthoDB. homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html tool_dev_url: https://gitlab.com/ezlab/busco doi: "10.1007/978-1-4939-9173-0_14" licence: ["MIT"] + identifier: biotools:busco input: - - short_summary_txt: - type: file - description: One or more short summary txt files from BUSCO - pattern: "short_summary.*.txt" + - - short_summary_txt: + type: file + description: One or more short summary txt files from BUSCO + pattern: "short_summary.*.txt" output: - png: - type: file - description: A summary plot in png format - pattern: "*.png" + - "*.png": + type: file + description: A summary plot in png format + pattern: "*.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/bwa/aln/meta.yml b/modules/nf-core/bwa/aln/meta.yml index ef2e6582dbb..40aabe86f99 100644 --- a/modules/nf-core/bwa/aln/meta.yml +++ b/modules/nf-core/bwa/aln/meta.yml @@ -18,40 +18,43 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sai: - type: file - description: Single or paired SA coordinate files - pattern: "*.sai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sai": + type: file + description: Single or paired SA coordinate files + pattern: "*.sai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 6bbc87a640b..4884bca2ab9 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -14,29 +14,32 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bwa: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@maxulysse" diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index 24f7f4436a6..ef7b966c0fa 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - bwa=0.7.18 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.20 - htslib=1.20.0 + - samtools=1.20 diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index b126dd86a8a..37467d2912a 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -17,55 +17,82 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fasta,fa}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fa}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - csi: - type: file - description: Optional index file for BAM file - pattern: "*.{csi}" + - meta: + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" + - "*.csi": + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" - crai: - type: file - description: Optional index file for CRAM file - pattern: "*.{crai}" + - meta: + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" + - "*.crai": + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@jeremy1805" diff --git a/modules/nf-core/bwa/sampe/meta.yml b/modules/nf-core/bwa/sampe/meta.yml index fa96499fcab..42041963a9c 100644 --- a/modules/nf-core/bwa/sampe/meta.yml +++ b/modules/nf-core/bwa/sampe/meta.yml @@ -19,43 +19,47 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ files specified alongside meta in input channel. - pattern: "*.{fastq,fq}.gz" - - sai: - type: file - description: SAI file specified alongside meta and reads in input channel. - pattern: "*.sai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: directory - description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX - pattern: "bwa/" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ files specified alongside meta in input channel. + pattern: "*.{fastq,fq}.gz" + - sai: + type: file + description: SAI file specified alongside meta and reads in input channel. + pattern: "*.sai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from + BWA_INDEX + pattern: "bwa/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bwa/samse/meta.yml b/modules/nf-core/bwa/samse/meta.yml index 45c396a3913..cd284575233 100644 --- a/modules/nf-core/bwa/samse/meta.yml +++ b/modules/nf-core/bwa/samse/meta.yml @@ -19,43 +19,47 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ files specified alongside meta in input channel. - pattern: "*.{fastq,fq}.gz" - - sai: - type: file - description: SAI file specified alongside meta and reads in input channel. - pattern: "*.sai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: directory - description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX - pattern: "bwa/" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ files specified alongside meta in input channel. + pattern: "*.{fastq,fq}.gz" + - sai: + type: file + description: SAI file specified alongside meta and reads in input channel. + pattern: "*.sai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from + BWA_INDEX + pattern: "bwa/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index c14a109252b..74f54ef0d8e 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -13,29 +13,32 @@ tools: homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: https://github.com/bwa-mem2/bwa-mem2#usage licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bwamem2: + type: file + description: BWA genome index files + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index 633712cf141..7e0b5a34795 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - bwa-mem2=2.2.1 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.19.2 - htslib=1.19.1 + - samtools=1.19.2 diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index 931f712943d..c6333ca171d 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -17,69 +17,96 @@ tools: documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference/index information - e.g. [ id:'test' ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fa,fasta,fna}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta,fna}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: Output SAM file containing read alignments - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.{sam}" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - crai: - type: file - description: Index file for CRAM file - pattern: "*.{crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Index file for CRAM file + pattern: "*.{crai}" - csi: - type: file - description: Index file for BAM file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Index file for BAM file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwameme/index/meta.yml b/modules/nf-core/bwameme/index/meta.yml index 2db1d3a82b7..e0cb04a630f 100644 --- a/modules/nf-core/bwameme/index/meta.yml +++ b/modules/nf-core/bwameme/index/meta.yml @@ -12,32 +12,33 @@ tools: documentation: https://github.com/kaist-ina/BWA-MEME#getting-started doi: "10.1093/bioinformatics/btac137" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fasta: - type: file - description: Input genome fasta file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: file - description: BWA-MEME genome index files - pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bwameme: + type: file + description: BWA-MEME genome index files + pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/mem/meta.yml b/modules/nf-core/bwameme/mem/meta.yml index e5d28db259d..070aefebfed 100644 --- a/modules/nf-core/bwameme/mem/meta.yml +++ b/modules/nf-core/bwameme/mem/meta.yml @@ -18,78 +18,103 @@ tools: documentation: https://github.com/kaist-ina/BWA-MEME#getting-started doi: "10.1093/bioinformatics/btac137" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference/index information - e.g. [ id:'test' ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fa,fasta,fna}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" - - mbuffer: - type: integer - description: memory for mbuffer in megabytes (default 3072) - - sort_threads: - type: integer - description: number of threads to used during samtools sort (default 2). - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta,fna}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" + - - mbuffer: + type: integer + description: memory for mbuffer in megabytes (default 3072) + - - samtools_threads: + type: integer + description: number of threads for samtools (default 2) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: Output SAM file containing read alignments - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.{sam}" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - crai: - type: file - description: Index file for CRAM file - pattern: "*.{crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Index file for CRAM file + pattern: "*.{crai}" - csi: - type: file - description: Index file for BAM file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Index file for BAM file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameth/align/meta.yml b/modules/nf-core/bwameth/align/meta.yml index a5338e4e7ea..6cd78268d11 100644 --- a/modules/nf-core/bwameth/align/meta.yml +++ b/modules/nf-core/bwameth/align/meta.yml @@ -21,34 +21,37 @@ tools: documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Directory containing bwameth genome index + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Directory containing bwameth genome index output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bwameth/index/meta.yml b/modules/nf-core/bwameth/index/meta.yml index 1836d2a2910..d92273c4d7e 100644 --- a/modules/nf-core/bwameth/index/meta.yml +++ b/modules/nf-core/bwameth/index/meta.yml @@ -17,19 +17,22 @@ tools: documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 licence: ["MIT"] + identifier: "" input: - - fasta: - type: file - description: Input genome fasta file + - - fasta: + type: file + description: Input genome fasta file output: - index: - type: directory - description: Directory containing bwameth genome index - pattern: "index" + - bwameth: + type: directory + description: Directory containing bwameth genome index + pattern: "index" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml index 230ed9c0f2e..751bea454c0 100644 --- a/modules/nf-core/cadd/meta.yml +++ b/modules/nf-core/cadd/meta.yml @@ -1,5 +1,6 @@ name: "cadd" -description: CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. +description: CADD is a tool for scoring the deleteriousness of single nucleotide variants + as well as insertion/deletions variants in the human genome. keywords: - cadd - annotate @@ -13,36 +14,39 @@ tools: doi: "10.1093/nar/gky1016" licence: - Restricted. Free for non-commercial users. + identifier: biotools:cadd_phred input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Input file for annotation in vcf or vcf.gz format - pattern: "*.{vcf,vcf.gz}" - - annotation_dir: - type: file - description: | - Path to folder containing the vcf files with precomputed CADD scores. - This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Input file for annotation in vcf or vcf.gz format + pattern: "*.{vcf,vcf.gz}" + - - annotation_dir: + type: file + description: | + Path to folder containing the vcf files with precomputed CADD scores. + This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Annotated tsv file - pattern: "*.{tsv,tsv.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv.gz": + type: file + description: Annotated tsv file + pattern: "*.{tsv,tsv.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cafe/meta.yml b/modules/nf-core/cafe/meta.yml index cc1e696c9da..6dc7c83c6aa 100644 --- a/modules/nf-core/cafe/meta.yml +++ b/modules/nf-core/cafe/meta.yml @@ -12,49 +12,57 @@ tools: tool_dev_url: "https://github.com/hahnlab/CAFE5" doi: "10.1093/bioinformatics/btaa1027" licence: ["IU OPEN SOURCE LICENSE (see https://github.com/hahnlab/CAFE5/blob/master/LICENSE)"] + identifier: biotools:CaFE_Calculation_of_Free_Energy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - infile: - type: file - description: Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder) - pattern: "*.{txt,tsv,tab}" - - tree: - type: file - description: Newick formatted tree - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - infile: + type: file + description: Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue + or OrthoFinder) + pattern: "*.{txt,tsv,tab}" + - - tree: + type: file + description: Newick formatted tree + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cafe: - type: directory - description: A folder with all the cafe output + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${prefix}: + type: directory + description: A folder with all the cafe output + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - cafe_base_count: - type: file - description: File containing counts of genes per orthogroup - pattern: "*_count.tab" + - $prefix/*_count.tab: + type: file + description: File containing counts of genes per orthogroup + pattern: "*_count.tab" - cafe_significant_trees: - type: file - description: File containing significant trees (newick format) - pattern: "*.tre" + - $prefix/*.tre: + type: file + description: File containing significant trees (newick format) + pattern: "*.tre" - cafe_report: - type: file - description: File containing the final report from cafe - pattern: "*_report.cafe" + - $prefix/*_report.cafe: + type: file + description: File containing the final report from cafe + pattern: "*_report.cafe" - cafe_results: - type: file - description: File containing the main result files from cafe - pattern: "*results.txt" + - $prefix/*results.txt: + type: file + description: File containing the main result files from cafe + pattern: "*results.txt" authors: - "@chriswyatt1" maintainers: diff --git a/modules/nf-core/calder2/meta.yml b/modules/nf-core/calder2/meta.yml index 24758928eec..e4d13266de9 100644 --- a/modules/nf-core/calder2/meta.yml +++ b/modules/nf-core/calder2/meta.yml @@ -15,31 +15,44 @@ tools: tool_dev_url: "https://github.com/CSOgroup/CALDER2" doi: "10.1038/s41467-021-22666-3" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool.mcool}" - - resolution: - type: integer - description: In case a .mcool file is provided, which resolution level to use for the analysis + - - meta: + type: map + description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false + ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool.mcool}" + - - resolution: + type: integer + description: In case a .mcool file is provided, which resolution level to use + for the analysis output: - - meta: - type: map - description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output_folder: - type: directory - description: Output folder containing sub-compartment (.tsv/.bed) and domain boundaries calls (.bed) + - meta: + type: map + description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false + ] + - ${prefix}/: + type: directory + description: Output folder containing sub-compartment (.tsv/.bed) and domain + boundaries calls (.bed) - intermediate_data_folder: - type: directory - description: Output folder containing intermediate data produced during the computation + - meta: + type: map + description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false + ] + - ${prefix}/intermediate_data/: + type: directory + description: Output folder containing intermediate data produced during the + computation + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucananni93" maintainers: diff --git a/modules/nf-core/canu/meta.yml b/modules/nf-core/canu/meta.yml index afcaa55b9e9..706c8f26702 100644 --- a/modules/nf-core/canu/meta.yml +++ b/modules/nf-core/canu/meta.yml @@ -1,5 +1,6 @@ name: "canu" -description: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. +description: Accurate assembly of segmental duplications, satellites, and allelic + variants from high-fidelity long reads. keywords: - Assembly - pacbio @@ -7,72 +8,122 @@ keywords: - nanopore tools: - "canu": - description: "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing." + description: "Canu is a fork of the Celera Assembler designed for high-noise single-molecule + sequencing." homepage: "https://canu.readthedocs.io/en/latest/index.html#" documentation: "https://canu.readthedocs.io/en/latest/tutorial.html" tool_dev_url: "https://github.com/marbl/canu" doi: "10.1101/gr.215087.116" licence: ["GPL v2 and others"] + identifier: biotools:canu input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:true ] - - reads: - type: file - description: fasta/fastq file - pattern: "*.{fasta,fastq}" - - mode: - type: string - description: Canu mode depending on the input data (source and error rate) - pattern: "-pacbio|-nanopore|-pacbio-hifi" - - genomesize: - type: string - description: An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g - pattern: "[g|m|k]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:true ] + - reads: + type: file + description: fasta/fastq file + pattern: "*.{fasta,fastq}" + - - mode: + type: string + description: Canu mode depending on the input data (source and error rate) + pattern: "-pacbio|-nanopore|-pacbio-hifi" + - - genomesize: + type: string + description: An estimate of the size of the genome. Common suffices are allowed, + for example, 3.7m or 2.8g + pattern: "[g|m|k]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Most of the analysis reported during assembly - pattern: "*.report" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.report": + type: file + description: Most of the analysis reported during assembly + pattern: "*.report" - assembly: - type: file - description: Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements. - pattern: "*.contigs.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.fasta.gz": + type: file + description: Everything which could be assembled and is the full assembly, including + both unique, repetitive, and bubble elements. + pattern: "*.contigs.fasta" - contigs: - type: file - description: Reads and low-coverage contigs which could not be incorporated into the primary assembly. - pattern: "*.unassembled.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unassembled.fasta.gz": + type: file + description: Reads and low-coverage contigs which could not be incorporated + into the primary assembly. + pattern: "*.unassembled.fasta" - corrected_reads: - type: file - description: The reads after correction. - pattern: "*.correctedReads.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.correctedReads.fasta.gz": + type: file + description: The reads after correction. + pattern: "*.correctedReads.fasta.gz" - corrected_trimmed_reads: - type: file - description: The corrected reads after overlap based trimming - pattern: "*.trimmedReads.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trimmedReads.fasta.gz": + type: file + description: The corrected reads after overlap based trimming + pattern: "*.trimmedReads.fasta.gz" - metadata: - type: file - description: (undocumented) - pattern: "*.contigs.layout" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.layout": + type: file + description: (undocumented) + pattern: "*.contigs.layout" - contig_position: - type: file - description: The position of each read in a contig - pattern: "*.contigs.layout.readToTig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.layout.readToTig": + type: file + description: The position of each read in a contig + pattern: "*.contigs.layout.readToTig" - contig_info: - type: file - description: A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line. - pattern: "*.contigs.layout.tigInfo" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.layout.tigInfo": + type: file + description: A list of the contigs, lengths, coverage, number of reads and other + metadata. Essentially the same information provided in the FASTA header line. + pattern: "*.contigs.layout.tigInfo" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" maintainers: diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml index 00a8db0bca8..81778a06710 100644 --- a/modules/nf-core/cat/cat/meta.yml +++ b/modules/nf-core/cat/cat/meta.yml @@ -9,25 +9,32 @@ tools: description: Just concatenation documentation: https://man7.org/linux/man-pages/man1/cat.1.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files_in: - type: file - description: List of compressed / uncompressed files - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files_in: + type: file + description: List of compressed / uncompressed files + pattern: "*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - file_out: - type: file - description: Concatenated file. Will be gzipped if file_out ends with ".gz" - pattern: "${file_out}" + - meta: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - ${prefix}: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index db4ac3c79af..91ff2fb5f64 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,30 +10,33 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/cdhit/cdhit/meta.yml b/modules/nf-core/cdhit/cdhit/meta.yml index fa3f204acc1..faa25b29114 100644 --- a/modules/nf-core/cdhit/cdhit/meta.yml +++ b/modules/nf-core/cdhit/cdhit/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: "https://github.com/weizhongli/cdhit" doi: "10.1093/bioinformatics/btl158" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: fasta file of sequences to be clustered - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: fasta file of sequences to be clustered + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: fasta file of the representative sequences for each cluster - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: fasta file of the representative sequences for each cluster + pattern: "*.{fasta}" - clusters: - type: file - description: List of clusters - pattern: "*.{clstr}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clstr": + type: file + description: List of clusters + pattern: "*.{clstr}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@timslittle" - "@Puumanamana" diff --git a/modules/nf-core/cdhit/cdhitest/meta.yml b/modules/nf-core/cdhit/cdhitest/meta.yml index c6b2dfc82b0..0a0e55af5cd 100644 --- a/modules/nf-core/cdhit/cdhitest/meta.yml +++ b/modules/nf-core/cdhit/cdhitest/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: "https://github.com/weizhongli/cdhit" doi: "10.1093/bioinformatics/btl158" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: fasta or fastq file of sequences to be clustered - pattern: "*.{fasta,fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: fasta or fastq file of sequences to be clustered + pattern: "*.{fasta,fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: fasta or fastq file of the representative sequences for each cluster - pattern: "*.{fasta,fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fq}": + type: file + description: fasta or fastq file of the representative sequences for each cluster + pattern: "*.{fasta,fastq}" - clusters: - type: file - description: List of clusters - pattern: "*.{clstr}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clstr": + type: file + description: List of clusters + pattern: "*.{clstr}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/celesta/meta.yml b/modules/nf-core/celesta/meta.yml index 9d6cae71840..50f57670ba0 100644 --- a/modules/nf-core/celesta/meta.yml +++ b/modules/nf-core/celesta/meta.yml @@ -1,6 +1,7 @@ ---- name: "celesta" -description: Unsupervised machine learning for cell type identification in multiplexed imaging using protein expression and cell neighborhood information without ground truth +description: Unsupervised machine learning for cell type identification in multiplexed + imaging using protein expression and cell neighborhood information without ground + truth keywords: - highly_multiplexed_imaging - cell_type_identification @@ -10,55 +11,65 @@ keywords: - machine_learning tools: - "celesta": - description: "Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information" + description: "Automate unsupervised machine learning cell type identification + using both protein expressions and cell spatial neighborhood information" homepage: https://github.com/SchapiroLabor/mcmicro-celesta documentation: https://github.com/SchapiroLabor/mcmicro-celesta/blob/main/README.md tool_dev_url: "https://github.com/plevritis-lab/CELESTA" doi: "10.1038/s41592-022-01498-z" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - img_data: - type: file - description: "Quantification table with single cells as rows, markers (e.g. CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as columns" - pattern: "*.csv" - - signature: - type: file - description: "Signature Matrix containing the definition of cell types according to markers" - pattern: "*.csv" - - high_thresholds: - type: file - description: "csv file with user-defined probability high thresholds for anchor cell (row 1) and index cell (row 2) definition" - pattern: "*.csv" - - low_thresholds: - type: file - description: "optional csv file with user-defined probability low thresholds for anchor cell (row 1) and index cell (row 2) definition" - pattern: "*.csv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - img_data: + type: file + description: "Quantification table with single cells as rows, markers (e.g. + CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as + columns" + pattern: "*.csv" + - - signature: + type: file + description: "Signature Matrix containing the definition of cell types according + to markers" + pattern: "*.csv" + - - high_thresholds: + type: file + description: "csv file with user-defined probability high thresholds for anchor + cell (row 1) and index cell (row 2) definition" + pattern: "*.csv" + - - low_thresholds: + type: file + description: "optional csv file with user-defined probability low thresholds + for anchor cell (row 1) and index cell (row 2) definition" + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - celltypes: - type: file - description: File with final celltype annotations concatenated to the original input quantification, due to the mechanism its non-deterministic - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*results.csv": + type: file + description: File with final celltype annotations concatenated to the original + input quantification, due to the mechanism its non-deterministic + pattern: "*.csv" - quality: - type: file - description: File with final calculated marker probabilities for inspection, non-deterministic - pattern: "*.csv" - + - "*quality.csv": + type: file + description: File with final calculated marker probabilities for inspection, + non-deterministic + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LukasHats" - "@ArozHada" diff --git a/modules/nf-core/cellbender/merge/meta.yml b/modules/nf-core/cellbender/merge/meta.yml index 333ad6a69c4..97f2c0e6479 100644 --- a/modules/nf-core/cellbender/merge/meta.yml +++ b/modules/nf-core/cellbender/merge/meta.yml @@ -1,42 +1,51 @@ name: cellbender_merge -description: Module to use CellBender to remove ambient RNA from single-cell RNA-seq data +description: Module to use CellBender to remove ambient RNA from single-cell RNA-seq + data keywords: - single-cell - scRNA-seq - ambient RNA removal tools: - cellbender: - description: CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. + description: CellBender is a software package for eliminating technical artifacts + from high-throughput single-cell RNA sequencing (scRNA-seq) data. documentation: https://cellbender.readthedocs.io/en/latest/ tool_dev_url: https://github.com/broadinstitute/CellBender licence: ["BSD-3-Clause"] + identifier: biotools:CellBender input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - filtered: - type: file - description: AnnData file containing filtered data (without empty droplets) - pattern: "*.h5ad" - - unfiltered: - type: file - description: AnnData file containing unfiltered data (with empty droplets) - pattern: "*.h5ad" - - cellbender_h5: - type: file - description: CellBender h5 file containing ambient RNA estimates - pattern: "*.h5" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - filtered: + type: file + description: AnnData file containing filtered data (without empty droplets) + pattern: "*.h5ad" + - unfiltered: + type: file + description: AnnData file containing unfiltered data (with empty droplets) + pattern: "*.h5ad" + - cellbender_h5: + type: file + description: CellBender h5 file containing ambient RNA estimates + pattern: "*.h5" output: - h5ad: - type: file - description: AnnData file containing decontaminated counts as `adata.X` - pattern: "*.h5ad" + - meta: + type: file + description: AnnData file containing decontaminated counts as `adata.X` + pattern: "*.h5ad" + - ${prefix}.h5ad: + type: file + description: AnnData file containing decontaminated counts as `adata.X` + pattern: "*.h5ad" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nictru" maintainers: diff --git a/modules/nf-core/cellbender/removebackground/meta.yml b/modules/nf-core/cellbender/removebackground/meta.yml index d70fa3fda1d..b037bf5c724 100644 --- a/modules/nf-core/cellbender/removebackground/meta.yml +++ b/modules/nf-core/cellbender/removebackground/meta.yml @@ -1,74 +1,135 @@ name: cellbender_removebackground -description: Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data +description: Module to use CellBender to estimate ambient RNA from single-cell RNA-seq + data keywords: - single-cell - scRNA-seq - ambient RNA removal tools: - cellbender: - description: CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. + description: CellBender is a software package for eliminating technical artifacts + from high-throughput single-cell RNA sequencing (scRNA-seq) data. documentation: https://cellbender.readthedocs.io/en/latest/ tool_dev_url: https://github.com/broadinstitute/CellBender licence: ["BSD-3-Clause"] + identifier: biotools:CellBender input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - h5ad: - type: file - description: AnnData file containing unfiltered data (with empty droplets) - pattern: "*.h5ad" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - h5ad: + type: file + description: AnnData file containing unfiltered data (with empty droplets) + pattern: "*.h5ad" output: - h5: - type: file - description: Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes. - pattern: "*.h5" + - meta: + type: file + description: Full count matrix as an h5 file, with background RNA removed. This + file contains all the original droplet barcodes. + pattern: "*.h5" + - ${prefix}.h5: + type: file + description: Full count matrix as an h5 file, with background RNA removed. This + file contains all the original droplet barcodes. + pattern: "*.h5" - filtered_h5: - type: file - description: | - Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. - pattern: "*.h5" + - meta: + type: file + description: | + Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. + pattern: "*.h5" + - ${prefix}_filtered.h5: + type: file + description: | + Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. + pattern: "*.h5" - posterior_h5: - type: file - description: | - The full posterior probability of noise counts. This is not normally used downstream. - pattern: "*.h5" + - meta: + type: file + description: | + The full posterior probability of noise counts. This is not normally used downstream. + pattern: "*.h5" + - ${prefix}_posterior.h5: + type: file + description: | + The full posterior probability of noise counts. This is not normally used downstream. + pattern: "*.h5" - barcodes: - type: file - description: | - CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | - Barcodes are written in plain text. This information is also contained in each of the above outputs, | - but is included as a separate output for convenient use in certain downstream applications. - pattern: "*.csv" + - meta: + type: file + description: | + CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | + Barcodes are written in plain text. This information is also contained in each of the above outputs, | + but is included as a separate output for convenient use in certain downstream applications. + pattern: "*.csv" + - ${prefix}_cell_barcodes.csv: + type: file + description: | + CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | + Barcodes are written in plain text. This information is also contained in each of the above outputs, | + but is included as a separate output for convenient use in certain downstream applications. + pattern: "*.csv" - metrics: - type: file - description: | - Metrics describing the run, potentially to be used to flag problematic runs | - when using CellBender as part of a large-scale automated pipeline. - pattern: "*.csv" + - meta: + type: file + description: | + Metrics describing the run, potentially to be used to flag problematic runs | + when using CellBender as part of a large-scale automated pipeline. + pattern: "*.csv" + - ${prefix}_metrics.csv: + type: file + description: | + Metrics describing the run, potentially to be used to flag problematic runs | + when using CellBender as part of a large-scale automated pipeline. + pattern: "*.csv" - report: - type: file - description: | - HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings. - pattern: "*.html" + - meta: + type: file + description: | + HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings. + pattern: "*.html" + - ${prefix}_report.html: + type: file + description: | + HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings. + pattern: "*.html" - pdf: - type: file - description: PDF file that provides a standard graphical summary of the inference procedure. - pattern: "*.pdf" + - meta: + type: file + description: PDF file that provides a standard graphical summary of the inference + procedure. + pattern: "*.pdf" + - ${prefix}.pdf: + type: file + description: PDF file that provides a standard graphical summary of the inference + procedure. + pattern: "*.pdf" - log: - type: file - description: Log file produced by the cellbender remove-background run. - pattern: "*.log" + - meta: + type: file + description: Log file produced by the cellbender remove-background run. + pattern: "*.log" + - ${prefix}.log: + type: file + description: Log file produced by the cellbender remove-background run. + pattern: "*.log" - checkpoint: - type: file - description: Checkpoint file which contains the trained model and the full posterior. - pattern: "*.ckpt" + - meta: + type: file + description: Checkpoint file which contains the trained model and the full posterior. + pattern: "*.ckpt" + - ckpt.tar.gz: + type: file + description: Checkpoint file which contains the trained model and the full posterior. + pattern: "*.ckpt" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nictru" maintainers: diff --git a/modules/nf-core/cellpose/meta.yml b/modules/nf-core/cellpose/meta.yml index 433d5204469..5397944baba 100644 --- a/modules/nf-core/cellpose/meta.yml +++ b/modules/nf-core/cellpose/meta.yml @@ -6,44 +6,54 @@ keywords: - cellpose tools: - "cellpose": - description: "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu" + description: "cellpose is an anatomical segmentation algorithm written in Python + 3 by Carsen Stringer and Marius Pachitariu" homepage: "https://github.com/MouseLand/cellpose" documentation: "https://cellpose.readthedocs.io/en/latest/command.html" tool_dev_url: "https://github.com/MouseLand/cellpose" doi: 10.1038/s41592-022-01663-4 licence: ["BSD 3-Clause"] + identifier: biotools:cellpose input: - - meta: - type: map - description: | - Groovy Map containing sample information - (sample id) - - image: - type: file - description: tif file for ready for segmentation - pattern: "*.{tif,tiff}" - - model: - type: file - description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach. + - - meta: + type: map + description: | + Groovy Map containing sample information + (sample id) + - image: + type: file + description: tif file for ready for segmentation + pattern: "*.{tif,tiff}" + - - model: + type: file + description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop + approach. output: - - meta: - type: map - description: | - Groovy Map containing sample information - [sample id] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mask: - type: file - description: labelled mask output from cellpose in tif format - pattern: "*.{tif, tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "*masks.tif": + type: file + description: labelled mask output from cellpose in tif format + pattern: "*.{tif, tiff}" - flows: - type: file - description: cell flow output from cellpose - pattern: "*.{tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "*flows.tif": + type: file + description: cell flow output from cellpose + pattern: "*.{tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@josenimo" - "@FloWuenne" diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index 1f1768a857b..046faf9fd64 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -1,49 +1,61 @@ name: cellranger_count -description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. +description: Module to use Cell Ranger's pipelines analyze sequencing data produced + from Chromium Single Cell Gene Expression. keywords: - align - count - reference tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: - 10x Genomics EULA + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files. The order of the input files MUST be ["sample1 R1", "sample1 R2", "sample2, R1", - "sample2, R2", ...]. This can usually be achieved by sorting the input files by file name. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files. The order of the input files MUST be ["sample1 R1", "sample1 R2", "sample2, R1", + "sample2, R2", ...]. This can usually be achieved by sorting the input files by file name. - Background: 10x data is always paired-end with R1 containing cell barcode and UMI - and R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name - convention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically - renames files to match this convention based on the order of input files to avoid various - issues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module - throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the "_R1"/"_R2" part. - Renaming the files does not affect the results (see README.md for detailed tests). - pattern: "*{R1,R2}*.fastq.gz" - - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + Background: 10x data is always paired-end with R1 containing cell barcode and UMI + and R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name + convention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically + renames files to match this convention based on the order of input files to avoid various + issues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module + throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the "_R1"/"_R2" part. + Renaming the files does not affect the results (see README.md for detailed tests). + pattern: "*{R1,R2}*.fastq.gz" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger output: - outs: - type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkfastq/meta.yml b/modules/nf-core/cellranger/mkfastq/meta.yml index 0077b069d68..fa7af86b673 100644 --- a/modules/nf-core/cellranger/mkfastq/meta.yml +++ b/modules/nf-core/cellranger/mkfastq/meta.yml @@ -1,5 +1,6 @@ name: cellranger_mkfastq -description: Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command. +description: Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. + Uses the cellranger mkfastq command. keywords: - reference - mkfastq @@ -8,29 +9,83 @@ keywords: - bcl2fastq tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: [10X Genomics EULA] + identifier: "" input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: Sample sheet + pattern: "*.csv" + - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" output: - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - "*_outs/outs/fastq_path/**/*.fastq.gz": + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - undetermined_fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/fastq_path/Undetermined*.fastq.gz": + type: file + description: Undetermined FastQ files + pattern: "Undetermined*.fastq.gz" + - reports: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/fastq_path/Reports": + type: directory + description: Reports + pattern: "Reports" + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/fastq_path/Stats": + type: directory + description: Stats + pattern: "Stats" + - interop: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/interop_path/*.bin": + type: file + description: InterOp files + pattern: "*.bin" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml index 282fcff0312..ceaca540923 100644 --- a/modules/nf-core/cellranger/mkgtf/meta.yml +++ b/modules/nf-core/cellranger/mkgtf/meta.yml @@ -1,30 +1,36 @@ name: cellranger_mkgtf -description: Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command. +description: Module to build a filtered GTF needed by the 10x Genomics Cell Ranger + tool. Uses the cellranger mkgtf command. keywords: - reference - mkref - index tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: [10X Genomics EULA] + identifier: "" input: - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" + - - gtf: + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" output: - gtf: - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" + - "*.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index bd8ad5a65ca..f4f595636fc 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -1,37 +1,43 @@ name: cellranger_mkref -description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command. +description: Module to build the reference needed by the 10x Genomics Cell Ranger + tool. Uses the cellranger mkref command. keywords: - reference - mkref - index tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: [10X Genomics EULA] + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/cellranger/mkvdjref/meta.yml b/modules/nf-core/cellranger/mkvdjref/meta.yml index c7d70dd1e85..23605d3f319 100644 --- a/modules/nf-core/cellranger/mkvdjref/meta.yml +++ b/modules/nf-core/cellranger/mkvdjref/meta.yml @@ -1,5 +1,6 @@ name: cellranger_mkvdjref -description: Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command. +description: Module to build the VDJ reference needed by the 10x Genomics Cell Ranger + tool. Uses the cellranger mkvdjref command. keywords: - reference - mkvdjref @@ -9,36 +10,46 @@ keywords: - cellranger tools: - cellranger: - description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser. + description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger + vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries + and performs sequence assembly and paired clonotype calling. It uses the Chromium + cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes + and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe + V(D)J Browser. homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references licence: ["10x Genomics EULA"] + identifier: "" input: - - reference_name: - type: string - description: The name to give the new reference folder, e.g. `my_vdj_ref`. This flag is required - pattern: str - - genes: - type: file - description: Reference transcriptome GTF file (optional) - pattern: "*.gtf" - - fasta: - type: file - description: Reference genome FASTA file (optional) - pattern: "*.{fasta,fa}" - - seqs: - type: file - description: Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional) - pattern: "*.{fasta,fa}" + - - fasta: + type: file + description: Reference genome FASTA file (optional) + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference genome GTF file (optional) + pattern: "*.gtf" + - - seqs: + type: file + description: Reference genome FASTA file from the 10X Genomics fetch-imgt workflow + (optional) + pattern: "*.{fasta,fa}" + - - reference_name: + type: string + description: The name to give the new reference folder, e.g. `my_vdj_ref`. This + flag is required + pattern: str output: - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@klkeys" diff --git a/modules/nf-core/cellranger/multi/meta.yml b/modules/nf-core/cellranger/multi/meta.yml index 5ac3ebdbb87..ccd329aecad 100644 --- a/modules/nf-core/cellranger/multi/meta.yml +++ b/modules/nf-core/cellranger/multi/meta.yml @@ -1,5 +1,7 @@ name: "cellranger_multi" -description: Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing. +description: Module to use Cell Ranger's pipelines to analyze sequencing data produced + from various Chromium technologies, including Single Cell Gene Expression, Single + Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing. keywords: - align - reference @@ -12,98 +14,150 @@ keywords: - crispr tools: - "cellranger": - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp licence: [10X Genomics EULA] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gex_fastqs: - type: file - description: FASTQ files for gene expression analysis - pattern: "*.fastq.gz" - - vdj_fastqs: - type: file - description: FASTQ files for V(D)J immunoprofiling analysis - pattern: "*.fastq.gz" - - ab_fastqs: - type: file - description: FASTQ files for antibody analysis - pattern: "*.fastq.gz" - - beam_fastqs: - type: file - description: FASTQ files for Barcode-Enabled Antigen Mapping (antigen analysis) - pattern: "*.fastq.gz" - - cmo_fastqs: - type: file - description: FASTQ files for cell multiplexing data - pattern: "*.fastq.gz" - - gex_reference: - type: directory - description: Folder containing Cellranger gene expression reference. Can also be a gzipped tarball - pattern: "*.tar.gz" - - gex_frna_probeset: - type: file - description: Fixed RNA profiling information containing custom probes in CSV format - pattern: "*.csv" - - gex_targetpanel: - type: file - description: Declaration of the target panel for Targeted Gene Expression analysis - pattern: "*.csv" - - vdj_reference: - type: directory - description: Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball - pattern: "*.tar.gz" - - vdj_primer_index: - type: file - description: List of custom V(D)J inner enrichment primers - pattern: "*.csv" - - fb_reference: - type: file - description: The Feature Barcodes used for reference in Feature Barcoding Analysis - pattern: "*.csv" - - beam_antigen_panel: - type: file - description: The BEAM manifest in Feature Barcode CSV format - pattern: "*.csv" - - beam_control_panel: - type: file - description: The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format - pattern: "*.csv" - - cmo_reference: - type: file - description: Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` option in Cellranger - pattern: "*.csv" - - cmo_barcodes: - type: file - description: A CSV file appended to the Cellranger multi config linking samples to CMO IDs - pattern: "*.csv" - - cmo_barcode_assignment: - type: file - description: A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis - pattern: "*.csv" - - frna_sampleinfo: - type: file - description: Sample information for fixed RNA analysis - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - - meta_gex: + type: map + description: | + Groovy Map containing sample information + - "gex_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_vdj: + type: map + description: | + Groovy Map containing sample information + - "vdj_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_ab: + type: map + description: | + Groovy Map containing sample information + - "ab_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_beam: + type: map + description: | + Groovy Map containing sample information + - "beam_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_cmo: + type: map + description: | + Groovy Map containing sample information + - "cmo_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_crispr: + type: map + description: | + Groovy Map containing sample information + - crispr_fastqs: + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - gex_reference: + type: directory + description: Folder containing Cellranger gene expression reference. Can also + be a gzipped tarball + pattern: "*.tar.gz" + - - gex_frna_probeset: + type: file + description: Fixed RNA profiling information containing custom probes in CSV + format + pattern: "*.csv" + - - gex_targetpanel: + type: file + description: Declaration of the target panel for Targeted Gene Expression analysis + pattern: "*.csv" + - - vdj_reference: + type: directory + description: Folder containing Cellranger V(D)J reference. Can also be a gzipped + tarball + pattern: "*.tar.gz" + - - vdj_primer_index: + type: file + description: List of custom V(D)J inner enrichment primers + pattern: "*.csv" + - - fb_reference: + type: file + description: The Feature Barcodes used for reference in Feature Barcoding Analysis + pattern: "*.csv" + - - beam_antigen_panel: + type: file + description: The BEAM manifest in Feature Barcode CSV format + pattern: "*.csv" + - - beam_control_panel: + type: file + description: The BEAM antigens set to control status, with corresponding MHC + alleles, in Feature Barcode CSV format + pattern: "*.csv" + - - cmo_reference: + type: file + description: Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` + option in Cellranger + pattern: "*.csv" + - - cmo_barcodes: + type: file + description: A CSV file appended to the Cellranger multi config linking samples + to CMO IDs + pattern: "*.csv" + - - cmo_barcode_assignment: + type: file + description: A CSV file that specifies the barcode-sample assignment in Cell + Multiplexing analysis + pattern: "*.csv" + - - frna_sampleinfo: + type: file + description: Sample information for fixed RNA analysis + pattern: "*.csv" + - - skip_renaming: + type: boolean + description: Skip renaming output: - config: - type: file - description: The resolved Cellranger multi config used for analysis - pattern: "cellranger_multi_config.csv" + - meta: + type: file + description: The resolved Cellranger multi config used for analysis + pattern: "cellranger_multi_config.csv" + - cellranger_multi_config.csv: + type: file + description: The resolved Cellranger multi config used for analysis + pattern: "cellranger_multi_config.csv" - outs: - type: file - description: Files containing the outputs of Cell Ranger - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@klkeys" maintainers: diff --git a/modules/nf-core/cellranger/vdj/meta.yml b/modules/nf-core/cellranger/vdj/meta.yml index 2bdafe5d167..8fbd75e802b 100644 --- a/modules/nf-core/cellranger/vdj/meta.yml +++ b/modules/nf-core/cellranger/vdj/meta.yml @@ -1,5 +1,6 @@ name: cellranger_vdj -description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling. +description: Module to use Cell Ranger's pipelines analyze sequencing data produced + from Chromium Single Cell Immune Profiling. keywords: - align - vdj @@ -9,35 +10,49 @@ keywords: - cellranger tools: - cellranger: - description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser. + description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger + vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries + and performs sequence assembly and paired clonotype calling. It uses the Chromium + cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes + and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe + V(D)J Browser. homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj licence: [10X Genomics EULA] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger output: - outs: - type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/count/meta.yml b/modules/nf-core/cellrangerarc/count/meta.yml index 8bc73c6fff5..6aa9d1f163e 100644 --- a/modules/nf-core/cellrangerarc/count/meta.yml +++ b/modules/nf-core/cellrangerarc/count/meta.yml @@ -1,39 +1,60 @@ name: cellrangerarc_count -description: Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command. +description: Module to use Cell Ranger's ARC pipelines analyze sequencing data produced + from Chromium Single Cell ARC. Uses the cellranger-arc count command. keywords: - align - count - reference tools: - cellrangerarc: - description: Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data. + description: Cell Ranger ARC is a set of analysis pipelines that process Chromium + Single Cell ARC data. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - lib_csv: - type: file - description: | - Path to a 3-column CSV file declaring FASTQ paths, sample names and library types of input ATAC and GEX FASTQs. - - reference: - type: directory - description: Directory containing all the reference indices needed by Cell Ranger ARC + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sample_type: + type: string + description: The type of sample + - sub_sample: + type: string + description: The name of sub sample + - reads: + type: file + description: FASTQ files produced using Cell Ranger ARC + pattern: "*.fastq.gz" + - - reference: + type: directory + description: Directory containing all the reference indices needed by Cell Ranger + ARC output: - outs: - type: file - description: Files containing the outputs of Cell Ranger ARC - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger ARC + pattern: "${meta.id}/outs/*" + - ${meta.id}/outs/**: + type: file + description: Files containing the outputs of Cell Ranger ARC + pattern: "${meta.id}/outs/*" + - lib: + - ${meta.id}_lib.csv: + type: file + description: Library + pattern: "*_lib.csv" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/mkfastq/meta.yml b/modules/nf-core/cellrangerarc/mkfastq/meta.yml index e344e900e81..f57487cdf29 100644 --- a/modules/nf-core/cellrangerarc/mkfastq/meta.yml +++ b/modules/nf-core/cellrangerarc/mkfastq/meta.yml @@ -1,5 +1,6 @@ name: cellrangerarc_mkfastq -description: Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command. +description: Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. + Uses the cellranger-arc mkfastq command. keywords: - reference - mkfastq @@ -8,30 +9,39 @@ keywords: - bcl2fastq tools: - cellrangerarc: - description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that + process Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" + - - csv: + type: file + description: Sample sheet + pattern: "*.csv" output: - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + - fastq: + - ${bcl.getSimpleName(: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - /*.fastq.gz: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/mkgtf/meta.yml b/modules/nf-core/cellrangerarc/mkgtf/meta.yml index 5fadc3eff55..8730f856fce 100644 --- a/modules/nf-core/cellrangerarc/mkgtf/meta.yml +++ b/modules/nf-core/cellrangerarc/mkgtf/meta.yml @@ -1,31 +1,37 @@ name: cellrangerarc_mkgtf -description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command. +description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger + Arc tool. Uses the cellranger-arc mkgtf command. keywords: - reference - mkref - index tools: - cellrangerarc: - description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that + process Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" + - - gtf: + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" output: - gtf: - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" + - "*.filtered.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/mkref/meta.yml b/modules/nf-core/cellrangerarc/mkref/meta.yml index cf98e60ca10..59dadcda1b0 100644 --- a/modules/nf-core/cellrangerarc/mkref/meta.yml +++ b/modules/nf-core/cellrangerarc/mkref/meta.yml @@ -1,46 +1,58 @@ name: cellrangerarc_mkref -description: Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command. +description: Module to build the reference needed by the 10x Genomics Cell Ranger + Arc tool. Uses the cellranger-arc mkref command. keywords: - reference - mkref - index tools: - cellrangerarc: - description: Cell Ranger Arc is a set of analysis pipelines that process Chromium Single Cell Arc data. + description: Cell Ranger Arc is a set of analysis pipelines that process Chromium + Single Cell Arc data. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - motifs: - type: file - description: Sequence motif file (e.g., from transcription factors) - pattern: "*.txt" - - reference_config: - type: file - description: JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path - pattern: config - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - motifs: + type: file + description: Sequence motif file (e.g., from transcription factors) + pattern: "*.txt" + - - reference_config: + type: file + description: JSON-like file holding organism, genome, reference fasta path, + reference annotation gtf path, contigs that should be excluded and sequence + format motif file path + pattern: config + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc + - ${reference_name}: + type: directory + description: Folder called like the reference_name containing all the reference + indices needed by Cell Ranger Arc + - config: + - config: + type: file + description: Configuration file - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@heylf" diff --git a/modules/nf-core/cellrangeratac/count/meta.yml b/modules/nf-core/cellrangeratac/count/meta.yml index 2bdef7f60d9..fd2599cdfdb 100644 --- a/modules/nf-core/cellrangeratac/count/meta.yml +++ b/modules/nf-core/cellrangeratac/count/meta.yml @@ -1,39 +1,49 @@ name: cellrangeratac_count -description: Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC. +description: Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced + from Chromium Single Cell ATAC. keywords: - align - count - reference tools: - cellranger-atac: - description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. + description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium + Single Cell ATAC data. homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac licence: ["10x Genomics EULA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively, plus an additional FastQ for the barcodes - - reference: - type: directory - description: Directory containing all the reference indices needed by Cell Ranger ATAC + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively, plus an additional FastQ for the barcodes + - - reference: + type: directory + description: Directory containing all the reference indices needed by Cell Ranger + ATAC output: - outs: - type: file - description: Files containing the outputs of Cell Ranger ATAC - pattern: "sample-${meta.gem}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger ATAC + pattern: "sample-${meta.gem}/outs/*" + - ${meta.id}/outs/*: + type: file + description: Files containing the outputs of Cell Ranger ATAC + pattern: "sample-${meta.gem}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangeratac/mkfastq/meta.yml b/modules/nf-core/cellrangeratac/mkfastq/meta.yml index fcee368d1ac..22441625c54 100644 --- a/modules/nf-core/cellrangeratac/mkfastq/meta.yml +++ b/modules/nf-core/cellrangeratac/mkfastq/meta.yml @@ -1,5 +1,6 @@ name: cellrangeratac_mkfastq -description: Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command. +description: Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. + Uses the cellranger-atac mkfastq command. keywords: - reference - mkfastq @@ -8,29 +9,38 @@ keywords: - bcl2fastq tools: - cellranger-atac: - description: Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that + process Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac licence: ["10x Genomics EULA"] + identifier: "" input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" + - - csv: + type: file + description: Sample sheet + pattern: "*.csv" output: - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + - fastq: + - ${bcl.getSimpleName(: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - /*.fastq.gz: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangeratac/mkref/meta.yml b/modules/nf-core/cellrangeratac/mkref/meta.yml index 4baed308375..caa46127bd1 100644 --- a/modules/nf-core/cellrangeratac/mkref/meta.yml +++ b/modules/nf-core/cellrangeratac/mkref/meta.yml @@ -1,45 +1,53 @@ name: cellrangeratac_mkref -description: Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command. +description: Module to build the reference needed by the 10x Genomics Cell Ranger + ATAC tool. Uses the cellranger-atac mkref command. keywords: - reference - mkref - index tools: - cellranger-atac: - description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. + description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium + Single Cell ATAC data. homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac licence: ["10x Genomics EULA"] + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - motifs: - type: file - description: Sequence motif file (e.g., of transcription factors) - pattern: "*.txt" - - reference_config: - type: file - description: JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path - pattern: config - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - motifs: + type: file + description: Sequence motif file (e.g., of transcription factors) + pattern: "*.txt" + - - reference_config: + type: file + description: JSON-like config file holding organism, genome, reference fasta + path, reference annotation gtf path, contigs that should be excluded and sequence + format motif file path + pattern: config + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC + - ${reference_name}: + type: directory + description: Folder called regarding reference_name containing all the reference + indices needed by Cell Ranger ATAC - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@heylf" diff --git a/modules/nf-core/cellsnp/modea/meta.yml b/modules/nf-core/cellsnp/modea/meta.yml index bed1bc482bd..886e5300548 100644 --- a/modules/nf-core/cellsnp/modea/meta.yml +++ b/modules/nf-core/cellsnp/modea/meta.yml @@ -1,7 +1,9 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cellsnp_modea" -description: Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data. +description: Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs + on single cells. You can use the mode A of cellsnp-lite after read alignment to + obtain the snp x cell pileup UMI or read count matrices for each alleles of given + or detected SNPs for droplet based single cell data. keywords: - genotyping - single cell @@ -15,65 +17,101 @@ tools: tool_dev_url: "https://github.com/single-cell-genetics/cellsnp-lite" doi: "10.1093/bioinformatics/btab358" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: A single BAM/SAM/CRAM file, e.g., from CellRanger. - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: The index of the BAM/CRAM file. - pattern: "*.{bai,crai}" - - region_vcf: - type: file - description: A optional vcf file listing all candidate SNPs for genotyping. - pattern: "*.{vcf, vcf.gz}" - - barcode: - type: file - description: A plain file listing all effective cell barcodes. - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: A single BAM/SAM/CRAM file, e.g., from CellRanger. + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: The index of the BAM/CRAM file. + pattern: "*.{bai,crai}" + - region_vcf: + type: file + description: A optional vcf file listing all candidate SNPs for genotyping. + pattern: "*.{vcf, vcf.gz}" + - barcode: + type: file + description: A plain file listing all effective cell barcodes. + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - base: - type: file - description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT). - pattern: "*.base.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.base.vcf.gz": + type: file + description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation + (without GT). + pattern: "*.base.vcf.gz" - cell: - type: file - description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample. - pattern: "*.cells.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.cells.vcf.gz": + type: file + description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation + & genotype (GT) information for each cell or sample. + pattern: "*.cells.vcf.gz" - sample: - type: file - description: A TSV file listing cell barcodes or sample IDs. - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.samples.tsv": + type: file + description: A TSV file listing cell barcodes or sample IDs. + pattern: "*.tsv" - allele_depth: - type: file - description: A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles. - pattern: "*.tag.AD.mtx" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tag.AD.mtx": + type: file + description: A file in “Matrix Market exchange formats”, containing the allele + depths of the alternative (ALT) alleles. + pattern: "*.tag.AD.mtx" - depth_coverage: - type: file - description: A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT). - pattern: "*.tag.DP.mtx" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tag.DP.mtx": + type: file + description: A file in “Matrix Market exchange formats”, containing the sum + of allele depths of the reference and alternative alleles (REF + ALT). + pattern: "*.tag.DP.mtx" - depth_other: - type: file - description: A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT. - pattern: "*.tag.OTH.mtx" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tag.OTH.mtx": + type: file + description: A file in “Matrix Market exchange formats”, containing the sum + of allele depths of all the alleles other than REF and ALT. + pattern: "*.tag.OTH.mtx" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@wxicu" maintainers: diff --git a/modules/nf-core/centrifuge/build/meta.yml b/modules/nf-core/centrifuge/build/meta.yml index d193ce1e833..65a34f6d7b0 100644 --- a/modules/nf-core/centrifuge/build/meta.yml +++ b/modules/nf-core/centrifuge/build/meta.yml @@ -13,56 +13,54 @@ tools: documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml doi: 10.1101/gr.210641.116 licence: ["GPL v3"] + identifier: biotools:centrifuge input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - - fasta: - type: file - description: Fasta file containing sequences to be used in centrifuge database. - pattern: "*.{fasta,fna}" - - - conversion_table: - type: file - description: A tab-separated file with sequence ID to taxonomy ID mapping - pattern: "*.{map}" - - - taxonomy_tree: - type: file - description: A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents - pattern: "*.{dmp}" - - - name_table: - type: file - description: A '|'-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name - pattern: "*.{dmp}" - - - size_table: - type: file - description: Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs. - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file containing sequences to be used in centrifuge database. + pattern: "*.{fasta,fna}" + - - conversion_table: + type: file + description: A tab-separated file with sequence ID to taxonomy ID mapping + pattern: "*.{map}" + - - taxonomy_tree: + type: file + description: A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from + the NCBI taxonomy dump. Links taxonomy IDs to their parents + pattern: "*.{dmp}" + - - name_table: + type: file + description: A '|'-separated file mapping taxonomy IDs to a name. Typically + names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific + name + pattern: "*.{dmp}" + - - size_table: + type: file + description: Optional list of taxonomic IDs and lengths of the sequences belonging + to the same taxonomic IDs. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - cf: - type: file - description: Index files for the centrifuge database - pattern: "*.{cf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cf": + type: file + description: Index files for the centrifuge database + pattern: "*.{cf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sarah-buddle" - "@jfy133" diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml index a06104e168a..17329e93355 100644 --- a/modules/nf-core/centrifuge/centrifuge/meta.yml +++ b/modules/nf-core/centrifuge/centrifuge/meta.yml @@ -12,59 +12,86 @@ tools: documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml doi: 10.1101/gr.210641.116 licence: ["GPL v3"] + identifier: biotools:centrifuge input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - db: - type: directory - description: Path to directory containing centrifuge database files - - save_unaligned: - type: boolean - description: If true unmapped fastq files are saved - - save_aligned: - type: boolean - description: If true mapped fastq files are saved + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - db: + type: directory + description: Path to directory containing centrifuge database files + - - save_unaligned: + type: boolean + description: If true unmapped fastq files are saved + - - save_aligned: + type: boolean + description: If true mapped fastq files are saved output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: | - File containing a classification summary - pattern: "*.{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: | + File containing a classification summary + pattern: "*.{report.txt}" - results: - type: file - description: | - File containing classification results - pattern: "*.{results.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*results.txt": + type: file + description: | + File containing classification results + pattern: "*.{results.txt}" - sam: - type: file - description: | - Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s - pattern: "*.{sam,tab}" - - fastq_unmapped: - type: file - description: Unmapped fastq files - pattern: "*.unmapped.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{sam,tab}": + type: file + description: | + Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s + pattern: "*.{sam,tab}" - fastq_mapped: - type: file - description: Mapped fastq files - pattern: "*.mapped.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapped.fastq{,.1,.2}.gz": + type: file + description: Mapped fastq files + pattern: "*.mapped.fastq.gz" + - fastq_unmapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unmapped.fastq{,.1,.2}.gz": + type: file + description: Unmapped fastq files + pattern: "*.unmapped.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@jfy133" diff --git a/modules/nf-core/centrifuge/kreport/meta.yml b/modules/nf-core/centrifuge/kreport/meta.yml index 5641152b675..e195eebf90b 100644 --- a/modules/nf-core/centrifuge/kreport/meta.yml +++ b/modules/nf-core/centrifuge/kreport/meta.yml @@ -14,35 +14,38 @@ tools: documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml doi: 10.1101/gr.210641.116 licence: ["GPL v3"] + identifier: biotools:centrifuge input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: File containing the centrifuge classification report - pattern: "*.{txt}" - - db: - type: directory - description: Path to directory containing centrifuge database files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: File containing the centrifuge classification report + pattern: "*.{txt}" + - - db: + type: directory + description: Path to directory containing centrifuge database files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - kreport: - type: file - description: | - File containing kraken-style report from centrifuge - out files. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: | + File containing kraken-style report from centrifuge + out files. + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@jfy133" diff --git a/modules/nf-core/checkm/lineagewf/meta.yml b/modules/nf-core/checkm/lineagewf/meta.yml index 239b8d2eba2..e32441d2475 100644 --- a/modules/nf-core/checkm/lineagewf/meta.yml +++ b/modules/nf-core/checkm/lineagewf/meta.yml @@ -1,5 +1,6 @@ name: checkm_lineagewf -description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. +description: CheckM provides a set of tools for assessing the quality of genomes recovered + from isolates, single cells, or metagenomes. keywords: - checkm - mag @@ -14,50 +15,68 @@ keywords: - genome bins tools: - checkm: - description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. + description: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes. homepage: https://ecogenomics.github.io/CheckM/ documentation: https://github.com/Ecogenomics/CheckM/wiki tool_dev_url: https://github.com/Ecogenomics/CheckM doi: "10.1101/gr.186072.114" licence: ["GPL v3"] + identifier: biotools:checkm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value - pattern: "*.{$fasta_ext}" - - fasta_ext: - type: string - description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) - - db: - type: directory - description: Optional directory pointing to checkM database to prevent re-downloading + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: One or a list of multiple FASTA files of each bin, with extension + defined with the fasta_ext value + pattern: "*.{$fasta_ext}" + - - fasta_ext: + type: string + description: The file-type extension suffix of the input FASTA files (e.g., + fasta, fna, fa, fas) + - - db: + type: directory + description: Optional directory pointing to checkM database to prevent re-downloading output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - checkm_output: - type: directory - description: CheckM output directory - pattern: "*/" - checkm_output: - type: file - description: Lineage markfer file - pattern: "lineage.ms" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}: + type: directory + description: CheckM output directory + pattern: "*/" + - marker_file: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/lineage.ms: + type: file + description: Lineage file + pattern: "*.ms" - checkm_tsv: - type: file - description: CheckM summary completeness statistics table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}.tsv: + type: file + description: CheckM summary completeness statistics table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/checkm/qa/meta.yml b/modules/nf-core/checkm/qa/meta.yml index 9f3d51ce62e..cd41eaecf7f 100644 --- a/modules/nf-core/checkm/qa/meta.yml +++ b/modules/nf-core/checkm/qa/meta.yml @@ -1,5 +1,6 @@ name: checkm_qa -description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. +description: CheckM provides a set of tools for assessing the quality of genomes recovered + from isolates, single cells, or metagenomes. keywords: - checkm - mag @@ -16,50 +17,63 @@ keywords: - quality assurnce tools: - checkm: - description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. + description: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes. homepage: https://ecogenomics.github.io/CheckM/ documentation: https://github.com/Ecogenomics/CheckM/wiki tool_dev_url: https://github.com/Ecogenomics/CheckM doi: "10.1101/gr.186072.114" licence: ["GPL v3"] + identifier: biotools:checkm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - analysis_dir: - type: file - description: Directory containing output of checkm/analyze or checkm/lineage_wf etc. - pattern: "*" - - marker_file: - type: file - description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf - pattern: "*.ms" - - coverage_file: - type: file - description: File containing coverage of each sequence (generated by checkm coverage) - - exclude_marker_file: - type: file - description: File specifying markers to exclude from marker sets + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - analysis_dir: + type: file + description: Directory containing output of checkm/analyze or checkm/lineage_wf + etc. + pattern: "*" + - marker_file: + type: file + description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf + pattern: "*.ms" + - coverage_file: + type: file + description: File containing coverage of each sequence (generated by checkm + coverage) + - - exclude_marker_file: + type: file + description: File specifying markers to exclude from marker sets output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)" - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: "Default completeness statistics in various formats, as specified + with --out_format (excluding option: 9)" + pattern: "*.txt" - fasta: - type: file - description: Output in fasta format (only if --out_format 9) - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fasta: + type: file + description: Output in fasta format (only if --out_format 9) + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/checkm2/databasedownload/meta.yml b/modules/nf-core/checkm2/databasedownload/meta.yml index 4672a1dcca5..09c69c923f5 100644 --- a/modules/nf-core/checkm2/databasedownload/meta.yml +++ b/modules/nf-core/checkm2/databasedownload/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkm2_databasedownload" description: CheckM2 database download @@ -16,17 +15,23 @@ tools: homepage: "https://github.com/chklovski/CheckM2" doi: "10.1038/s41592-023-01940-w" licence: ["GPL v3"] + identifier: "" output: - - meta: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test', version:1 ]` + - database: + - meta: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test', version:1 ]` + - checkm2_db_v${db_version}.dmnd: + type: file + description: CheckM2 database file + pattern: "checkm2_db_v*.dmnd" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@dialvarezs" diff --git a/modules/nf-core/checkm2/predict/meta.yml b/modules/nf-core/checkm2/predict/meta.yml index db17500e344..48cc9fbccaa 100644 --- a/modules/nf-core/checkm2/predict/meta.yml +++ b/modules/nf-core/checkm2/predict/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkm2_predict" description: CheckM2 bin quality prediction @@ -16,44 +15,51 @@ tools: homepage: "https://github.com/chklovski/CheckM2" doi: "10.1038/s41592-023-01940-w" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - dbmeta: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test', version:1 ]` - - fasta: - type: file - description: One or multiple FASTA files of each bin - pattern: "*.{fasta,fna,fa}" - - db: - type: file - description: CheckM2 database - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: One or multiple FASTA files of each bin + pattern: "*.{fasta,fna,fa}" + - - dbmeta: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test', version:1 ]` + - db: + type: file + description: CheckM2 database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checkm2_output: - type: directory - description: CheckM2 output directory - pattern: "${prefix}/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}: + type: directory + description: CheckM2 output directory + pattern: "${prefix}/" - checkm2_tsv: - type: file - description: CheckM2 summary completeness statistics table - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}/quality_report.tsv: + type: file + description: CheckM2 summary completeness statistics table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@dialvarezs" diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml index 0c3d98ba916..42d0017f6ba 100644 --- a/modules/nf-core/checkqc/meta.yml +++ b/modules/nf-core/checkqc/meta.yml @@ -1,43 +1,50 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkqc" -description: A simple program to parse Illumina NGS data and check it for quality criteria +description: A simple program to parse Illumina NGS data and check it for quality + criteria keywords: - QC - Illumina - genomics tools: - "checkqc": - description: "A simple program to parse Illumina NGS data and check it for quality criteria." + description: "A simple program to parse Illumina NGS data and check it for quality + criteria." homepage: "https://github.com/Molmed/checkQC" documentation: "http://checkqc.readthedocs.io/en/latest/" doi: "10.21105/joss.00556" licence: ["GPL v3"] + identifier: "" input: - - run_dir: - type: file - description: | - Illumina sequencing run directory - Can be directory or a compressed tar (tar.gz) of the directory - - checkqc_config: - type: file - description: CheckQC configuration file - pattern: "*.{yml,yaml}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - run_dir: + type: file + description: | + Illumina sequencing run directory + Can be directory or a compressed tar (tar.gz) of the directory + - - checkqc_config: + type: file + description: CheckQC configuration file + pattern: "*.{yml,yaml}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: CheckQC report in json format - pattern: "*checkqc_report.json" - - log: - type: file - description: CheckQC log in txt format - pattern: "*_log.txt" - + - meta: + type: file + description: CheckQC report in json format + pattern: "*checkqc_report.json" + - "*checkqc_report.json": + type: file + description: CheckQC report in json format + pattern: "*checkqc_report.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matrulda" diff --git a/modules/nf-core/checkv/downloaddatabase/meta.yml b/modules/nf-core/checkv/downloaddatabase/meta.yml index 1ca54150723..533ab8c69bf 100644 --- a/modules/nf-core/checkv/downloaddatabase/meta.yml +++ b/modules/nf-core/checkv/downloaddatabase/meta.yml @@ -20,15 +20,18 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/checkv/src/master/ doi: "10.1038/s41587-020-00774-7" licence: ["BSD License"] + identifier: biotools:checkv output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checkv_db: - type: directory - description: directory pointing to database - pattern: "${prefix}/" + - ${prefix}/*: + type: directory + description: directory pointing to database + pattern: "${prefix}/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/checkv/endtoend/meta.yml b/modules/nf-core/checkv/endtoend/meta.yml index 2bb4d330ed3..a8a6deaf0e6 100644 --- a/modules/nf-core/checkv/endtoend/meta.yml +++ b/modules/nf-core/checkv/endtoend/meta.yml @@ -18,53 +18,89 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/checkv/src/master/ doi: "10.1038/s41587-020-00774-7" licence: ["BSD License"] + identifier: biotools:checkv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta,fna,fa}" - - db: - type: directory - description: Directory pointing to checkV database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file + pattern: "*.{fasta,fna,fa}" + - - db: + type: directory + description: Directory pointing to checkV database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - quality_summary: - type: file - description: CheckV's main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs - pattern: "${prefix}/quality_summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/quality_summary.tsv: + type: file + description: CheckV's main output containing integrated results from the three + main modules (contamination, completeness, complete genomes) with overall + quality of contigs + pattern: "${prefix}/quality_summary.tsv" - completeness: - type: file - description: CheckV's detailed overview table on estimating completeness - pattern: "${prefix}/completeness.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/completeness.tsv: + type: file + description: CheckV's detailed overview table on estimating completeness + pattern: "${prefix}/completeness.tsv" - contamination: - type: file - description: CheckV's detailed overview table on estimating contamination - pattern: "${prefix}/contamination.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/contamination.tsv: + type: file + description: CheckV's detailed overview table on estimating contamination + pattern: "${prefix}/contamination.tsv" - complete_genomes: - type: file - description: CheckV's detailed overview table on the identified putative complete genomes - pattern: "${prefix}/complete_genomes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/complete_genomes.tsv: + type: file + description: CheckV's detailed overview table on the identified putative complete + genomes + pattern: "${prefix}/complete_genomes.tsv" - proviruses: - type: file - description: CheckV's extracted proviruses contigs - pattern: "${prefix}/proviruses.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/proviruses.fna: + type: file + description: CheckV's extracted proviruses contigs + pattern: "${prefix}/proviruses.fna" - viruses: - type: file - description: CheckV's extracted virus contigs - pattern: "${prefix}/viruses.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/viruses.fna: + type: file + description: CheckV's extracted virus contigs + pattern: "${prefix}/viruses.fna" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/checkv/updatedatabase/meta.yml b/modules/nf-core/checkv/updatedatabase/meta.yml index 2bed0c4cf02..fe411c63323 100644 --- a/modules/nf-core/checkv/updatedatabase/meta.yml +++ b/modules/nf-core/checkv/updatedatabase/meta.yml @@ -18,32 +18,37 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/checkv/src/master/ doi: "10.1038/s41587-020-00774-7" licence: ["BSD License"] + identifier: biotools:checkv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - fasta: - type: file - description: fasta file containing additional sequences for the existing checkv database - pattern: "*.{fasta,fna,fa}" - - db: - type: directory - description: directory pointing to existing checkV database to avoid redownloading the database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - fasta: + type: file + description: fasta file containing additional sequences for the existing checkv + database + pattern: "*.{fasta,fna,fa}" + - - db: + type: directory + description: directory pointing to existing checkV database to avoid redownloading + the database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checkv_db: - type: directory - description: directory pointing to database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/*: + type: directory + description: directory pointing to database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index 1c7be66e2ea..ef761f8a395 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -12,55 +12,57 @@ tools: tool_dev_url: "https://github.com/B-UMMI/chewBBACA" doi: "10.1099/mgen.0.000166" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - fasta: - type: directory - description: One or multiple FASTA files to create schema from - pattern: "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" - - - prodigal_tf: - type: file - description: File containing the prodigal training file - pattern: "*.ptf" - - - cds: - type: file - description: File containing the prodigal cds file - pattern: "*.cds" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: directory + description: One or multiple FASTA files to create schema from + pattern: "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" + - - prodigal_tf: + type: file + description: File containing the prodigal training file + pattern: "*.ptf" + - - cds: + type: file + description: File containing the prodigal cds file + pattern: "*.cds" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - schema: - type: directory - description: Schema directory - pattern: "*/" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - results/$meta.id: + type: directory + description: Schema directory + pattern: "*/" - cds_coordinates: - type: file - description: File containing the coordinates of the CDS in the input sample - pattern: "*_cds_coordinates.tsv" - + - results/cds_coordinates.tsv: + type: file + description: File containing the coordinates of the CDS in the input sample + pattern: "*_cds_coordinates.tsv" - invalid_cds: - type: file - description: File containing the list of alleles predicted by Prodigal that were excluded - pattern: "*_invalid_cds.txt" - + - results/invalid_cds.txt: + type: file + description: File containing the list of alleles predicted by Prodigal that + were excluded + pattern: "*_invalid_cds.txt" + - id_cds: + type: file + description: File containing the list of alleles predicted by Prodigal that + were excluded + pattern: "*_invalid_cds.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anwarMZ" diff --git a/modules/nf-core/chopper/meta.yml b/modules/nf-core/chopper/meta.yml index 9d8093d66bc..916c865e839 100644 --- a/modules/nf-core/chopper/meta.yml +++ b/modules/nf-core/chopper/meta.yml @@ -8,9 +8,11 @@ keywords: - qc tools: - "zcat": - description: "zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output." + description: "zcat uncompresses either a list of files on the command line or + its standard input and writes the uncompressed data on standard output." documentation: "https://linux.die.net/man/1/zcat" args_id: "$args" + identifier: "" - "chopper": description: "A rust command line for filtering and trimming long reads." homepage: "https://github.com/wdecoster/chopper" @@ -19,34 +21,39 @@ tools: doi: "10.1093/bioinformatics/bty149" licence: ["MIT"] args_id: "$args2" + identifier: "" - "gzip": - description: "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77)." + description: "Gzip reduces the size of the named files using Lempel-Ziv coding + (LZ77)." documentation: "https://linux.die.net/man/1/gzip" args_id: "$args3" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FastQ with reads from long read sequencing e.g. PacBio or ONT - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FastQ with reads from long read sequencing e.g. PacBio or ONT + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Filtered and trimmed FastQ file - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Filtered and trimmed FastQ file + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FynnFreyer" maintainers: diff --git a/modules/nf-core/chromap/chromap/meta.yml b/modules/nf-core/chromap/chromap/meta.yml index 140299ed6d4..5eefb46169c 100644 --- a/modules/nf-core/chromap/chromap/meta.yml +++ b/modules/nf-core/chromap/chromap/meta.yml @@ -21,77 +21,98 @@ tools: documentation: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing information for the fasta - e.g. [ id:'test' ] - - fasta: - type: file - description: | - The fasta reference file. - - meta3: - type: map - description: | - Groovy Map containing information for the index - e.g. [ id:'test' ] - - index: - type: file - description: | - Chromap genome index files (*.index) - - barcodes: - type: file - description: | - Cell barcode files - - whitelist: - type: file - description: | - Cell barcode whitelist file - - chr_order: - type: file - description: | - Custom chromosome order - - pairs_chr_order: - type: file - description: | - Natural chromosome order for pairs flipping + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing information for the fasta + e.g. [ id:'test' ] + - fasta: + type: file + description: | + The fasta reference file. + - - meta3: + type: map + description: | + Groovy Map containing information for the index + e.g. [ id:'test' ] + - index: + type: file + description: | + Chromap genome index files (*.index) + - - barcodes: + type: file + description: | + Cell barcode files + - - whitelist: + type: file + description: | + Cell barcode whitelist file + - - chr_order: + type: file + description: | + Custom chromosome order + - - pairs_chr_order: + type: file + description: | + Natural chromosome order for pairs flipping output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: BED file - pattern: "*.bed.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: BED file + pattern: "*.bed.gz" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.bam" - tagAlign: - type: file - description: tagAlign file - pattern: "*.tagAlign.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tagAlign.gz": + type: file + description: tagAlign file + pattern: "*.tagAlign.gz" - pairs: - type: file - description: pairs file - pattern: "*.pairs.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: pairs file + pattern: "*.pairs.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" - "@joseespinosa" diff --git a/modules/nf-core/chromap/index/meta.yml b/modules/nf-core/chromap/index/meta.yml index 6559509ca11..057847fd726 100644 --- a/modules/nf-core/chromap/index/meta.yml +++ b/modules/nf-core/chromap/index/meta.yml @@ -12,29 +12,32 @@ tools: documentation: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Fasta reference file. + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Fasta reference file. output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - index: - type: file - description: Index file of the reference genome - pattern: "*.{index}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - "*.index": + type: file + description: Index file of the reference genome + pattern: "*.{index}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" - "@joseespinosa" diff --git a/modules/nf-core/chromograph/meta.yml b/modules/nf-core/chromograph/meta.yml index 6540d9f077e..4a986dbbb99 100644 --- a/modules/nf-core/chromograph/meta.yml +++ b/modules/nf-core/chromograph/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "chromograph" -description: Chromograph is a python package to create PNG images from genetics data such as BED and WIG files. +description: Chromograph is a python package to create PNG images from genetics data + such as BED and WIG files. keywords: - chromosome_visualization - bed @@ -9,83 +9,87 @@ keywords: - png tools: - "chromograph": - description: "Chromograph is a python package to create PNG images from genetics data such as BED and WIG files." + description: "Chromograph is a python package to create PNG images from genetics + data such as BED and WIG files." homepage: "https://github.com/Clinical-Genomics/chromograph" documentation: "https://github.com/Clinical-Genomics/chromograph/blob/master/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta6: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta7: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - autozyg: - type: file - description: Bed file containing the regions of autozygosity - - coverage: - type: file - description: Wig file containing the coverage information - - exome: - type: file - description: Bed file containing the coverage for exome. - - fracsnp: - type: file - description: Wig file containing the fraction of homozygous SNPs - - ideogram: - type: file - description: | - Bed file containing information necessary for ideogram plots. - Format ['chrom', 'start', 'end', 'name', 'gStain'] - - regions: - type: file - description: Bed file containing UPD regions - - sites: - type: file - description: Bed file containing UPD sites + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - autozyg: + type: file + description: Bed file containing the regions of autozygosity + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage: + type: file + description: Wig file containing the coverage information + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exome: + type: file + description: Bed file containing the coverage for exome. + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fracsnp: + type: file + description: Wig file containing the fraction of homozygous SNPs + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ideogram: + type: file + description: | + Bed file containing information necessary for ideogram plots. + Format ['chrom', 'start', 'end', 'name', 'gStain'] + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: Bed file containing UPD regions + - - meta7: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sites: + type: file + description: Bed file containing UPD sites output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - plots: - type: file - description: Directory containing the plots in png format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Directory containing the plots in png format + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/circexplorer2/annotate/meta.yml b/modules/nf-core/circexplorer2/annotate/meta.yml index aac031ce3db..20b853104ee 100644 --- a/modules/nf-core/circexplorer2/annotate/meta.yml +++ b/modules/nf-core/circexplorer2/annotate/meta.yml @@ -11,38 +11,41 @@ tools: documentation: "https://circexplorer2.readthedocs.io/en/latest/" doi: "10.1101/gr.202895.115" licence: ["MIT License"] + identifier: biotools:CIRCexplorer2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - junctions: - type: file - description: Reformatted junctions file - pattern: "*.{junction}" - - fasta: - type: file - description: Genome FASTA file - pattern: "*.{fa,fasta}" - - gene_annotation: - type: file - description: Reformatted GTF file for CIRCexplorer2 - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - junctions: + type: file + description: Reformatted junctions file + pattern: "*.{junction}" + - - fasta: + type: file + description: Genome FASTA file + pattern: "*.{fa,fasta}" + - - gene_annotation: + type: file + description: Reformatted GTF file for CIRCexplorer2 + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Annotated circRNA TXT file - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Annotated circRNA TXT file + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/circexplorer2/parse/meta.yml b/modules/nf-core/circexplorer2/parse/meta.yml index 83e6e9d35b4..382c64f3099 100644 --- a/modules/nf-core/circexplorer2/parse/meta.yml +++ b/modules/nf-core/circexplorer2/parse/meta.yml @@ -1,5 +1,6 @@ name: "circexplorer2_parse" -description: CIRCexplorer2 parses fusion junction files from multiple aligners to prepare them for CIRCexplorer2 annotate. +description: CIRCexplorer2 parses fusion junction files from multiple aligners to + prepare them for CIRCexplorer2 annotate. keywords: - parse - circrna @@ -11,30 +12,34 @@ tools: documentation: "https://circexplorer2.readthedocs.io/en/latest/" doi: "10.1101/gr.202895.115" licence: ["MIT License"] + identifier: biotools:CIRCexplorer2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fusions: - type: file - description: BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) file. Aligner will be autodetected based on file suffix. - pattern: "*.{bam,junction,bed,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fusions: + type: file + description: BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) + file. Aligner will be autodetected based on file suffix. + pattern: "*.{bam,junction,bed,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Standardized fusion junction file suitable for CIRCexplorer2 annotate module. - pattern: "*.{bam,cram,sam}" + - junction: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/circularmapper/circulargenerator/meta.yml b/modules/nf-core/circularmapper/circulargenerator/meta.yml index baa39e74b90..637b38d4d96 100644 --- a/modules/nf-core/circularmapper/circulargenerator/meta.yml +++ b/modules/nf-core/circularmapper/circulargenerator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "circularmapper_circulargenerator" description: A method to improve mappings on circular genomes, using the BWA mapper. @@ -8,56 +7,68 @@ keywords: - genomics tools: - "circulargenerator": - description: "Creating a modified reference genome, with an elongation of the an specified amount of bases" + description: "Creating a modified reference genome, with an elongation of the + an specified amount of bases" homepage: "https://github.com/apeltzer/CircularMapper" documentation: "https://github.com/apeltzer/CircularMapper/blob/master/docs/contents/userguide.rst" tool_dev_url: "https://github.com/apeltzer/CircularMapper" doi: "no DOI available" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'sample1' ]` - - reference: - type: file - description: Genome fasta file - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'sample1' ]` - - elongation_factor: - type: integer - description: The number of bases that the ends of the target chromosome in the reference genome should be elongated by - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'sample1' ]` - - target: - type: string - description: The name of the chromosome in the reference genome that should be elongated + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'sample1' ]` + - reference: + type: file + description: Genome fasta file + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'sample1' ]` + - elongation_factor: + type: integer + description: The number of bases that the ends of the target chromosome in the + reference genome should be elongated by + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'sample1' ]` + - target: + type: string + description: The name of the chromosome in the reference genome that should + be elongated output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Genome fasta file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_${elongation_factor}.fasta": + type: file + description: Genome fasta file + pattern: "*.fasta" - elongated: - type: file - description: File listing the chromosomes that were elongated - pattern: "*_elongated" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*${elongation_factor}_elongated": + type: file + description: File listing the chromosomes that were elongated + pattern: "*_elongated" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apalleja" - "@TCLamnidis" diff --git a/modules/nf-core/circularmapper/realignsamfile/meta.yml b/modules/nf-core/circularmapper/realignsamfile/meta.yml index 94f74069e56..52b2fdd5a33 100644 --- a/modules/nf-core/circularmapper/realignsamfile/meta.yml +++ b/modules/nf-core/circularmapper/realignsamfile/meta.yml @@ -17,55 +17,60 @@ tools: tool_dev_url: "https://github.com/apeltzer/CircularMapper/" doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - fasta: - type: file - description: Input elongated genome fasta - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - elongation_factor: - type: integer - description: The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - elongated_chr_list: - type: file - description: File listing the chromosomes that were elongated - pattern: "*_elongated" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Input elongated genome fasta + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - elongation_factor: + type: integer + description: The elongation factor used when running circulargenerator, i.e. + the number of bases that the ends of the target chromosome in the reference + genome was elongated by + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - elongated_chr_list: + type: file + description: File listing the chromosomes that were elongated + pattern: "*_elongated" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - bam: - type: file - description: Realigned BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_realigned.bam": + type: file + description: Realigned BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@shyama-mama" - "@jbv2" diff --git a/modules/nf-core/clame/meta.yml b/modules/nf-core/clame/meta.yml index 24e17af00f5..c5a7f763515 100644 --- a/modules/nf-core/clame/meta.yml +++ b/modules/nf-core/clame/meta.yml @@ -6,56 +6,92 @@ keywords: - genomics tools: - "clame": - description: "CLAME is a binning software for metagenomic reads. It immplements a fm-index search algorithm for nucleotide sequence alignment. Then it uses strongly connected component strategy to bin sequences with similar DNA composition." + description: "CLAME is a binning software for metagenomic reads. It immplements + a fm-index search algorithm for nucleotide sequence alignment. Then it uses + strongly connected component strategy to bin sequences with similar DNA composition." homepage: "https://github.com/andvides/CLAME" documentation: "https://github.com/andvides/CLAME" tool_dev_url: "https://github.com/andvides/CLAME" doi: "10.1186/s12864-018-5191-y" licence: ["GPLv3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Nucleotide sequences in FASTA format - pattern: "*.{fasta,fa,fna,faa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Nucleotide sequences in FASTA format + pattern: "*.{fasta,fa,fna,faa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Output fasta file for all the bins reported, optional since it will be created when bins can be found - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta": + type: file + description: Output fasta file for all the bins reported, optional since it + will be created when bins can be found + pattern: "*.{fasta}" - bins: - type: file - description: All bins reported - pattern: "*.{binning}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.binning": + type: file + description: All bins reported + pattern: "*.{binning}" - fm: - type: file - description: FM-index output - pattern: "*.{fm9}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fm9": + type: file + description: FM-index output + pattern: "*.{fm9}" - index: - type: file - description: 1st column contains the original name for each read, 2nd column the index used by CLAME - pattern: "*.{index}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.index": + type: file + description: 1st column contains the original name for each read, 2nd column + the index used by CLAME + pattern: "*.{index}" - links: - type: file - description: Histogram links by number of reads - pattern: "*.{links}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.links": + type: file + description: Histogram links by number of reads + pattern: "*.{links}" - result: - type: file - description: Adjacency list for the overlap detected by each read - pattern: "*.{result}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.result": + type: file + description: Adjacency list for the overlap detected by each read + pattern: "*.{result}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" diff --git a/modules/nf-core/clippy/meta.yml b/modules/nf-core/clippy/meta.yml index cdb9f00b843..7ccd8266048 100644 --- a/modules/nf-core/clippy/meta.yml +++ b/modules/nf-core/clippy/meta.yml @@ -1,4 +1,3 @@ ---- name: clippy description: Runs the Clippy CLIP peak caller keywords: @@ -13,37 +12,59 @@ tools: tool_dev_url: "https://github.com/ulelab/clippy" doi: "10.7554/eLife.84034" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - pattern: "*.{bed,bed.gz}" - - gtf: - type: file - description: A GTF file of genes to call peaks on - pattern: "*.{gtf}" - - fai: - type: file - description: FAI file corresponding to the reference sequence - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + pattern: "*.{bed,bed.gz}" + - - gtf: + type: file + description: A GTF file of genes to call peaks on + pattern: "*.{gtf}" + - - fai: + type: file + description: FAI file corresponding to the reference sequence + pattern: "*.{fai}" output: - peaks: - type: file - description: BED file of peaks called by Clippy - pattern: "*_broadPeaks.bed.gz" + - meta: + type: file + description: BED file of peaks called by Clippy + pattern: "*_broadPeaks.bed.gz" + - "*_Peaks.bed": + type: file + description: BED file of peaks called by Clippy + pattern: "*_broadPeaks.bed.gz" - summits: - type: file - description: BED file of peak summits called by Clippy - pattern: "*[0-9].bed.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: file + description: BED file of peak summits called by Clippy + pattern: "*[0-9].bed.gz" + - "*_Summits.bed": + type: file + description: BED file of peak summits called by Clippy + pattern: "*[0-9].bed.gz" + - intergenic_gtf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_intergenic_regions.gtf": + type: file + description: GTF file of intergenic regions + pattern: "*_intergenic_regions.gtf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@CharlotteAnne" diff --git a/modules/nf-core/clonalframeml/meta.yml b/modules/nf-core/clonalframeml/meta.yml index 5abe2cc5216..2696edd872a 100644 --- a/modules/nf-core/clonalframeml/meta.yml +++ b/modules/nf-core/clonalframeml/meta.yml @@ -12,54 +12,87 @@ tools: tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML doi: "10.1371/journal.pcbi.1004041" licence: ["GPL v3"] + identifier: biotools:clonalframeml input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - msa: - type: file - description: A multiple seqeunce alignmnet in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - newick: - type: file - description: A Newick formated tree based on multiple sequence alignment - pattern: "*.{newick,treefile,dnd}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - newick: + type: file + description: A Newick formated tree based on multiple sequence alignment + pattern: "*.{newick,treefile,dnd}" + - msa: + type: file + description: A multiple seqeunce alignmnet in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - emsim: - type: file - description: Bootstrapped values for the three parameters R/theta, nu and delta - pattern: "*.emsim.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.emsim.txt": + type: file + description: Bootstrapped values for the three parameters R/theta, nu and delta + pattern: "*.emsim.txt" - em: - type: file - description: Point estimates for R/theta, nu, delta and the branch lengths - pattern: "*.em.txt" - - fasta: - type: file - description: Sequence reconstructed by maximum likelihood - pattern: "*.ML_sequence.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.em.txt": + type: file + description: Point estimates for R/theta, nu, delta and the branch lengths + pattern: "*.em.txt" + - status: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.importation_status.txt": + type: file + description: List of reconstructed recombination events + pattern: "*.importation_status.txt" - newick: - type: file - description: Tree with all nodes labelled - pattern: "*.labelled_tree.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.labelled_tree.newick": + type: file + description: Tree with all nodes labelled + pattern: "*.labelled_tree.newick" + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ML_sequence.fasta": + type: file + description: Sequence reconstructed by maximum likelihood + pattern: "*.ML_sequence.fasta" - pos_ref: - type: file - description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta - pattern: "*.position_cross_reference.txt" - - status: - type: file - description: List of reconstructed recombination events - pattern: "*.importation_status.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.position_cross_reference.txt": + type: file + description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta + pattern: "*.position_cross_reference.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/clustalo/align/meta.yml b/modules/nf-core/clustalo/align/meta.yml index 469b3a37691..c97ebf722e9 100644 --- a/modules/nf-core/clustalo/align/meta.yml +++ b/modules/nf-core/clustalo/align/meta.yml @@ -6,52 +6,59 @@ keywords: - genomics tools: - "clustalo": - description: "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins" + description: "Latest version of Clustal: a multiple sequence alignment program + for DNA or proteins" homepage: "http://www.clustal.org/omega/" documentation: "http://www.clustal.org/omega/" tool_dev_url: "http://www.clustal.org/omega/" doi: "10.1038/msb.2011.75" licence: ["GPL v2"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in gzipped fasta format - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in gzipped fasta format + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@joseespinosa" diff --git a/modules/nf-core/clustalo/guidetree/meta.yml b/modules/nf-core/clustalo/guidetree/meta.yml index b8e02352a2f..e006bad7866 100644 --- a/modules/nf-core/clustalo/guidetree/meta.yml +++ b/modules/nf-core/clustalo/guidetree/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "clustalo_guidetree" description: Renders a guidetree in clustalo @@ -8,36 +7,40 @@ keywords: - newick tools: - "clustalo": - description: "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins" + description: "Latest version of Clustal: a multiple sequence alignment program + for DNA or proteins" homepage: "http://www.clustal.org/omega/" documentation: "http://www.clustal.org/omega/" tool_dev_url: "http://www.clustal.org/omega/" doi: "10.1038/msb.2011.75" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - tree: - type: file - description: Guide tree file in Newick format - pattern: "*.{dnd}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.dnd": + type: file + description: Guide tree file in Newick format + pattern: "*.{dnd}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/cmseq/polymut/meta.yml b/modules/nf-core/cmseq/polymut/meta.yml index 182a75e0b26..8c0f52a9a66 100644 --- a/modules/nf-core/cmseq/polymut/meta.yml +++ b/modules/nf-core/cmseq/polymut/meta.yml @@ -18,42 +18,46 @@ tools: documentation: https://github.com/SegataLab/cmseq tool_dev_url: https://github.com/SegataLab/cmseq licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - gff: - type: file - description: GFF file used to extract protein-coding genes - pattern: "*.gff" - - fasta: - type: file - description: Optional fasta file to run on a subset of references in the BAM file. - pattern: .{fa,fasta,fas,fna} + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - gff: + type: file + description: GFF file used to extract protein-coding genes + pattern: "*.gff" + - fasta: + type: file + description: Optional fasta file to run on a subset of references in the BAM + file. + pattern: .{fa,fasta,fas,fna} output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - polymut: - type: file - description: Polymut report in `.txt` format. - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Polymut report in `.txt` format. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/cnvkit/access/meta.yml b/modules/nf-core/cnvkit/access/meta.yml index 259ae3471c1..4627fe0abd0 100644 --- a/modules/nf-core/cnvkit/access/meta.yml +++ b/modules/nf-core/cnvkit/access/meta.yml @@ -1,5 +1,6 @@ name: cnvkit_access -description: Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file. +description: Calculate the sequence-accessible coordinates in chromosomes from the + given reference genome, output as a BED file. keywords: - cvnkit - access @@ -15,38 +16,42 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome FASTA. - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - exclude_bed: - type: file - description: Additional regions to exclude, in BED format. Can be used multiple times. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome FASTA. + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exclude_bed: + type: file + description: Additional regions to exclude, in BED format. Can be used multiple + times. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing accessible regions. - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing accessible regions. + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml index d879092d33a..13f12a10c0e 100644 --- a/modules/nf-core/cnvkit/antitarget/meta.yml +++ b/modules/nf-core/cnvkit/antitarget/meta.yml @@ -15,30 +15,33 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - targets: - type: file - description: File containing genomic regions - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - targets: + type: file + description: File containing genomic regions + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing off-target regions - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing off-target regions + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml index f14efe553c3..30f7a1a29b8 100644 --- a/modules/nf-core/cnvkit/batch/meta.yml +++ b/modules/nf-core/cnvkit/batch/meta.yml @@ -12,94 +12,127 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tumor: - type: file - description: | - Input tumour sample bam file (or cram) - - normal: - type: file - description: | - Input normal sample bam file (or cram) - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: | - Input reference genome fasta index (optional, but recommended for cram_input) - - meta4: - type: map - description: | - Groovy Map containing information about target file - e.g. [ id:'test' ] - - targets: - type: file - description: | - Input target bed file - - meta5: - type: map - description: | - Groovy Map containing information about reference file - e.g. [ id:'test' ] - - reference: - type: file - description: | - Input reference cnn-file (only for germline and tumor-only running) - - panel_of_normals: - type: file - description: | - Input panel of normals file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tumor: + type: file + description: | + Input tumour sample bam file (or cram) + - normal: + type: file + description: | + Input normal sample bam file (or cram) + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: | + Input reference genome fasta index (optional, but recommended for cram_input) + - - meta4: + type: map + description: | + Groovy Map containing information about target file + e.g. [ id:'test' ] + - targets: + type: file + description: | + Input target bed file + - - meta5: + type: map + description: | + Groovy Map containing information about reference file + e.g. [ id:'test' ] + - reference: + type: file + description: | + Input reference cnn-file (only for germline and tumor-only running) + - - panel_of_normals: + type: file + description: | + Input panel of normals file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing genomic regions - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing genomic regions + pattern: "*.{bed}" - cnn: - type: file - description: File containing coverage information - pattern: "*.{cnn}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cnn": + type: file + description: File containing coverage information + pattern: "*.{cnn}" - cnr: - type: file - description: File containing copy number ratio information - pattern: "*.{cnr}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cnr": + type: file + description: File containing copy number ratio information + pattern: "*.{cnr}" - cns: - type: file - description: File containing copy number segment information - pattern: "*.{cns}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cns": + type: file + description: File containing copy number segment information + pattern: "*.{cns}" - pdf: - type: file - description: File with plot of copy numbers or segments on chromosomes - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: File with plot of copy numbers or segments on chromosomes + pattern: "*.{pdf}" - png: - type: file - description: File with plot of bin-level log2 coverages and segmentation calls - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: File with plot of bin-level log2 coverages and segmentation calls + pattern: "*.{png}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@drpatelh" diff --git a/modules/nf-core/cnvkit/call/meta.yml b/modules/nf-core/cnvkit/call/meta.yml index 64dc336869f..b3b4a4a78af 100644 --- a/modules/nf-core/cnvkit/call/meta.yml +++ b/modules/nf-core/cnvkit/call/meta.yml @@ -1,5 +1,6 @@ name: cnvkit_call -description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number +description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute + integer copy number keywords: - cnvkit - bam @@ -12,34 +13,37 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cns: - type: file - description: CNVKit CNS file. - pattern: "*.cns" - - vcf: - type: file - description: Germline VCF file for BAF. - pattern: "*.vcf{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cns: + type: file + description: CNVKit CNS file. + pattern: "*.cns" + - vcf: + type: file + description: Germline VCF file for BAF. + pattern: "*.vcf{,.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - cns: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cns": + type: file + description: CNS file. + pattern: "*.cns" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: File containing copy number information in new format. - pattern: "*.{bed,vcf,cdt,jtv,seg,interval_count}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/export/meta.yml b/modules/nf-core/cnvkit/export/meta.yml index 836baa1b58e..a573e03bac5 100644 --- a/modules/nf-core/cnvkit/export/meta.yml +++ b/modules/nf-core/cnvkit/export/meta.yml @@ -1,5 +1,6 @@ name: cnvkit_export -description: Convert copy number ratio tables (.cnr files) or segments (.cns) to another format. +description: Convert copy number ratio tables (.cnr files) or segments (.cns) to another + format. keywords: - cnvkit - copy number @@ -11,30 +12,32 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cns: - type: file - description: CNVKit CNS file. - pattern: "*.cns" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cns: + type: file + description: CNVKit CNS file. + pattern: "*.cns" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${suffix}: + type: file + description: Output file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - cns: - type: file - description: File containing copy number segment information - pattern: "*.{cns}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml index 4bef28c7d5e..6b110accc23 100644 --- a/modules/nf-core/cnvkit/genemetrics/meta.yml +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -12,34 +12,47 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cnr: - type: file - description: CNR file - pattern: "*.cnr" - - cns: - type: file - description: CNS file [Optional] - pattern: "*.cns" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cnr: + type: file + description: CNR file + pattern: "*.cnr" + - cns: + type: file + description: CNS file [Optional] + pattern: "*.cns" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - txt: - type: file - description: TXT file - pattern: "*.txt" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file + pattern: "*.tsv" + - cnn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cnn": + type: file + description: CNN file + pattern: "*.cnn" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@marrip" diff --git a/modules/nf-core/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml index 8747893b6fb..965a7b57953 100644 --- a/modules/nf-core/cnvkit/reference/meta.yml +++ b/modules/nf-core/cnvkit/reference/meta.yml @@ -15,33 +15,32 @@ tools: tool_dev_url: https://github.com/etal/cnvkit doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - fasta: - type: file - description: File containing reference genome - pattern: "*.{fasta}" - - targets: - type: file - description: File containing genomic regions - pattern: "*.{bed}" - - antitargets: - type: file - description: File containing off-target genomic regions - pattern: "*.{bed}" + - - fasta: + type: file + description: File containing reference genome + pattern: "*.{fasta}" + - - targets: + type: file + description: File containing genomic regions + pattern: "*.{bed}" + - - antitargets: + type: file + description: File containing off-target genomic regions + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - cnn: - type: file - description: File containing a copy-number reference (required for CNV calling in tumor_only mode) - pattern: "*.{cnn}" + - "*.cnn": + type: file + description: File containing a copy-number reference (required for CNV calling + in tumor_only mode) + pattern: "*.{cnn}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/target/meta.yml b/modules/nf-core/cnvkit/target/meta.yml index 1f0e31dc8ff..94e1f57b1ab 100644 --- a/modules/nf-core/cnvkit/target/meta.yml +++ b/modules/nf-core/cnvkit/target/meta.yml @@ -15,39 +15,42 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - baits: - type: file - description: BED or interval file listing the targeted regions. - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - annotation: - type: file - description: Use gene models from this file to assign names to the target regions. - pattern: "*.{txt,bed,gff3,pil}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - baits: + type: file + description: BED or interval file listing the targeted regions. + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - annotation: + type: file + description: Use gene models from this file to assign names to the target regions. + pattern: "*.{txt,bed,gff3,pil}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing target regions - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing target regions + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml index 627b76b993d..7ad6b4068b8 100644 --- a/modules/nf-core/cnvnator/cnvnator/meta.yml +++ b/modules/nf-core/cnvnator/cnvnator/meta.yml @@ -1,5 +1,6 @@ name: "cnvnator_cnvnator" -description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads. +description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage + by mapped reads. keywords: - cnvnator - cnv @@ -11,65 +12,74 @@ tools: documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" licence: ["MIT"] + identifier: biotools:cnvnator input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.bam" - - bai: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.bam" - - root: - type: file - description: ROOT file - pattern: "*.root" - - fasta: - type: file - description: Path to a directory containing fasta files or a fasta file - pattern: "*.fa" - - fai: - type: file - description: Path to a fasta file index - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.bam" + - bai: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - root: + type: file + description: ROOT file + pattern: "*.root" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Path to a directory containing fasta files or a fasta file + pattern: "*.fa" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fai: + type: file + description: Path to a fasta file index + pattern: "*.fai" output: - - output_meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - root: - type: file - description: A ROOT file - pattern: "*.root" + - output_meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.root: + type: file + description: A ROOT file + pattern: "*.root" - tab: - type: file - description: A tab file containing cnvnator calls - pattern: "*.tab" + - output_meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.tab: + type: file + description: A tab file containing cnvnator calls + pattern: "*.tab" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvnator/convert2vcf/meta.yml b/modules/nf-core/cnvnator/convert2vcf/meta.yml index b7d269e0480..3d686c2f17f 100644 --- a/modules/nf-core/cnvnator/convert2vcf/meta.yml +++ b/modules/nf-core/cnvnator/convert2vcf/meta.yml @@ -1,5 +1,6 @@ name: "cnvnator_convert2vcf" -description: convert2vcf.pl is command line tool to convert CNVnator calls to vcf format. +description: convert2vcf.pl is command line tool to convert CNVnator calls to vcf + format. keywords: - cnvnator - cnv @@ -11,30 +12,33 @@ tools: documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" licence: ["MIT"] + identifier: biotools:cnvnator input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - calls: - type: file - description: A tab file containing CNVnator calls - pattern: "*.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - calls: + type: file + description: A tab file containing CNVnator calls + pattern: "*.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: CNVnator calls in vcf format - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf": + type: file + description: CNVnator calls in vcf format + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvpytor/callcnvs/meta.yml b/modules/nf-core/cnvpytor/callcnvs/meta.yml index 25e22941c7e..cdc96d8c0dc 100644 --- a/modules/nf-core/cnvpytor/callcnvs/meta.yml +++ b/modules/nf-core/cnvpytor/callcnvs/meta.yml @@ -12,33 +12,37 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - pytor: - type: file - description: pytor file containing partitions of read depth histograms using mean-shift method - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - pytor: + type: file + description: pytor file containing partitions of read depth histograms using + mean-shift method + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - pytor: - type: file - description: pytor files containing cnv calls - pattern: "*.{pytor}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${pytor.baseName}.pytor: + type: file + description: pytor files containing cnv calls + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" maintainers: diff --git a/modules/nf-core/cnvpytor/histogram/meta.yml b/modules/nf-core/cnvpytor/histogram/meta.yml index e8fcedd47f6..d53733b2132 100644 --- a/modules/nf-core/cnvpytor/histogram/meta.yml +++ b/modules/nf-core/cnvpytor/histogram/meta.yml @@ -12,33 +12,37 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pytor: - type: file - description: pytor file containing read depth data - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pytor: + type: file + description: pytor file containing read depth data + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - pytor: - type: file - description: pytor file containing read depth histograms binned based on given bin size(s) - pattern: "*.{pytor}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${pytor.baseName}.pytor: + type: file + description: pytor file containing read depth histograms binned based on given + bin size(s) + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/importreaddepth/meta.yml b/modules/nf-core/cnvpytor/importreaddepth/meta.yml index 660a7bdd77a..0e1acff3285 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/meta.yml +++ b/modules/nf-core/cnvpytor/importreaddepth/meta.yml @@ -1,5 +1,6 @@ name: cnvpytor_importreaddepth -description: command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file. +description: command line tool for CNV/CNA analysis. This step imports the read depth + data into a root pytor file. keywords: - read depth - cnv @@ -13,42 +14,47 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input_file: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: bam file index - pattern: "*.{bai,crai}" - - fasta: - type: file - description: specifies reference genome file (only for cram file without reference genome) - pattern: "*.{fasta,fasta.gz,fa,fa.gz}" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input_file: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: bam file index + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: specifies reference genome file (only for cram file without reference + genome) + pattern: "*.{fasta,fasta.gz,fa,fa.gz}" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - pytor: - type: file - description: read depth root file in which read depth data binned to 100 base pair bins will be stored. - pattern: "*.{pytor}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.pytor": + type: file + description: read depth root file in which read depth data binned to 100 base + pair bins will be stored. + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/partition/meta.yml b/modules/nf-core/cnvpytor/partition/meta.yml index c9a04d30516..014e0d40702 100644 --- a/modules/nf-core/cnvpytor/partition/meta.yml +++ b/modules/nf-core/cnvpytor/partition/meta.yml @@ -12,33 +12,36 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pytor: - type: file - description: pytor file containing read depth data - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pytor: + type: file + description: pytor file containing read depth data + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - partitions: - type: file - description: pytor file containing partitions of read depth histograms using mean-shift method - pattern: "*.{pytor}" + - pytor: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${pytor.baseName}.pytor: + type: file + description: pytor file + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/view/meta.yml b/modules/nf-core/cnvpytor/view/meta.yml index 7c2088b4c35..9cab351a26f 100644 --- a/modules/nf-core/cnvpytor/view/meta.yml +++ b/modules/nf-core/cnvpytor/view/meta.yml @@ -12,44 +12,61 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pytor_files: - type: file - description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files. - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" - - output_format: - type: string - description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pytor_files: + type: file + description: pytor file containing cnv calls. To merge calls from multiple samples + use a list of files. + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - output_format: + type: string + description: output format of the cnv calls. Valid entries are "tsv", "vcf", + and "xls" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - tsv: - type: file - description: tsv file containing cnv calls - pattern: "*.{tsv}" - vcf: - type: file - description: vcf file containing cnv calls - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: vcf file containing cnv calls + pattern: "*.{vcf}" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.tsv": + type: file + description: tsv file containing cnv calls + pattern: "*.{tsv}" - xls: - type: file - description: xls file containing cnv calls - pattern: "*.{xls}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xls": + type: file + description: xls file containing cnv calls + pattern: "*.{xls}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cobrameta/meta.yml b/modules/nf-core/cobrameta/meta.yml index 5885f079bc4..1a5820d6c64 100644 --- a/modules/nf-core/cobrameta/meta.yml +++ b/modules/nf-core/cobrameta/meta.yml @@ -1,5 +1,6 @@ name: cobrameta -description: A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly. +description: A tool to raise the quality of viral genomes assembled from short-read + metagenomes via resolving and joining of contigs fragmented during de novo assembly. keywords: - cobra - contig @@ -10,111 +11,168 @@ keywords: - phage tools: - cobra-meta: - description: COBRA is a tool to get higher quality viral genomes assembled from metagenomes. + description: COBRA is a tool to get higher quality viral genomes assembled from + metagenomes. homepage: https://github.com/linxingchen/cobra documentation: https://github.com/linxingchen/cobra tool_dev_url: https://github.com/linxingchen/cobra doi: 10.1038/s41564-023-01598-2 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: | - Assembly file (contigs/scaffolds) in FASTA format - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" - - coverage: - type: file - description: | - TSV file with 2 columns containing 1) the contig/scaffold id and - 2) the coverage depth of the sequence specified in column 1 - pattern: "*.{tsv,txt}" - - query: - type: file - description: | - File containing the query contigs that the user wants COBRA to extend. This - can be provided in one-column TXT or FASTA format. (The IDs must match the IDs - in the `--fasta` file exactly) - pattern: "*.{txt,fasta}" - - bam: - type: file - description: | - Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly - to the resulting assembly FASTA - pattern: "*.{bam,cram,sam}" - - assembler: - type: string - description: The name of the tool used to assemble contigs - pattern: "{metaspades,megahit,idba}" - - mink: - type: integer - description: The minimum kmer size used to assemble contigs - pattern: "[0-9]+" - - maxk: - type: integer - description: The maximum kmer size used to assemble contigs - pattern: "[0-9]+" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: | + Assembly file (contigs/scaffolds) in FASTA format + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage: + type: file + description: | + TSV file with 2 columns containing 1) the contig/scaffold id and + 2) the coverage depth of the sequence specified in column 1 + pattern: "*.{tsv,txt}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: | + File containing the query contigs that the user wants COBRA to extend. This + can be provided in one-column TXT or FASTA format. (The IDs must match the IDs + in the `--fasta` file exactly) + pattern: "*.{txt,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly + to the resulting assembly FASTA + pattern: "*.{bam,cram,sam}" + - - assembler: + type: string + description: The name of the tool used to assemble contigs + pattern: "{metaspades,megahit,idba}" + - - mink: + type: integer + description: The minimum kmer size used to assemble contigs + pattern: "[0-9]+" + - - maxk: + type: integer + description: The maximum kmer size used to assemble contigs + pattern: "[0-9]+" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - extended_assemblies: - type: file - description: | - Gzipped FASTA file containing query contigs that are already circular - pattern: "${prefix}/COBRA_category_i_self_circular.fasta.gz" + - self_circular: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_i_self_circular.fasta.gz: + type: file + description: fasta file + pattern: "*/COBRA_category_i_self_circular.fasta.gz" - extended_circular: - type: file - description: | - Gzipped FASTA file containing query contigs that were joined and extended - into a circular genome - pattern: "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs that were joined and extended + into a circular genome + pattern: "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz" - extended_partial: - type: file - description: | - Gzipped FASTA file containing query contigs were joined and extended, but - not into circular sequences - pattern: "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs were joined and extended, but + not into circular sequences + pattern: "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz" - extended_failed: - type: file - description: | - Gzipped FASTA file containing query contigs that could not be extended due - to COBRA rules - pattern: "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs that could not be extended due + to COBRA rules + pattern: "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz" - orphan_end: - type: file - description: | - Gzipped FASTA file containing query contigs that do not shared the - "expected overlap length" with other contigs - pattern: "${prefix}/COBRA_category_iii_orphan_end.fasta.gz" - - all_assemblies: - type: file - description: | - Gzipped FASTA file containing all FASTA outputs combined into one file - pattern: "${prefix}/COBRA_all_assemblies.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_iii_orphan_end.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs that do not shared the + "expected overlap length" with other contigs + pattern: "${prefix}/COBRA_category_iii_orphan_end.fasta.gz" + - all_cobra_assemblies: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_all_assemblies.fasta.gz: + type: file + description: Gzipped FASTA file containing all the assemblies generated by COBRA + pattern: "*/COBRA_all_assemblies.fasta.gz" - joining_summary: - type: file - description: | - TSV file containing information regarding COBRA's extension results - pattern: "${prefix}/COBRA_joining_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_joining_summary.txt: + type: file + description: | + TSV file containing information regarding COBRA's extension results + pattern: "${prefix}/COBRA_joining_summary.txt" - log: - type: file - description: | - Log file containing the contents of each processing - pattern: "${prefix}/log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/log: + type: file + description: | + Log file containing the contents of each processing + pattern: "${prefix}/log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/cobs/classicconstruct/meta.yml b/modules/nf-core/cobs/classicconstruct/meta.yml index 07488abd277..3f661b02668 100644 --- a/modules/nf-core/cobs/classicconstruct/meta.yml +++ b/modules/nf-core/cobs/classicconstruct/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cobs_classicconstruct" description: Builds a classic bloom filter COBS index @@ -15,45 +14,43 @@ tools: tool_dev_url: "https://github.com/iqbal-lab-org/cobs" doi: "10.1007/978-3-030-32686-9_21" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: | - The file or directory to be indexed. - COBS can read: - 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz), - 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz), - 3. "Multi-FASTA" and "Multi-FASTQ" files (*.mfasta, *.mfastq), - 4. McCortex files (*.ctx), - 5. or text files (*.txt). - You can either recursively scan a directory for all files matching any of these files, - or pass a *.list file which lists all paths COBS should index. - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: | + The file or directory to be indexed. + COBS can read: + 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz), + 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz), + 3. "Multi-FASTA" and "Multi-FASTQ" files (*.mfasta, *.mfastq), + 4. McCortex files (*.ctx), + 5. or text files (*.txt). + You can either recursively scan a directory for all files matching any of these files, + or pass a *.list file which lists all paths COBS should index. + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - index: - type: file - description: The COBS classic index - pattern: "*.index.cobs_classic" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.index.cobs_classic": + type: file + description: The COBS classic index + pattern: "*.index.cobs_classic" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/cobs/compactconstruct/meta.yml b/modules/nf-core/cobs/compactconstruct/meta.yml index a9fc6c27c84..1f1dfa2e6ed 100644 --- a/modules/nf-core/cobs/compactconstruct/meta.yml +++ b/modules/nf-core/cobs/compactconstruct/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cobs_compactconstruct" description: Builds a compact bloom filter COBS index @@ -14,45 +13,43 @@ tools: documentation: "https://github.com/iqbal-lab-org/cobs" doi: "10.1007/978-3-030-32686-9_21" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - input: - type: file - description: | - The file or directory to be indexed. - COBS can read: - 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`), - 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`), - 3. "Multi-FASTA" and "Multi-FASTQ" files (`*.mfasta`, `*.mfastq`), - 4. McCortex files (`*.ctx`), - 5. or text files (`*.txt`). - You can either recursively scan a directory for all files matching any of these files, - or pass a `*.list` file which lists all paths COBS should index. - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - input: + type: file + description: | + The file or directory to be indexed. + COBS can read: + 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`), + 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`), + 3. "Multi-FASTA" and "Multi-FASTQ" files (`*.mfasta`, `*.mfastq`), + 4. McCortex files (`*.ctx`), + 5. or text files (`*.txt`). + You can either recursively scan a directory for all files matching any of these files, + or pass a `*.list` file which lists all paths COBS should index. + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - index: - type: file - description: The COBS compact index - pattern: "*.index.cobs_compact" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.index.cobs_compact": + type: file + description: The COBS compact index + pattern: "*.index.cobs_compact" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/concoct/concoct/meta.yml b/modules/nf-core/concoct/concoct/meta.yml index d92455cf850..d47d1672c3b 100644 --- a/modules/nf-core/concoct/concoct/meta.yml +++ b/modules/nf-core/concoct/concoct/meta.yml @@ -1,5 +1,6 @@ name: "concoct_concoct" -description: Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples +description: Unsupervised binning of metagenomic contigs by using nucleotide composition + - kmer frequencies - and coverage data for multiple samples keywords: - contigs - fragment @@ -18,54 +19,88 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_file: - type: file - description: Subcontig coverage TSV table (typically generated with concoct_coverage_table.py) - pattern: "*.tsv" - - fasta: - type: file - description: FASTA file containing subcontigs (typically generated with cutup_fasta.py) - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_file: + type: file + description: Subcontig coverage TSV table (typically generated with concoct_coverage_table.py) + pattern: "*.tsv" + - fasta: + type: file + description: FASTA file containing subcontigs (typically generated with cutup_fasta.py) + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - args_txt: - type: file - description: File containing execution parameters - pattern: "*_args.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_args.txt": + type: file + description: File containing execution parameters + pattern: "*_args.txt" - clustering_csv: - type: file - description: CSV containing information which subcontig is assigned to which cluster - pattern: "*_clustering_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_clustering_gt1000.csv": + type: file + description: CSV containing information which subcontig is assigned to which + cluster + pattern: "*_clustering_gt1000.csv" - log_txt: - type: file - description: Log file of tool execution - pattern: "*_log.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_log.txt": + type: file + description: Log file of tool execution + pattern: "*_log.txt" - original_data_csv: - type: file - description: Original CONCOCT GT1000 output - pattern: "*_original_data_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_original_data_gt1000.csv": + type: file + description: Original CONCOCT GT1000 output + pattern: "*_original_data_gt1000.csv" - pca_components_csv: - type: file - description: Untransformed PCA component values - pattern: "*_PCA_components_data_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PCA_components_data_gt1000.csv": + type: file + description: Untransformed PCA component values + pattern: "*_PCA_components_data_gt1000.csv" - pca_transformed_csv: - type: file - description: Transformed PCA compontent values - pattern: "*_PCA_transformed_data_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PCA_transformed_data_gt1000.csv": + type: file + description: Transformed PCA compontent values + pattern: "*_PCA_transformed_data_gt1000.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/concoctcoveragetable/meta.yml b/modules/nf-core/concoct/concoctcoveragetable/meta.yml index 26b9793c9c8..ce878eb6f04 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/meta.yml +++ b/modules/nf-core/concoct/concoctcoveragetable/meta.yml @@ -17,38 +17,43 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file describing where each contig was cut up (typically output from CONCOCT's cut_up_fasta.py) - pattern: "*.bed" - - bamfiles: - type: file - description: A single or list of BAM files of reads mapped back to original contigs (prior cutting up) - pattern: "*.bam" - - baifiles: - type: file - description: A single or list of BAM index files (.bai) corresponding to BAM - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file describing where each contig was cut up (typically output + from CONCOCT's cut_up_fasta.py) + pattern: "*.bed" + - bamfiles: + type: file + description: A single or list of BAM files of reads mapped back to original + contigs (prior cutting up) + pattern: "*.bam" + - baifiles: + type: file + description: A single or list of BAM index files (.bai) corresponding to BAM + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Contig coverage table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Contig coverage table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/cutupfasta/meta.yml b/modules/nf-core/concoct/cutupfasta/meta.yml index 44a28723300..02146640847 100644 --- a/modules/nf-core/concoct/cutupfasta/meta.yml +++ b/modules/nf-core/concoct/cutupfasta/meta.yml @@ -16,37 +16,49 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: (Uncompressed) FASTA file containing contigs - pattern: "*.{fasta,fna,fa,fas}" - - bed: - type: boolean - description: Specify whether to generate a BED file describing where each contig was cut up + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: (Uncompressed) FASTA file containing contigs + pattern: "*.{fasta,fna,fa,fas}" + - - bed: + type: boolean + description: Specify whether to generate a BED file describing where each contig + was cut up output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Cut up fasta file in non-overlapping or overlapping parts of equal length. - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Cut up fasta file in non-overlapping or overlapping parts of equal + length. + pattern: "*.fasta" - bed: - type: file - description: Optional BED File containing locations on original contigs where they were cut up. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Optional BED File containing locations on original contigs where + they were cut up. + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/extractfastabins/meta.yml b/modules/nf-core/concoct/extractfastabins/meta.yml index a9ac00a304c..4e6effda3a8 100644 --- a/modules/nf-core/concoct/extractfastabins/meta.yml +++ b/modules/nf-core/concoct/extractfastabins/meta.yml @@ -18,34 +18,38 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - original_fasta: - type: file - description: Original input FASTA file to CONOCT cut_up_fasta - pattern: "*.{fasta,fna,fa,fas}" - - csv: - type: boolean - description: Output table of merge_cutup_clustering with new cluster assignments - pattern: ".csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - original_fasta: + type: file + description: Original input FASTA file to CONOCT cut_up_fasta + pattern: "*.{fasta,fna,fa,fas}" + - csv: + type: boolean + description: Output table of merge_cutup_clustering with new cluster assignments + pattern: ".csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: FASTA files containing CONCOCT predicted bin clusters, named numerically by CONCOCT cluster ID in a directory called `fasta_bins` - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.fa.gz: + type: file + description: FASTA files containing CONCOCT predicted bin clusters, named numerically + by CONCOCT cluster ID in a directory called `fasta_bins` + pattern: "*.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/mergecutupclustering/meta.yml b/modules/nf-core/concoct/mergecutupclustering/meta.yml index e34a423c22b..69a839928d4 100644 --- a/modules/nf-core/concoct/mergecutupclustering/meta.yml +++ b/modules/nf-core/concoct/mergecutupclustering/meta.yml @@ -17,30 +17,33 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - clustering_csv: - type: file - description: Input cutup clustering result. Typically *_gt1000.csv from concoct - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - clustering_csv: + type: file + description: Input cutup clustering result. Typically *_gt1000.csv from concoct + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Cluster assignments per contig part with concensus cluster - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Cluster assignments per contig part with concensus cluster + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/conifer/meta.yml b/modules/nf-core/conifer/meta.yml index d70ca4630fa..795d8f85951 100644 --- a/modules/nf-core/conifer/meta.yml +++ b/modules/nf-core/conifer/meta.yml @@ -12,34 +12,37 @@ tools: documentation: "https://github.com/Ivarz/Conifer" tool_dev_url: "https://github.com/Ivarz/Conifer" licence: ["BSD / BSD-2-Clause"] + identifier: biotools:conifer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kraken_result: - type: file - description: | - Raw Kraken2 standard output file - - kraken_taxon_db: - type: file - description: Kraken2 taxo.k2d database file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_result: + type: file + description: | + Raw Kraken2 standard output file + - - kraken_taxon_db: + type: file + description: Kraken2 taxo.k2d database file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - score: - type: file - description: | - Conifer report file containing confidence scores of Kraken2 classified reads. - pattern: "*.score" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.score": + type: file + description: | + Conifer report file containing confidence scores of Kraken2 classified reads. + pattern: "*.score" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@icaromsc" - "@rpetit3" diff --git a/modules/nf-core/controlfreec/assesssignificance/meta.yml b/modules/nf-core/controlfreec/assesssignificance/meta.yml index b8cda6dd505..8a6ab47edb9 100644 --- a/modules/nf-core/controlfreec/assesssignificance/meta.yml +++ b/modules/nf-core/controlfreec/assesssignificance/meta.yml @@ -1,5 +1,6 @@ name: controlfreec_assesssignificance -description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC +description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV + output of FREEC keywords: - cna - cnv @@ -8,41 +9,49 @@ keywords: - tumor-only tools: - controlfreec/assesssignificance: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cnvs: - type: file - description: _CNVs file generated by FREEC - pattern: "*._CNVs" - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cnvs: + type: file + description: _CNVs file generated by FREEC + pattern: "*._CNVs" + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - p_value_txt: - type: file - description: CNV file containing p_values for each call - pattern: "*.p.value.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.p.value.txt": + type: file + description: CNV file containing p_values for each call + pattern: "*.p.value.txt" + - ue_txt: + type: file + description: CNV file containing p_values for each call + pattern: "*.p.value.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/freec/meta.yml b/modules/nf-core/controlfreec/freec/meta.yml index 1442bbe44a7..6b35a38be72 100644 --- a/modules/nf-core/controlfreec/freec/meta.yml +++ b/modules/nf-core/controlfreec/freec/meta.yml @@ -1,5 +1,6 @@ name: controlfreec_freec -description: Copy number and genotype annotation from whole genome and whole exome sequencing data +description: Copy number and genotype annotation from whole genome and whole exome + sequencing data keywords: - cna - cnv @@ -8,172 +9,176 @@ keywords: - tumor-only tools: - controlfreec/freec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: - - args: - type: map - description: | - Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. - Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`: - For default values, please check the documentation above. - - ``` - { - [ - "general" :[ - "bedgraphoutput": (optional), - "breakpointthreshold": (optional), - "breakpointtype": (optional), - "coefficientofvariation": (optional), - "contamination": (optional), - "contaminationadjustment": (optional), - "degree": (optional), - "forcegccontentnormalization": (optional), - "gccontentprofile": (optional), - "intercept": (optional), - "mincnalength": (optional), - "minmappabilityperwindow": (optional), - "minexpectedgc": (optional), - "maxexpectedgc": (optional), - "minimalsubclonepresence": (optional), - "noisydata": (optional), - "ploidy": (optional), - "printNA": (optional), - "readcountthreshold": (optional), - "sex": (optional), - "step": (optional), - "telocentromeric": (optional), - "uniquematch": (optional), - "window": (optional) - ], - "control":[ - "inputformat": (required), - "mateorientation": (optional), - ], - "sample":[ - "inputformat": (required), - "mateorientation": (optional), - ], - "BAF":[ - "minimalcoverageperposition": (optional), - "minimalqualityperposition": (optional), - "shiftinquality": (optional) - ] - ] - } - ``` - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mateFile_normal: - type: file - description: File with mapped reads - pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - - mateFile_tumor: - type: file - description: File with mapped reads - pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - - cpn_normal: - type: file - description: Raw copy number profiles (optional) - pattern: "*.cpn" - - cpn_tumor: - type: file - description: Raw copy number profiles (optional) - pattern: "*.cpn" - - minipileup_normal: - type: file - description: miniPileup file from previous run (optional) - pattern: "*.pileup" - - minipileup_tumor: - type: file - description: miniPileup file from previous run (optional) - pattern: "*.pileup" - - fasta: - type: file - description: Reference file (optional; required if args 'makePileup' is set) - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: Fasta index - pattern: "*.fai" - - snp_position: - type: file - description: Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional) - pattern: "*.{bed,vcf}" - - known_snps: - type: file - description: File with known SNPs - pattern: "*.{vcf,vcf.gz}" - - known_snps_tbi: - type: file - description: Index of known_snps - pattern: "*.tbi" - - chr_directory: - type: file - description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided) - pattern: "*/" - - mappability: - type: file - description: Contains information of mappable positions (optional) - pattern: "*.gem" - - target_bed: - type: file - description: Sorted bed file containing capture regions (optional) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mpileup_normal: + type: file + description: miniPileup file + - mpileup_tumor: + type: file + description: miniPileup file + - cpn_normal: + type: file + description: Raw copy number profiles (optional) + pattern: "*.cpn" + - cpn_tumor: + type: file + description: Raw copy number profiles (optional) + pattern: "*.cpn" + - minipileup_normal: + type: file + description: miniPileup file from previous run (optional) + pattern: "*.pileup" + - minipileup_tumor: + type: file + description: miniPileup file from previous run (optional) + pattern: "*.pileup" + - - fasta: + type: file + description: Reference file (optional; required if args 'makePileup' is set) + pattern: "*.{fasta,fna,fa}" + - - fai: + type: file + description: Fasta index + pattern: "*.fai" + - - snp_position: + type: file + description: Path to a BED or VCF file with SNP positions to create a mini pileup + file from the initial BAM file provided in mateFile (optional) + pattern: "*.{bed,vcf}" + - - known_snps: + type: file + description: File with known SNPs + pattern: "*.{vcf,vcf.gz}" + - - known_snps_tbi: + type: file + description: Index of known_snps + pattern: "*.tbi" + - - chr_directory: + type: file + description: Path to directory with chromosome fasta files (optional, required + if gccontentprofile is not provided) + pattern: "*/" + - - mappability: + type: file + description: Contains information of mappable positions (optional) + pattern: "*.gem" + - - target_bed: + type: file + description: Sorted bed file containing capture regions (optional) + pattern: "*.bed" + - - gccontent_profile: + type: file + description: File with GC-content profile output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: Bedgraph format for the UCSC genome browser - pattern: ".bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.BedGraph": + type: file + description: Bedgraph format for the UCSC genome browser + pattern: ".bedgraph" - control_cpn: - type: file - description: files with raw copy number profiles - pattern: "*_control.cpn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_control.cpn": + type: file + description: files with raw copy number profiles + pattern: "*_control.cpn" - sample_cpn: - type: file - description: files with raw copy number profiles - pattern: "*_sample.cpn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_sample.cpn": + type: file + description: files with raw copy number profiles + pattern: "*_sample.cpn" - gcprofile_cpn: - type: file - description: file with GC-content profile. - pattern: "GC_profile.*.cpn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - GC_profile.*.cpn: + type: file + description: file with GC-content profile. + pattern: "GC_profile.*.cpn" - BAF: - type: file - description: file B-allele frequencies for each possibly heterozygous SNP position - pattern: "*_BAF.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BAF.txt": + type: file + description: file B-allele frequencies for each possibly heterozygous SNP position + pattern: "*_BAF.txt" - CNV: - type: file - description: file with coordinates of predicted copy number alterations. - pattern: "*_CNVs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_CNVs": + type: file + description: file with coordinates of predicted copy number alterations. + pattern: "*_CNVs" - info: - type: file - description: parsable file with information about FREEC run - pattern: "*_info.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_info.txt": + type: file + description: parsable file with information about FREEC run + pattern: "*_info.txt" - ratio: - type: file - description: file with ratios and predicted copy number alterations for each window - pattern: "*_ratio.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.txt": + type: file + description: file with ratios and predicted copy number alterations for each + window + pattern: "*_ratio.txt" - config: - type: file - description: Config file used to run Control-FREEC - pattern: "config.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - config.txt: + type: file + description: Config file used to run Control-FREEC + pattern: "config.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/freec2bed/meta.yml b/modules/nf-core/controlfreec/freec2bed/meta.yml index b10c8ab377a..e01f870f4dc 100644 --- a/modules/nf-core/controlfreec/freec2bed/meta.yml +++ b/modules/nf-core/controlfreec/freec2bed/meta.yml @@ -8,36 +8,40 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Bed file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/freec2circos/meta.yml b/modules/nf-core/controlfreec/freec2circos/meta.yml index 2c6b77d611b..5368c0429ea 100644 --- a/modules/nf-core/controlfreec/freec2circos/meta.yml +++ b/modules/nf-core/controlfreec/freec2circos/meta.yml @@ -8,36 +8,40 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - circos: - type: file - description: Txt file - pattern: "*.circos.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.circos.txt": + type: file + description: Txt file + pattern: "*.circos.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml index 6f91db38aa4..f9dff86eeb8 100644 --- a/modules/nf-core/controlfreec/makegraph/meta.yml +++ b/modules/nf-core/controlfreec/makegraph/meta.yml @@ -8,52 +8,68 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" - - baf: - type: file - description: .BAF file generated by FREEC - pattern: "*.BAF" - - ploidy: - type: integer - description: Ploidy value for which graph should be created + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" + - baf: + type: file + description: .BAF file generated by FREEC + pattern: "*.BAF" + - ploidy: + type: integer + description: Ploidy value for which graph should be created output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png_baf: - type: file - description: Image of BAF plot - pattern: "*_BAF.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BAF.png": + type: file + description: Image of BAF plot + pattern: "*_BAF.png" - png_ratio_log2: - type: file - description: Image of ratio log2 plot - pattern: "*_ratio.log2.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.log2.png": + type: file + description: Image of ratio log2 plot + pattern: "*_ratio.log2.png" - png_ratio: - type: file - description: Image of ratio plot - pattern: "*_ratio.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.png": + type: file + description: Image of ratio plot + pattern: "*_ratio.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/makegraph2/meta.yml b/modules/nf-core/controlfreec/makegraph2/meta.yml index 1325da4a8b9..6614b39ba90 100644 --- a/modules/nf-core/controlfreec/makegraph2/meta.yml +++ b/modules/nf-core/controlfreec/makegraph2/meta.yml @@ -8,51 +8,65 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" - - baf: - type: file - description: .BAF file generated by FREEC - pattern: "*.BAF" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" + - baf: + type: file + description: .BAF file generated by FREEC + pattern: "*.BAF" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png_baf: - type: file - description: Image of BAF plot - pattern: "*_BAF.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BAF.png": + type: file + description: Image of BAF plot + pattern: "*_BAF.png" - png_ratio_log2: - type: file - description: Image of ratio log2 plot - pattern: "*_ratio.log2.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.log2.png": + type: file + description: Image of ratio log2 plot + pattern: "*_ratio.log2.png" - png_ratio: - type: file - description: Image of ratio plot - pattern: "*_ratio.png" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.png": + type: file + description: Image of ratio plot + pattern: "*_ratio.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" diff --git a/modules/nf-core/cooler/balance/meta.yml b/modules/nf-core/cooler/balance/meta.yml index 9b890638721..ace840ec598 100644 --- a/modules/nf-core/cooler/balance/meta.yml +++ b/modules/nf-core/cooler/balance/meta.yml @@ -13,33 +13,36 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" - - resolution: - type: integer - description: Resolution + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" + - resolution: + type: integer + description: Resolution output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cool: - type: file - description: Output COOL file balancing weigths - pattern: "*.cool" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}: + type: file + description: Output COOL file balancing weigths + pattern: "*.cool" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" - "@muffato" diff --git a/modules/nf-core/cooler/cload/meta.yml b/modules/nf-core/cooler/cload/meta.yml index fa5474aeb61..1bb9f7485a0 100644 --- a/modules/nf-core/cooler/cload/meta.yml +++ b/modules/nf-core/cooler/cload/meta.yml @@ -13,41 +13,45 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: Path to contacts (i.e. read pairs) file. - - index: - type: file - description: Path to index file of the contacts. - - cool_bin: - type: integer - description: Bins size in bp - - chromsizes: - type: file - description: Path to a chromsizes file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: Path to contacts (i.e. read pairs) file. + - index: + type: file + description: Path to index file of the contacts. + - cool_bin: + type: integer + description: Bins size in bp + - - chromsizes: + type: file + description: Path to a chromsizes file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - version: - type: file - description: File containing software version - pattern: "versions.yml" - cool: - type: file - description: Output COOL file path - pattern: "*.cool" - - cool_bin: - type: integer - description: Bins size in bp + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cool": + type: file + description: Output COOL file path + pattern: "*.cool" + - cool_bin: + type: file + description: Output COOL file path + pattern: "*.cool" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@muffato" diff --git a/modules/nf-core/cooler/digest/meta.yml b/modules/nf-core/cooler/digest/meta.yml index a52e21b0396..e3ec3f079ea 100644 --- a/modules/nf-core/cooler/digest/meta.yml +++ b/modules/nf-core/cooler/digest/meta.yml @@ -12,27 +12,30 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - fasta: - type: file - description: Genome assembly FASTA file or folder containing FASTA files (uncompressed). - pattern: "*.{fasta,fa}" - - chromsizes: - type: file - description: Path to a chromsizes file. - - enzyme: - type: string - description: Name of restriction enzyme. e.g. CviQI. - documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html + - - fasta: + type: file + description: Genome assembly FASTA file or folder containing FASTA files (uncompressed). + pattern: "*.{fasta,fa}" + - - chromsizes: + type: file + description: Path to a chromsizes file. + - - enzyme: + type: string + description: Name of restriction enzyme. e.g. CviQI. + documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: A genome segmentation of restriction fragments as a BED file. - pattern: "*.{bed}" + - "*.bed": + type: file + description: A genome segmentation of restriction fragments as a BED file. + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/cooler/dump/meta.yml b/modules/nf-core/cooler/dump/meta.yml index 2f882aeb983..e8150097e2b 100644 --- a/modules/nf-core/cooler/dump/meta.yml +++ b/modules/nf-core/cooler/dump/meta.yml @@ -12,33 +12,36 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" - - resolution: - type: integer - description: Resolution + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" + - resolution: + type: integer + description: Resolution output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedpe: - type: file - description: Output text file - pattern: "*.bedpe" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedpe": + type: file + description: Output text file + pattern: "*.bedpe" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@muffato" diff --git a/modules/nf-core/cooler/makebins/meta.yml b/modules/nf-core/cooler/makebins/meta.yml index 16e2c59815d..73bc62577ed 100644 --- a/modules/nf-core/cooler/makebins/meta.yml +++ b/modules/nf-core/cooler/makebins/meta.yml @@ -12,22 +12,34 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - chromsize: - type: file - description: Path to chromosome size file - - cool_bin: - type: integer - description: Resolution (bin size) in base pairs + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - chromsizes: + type: file + description: Path to a chromsizes file. + - cool_bin: + type: integer + description: Resolution (bin size) in base pairs output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Genome segmentation at a fixed resolution as a BED file. - pattern: "*.bed" + - meta: + type: file + description: Genome segmentation at a fixed resolution as a BED file. + pattern: "*.bed" + - "*.bed": + type: file + description: Genome segmentation at a fixed resolution as a BED file. + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" - "@muffato" diff --git a/modules/nf-core/cooler/merge/meta.yml b/modules/nf-core/cooler/merge/meta.yml index 3ef7f16c45f..d097b84dd10 100644 --- a/modules/nf-core/cooler/merge/meta.yml +++ b/modules/nf-core/cooler/merge/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - cool: - type: file - description: Path to COOL file - pattern: "*.cool" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cool": + type: file + description: Path to COOL file + pattern: "*.cool" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/cooler/zoomify/meta.yml b/modules/nf-core/cooler/zoomify/meta.yml index d87aaf298a3..3f928781b9a 100644 --- a/modules/nf-core/cooler/zoomify/meta.yml +++ b/modules/nf-core/cooler/zoomify/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mcool: - type: file - description: Output mcool file - pattern: "*.mcool" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mcool": + type: file + description: Output mcool file + pattern: "*.mcool" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/coreograph/meta.yml b/modules/nf-core/coreograph/meta.yml index fa61fec708e..4cf3b08ef2f 100644 --- a/modules/nf-core/coreograph/meta.yml +++ b/modules/nf-core/coreograph/meta.yml @@ -1,5 +1,8 @@ name: "coreograph" -description: Great....yet another TMA dearray program. What does this one do? Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types. +description: Great....yet another TMA dearray program. What does this one do? Coreograph + uses UNet, a deep learning model, to identify complete/incomplete tissue cores on + a tissue microarray. It has been trained on 9 TMA slides of different sizes and + tissue types. keywords: - UNet - TMA dearray @@ -7,47 +10,66 @@ keywords: - Cores tools: - "coreograph": - description: "A TMA dearray porgram that uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray." + description: "A TMA dearray porgram that uses UNet, a deep learning model, to + identify complete/incomplete tissue cores on a tissue microarray." homepage: "https://mcmicro.org/parameters/core.html#coreograph" documentation: "https://mcmicro.org/troubleshooting/tuning/coreograph.html" tool_dev_url: "https://github.com/HMS-IDAC/UNetCoreograph" doi: 10.1038/s41592-021-01308-y license: ["MIT License"] + identifier: "" input: - - image: - type: file - description: ome.tif/tif file - pattern: "*.{ome.tif,tif}" - - meta: - type: map - description: | - Groovy Map containing sample information + - - meta: + type: map + description: | + Groovy Map containing sample information + - image: + type: file + description: ome.tif/tif file + pattern: "*.{ome.tif,tif}" output: # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cores: - type: file - description: Complete/Incomplete tissue cores - pattern: "*.{tif}" + - meta: + type: file + description: Complete/Incomplete tissue cores + pattern: "*.{tif}" + - "*[0-9]*.tif": + type: file + description: Complete/Incomplete tissue cores + pattern: "*.{tif}" - masks: - type: file - description: Binary masks for the Complete/Incomplete tissue cores - pattern: "./masks/*.{tif}" + - meta: + type: file + description: Binary masks for the Complete/Incomplete tissue cores + pattern: "./masks/*.{tif}" + - ./masks/: + type: file + description: Binary masks for the Complete/Incomplete tissue cores + pattern: "./masks/*.{tif}" - tma_map: - type: file - description: A TMA map showing labels and outlines - pattern: "TMA_MAP.tif" + - meta: + type: file + description: A TMA map showing labels and outlines + pattern: "TMA_MAP.tif" + - TMA_MAP.tif: + type: file + description: A TMA map showing labels and outlines + pattern: "TMA_MAP.tif" - centroids: - type: file - description: A text file listing centroids of each core in format Y, X - pattern: "centroidsY-X.txt" - - meta: - type: map - description: | - Groovy Map containing sample information + - meta: + type: file + description: A text file listing centroids of each core in format Y, X + pattern: "centroidsY-X.txt" + - centroidsY-X.txt: + type: file + description: A text file listing centroids of each core in format Y, X + pattern: "centroidsY-X.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@arozhada" - "@MargotCh" diff --git a/modules/nf-core/crabz/compress/meta.yml b/modules/nf-core/crabz/compress/meta.yml index bd7cc8a6a87..6c69b81d343 100644 --- a/modules/nf-core/crabz/compress/meta.yml +++ b/modules/nf-core/crabz/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "crabz_compress" description: Compress files with crabz @@ -13,37 +12,36 @@ tools: documentation: "https://github.com/sstadick/crabz" tool_dev_url: "https://github.com/sstadick/crabz" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - file: - type: file - description: File to be compressed - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - file: + type: file + description: File to be compressed + pattern: "*.*" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - archive: - type: file - description: The compressed file - pattern: "*.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gz": + type: file + description: The compressed file + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@camlloyd" maintainers: diff --git a/modules/nf-core/crabz/decompress/meta.yml b/modules/nf-core/crabz/decompress/meta.yml index 9072694c2a7..dd25233e899 100644 --- a/modules/nf-core/crabz/decompress/meta.yml +++ b/modules/nf-core/crabz/decompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "crabz_decompress" description: Decompress files with crabz @@ -13,37 +12,36 @@ tools: documentation: "https://github.com/sstadick/crabz" tool_dev_url: "https://github.com/sstadick/crabz" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - archive: - type: file - description: File to be decompressed - pattern: "*.gz" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - archive: + type: file + description: File to be decompressed + pattern: "*.gz" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - file: - type: file - description: The decompressed file - pattern: "*.*" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.*": + type: file + description: The decompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@camlloyd" maintainers: diff --git a/modules/nf-core/crisprcleanr/normalize/meta.yml b/modules/nf-core/crisprcleanr/normalize/meta.yml index f20492fd744..28be35cd894 100644 --- a/modules/nf-core/crisprcleanr/normalize/meta.yml +++ b/modules/nf-core/crisprcleanr/normalize/meta.yml @@ -7,40 +7,50 @@ keywords: - CRISPR tools: - "crisprcleanr": - description: "Analysis of CRISPR functional genomics, remove false positive due to CNVs." + description: "Analysis of CRISPR functional genomics, remove false positive due + to CNVs." homepage: "https://github.com/francescojm/CRISPRcleanR" documentation: "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf" tool_dev_url: "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0" doi: "10.1186/s12864-018-4989-y" licence: ["MIT"] + identifier: biotools:crisprcleanr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - count_file: - type: file - description: sgRNA raw counts - pattern: "*.tsv" - - library_file: - type: file - description: sgRNA library - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - count_file: + type: file + description: sgRNA raw counts + pattern: "*.tsv" + - library_file: + type: file + description: sgRNA library + pattern: "*.tsv" + - - min_reads: + type: integer + description: Minimum number of reads + - - min_targeted_genes: + type: integer + description: Minimum number of targeted genes output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - norm_count_file: - type: file - description: normalized count file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_norm_table.tsv": + type: file + description: normalized count file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/crumble/meta.yml b/modules/nf-core/crumble/meta.yml index 66665f127f6..cc63012dd3a 100644 --- a/modules/nf-core/crumble/meta.yml +++ b/modules/nf-core/crumble/meta.yml @@ -13,48 +13,69 @@ tools: tool_dev_url: "https://github.com/jkbonfield/crumble" doi: "10.1093/bioinformatics/bty608" licence: ["multiple BSD style licenses"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - keepbed: - type: file - description: BED file defining regions to keep quality - - bedout: - type: boolean - description: set to true to ouput suspicious regions to a BED file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - keepbed: + type: file + description: BED file defining regions to keep quality + - - bedout: + type: boolean + description: set to true to ouput suspicious regions to a BED file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: optional filtered/compressed BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: optional filtered/compressed BAM file + pattern: "*.{bam}" - cram: - type: file - description: optional filtered/compressed CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: optional filtered/compressed CRAM file + pattern: "*.{cram}" - sam: - type: file - description: optional filtered/compressed SAM file - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: optional filtered/compressed SAM file + pattern: "*.{sam}" - bed: - type: file - description: optional suspicious regions BED file - pattern: "*{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: optional suspicious regions BED file + pattern: "*{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/csvtk/concat/meta.yml b/modules/nf-core/csvtk/concat/meta.yml index 5f53229cf64..27ffc1caf09 100644 --- a/modules/nf-core/csvtk/concat/meta.yml +++ b/modules/nf-core/csvtk/concat/meta.yml @@ -11,38 +11,41 @@ tools: documentation: http://bioinf.shenwei.me/csvtk tool_dev_url: https://github.com/shenwei356/csvtk licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: CSV/TSV formatted files - pattern: "*.{csv,tsv}" - - in_format: - type: string - description: Input format (csv, tab, or a delimiting character) - pattern: "*" - - out_format: - type: string - description: Output format (csv, tab, or a delimiting character) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV formatted files + pattern: "*.{csv,tsv}" + - - in_format: + type: string + description: Input format (csv, tab, or a delimiting character) + pattern: "*" + - - out_format: + type: string + description: Output format (csv, tab, or a delimiting character) + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "version.yml" - csv: - type: file - description: Concatenated CSV/TSV file - pattern: "*.{csv,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${out_extension}: + type: file + description: Concatenated CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "version.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml index a75ec40f036..d8671b176e7 100644 --- a/modules/nf-core/csvtk/join/meta.yml +++ b/modules/nf-core/csvtk/join/meta.yml @@ -1,5 +1,6 @@ name: csvtk_join -description: Join two or more CSV (or TSV) tables by selected fields into a single table +description: Join two or more CSV (or TSV) tables by selected fields into a single + table keywords: - join - tsv @@ -11,30 +12,33 @@ tools: documentation: http://bioinf.shenwei.me/csvtk tool_dev_url: https://github.com/shenwei356/csvtk licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: CSV/TSV formatted files - pattern: "*.{csv,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV formatted files + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "version.yml" - csv: - type: file - description: Joined CSV/TSV file - pattern: "*.{csv,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${out_extension}: + type: file + description: Joined CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "version.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/csvtk/split/meta.yml b/modules/nf-core/csvtk/split/meta.yml index 6ff78aa0168..fc220506818 100644 --- a/modules/nf-core/csvtk/split/meta.yml +++ b/modules/nf-core/csvtk/split/meta.yml @@ -6,43 +6,47 @@ keywords: - tsv tools: - csvtk: - description: CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit that allows rapid data investigation and manipulation. + description: CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit + that allows rapid data investigation and manipulation. homepage: https://bioinf.shenwei.me/csvtk/ documentation: https://bioinf.shenwei.me/csvtk/ tool_dev_url: https://github.com/shenwei356/csvtk licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: CSV/TSV file - pattern: "*.{csv,tsv}" - - in_format: - type: string - description: Input format (csv, tab, or a delimiting character) - pattern: "*" - - out_format: - type: string - description: Output format (csv, tab, or a delimiting character) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV file + pattern: "*.{csv,tsv}" + - - in_format: + type: string + description: Input format (csv, tab, or a delimiting character) + pattern: "*" + - - out_format: + type: string + description: Output format (csv, tab, or a delimiting character) + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_csv: - type: file - description: Split CSV/TSV file - pattern: "*.{csv,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_extension}": + type: file + description: Split CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@SusiJo" maintainers: diff --git a/modules/nf-core/custom/catadditionalfasta/meta.yml b/modules/nf-core/custom/catadditionalfasta/meta.yml index 8a9505d30a4..e6c313d3999 100644 --- a/modules/nf-core/custom/catadditionalfasta/meta.yml +++ b/modules/nf-core/custom/catadditionalfasta/meta.yml @@ -1,60 +1,67 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_catadditionalfasta" -description: Custom module to Add a new fasta file to an old one and update an associated GTF +description: Custom module to Add a new fasta file to an old one and update an associated + GTF keywords: - fasta - gtf - genomics tools: - "custom": - description: "Custom module to Add a new fasta file to an old one and update an associated GTF" + description: "Custom module to Add a new fasta file to an old one and update an + associated GTF" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing fasta information - - meta2: - type: map - description: | - Groovy Map containing additional fasta information - - fasta: - type: file - description: FASTA-format sequence file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: GTF-format annotation file for fasta - pattern: "*.gtf" - - add_fasta: - type: file - description: FASTA-format file of additional sequences - pattern: "*.fa" - - biotype: - type: string - description: Biotype to apply to new GTF entries - + - - meta: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: FASTA-format sequence file + pattern: "*.{fasta,fa}" + - gtf: + type: file + description: GTF-format annotation file for fasta + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing additional fasta information + - add_fasta: + type: file + description: FASTA-format file of additional sequences + pattern: "*.fa" + - - biotype: + type: string + description: Biotype to apply to new GTF entries output: - - meta: - type: map - description: | - Groovy Map containing fasta information - fasta: - type: file - description: FASTA-format combined sequence file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.fasta": + type: file + description: FASTA-format combined sequence file + pattern: "*.{fasta,fa}" - gtf: - type: file - description: GTF-format combined annotation file - pattern: "*.gtf" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.gtf": + type: file + description: GTF-format combined annotation file + pattern: "*.gtf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 5f15a5fde05..dc1e412fbcd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,34 +1,40 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template +description: Custom module used to dump software versions within the nf-core pipeline + template keywords: - custom - dump - version tools: - custom: - description: Custom module used to dump software versions within the nf-core pipeline template + description: Custom module used to dump software versions within the nf-core pipeline + template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools licence: ["MIT"] + identifier: "" input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" + - - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" output: - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" + - software_versions.yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" + - software_versions_mqc.yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index da2df5e43a4..b98cbb99092 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.20 - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml index 529be07e443..2a0e8da0a63 100644 --- a/modules/nf-core/custom/getchromsizes/meta.yml +++ b/modules/nf-core/custom/getchromsizes/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna,fas}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna,fas}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sizes: - type: file - description: File containing chromosome lengths - pattern: "*.{sizes}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: File containing chromosome lengths + pattern: "*.{sizes}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/custom/gtffilter/meta.yml b/modules/nf-core/custom/gtffilter/meta.yml index 2c8692218de..67225649435 100644 --- a/modules/nf-core/custom/gtffilter/meta.yml +++ b/modules/nf-core/custom/gtffilter/meta.yml @@ -1,50 +1,53 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_gtffilter" -description: Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file +description: Filter a gtf file to keep only regions that are located on a chromosome + represented in a given fasta file keywords: - gtf - fasta - filter tools: - "gtffilter": - description: "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file" + description: "Filter a gtf file to keep only regions that are located on a chromosome + represented in a given fasta file" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fasta,fa}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gtf: - type: file - description: Filtered GTF file - pattern: "*.{gtf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.${suffix}: + type: file + description: Filtered GTF file + pattern: "*.{gtf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nictru" maintainers: diff --git a/modules/nf-core/custom/matrixfilter/meta.yml b/modules/nf-core/custom/matrixfilter/meta.yml index 99d7ca4e864..ce9601b580f 100644 --- a/modules/nf-core/custom/matrixfilter/meta.yml +++ b/modules/nf-core/custom/matrixfilter/meta.yml @@ -1,5 +1,6 @@ name: "custom_matrixfilter" -description: filter a matrix based on a minimum value and numbers of samples that must pass. +description: filter a matrix based on a minimum value and numbers of samples that + must pass. keywords: - matrix - filter @@ -9,93 +10,67 @@ tools: - "matrixfilter": description: "filter a matrix based on a minimum value and numbers of samples" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on matrix to be filtered, at a - minimum an id. e.g. [ id:'test' ] - - abundance: - type: file - description: | - Raw TSV or CSV format abundance matrix with features (e.g. - genes) by row and observations (e.g. samples) by column. All rownames - from the sample sheet should be present in the columns. - - samplesheet_meta: - type: map - description: | - Where samplesheet is provided, aroovy Map containing information on - sample sheet, at a minimum an id. e.g. [ id:'test' ] - - samplesheet: - type: file - description: | - Optional CSV or TSV format sample sheet with sample metadata. If - provided this is used to infer minimum passing samples from group sizes - present (see grouping_variable), but also to validate matrix columns. - If not provided, all numeric columns are selected. - - minimum_abundance: - type: float - description: | - Minimum abundance value, supplied via task.ext.args as --minimum_abundance - default: 1 - - minimum_samples: - type: integer - description: | - Minimum observations that must pass the threshold to retain - the row/ feature (e.g. gene). Supplied via task.ext.args as - --minimum_samples - default: 1 - - minimum_proportion: - type: float - description: | - A minimum proportion of observations that must pass the threshold. - Supplied via task.ext.args as --minimum_proportion. Overrides - minimum_samples - default: 0 - - grouping_variable: - type: string - description: | - Optionally supply a variable from the sample sheet that can be used to - define groups and derive a minimum group size upon which to base - minimum observation numbers. The rationale being to allow retention of - features that might be present in only one group. Supplied via - task.ext.args as --grouping_variable - - minimum_proportion_not_na: - type: float - description: | - A minimum proportion of observations that must have a numeric value (not be NA). - Supplied via task.ext.args as --minimum_proportion_not_na - default: 0.5 - - minimum_samples_not_na: - type: integer - description: | - Minimum observations that must have a numeric value (not be NA) to retain - the row/ feature (e.g. gene). Supplied via task.ext.args as - --minimum_samples_not_na. Overrides minimum_proportion_not_na - - most_variant_features: - type: integer - description: | - Variance filter for the number of row/ feature (e.g. gene) observations returned. - Supplied via task.ext.args as --most_variant_features - + - - meta: + type: map + description: | + Groovy Map containing information on matrix to be filtered, at a + minimum an id. e.g. [ id:'test' ] + - abundance: + type: file + description: | + Raw TSV or CSV format abundance matrix with features (e.g. + genes) by row and observations (e.g. samples) by column. All rownames + from the sample sheet should be present in the columns. + - - samplesheet_meta: + type: map + description: | + Where samplesheet is provided, aroovy Map containing information on + sample sheet, at a minimum an id. e.g. [ id:'test' ] + - samplesheet: + type: file + description: | + Optional CSV or TSV format sample sheet with sample metadata. If + provided this is used to infer minimum passing samples from group sizes + present (see grouping_variable), but also to validate matrix columns. + If not provided, all numeric columns are selected. output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing information on experiment. - e.g. [ id:'test' ] - filtered: - type: file - description: Filtered version of input matrix - pattern: "*.filtered.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*.filtered.tsv": + type: file + description: Filtered version of input matrix + pattern: "*.filtered.tsv" - tests: - type: file - description: Boolean matrix with pass/ fail status for each test on each feature - pattern: "*.tests.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*.tests.tsv": + type: file + description: Boolean matrix with pass/ fail status for each test on each feature + pattern: "*.tests.tsv" + - session_info: + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - R_sessionInfo.log: + type: file + description: Log file containing R session information + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml index 46a6cd329c2..2938a35dc84 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/meta.yml +++ b/modules/nf-core/custom/sratoolsncbisettings/meta.yml @@ -1,5 +1,6 @@ name: "custom_sratoolsncbisettings" -description: Test for the presence of suitable NCBI settings or create them on the fly. +description: Test for the presence of suitable NCBI settings or create them on the + fly. keywords: - NCBI - settings @@ -13,15 +14,18 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ncbi_settings: - type: file - description: An NCBI user settings file. - pattern: "*.mkfg" + - "*.mkfg": + type: file + description: An NCBI user settings file. + pattern: "*.mkfg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/custom/tabulartogseacls/meta.yml b/modules/nf-core/custom/tabulartogseacls/meta.yml index 2d1ec0b8d32..e0d8c340a46 100644 --- a/modules/nf-core/custom/tabulartogseacls/meta.yml +++ b/modules/nf-core/custom/tabulartogseacls/meta.yml @@ -9,37 +9,41 @@ tools: - custom: description: "Make a GSEA class file (.cls) from tabular inputs" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing metadata including an id, the sample sheet column - used to define groups, and optionally a separator to override defaults e.g. [ - id:'test', variable:'treatment', separator:',' ]. The way these values are - passed to the associated module parameters is then defined via an ext.args - specification for the process from the workflow, like: ext.args = { [ - "separator": "\t", "variable": "$meta.variable" ] } ('variable' is - compulsory here). - - samples: - type: file - description: Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column. - pattern: "*.{csv,tsv}" + - - meta: + type: map + description: | + Groovy Map containing metadata including an id, the sample sheet column + used to define groups, and optionally a separator to override defaults e.g. [ + id:'test', variable:'treatment', separator:',' ]. The way these values are + passed to the associated module parameters is then defined via an ext.args + specification for the process from the workflow, like: ext.args = { [ + "separator": "\t", "variable": "$meta.variable" ] } ('variable' is + compulsory here). + - samples: + type: file + description: Tabular (e.g. TSV/CSV) samples file with sample IDs by row and + variables by column. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing metadata e.g. [ id:'test', variable:'treatment', - separator:',' ] - cls: - type: file - description: | - A categorical class format file (.cls) as defined by the Broad - documentation at - https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats + - meta: + type: map + description: | + Groovy Map containing metadata e.g. [ id:'test', variable:'treatment', + separator:',' ] + - "*.cls": + type: file + description: | + A categorical class format file (.cls) as defined by the Broad + documentation at + https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/tabulartogseagct/meta.yml b/modules/nf-core/custom/tabulartogseagct/meta.yml index 4f4a806429c..055cd9e4d32 100644 --- a/modules/nf-core/custom/tabulartogseagct/meta.yml +++ b/modules/nf-core/custom/tabulartogseagct/meta.yml @@ -1,37 +1,43 @@ name: "custom_tabulartogseagct" -description: Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA +description: Convert a TSV or CSV with features by row and observations by column + to a GCT format file as consumed by GSEA keywords: - gsea - gct - tabular tools: - tabulartogseagct: - description: "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA" + description: "Convert a TSV or CSV with features by row and observations by column + to a GCT format file as consumed by GSEA" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing matrix information - e.g. [ id:'test' ] - - tabular: - type: file - description: Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column. - pattern: "*.{tsv,csv}" + - - meta: + type: map + description: | + Groovy Map containing matrix information + e.g. [ id:'test' ] + - tabular: + type: file + description: Tabular (e.g. TSV or CSV file) containing a numeric matrix with + features (e.g. genes) by row and samples by column. + pattern: "*.{tsv,csv}" output: - - meta: - type: map - description: | - Groovy Map containing matrix information - e.g. [ id:'test' ] - gct: - type: file - description: GCT format version of input TSV - pattern: "*.{gct}" + - meta: + type: map + description: | + Groovy Map containing matrix information + e.g. [ id:'test' ] + - "*.gct": + type: file + description: GCT format version of input TSV + pattern: "*.{gct}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/tx2gene/meta.yml b/modules/nf-core/custom/tx2gene/meta.yml index d991bf1be95..8254afa08da 100644 --- a/modules/nf-core/custom/tx2gene/meta.yml +++ b/modules/nf-core/custom/tx2gene/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_tx2gene" -description: Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. +description: Make a transcript/gene mapping from a GTF and cross-reference with transcript + quantifications. keywords: - gene - gtf @@ -14,51 +14,51 @@ tools: check it against transcript quantifications" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" - - meta2: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - - id: - type: string - description: Gene ID attribute in the GTF file (default= gene_id) - - extra: - type: string - description: Extra gene attribute in the GTF file (default= gene_name) - + - - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: file + description: quants file + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' + - - id: + type: string + description: Gene ID attribute in the GTF file (default= gene_id) + - - extra: + type: string + description: Extra gene attribute in the GTF file (default= gene_name) output: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - tx2gene: - type: file - description: A transcript/ gene mapping table in TSV format - pattern: "*.tx2gene.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - "*tx2gene.tsv": + type: file + description: A transcript/ gene mapping table in TSV format + pattern: "*.tx2gene.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/cutadapt/meta.yml b/modules/nf-core/cutadapt/meta.yml index 5ecfe27a9bb..8844d86c8ca 100644 --- a/modules/nf-core/cutadapt/meta.yml +++ b/modules/nf-core/cutadapt/meta.yml @@ -12,35 +12,44 @@ tools: documentation: https://cutadapt.readthedocs.io/en/stable/index.html doi: 10.14806/ej.17.1.200 licence: ["MIT"] + identifier: biotools:cutadapt input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trim.fastq.gz": + type: file + description: The trimmed/modified fastq reads + pattern: "*fastq.gz" - log: - type: file - description: cuatadapt log file - pattern: "*cutadapt.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: cuatadapt log file + pattern: "*cutadapt.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/cutesv/meta.yml b/modules/nf-core/cutesv/meta.yml index 480efafd099..409fd1fc010 100644 --- a/modules/nf-core/cutesv/meta.yml +++ b/modules/nf-core/cutesv/meta.yml @@ -6,48 +6,52 @@ keywords: - sv tools: - cutesv: - description: a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. + description: a clustering-and-refinement method to analyze the signatures to implement + sensitive SV detection. homepage: https://github.com/tjiangHIT/cuteSV documentation: https://github.com/tjiangHIT/cuteSV#readme tool_dev_url: https://github.com/tjiangHIT/cuteSV licence: ["MIT"] + identifier: biotools:cuteSV input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: Index of BAM file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: | - Reference database in FASTA format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: Index of BAM file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: | + Reference database in FASTA format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: VCF file containing called variants from CuteSV - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: VCF file containing called variants from CuteSV + pattern: "*.vcf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-hakkaart" - "@yuukiiwa" diff --git a/modules/nf-core/damageprofiler/meta.yml b/modules/nf-core/damageprofiler/meta.yml index 7cf1a4a5146..0c3360e893b 100644 --- a/modules/nf-core/damageprofiler/meta.yml +++ b/modules/nf-core/damageprofiler/meta.yml @@ -1,5 +1,6 @@ name: damageprofiler -description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage +description: A Java based tool to determine damage patterns on ancient DNA as a replacement + for mapDamage keywords: - damage - deamination @@ -13,43 +14,51 @@ keywords: - archaeogenetics tools: - damageprofiler: - description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage + description: A Java based tool to determine damage patterns on ancient DNA as + a replacement for mapDamage homepage: https://github.com/Integrative-Transcriptomics/DamageProfiler documentation: https://damageprofiler.readthedocs.io/ tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler doi: "10.1093/bioinformatics/btab190" licence: ["GPL v3"] + identifier: biotools:damageprofiler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: OPTIONAL FASTA reference file - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: OPTIONAL FASTA index file from samtools faidx - pattern: "*.{fai}" - - specieslist: - type: file - description: OPTIONAL text file with list of target reference headers - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: OPTIONAL FASTA reference file + pattern: "*.{fasta,fna,fa}" + - - fai: + type: file + description: OPTIONAL FASTA index file from samtools faidx + pattern: "*.{fai}" + - - specieslist: + type: file + description: OPTIONAL text file with list of target reference headers + pattern: "*.{txt}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: DamageProfiler results directory - pattern: "*/*" + - meta: + type: directory + description: DamageProfiler results directory + pattern: "*/*" + - ${prefix}: + type: directory + description: DamageProfiler results directory + pattern: "*/*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/dastool/dastool/meta.yml b/modules/nf-core/dastool/dastool/meta.yml index c661de8db6b..7eab655a842 100644 --- a/modules/nf-core/dastool/dastool/meta.yml +++ b/modules/nf-core/dastool/dastool/meta.yml @@ -20,81 +20,155 @@ tools: tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" licence: ["BSD"] + identifier: biotools:dastool input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - contigs: - type: file - description: fasta file - pattern: "*.{fa.gz,fas.gz,fasta.gz}" - - bins: - type: file - description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin" - pattern: "*.tsv" - - proteins: - type: file - description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo) - pattern: "*.{fa.gz,fas.gz,fasta.gz}" - - db_directory: - type: file - description: (optional) Directory of single copy gene database. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs: + type: file + description: fasta file + pattern: "*.{fa.gz,fas.gz,fasta.gz}" + - bins: + type: file + description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin" + pattern: "*.tsv" + - - proteins: + type: file + description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo) + pattern: "*.{fa.gz,fas.gz,fasta.gz}" + - - db_directory: + type: file + description: (optional) Directory of single copy gene database. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - version: - type: file - description: File containing software version - pattern: "versions.yml" - log: - type: file - description: Log file of the run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file of the run + pattern: "*.log" - summary: - type: file - description: Summary of output bins including quality and completeness estimates - pattern: "*summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary.tsv": + type: file + description: Summary of output bins including quality and completeness estimates + pattern: "*summary.txt" - contig2bin: - type: file - description: Scaffolds to bin file of output bins - pattern: "*.contig2bin.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_DASTool_contig2bin.tsv": + type: file + description: Scaffolds to bin file of output bins + pattern: "*.contig2bin.txt" - eval: - type: file - description: Quality and completeness estimates of input bin sets - pattern: "*.eval" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.eval": + type: file + description: Quality and completeness estimates of input bin sets + pattern: "*.eval" - bins: - type: file - description: Final refined bins in fasta format - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_DASTool_bins/*.fa": + type: file + description: Final refined bins in fasta format + pattern: "*.fa" - pdfs: - type: file - description: Plots showing the amount of high quality bins and score distribution of bins per method - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: Plots showing the amount of high quality bins and score distribution + of bins per method + pattern: "*.pdf" - fasta_proteins: - type: file - description: Output from prodigal if not already supplied - pattern: "*.proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidates.faa": + type: file + description: Output from prodigal if not already supplied + pattern: "*.proteins.faa" + - candidates_faa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.faa": + type: file + description: FAA file + pattern: "*.faa" - fasta_archaea_scg: - type: file - description: Results of archaeal single-copy-gene prediction - pattern: "*.archaea.scg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.archaea.scg": + type: file + description: Results of archaeal single-copy-gene prediction + pattern: "*.archaea.scg" - fasta_bacteria_scg: - type: file - description: Results of bacterial single-copy-gene prediction - pattern: "*.bacteria.scg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bacteria.scg": + type: file + description: Results of bacterial single-copy-gene prediction + pattern: "*.bacteria.scg" - b6: - type: file - description: Results in b6 format - pattern: "*.b6" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.b6": + type: file + description: Results in b6 format + pattern: "*.b6" - seqlength: - type: file - description: Summary of contig lengths - pattern: "*.seqlength" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.seqlength": + type: file + description: Summary of contig lengths + pattern: "*.seqlength" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/dastool/fastatocontig2bin/meta.yml b/modules/nf-core/dastool/fastatocontig2bin/meta.yml index bbecfd27ef7..97b140bb974 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/meta.yml +++ b/modules/nf-core/dastool/fastatocontig2bin/meta.yml @@ -1,5 +1,6 @@ name: dastool_fastatocontig2bin -description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format +description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin + format keywords: - binning - das tool @@ -20,33 +21,38 @@ tools: tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" licence: ["BSD"] + identifier: biotools:dastool input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins - pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - - extension: - type: string - description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta of list of fasta files recommended to be gathered via with + .collect() of bins + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + - - extension: + type: string + description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, + if gzipped input. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastatocontig2bin: - type: file - description: tabular contig2bin file for DAS tool input - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: tabular contig2bin file for DAS tool input + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/dastool/scaffolds2bin/meta.yml b/modules/nf-core/dastool/scaffolds2bin/meta.yml index f57c50ab017..2fcc05bdc1f 100644 --- a/modules/nf-core/dastool/scaffolds2bin/meta.yml +++ b/modules/nf-core/dastool/scaffolds2bin/meta.yml @@ -1,5 +1,6 @@ name: dastool_scaffolds2bin -description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format +description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin + format keywords: - binning - das tool @@ -20,33 +21,38 @@ tools: tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" licence: ["BSD"] + identifier: biotools:dastool input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins - pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - - extension: - type: string - description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta or list of fasta files recommended to be gathered via with + .collect() of bins + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + - - extension: + type: string + description: Fasta file extension (fa | fas | fasta | ...), but without .gz + suffix, even if gzipped input. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scaffolds2bin: - type: file - description: tabular scaffolds2bin file for DAS tool input - pattern: "*.scaffolds2bin.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: tabular scaffolds2bin file for DAS tool input + pattern: "*.scaffolds2bin.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/datavzrd/meta.yml b/modules/nf-core/datavzrd/meta.yml index 8ac5f55d0d5..44d6bd6932e 100644 --- a/modules/nf-core/datavzrd/meta.yml +++ b/modules/nf-core/datavzrd/meta.yml @@ -1,44 +1,42 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "datavzrd" -description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables. +description: Datavzrd is a tool to create visual HTML reports from collections of + CSV/TSV tables. keywords: - visualisation - tsv - csv tools: - datavzrd: - description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables. + description: Datavzrd is a tool to create visual HTML reports from collections + of CSV/TSV tables. homepage: https://datavzrd.github.io/ documentation: https://datavzrd.github.io/docs/index.html tool_dev_url: https://github.com/datavzrd/datavzrd licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - config_file: - type: file - description: configuration file used for visualisation - pattern: "*.{yml,yaml}" - - table: - type: file - description: file used for visualisation - pattern: "*.{tsv,csv}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: directory - description: directory with HTML report of provided CSV/TSV files - pattern: "/output/" - + - meta: + type: directory + description: directory with HTML report of provided CSV/TSV files + pattern: "/output/" + - ${prefix}: + type: directory + description: directory with HTML report of provided CSV/TSV files + pattern: "/output/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vickylaram" - "@famosab" diff --git a/modules/nf-core/decoupler/decoupler/meta.yml b/modules/nf-core/decoupler/decoupler/meta.yml index 4188611897b..8f502254188 100644 --- a/modules/nf-core/decoupler/decoupler/meta.yml +++ b/modules/nf-core/decoupler/decoupler/meta.yml @@ -25,58 +25,62 @@ tools: tool_dev_url: "https://decoupler-py.readthedocs.io" doi: "10.1093/bioadv/vbac016" licence: ["GPL v3"] + identifier: biotools:decoupler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:‘test’, single_end ] - - mat: - type: file - description: | - Path to the matrix file (e.g. gene/protein expression, etc.). - Should be in in tab-separated format (`*.tab`) - pattern: "*.tsv" - - net: - type: file - description: | - The prior knowledge network linking the features of the - expression matrix to a process/component (e.g. gene set, - transcription factor, kinase, etc.) - pattern: "*.tsv" - - args: - type: string - description: | - Keyword arguments passed to `decoupler.decouple()` (see - documentation for more information here: - https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.decouple.html#decoupler.decouple). - Arguments specific for a method must be specified with - the method name as a prefix e.g. `'gsea_batch_size'` - pattern: "{arg: val, ..., method_arg: val}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:‘test’, single_end ] + - mat: + type: file + description: | + Path to the matrix file (e.g. gene/protein expression, etc.). + Should be in in tab-separated format (`*.tab`) + pattern: "*.tsv" + - - net: + type: file + description: | + The prior knowledge network linking the features of the + expression matrix to a process/component (e.g. gene set, + transcription factor, kinase, etc.) + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:‘test’, single_end ] - dc_estimate: - type: file - description: | - The file containing the estimation results of the enrichment(s) - pattern: "*estimate__decoupler.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:‘test’, single_end ] + - "*estimate__decoupler.tsv": + type: file + description: | + The file containing the estimation results of the enrichment(s) + pattern: "*estimate__decoupler.tsv" - dc_pvals: - type: file - description: | - The file containing the p-value associated to the estimation - results of the enrichment(s) - pattern: "*pvals__decoupler.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:‘test’, single_end ] + - "*pvals__decoupler.tsv": + type: file + description: | + The file containing the p-value associated to the estimation + results of the enrichment(s) + pattern: "*pvals__decoupler.tsv" + - s: + type: file + description: | + The file containing the p-value associated to the estimation + results of the enrichment(s) + pattern: "*pvals__decoupler.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gabora" - "@vicpaton" diff --git a/modules/nf-core/dedup/meta.yml b/modules/nf-core/dedup/meta.yml index 3a626587842..614236f2297 100644 --- a/modules/nf-core/dedup/meta.yml +++ b/modules/nf-core/dedup/meta.yml @@ -1,5 +1,6 @@ name: dedup -description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). +description: DeDup is a tool for read deduplication in paired-end read merging (e.g. + for ancient DNA experiments). keywords: - dedup - deduplication @@ -9,48 +10,70 @@ keywords: - bam tools: - dedup: - description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). + description: DeDup is a tool for read deduplication in paired-end read merging + (e.g. for ancient DNA experiments). homepage: https://github.com/apeltzer/DeDup documentation: https://dedup.readthedocs.io/en/latest/ tool_dev_url: https://github.com/apeltzer/DeDup doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Deduplicated BAM file - pattern: "*_rmdup.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rmdup.bam": + type: file + description: Deduplicated BAM file + pattern: "*_rmdup.bam" - json: - type: file - description: JSON file for MultiQC - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file for MultiQC + pattern: "*.json" - hist: - type: file - description: Histogram data of amount of deduplication - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram data of amount of deduplication + pattern: "*.hist" - log: - type: file - description: Dedup log information - pattern: "*log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*log": + type: file + description: Dedup log information + pattern: "*log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/deeparg/downloaddata/meta.yml b/modules/nf-core/deeparg/downloaddata/meta.yml index 65fb39039ed..5df2887ba0e 100644 --- a/modules/nf-core/deeparg/downloaddata/meta.yml +++ b/modules/nf-core/deeparg/downloaddata/meta.yml @@ -1,5 +1,6 @@ name: deeparg_downloaddata -description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes +description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes keywords: - download - database @@ -9,22 +10,26 @@ keywords: - prediction tools: - deeparg: - description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes + description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes homepage: https://github.com/gaarangoa/deeparg documentation: https://github.com/gaarangoa/deeparg tool_dev_url: https://github.com/gaarangoa/deeparg doi: "10.1186/s40168-018-0401-z" licence: ["MIT"] + identifier: "" # No input required for download module. output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: Directory containing database required for deepARG. - pattern: "db/" + - db/: + type: directory + description: Directory containing database required for deepARG. + pattern: "db/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/deeparg/predict/meta.yml b/modules/nf-core/deeparg/predict/meta.yml index d62c2c5fb26..dbd63945dbb 100644 --- a/modules/nf-core/deeparg/predict/meta.yml +++ b/modules/nf-core/deeparg/predict/meta.yml @@ -1,5 +1,6 @@ name: deeparg_predict -description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes +description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes keywords: - deeparg - antimicrobial resistance @@ -11,56 +12,81 @@ keywords: - metagenomes tools: - deeparg: - description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes + description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes homepage: https://github.com/gaarangoa/deeparg documentation: https://github.com/gaarangoa/deeparg tool_dev_url: https://github.com/gaarangoa/deeparg doi: "10.1186/s40168-018-0401-z" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file containing gene-like sequences - pattern: "*.{fasta,fa,fna}" - - model: - type: string - description: Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively - pattern: "LS|LS" - - db: - type: directory - description: Path to a directory containing the deepARG pre-built models - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file containing gene-like sequences + pattern: "*.{fasta,fa,fna}" + - model: + type: string + description: Which model to use, depending on input data. Either 'LS' or 'SS' + for long or short sequences respectively + pattern: "LS|LS" + - - db: + type: directory + description: Path to a directory containing the deepARG pre-built models + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - daa: - type: file - description: Sequences of ARG-like sequences from DIAMOND alignment - pattern: "*.align.daa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.align.daa": + type: file + description: Sequences of ARG-like sequences from DIAMOND alignment + pattern: "*.align.daa" - daa_tsv: - type: file - description: Alignments scores against ARG-like sequences from DIAMOND alignment - pattern: "*.align.daa.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.align.daa.tsv": + type: file + description: Alignments scores against ARG-like sequences from DIAMOND alignment + pattern: "*.align.daa.tsv" - arg: - type: file - description: Table containing sequences with an ARG-like probability of more than specified thresholds - pattern: "*.mapping.ARG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapping.ARG": + type: file + description: Table containing sequences with an ARG-like probability of more + than specified thresholds + pattern: "*.mapping.ARG" - potential_arg: - type: file - description: Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection - pattern: "*.mapping.potential.ARG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapping.potential.ARG": + type: file + description: Table containing sequences with an ARG-like probability of less + than specified thresholds, and requires manual inspection + pattern: "*.mapping.potential.ARG" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/deepbgc/download/meta.yml b/modules/nf-core/deepbgc/download/meta.yml index 6444dd41d49..4551e9a00df 100644 --- a/modules/nf-core/deepbgc/download/meta.yml +++ b/modules/nf-core/deepbgc/download/meta.yml @@ -1,5 +1,6 @@ name: "deepbgc_download" -description: Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning. +description: Database download module for DeepBGC which detects BGCs in bacterial + and fungal genomes using deep learning. keywords: - database - download @@ -19,15 +20,18 @@ tools: tool_dev_url: "https://github.com/Merck/deepbgc" doi: "10.1093/nar/gkz654" licence: ["MIT"] + identifier: biotools:DeepBGC output: + - db: + - deepbgc_db/: + type: directory + description: Directory containing the DeepBGC database + pattern: "deepbgc_db/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - deepbgc_db: - type: directory - description: Contains reference database files - pattern: "deepbgc_db" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/deepbgc/pipeline/meta.yml b/modules/nf-core/deepbgc/pipeline/meta.yml index 5f939eaa4fd..186c7d30c75 100644 --- a/modules/nf-core/deepbgc/pipeline/meta.yml +++ b/modules/nf-core/deepbgc/pipeline/meta.yml @@ -17,73 +17,138 @@ tools: tool_dev_url: "https://github.com/Merck/deepbgc" doi: "10.1093/nar/gkz654" licence: ["MIT"] + identifier: biotools:DeepBGC input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - genome: - type: file - description: FASTA/GenBank/Pfam CSV file - pattern: "*.{fasta,fa,fna,gbk,csv}" - - db: - type: directory - description: Database path + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - genome: + type: file + description: FASTA/GenBank/Pfam CSV file + pattern: "*.{fasta,fa,fna,gbk,csv}" + - - db: + type: directory + description: Database path output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - readme: - type: file - description: txt file containing description of output files - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/README.txt: + type: file + description: txt file containing description of output files + pattern: "*.{txt}" - log: - type: file - description: Log output of DeepBGC - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/LOG.txt: + type: file + description: Log output of DeepBGC + pattern: "*.{txt}" - json: - type: file - description: AntiSMASH JSON file for sideloading - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.antismash.json: + type: file + description: AntiSMASH JSON file for sideloading + pattern: "*.{json}" - bgc_gbk: - type: file - description: Sequences and features of all detected BGCs in GenBank format - pattern: "*.{bgc.gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.bgc.gbk: + type: file + description: Sequences and features of all detected BGCs in GenBank format + pattern: "*.{bgc.gbk}" - bgc_tsv: - type: file - description: Table of detected BGCs and their properties - pattern: "*.{bgc.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.bgc.tsv: + type: file + description: Table of detected BGCs and their properties + pattern: "*.{bgc.tsv}" - full_gbk: - type: file - description: Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features) - pattern: "*.{full.gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.full.gbk: + type: file + description: Fully annotated input sequence with proteins, Pfam domains (PFAM_domain + features) and BGCs (cluster features) + pattern: "*.{full.gbk}" - pfam_tsv: - type: file - description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores - pattern: "*.{pfam.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.pfam.tsv: + type: file + description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) + in genomic order, with BGC detection scores + pattern: "*.{pfam.tsv}" - bgc_png: - type: file - description: Detected BGCs plotted by their nucleotide coordinates - pattern: "*.{bgc.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.bgc.png: + type: file + description: Detected BGCs plotted by their nucleotide coordinates + pattern: "*.{bgc.png}" - pr_png: - type: file - description: Precision-Recall curve based on predicted per-Pfam BGC scores - pattern: "*.{pr.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.pr.png: + type: file + description: Precision-Recall curve based on predicted per-Pfam BGC scores + pattern: "*.{pr.png}" - roc_png: - type: file - description: ROC curve based on predicted per-Pfam BGC scores - pattern: "*.{roc.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.roc.png: + type: file + description: ROC curve based on predicted per-Pfam BGC scores + pattern: "*.{roc.png}" - score_png: - type: file - description: BGC detection scores of each Pfam domain in genomic order - pattern: "*.{score.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.score.png: + type: file + description: BGC detection scores of each Pfam domain in genomic order + pattern: "*.{score.png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" - "@jfy133" diff --git a/modules/nf-core/deepcell/mesmer/meta.yml b/modules/nf-core/deepcell/mesmer/meta.yml index dec360b9c38..0292aa79e7d 100644 --- a/modules/nf-core/deepcell/mesmer/meta.yml +++ b/modules/nf-core/deepcell/mesmer/meta.yml @@ -12,42 +12,44 @@ tools: tool_dev_url: "https://githu/b.com/vanvalenlab/deepcell-tf" doi: 10.1038/s41587-021-01094-0 licence: ["APACHE2"] + identifier: biotools:deepcell input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - img: - type: file - description: Multichannel image file - pattern: "*.{tiff,tif,h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - membrane_img: - type: file - description: Optional membrane image to be provided separately. - pattern: "*.{tiff,tif,h5,hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - img: + type: file + description: Multichannel image file + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - membrane_img: + type: file + description: Optional membrane image to be provided separately. + pattern: "*.{tiff,tif,h5,hdf5}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mask: - type: file - description: File containing the mask. - pattern: "*.{tif, tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tif": + type: file + description: File containing the mask. + pattern: "*.{tif, tiff}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" - "@chiarasch" diff --git a/modules/nf-core/deeptmhmm/meta.yml b/modules/nf-core/deeptmhmm/meta.yml index 5abcf1e306d..dc51ec59b02 100644 --- a/modules/nf-core/deeptmhmm/meta.yml +++ b/modules/nf-core/deeptmhmm/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: deeptmhmm description: A Deep Learning Model for Transmembrane Topology Prediction and Classification @@ -8,51 +7,84 @@ keywords: - classification tools: - deeptmhmm: - description: Deep Learning model for Transmembrane Helices protein domain prediction through the BioLib Python Client + description: Deep Learning model for Transmembrane Helices protein domain prediction + through the BioLib Python Client homepage: https://dtu.biolib.com/DeepTMHMM documentation: https://dtu.biolib.com/DeepTMHMM doi: 10.1101/2022.04.08.487609 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Database of sequences in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Database of sequences in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gff3: - type: file - description: Predicted topologies (inside, outside, TMhelix) in general Feature Format Version 3 - pattern: "biolib_results/TMRs.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/TMRs.gff3: + type: file + description: Predicted topologies (inside, outside, TMhelix) in general Feature + Format Version 3 + pattern: "biolib_results/TMRs.gff3" - line3: - type: file - description: Predicted topologies and information of protein sequences in three lines (name, sequence, topology) - pattern: "biolib_results/predicted_topologies.3line" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/predicted_topologies.3line: + type: file + description: Predicted topologies and information of protein sequences in three + lines (name, sequence, topology) + pattern: "biolib_results/predicted_topologies.3line" - md: - type: file - description: Markdown results file - pattern: "biolib_results/deeptmhmm_results.md" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/deeptmhmm_results.md: + type: file + description: Markdown results file + pattern: "biolib_results/deeptmhmm_results.md" - csv: - type: file - description: CSV file with per-residue predictions for the likelihood of each amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, Inside, Outside or Signal (only when querying against genomic fasta) - pattern: "biolib_results/*_probs.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/*_probs.csv: + type: file + description: CSV file with per-residue predictions for the likelihood of each + amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, + Inside, Outside or Signal (only when querying against genomic fasta) + pattern: "biolib_results/*_probs.csv" - png: - type: file - description: Most likely topology probability line plots (only when querying against genomic fasta) - pattern: "biolib_results/plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/plot.png: + type: file + description: Most likely topology probability line plots (only when querying + against genomic fasta) + pattern: "biolib_results/plot.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/deeptools/bamcoverage/meta.yml b/modules/nf-core/deeptools/bamcoverage/meta.yml index 89cf05ff903..c349bfb9319 100644 --- a/modules/nf-core/deeptools/bamcoverage/meta.yml +++ b/modules/nf-core/deeptools/bamcoverage/meta.yml @@ -1,57 +1,69 @@ name: deeptools_bamcoverage -description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. +description: This tool takes an alignment of reads or fragments as input (BAM file) + and generates a coverage track (bigWig or bedGraph) as output. keywords: - coverage - depth - track tools: - deeptools: - description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data + description: A set of user-friendly tools for normalization and visualzation of + deep-sequencing data homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html tool_dev_url: https://github.com/deeptools/deepTools/ doi: "10.1093/nar/gkw257" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Reference file the CRAM file was created with (required with CRAM input) - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference file (optional, but recommended) - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Reference file the CRAM file was created with (required with CRAM + input) + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference file (optional, but recommended) + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bigWig: - type: file - description: BigWig file - pattern: "*.bigWig" + - bigwig: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigWig": + type: file + description: BigWig file + pattern: "*.bigWig" - bedgraph: - type: file - description: Bedgraph file - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedgraph": + type: file + description: Bedgraph file + pattern: "*.bedgraph" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@SusiJo" diff --git a/modules/nf-core/deeptools/computematrix/meta.yml b/modules/nf-core/deeptools/computematrix/meta.yml index a48dec39262..1ab222081bb 100644 --- a/modules/nf-core/deeptools/computematrix/meta.yml +++ b/modules/nf-core/deeptools/computematrix/meta.yml @@ -7,46 +7,56 @@ keywords: - matrix tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bigwig: - type: file - description: bigwig file containing genomic scores - pattern: "*.{bw,bigwig}" - - bed: - type: file - description: bed file containing genomic regions - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bigwig: + type: file + description: bigwig file containing genomic scores + pattern: "*.{bw,bigwig}" + - - bed: + type: file + description: bed file containing genomic regions + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - matrix: - type: file - description: | - gzipped matrix file needed by the plotHeatmap and plotProfile - deeptools utilities - pattern: "*.{computeMatrix.mat.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mat.gz": + type: file + description: | + gzipped matrix file needed by the plotHeatmap and plotProfile + deeptools utilities + pattern: "*.{computeMatrix.mat.gz}" - table: - type: file - description: | - tabular file containing the scores of the generated matrix - pattern: "*.{computeMatrix.vals.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mat.tab": + type: file + description: | + tabular file containing the scores of the generated matrix + pattern: "*.{computeMatrix.vals.mat.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jeremy1805" - "@edmundmiller" diff --git a/modules/nf-core/deeptools/multibamsummary/meta.yml b/modules/nf-core/deeptools/multibamsummary/meta.yml index 25362587b92..035f7f02241 100644 --- a/modules/nf-core/deeptools/multibamsummary/meta.yml +++ b/modules/nf-core/deeptools/multibamsummary/meta.yml @@ -7,44 +7,48 @@ keywords: - bin tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: One or more BAM files - pattern: "*.{bam}" - - bais: - type: file - description: Corresponding BAM file indexes - pattern: "*.bam.bai" - - labels: - type: string - description: User specified labels instead of default labels (file names). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: One or more BAM files + pattern: "*.{bam}" + - bais: + type: file + description: Corresponding BAM file indexes + pattern: "*.bam.bai" + - labels: + type: string + description: User specified labels instead of default labels (file names). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - matrix: - type: file - description: | - compressed numpy array of read coverage data used by plotCorrelation and plotPCA - deeptool utilities - pattern: "all_bam.bamSummary.npz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.npz": + type: file + description: | + compressed numpy array of read coverage data used by plotCorrelation and plotPCA + deeptool utilities + pattern: "all_bam.bamSummary.npz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/deeptools/plotcorrelation/meta.yml b/modules/nf-core/deeptools/plotcorrelation/meta.yml index 4b32e7b7ef4..d82ae170508 100644 --- a/modules/nf-core/deeptools/plotcorrelation/meta.yml +++ b/modules/nf-core/deeptools/plotcorrelation/meta.yml @@ -1,5 +1,6 @@ name: "deeptools_plotcorrelation" -description: Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input. +description: Visualises sample correlations using a compressed matrix generated by + mutlibamsummary or multibigwigsummary as input. keywords: - corrrelation - matrix @@ -7,53 +8,63 @@ keywords: - scatterplot tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - matrix: - type: file - description: | - compressed matrix file produced by - mutlibamsummary or multibigwigsummary - pattern: "*.{npz}" - - method: - type: string - description: | - Correlation coefficient to use for heatmap or scatterplot generation - pattern: "{spearman,pearson}" - - plot_type: - type: string - description: | - Type of output plot to display sample correlation - pattern: "{heatmap,scatterplot}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - matrix: + type: file + description: | + compressed matrix file produced by + mutlibamsummary or multibigwigsummary + pattern: "*.{npz}" + - - method: + type: string + description: | + Correlation coefficient to use for heatmap or scatterplot generation + pattern: "{spearman,pearson}" + - - plot_type: + type: string + description: | + Type of output plot to display sample correlation + pattern: "{heatmap,scatterplot}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotCorrelation.pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotCorrelation.pdf}" - matrix: - type: file - description: | - Tab-separated file containing a matrix of pairwise correlations - pattern: "*.{plotCorrelation.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: | + Tab-separated file containing a matrix of pairwise correlations + pattern: "*.{plotCorrelation.mat.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/deeptools/plotfingerprint/meta.yml b/modules/nf-core/deeptools/plotfingerprint/meta.yml index f8217440104..d659f02cf72 100644 --- a/modules/nf-core/deeptools/plotfingerprint/meta.yml +++ b/modules/nf-core/deeptools/plotfingerprint/meta.yml @@ -7,50 +7,66 @@ keywords: - bam tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: One or more BAM files - pattern: "*.{bam}" - - bais: - type: file - description: Corresponding BAM file indexes - pattern: "*.bam.bai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bams: + type: file + description: BAM files + pattern: "*.bam" + - bais: + type: file + description: Corresponding BAM file indexes + pattern: "*.bam.bai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotFingerprint.pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotFingerprint.pdf}" - matrix: - type: file - description: | - Output file summarizing the read counts per bin - pattern: "*.{plotFingerprint.raw.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.raw.txt": + type: file + description: | + Output file summarizing the read counts per bin + pattern: "*.{plotFingerprint.raw.txt}" - metrics: - type: file - description: | - file containing BAM file quality metrics - pattern: "*.{qcmetrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.qcmetrics.txt": + type: file + description: | + file containing BAM file quality metrics + pattern: "*.{qcmetrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@drpatelh" diff --git a/modules/nf-core/deeptools/plotheatmap/meta.yml b/modules/nf-core/deeptools/plotheatmap/meta.yml index 54ddeb0a004..7c4828ca2fd 100644 --- a/modules/nf-core/deeptools/plotheatmap/meta.yml +++ b/modules/nf-core/deeptools/plotheatmap/meta.yml @@ -7,44 +7,51 @@ keywords: - matrix tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - matrix: - type: file - description: | - gzipped matrix file produced by deeptools_ - computematrix deeptools utility - pattern: "*.{mat.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - matrix: + type: file + description: | + gzipped matrix file produced by deeptools_ + computematrix deeptools utility + pattern: "*.{mat.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotHeatmap.pdf}" - - matrix: - type: file - description: | - File containing the matrix of values - used to generate the heatmap - pattern: "*.{plotHeatmap.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotHeatmap.pdf}" + - table: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: Output table - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@drpatelh" diff --git a/modules/nf-core/deeptools/plotpca/meta.yml b/modules/nf-core/deeptools/plotpca/meta.yml index b04b60ccebc..ea999922695 100644 --- a/modules/nf-core/deeptools/plotpca/meta.yml +++ b/modules/nf-core/deeptools/plotpca/meta.yml @@ -1,5 +1,6 @@ name: "deeptools_plotpca" -description: Generates principal component analysis (PCA) plot using a compressed matrix generated by multibamsummary or multibigwigsummary as input. +description: Generates principal component analysis (PCA) plot using a compressed + matrix generated by multibamsummary or multibigwigsummary as input. keywords: - PCA - matrix @@ -7,43 +8,53 @@ keywords: - bigwig tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - matrix: - type: file - description: | - compressed matrix file produced by - mutlibamsummary or multibigwigsummary - pattern: "*.{npz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - matrix: + type: file + description: | + compressed matrix file produced by + mutlibamsummary or multibigwigsummary + pattern: "*.{npz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotPCA.pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotPCA.pdf}" - tab: - type: file - description: | - Tab file containing data used to generate the PCA plot - pattern: "*.{plotPCA.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: | + Tab file containing data used to generate the PCA plot + pattern: "*.{plotPCA.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/deeptools/plotprofile/meta.yml b/modules/nf-core/deeptools/plotprofile/meta.yml index f7f10505532..8056816a8d9 100644 --- a/modules/nf-core/deeptools/plotprofile/meta.yml +++ b/modules/nf-core/deeptools/plotprofile/meta.yml @@ -7,44 +7,52 @@ keywords: - matrix tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - matrix: - type: file - description: | - gzipped matrix file produced by deeptools_ - computematrix deeptools utility - pattern: "*.{mat.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - matrix: + type: file + description: | + gzipped matrix file produced by deeptools_ + computematrix deeptools utility + pattern: "*.{mat.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotProfile.pdf}" - - matrix: - type: file - description: | - File containing the matrix of values - used to generate the profile - pattern: "*.{plotProfile.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotProfile.pdf}" + - table: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: Output table + pattern: "*.tab" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@drpatelh" diff --git a/modules/nf-core/deepvariant/callvariants/meta.yml b/modules/nf-core/deepvariant/callvariants/meta.yml index db779c62ba0..4507192ca2f 100644 --- a/modules/nf-core/deepvariant/callvariants/meta.yml +++ b/modules/nf-core/deepvariant/callvariants/meta.yml @@ -6,31 +6,39 @@ keywords: - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - make_examples_tfrecords: - type: file - description: The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process - pattern: "*.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - make_examples_tfrecords: + type: file + description: The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process + pattern: "*.gz" output: - call_variants_tfrecords: - type: list - description: | - Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. + - meta: + type: list + description: | + Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. + - ${prefix}.call-*-of-*.tfrecord.gz: + type: list + description: | + Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/makeexamples/meta.yml b/modules/nf-core/deepvariant/makeexamples/meta.yml index ab1d2e589a1..6fb9f1b8143 100644 --- a/modules/nf-core/deepvariant/makeexamples/meta.yml +++ b/modules/nf-core/deepvariant/makeexamples/meta.yml @@ -1,84 +1,98 @@ name: deepvariant_makeexamples -description: Transforms the input alignments to a format suitable for the deep neural network variant caller +description: Transforms the input alignments to a format suitable for the deep neural + network variant caller keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - intervals: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - pattern: "*.gzi" - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: Interval file for targeted regions + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + pattern: "*.gzi" + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" output: - examples: - type: list - description: | - Tuple containing sample metadata and examples that can be used for calling + - meta: + type: list + description: | + Tuple containing sample metadata and examples that can be used for calling + - ${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}: + type: list + description: | + Tuple containing sample metadata and examples that can be used for calling - gvcf: - type: list - description: | - Tuple containing sample metadata and the GVCF data in tfrecord format + - meta: + type: list + description: | + Tuple containing sample metadata and the GVCF data in tfrecord format + - ${prefix}.gvcf.tfrecord-*-of-*.gz: + type: list + description: | + Tuple containing sample metadata and the GVCF data in tfrecord format - versions: - type: file - description: File containing the DeepVariant software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing the DeepVariant software version + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml index 30c0285ae3e..77dbf438c3f 100644 --- a/modules/nf-core/deepvariant/meta.yml +++ b/modules/nf-core/deepvariant/meta.yml @@ -1,89 +1,120 @@ name: deepvariant -description: (DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: (DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses + a deep neural network to call genetic variants from next-generation DNA sequencing + data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - interval: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: file containing intervals + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - vcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Tabix index of compressed VCF file + pattern: "*.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - gvcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Tabix index of compressed GVCF file + pattern: "*.g.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/postprocessvariants/meta.yml b/modules/nf-core/deepvariant/postprocessvariants/meta.yml index 03a0a6b8235..132a5263226 100644 --- a/modules/nf-core/deepvariant/postprocessvariants/meta.yml +++ b/modules/nf-core/deepvariant/postprocessvariants/meta.yml @@ -1,86 +1,109 @@ name: deepvariant_postprocessvariants -description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: DeepVariant is an analysis pipeline that uses a deep neural network to + call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variant_calls_tfrecord_files: - type: file - description: | - One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS - pattern: "*.tfrecord.gz" - - gvcf_tfrecords: - type: file - description: | - Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output - pattern: "*.gz" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variant_calls_tfrecord_files: + type: file + description: | + One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS + pattern: "*.tfrecord.gz" + - gvcf_tfrecords: + type: file + description: | + Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output + pattern: "*.gz" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - vcf_tbi: - type: file - description: Index for VCF - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Index for VCF + pattern: "*.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" - gvcf_tbi: - type: file - description: Index for GVCF - pattern: "*.g.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Index for GVCF + pattern: "*.g.vcf.gz.tbi" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml index a6ee5499285..29b45ff9173 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/meta.yml +++ b/modules/nf-core/deepvariant/rundeepvariant/meta.yml @@ -1,89 +1,119 @@ name: deepvariant_rundeepvariant -description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: DeepVariant is an analysis pipeline that uses a deep neural network to + call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - interval: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: file containing intervals + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - vcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Tabix index file of compressed VCF + pattern: "*.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - gvcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Tabix index file of compressed GVCF + pattern: "*.g.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/delly/call/meta.yml b/modules/nf-core/delly/call/meta.yml index cc378ffd62a..ef7c238d6b6 100644 --- a/modules/nf-core/delly/call/meta.yml +++ b/modules/nf-core/delly/call/meta.yml @@ -7,73 +7,88 @@ keywords: - bcf tools: - delly: - description: Structural variant discovery by integrated paired-end and split-read analysis + description: Structural variant discovery by integrated paired-end and split-read + analysis homepage: https://github.com/dellytools/delly documentation: https://github.com/dellytools/delly/blob/master/README.md doi: "10.1093/bioinformatics/bts378" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked - pattern: "*.{bam,cram}" - - input_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - vcf: - type: file - description: A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped - pattern: "*.{vcf.gz,bcf}" - - vcf_index: - type: file - description: The index of the BCF/VCF file - pattern: "*.{tbi,csi}" - - exclude_bed: - type: file - description: An optional bed file containing regions to exclude from the called VCF - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing fasta index information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference fasta file to identify split-reads - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate + marked + pattern: "*.{bam,cram}" + - input_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - vcf: + type: file + description: A BCF/VCF file to genotype with Delly. If this is supplied, the + variant calling will be skipped + pattern: "*.{vcf.gz,bcf}" + - vcf_index: + type: file + description: The index of the BCF/VCF file + pattern: "*.{tbi,csi}" + - exclude_bed: + type: file + description: An optional bed file containing regions to exclude from the called + VCF + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing fasta index information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference fasta file to identify split-reads + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bcf: - type: file - description: Called variants in BCF/VCF format. Specify either "bcf" or "vcf" in ext.suffix to define the output type - pattern: "*.{bcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf.gz}": + type: file + description: Called variants in BCF/VCF format. Specify either "bcf" or "vcf" + in ext.suffix to define the output type + pattern: "*.{bcf,vcf.gz}" - csi: - type: file - description: A generated csi index that matches the bcf output (not generated for vcf files) - pattern: "*.{bcf.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: A generated csi index that matches the bcf output (not generated + for vcf files) + pattern: "*.{bcf.csi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@nvnieuwk" diff --git a/modules/nf-core/demuxem/meta.yml b/modules/nf-core/demuxem/meta.yml index 0aa94d1de60..2fb43f5780e 100644 --- a/modules/nf-core/demuxem/meta.yml +++ b/modules/nf-core/demuxem/meta.yml @@ -1,73 +1,81 @@ name: "demuxem" -description: Demultiplexing cell nucleus hashing data, using the estimated antibody background probability. +description: Demultiplexing cell nucleus hashing data, using the estimated antibody + background probability. keywords: - demultiplexing - hashing-based deconvoltion - single-cell tools: - demuxem: - description: "DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data." + description: "DemuxEM is the demultiplexing module of Pegasus, which works on + cell-hashing and nucleus-hashing genomics data." homepage: "https://demuxEM.readthedocs.io" documentation: "https://demuxEM.readthedocs.io" tool_dev_url: "https://github.com/lilab-bcb/pegasus/tree/master" doi: "10.1038/s41467-019-10756-2" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input_raw_gene_bc_matrices_h5: - type: string - description: | - Path to file containing input raw RNA expression matrix in 10x hdf5 format - pattern: "*.{h5}" - - input_hto_csv_file: - type: string - description: | - Path to file containing input HTO (antibody tag) count matrix in CSV format. - pattern: "*.{csv}" - - output_name: - type: string - description: | - Output name. All outputs will use it as the prefix. - - generate_gender_plot: - type: string - description: | - Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names. - - genome: - type: string - description: | - Reference genome name. If not provided, the tools infers it from the expression matrix file - - generate_diagnostic_plots: - type: string - description: | - Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input_raw_gene_bc_matrices_h5: + type: string + description: | + Path to file containing input raw RNA expression matrix in 10x hdf5 format + pattern: "*.{h5}" + - input_hto_csv_file: + type: string + description: | + Path to file containing input HTO (antibody tag) count matrix in CSV format. + pattern: "*.{csv}" + - - output_name: + type: string + description: | + Output name. All outputs will use it as the prefix. + - - generate_gender_plot: + type: string + description: | + Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names. + - - genome: + type: string + description: | + Reference genome name. If not provided, the tools infers it from the expression matrix file + - - generate_diagnostic_plots: + type: string + description: | + Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample1' ] - zarr: - type: file - description: | - RNA expression matrix with demultiplexed sample identities in Zarr format. - pattern: "*_demux.zarr.zip" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*_demux.zarr.zip": + type: file + description: | + RNA expression matrix with demultiplexed sample identities in Zarr format. + pattern: "*_demux.zarr.zip" - out_zarr: - type: file - description: | - DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA. - pattern: "*.out.demuxEM.zarr.zip" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*.out.demuxEM.zarr.zip": + type: file + description: | + DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA. + pattern: "*.out.demuxEM.zarr.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/deseq2/differential/meta.yml b/modules/nf-core/deseq2/differential/meta.yml index 41fcc014f02..be8cec47cb1 100644 --- a/modules/nf-core/deseq2/differential/meta.yml +++ b/modules/nf-core/deseq2/differential/meta.yml @@ -7,114 +7,167 @@ keywords: - deseq2 tools: - "deseq2": - description: "Differential gene expression analysis based on the negative binomial distribution" + description: "Differential gene expression analysis based on the negative binomial + distribution" homepage: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" tool_dev_url: "https://github.com/mikelove/DESeq2" doi: "10.1186/s13059-014-0550-8" licence: ["LGPL >=3"] + identifier: biotools:deseq2 input: - - meta: - type: map - description: | - Groovy Map containing contrast information. This can be used at the - workflow level to pass optional parameters to the module, e.g. - [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: - '--blocking_variable $meta.blocking'. - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - counts: - type: file - description: | - Raw TSV or CSV format expression matrix as output from the nf-core - RNA-seq workflow - - meta3: - type: file - description: | - Meta map describing control genes, e.g. [ id: 'ERCC' ] - - control_genes_file: - type: file - description: | - Text file listing control genes, one per line - - meta4: - type: map - description: | - Groovy map containing study-wide metadata related to the transcript - lengths file - - transcript_lengths_file: - type: file - description: | - Optional file of transcript lengths, with the same sample columns as - counts. If supplied, lengths will be supplied to DESeq2 to correct for - differences in average transcript lengths across samples. - + - - meta: + type: map + description: | + Groovy Map containing contrast information. This can be used at the + workflow level to pass optional parameters to the module, e.g. + [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: + '--blocking_variable $meta.blocking'. + - contrast_variable: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata + - counts: + type: file + description: | + Raw TSV or CSV format expression matrix as output from the nf-core + RNA-seq workflow + - - meta3: + type: file + description: | + Meta map describing control genes, e.g. [ id: 'ERCC' ] + - control_genes_file: + type: file + description: | + Text file listing control genes, one per line + - - meta4: + type: map + description: | + Groovy map containing study-wide metadata related to the transcript + lengths file + - transcript_lengths_file: + type: file + description: | + Optional file of transcript lengths, with the same sample columns as + counts. If supplied, lengths will be supplied to DESeq2 to correct for + differences in average transcript lengths across samples. output: - results: - type: file - description: TSV-format table of differential expression information as output by DESeq2 - pattern: "deseq2.results.tsv" + - meta: + type: file + description: TSV-format table of differential expression information as output + by DESeq2 + pattern: "deseq2.results.tsv" + - "*.deseq2.results.tsv": + type: file + description: TSV-format table of differential expression information as output + by DESeq2 + pattern: "deseq2.results.tsv" - dispersion_plot: - type: file - description: DESeq2 dispersion plot - pattern: "deseq2.dispersion.png" + - meta: + type: file + description: DESeq2 dispersion plot + pattern: "deseq2.dispersion.png" + - "*.deseq2.dispersion.png": + type: file + description: DESeq2 dispersion plot + pattern: "deseq2.dispersion.png" - rdata: - type: file - description: Serialised DESeq2 object - pattern: "dds.rld.rds" + - meta: + type: file + description: Serialised DESeq2 object + pattern: "dds.rld.rds" + - "*.dds.rld.rds": + type: file + description: Serialised DESeq2 object + pattern: "dds.rld.rds" - size_factors: - type: file - description: Size factors - pattern: "deseq2.sizefactors.tsv" + - meta: + type: file + description: Size factors + pattern: "deseq2.sizefactors.tsv" + - "*.deseq2.sizefactors.tsv": + type: file + description: Size factors + pattern: "deseq2.sizefactors.tsv" - normalised_counts: - type: file - description: TSV-format counts matrix, normalised to size factors - pattern: "normalised_counts.tsv" + - meta: + type: file + description: TSV-format counts matrix, normalised to size factors + pattern: "normalised_counts.tsv" + - "*.normalised_counts.tsv": + type: file + description: TSV-format counts matrix, normalised to size factors + pattern: "normalised_counts.tsv" - rlog_counts: - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `rlog()`. - pattern: "rlog.tsv" + - meta: + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `rlog()`. + pattern: "rlog.tsv" + - "*.rlog.tsv": + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `rlog()`. + pattern: "rlog.tsv" - vst_counts: - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `vst()`. - pattern: "vst_counts.tsv" + - meta: + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `vst()`. + pattern: "vst_counts.tsv" + - "*.vst.tsv": + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `vst()`. + pattern: "vst_counts.tsv" - model: - type: file - description: TXT-format DESeq2 model - pattern: "deseq2.model.tsv" + - meta: + type: file + description: TXT-format DESeq2 model + pattern: "deseq2.model.tsv" + - "*.deseq2.model.txt": + type: file + description: TXT-format DESeq2 model + pattern: "deseq2.model.tsv" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: file + description: dump of R SessionInfo + pattern: "*.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/diamond/blastp/meta.yml b/modules/nf-core/diamond/blastp/meta.yml index bab6801eaa2..fbddfbd00f1 100644 --- a/modules/nf-core/diamond/blastp/meta.yml +++ b/modules/nf-core/diamond/blastp/meta.yml @@ -13,77 +13,116 @@ tools: tool_dev_url: https://github.com/bbuchfink/diamond doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3.0"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: file - description: File of the indexed DIAMOND database - pattern: "*.dmnd" - - out_ext: - type: string - description: | - Specify the type of output file to be generated. `blast` corresponds to - BLAST pairwise format. `xml` corresponds to BLAST xml format. - `txt` corresponds to to BLAST tabular format. `tsv` corresponds to - taxonomic classification format. - pattern: "blast|xml|txt|daa|sam|tsv|paf" - - blast_columns: - type: string - description: | - Optional space separated list of DIAMOND tabular BLAST output keywords - used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: - qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: file + description: File of the indexed DIAMOND database + pattern: "*.dmnd" + - - out_ext: + type: string + description: | + Specify the type of output file to be generated. `blast` corresponds to + BLAST pairwise format. `xml` corresponds to BLAST xml format. + `txt` corresponds to to BLAST tabular format. `tsv` corresponds to + taxonomic classification format. + pattern: "blast|xml|txt|daa|sam|tsv|paf" + - - blast_columns: + type: string + description: | + Optional space separated list of DIAMOND tabular BLAST output keywords + used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: + qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - blast: - type: file - description: File containing blastp hits - pattern: "*.{blast}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.blast": + type: file + description: File containing blastp hits + pattern: "*.{blast}" - xml: - type: file - description: File containing blastp hits - pattern: "*.{xml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xml": + type: file + description: File containing blastp hits + pattern: "*.{xml}" - txt: - type: file - description: File containing hits in tabular BLAST format. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing hits in tabular BLAST format. + pattern: "*.{txt}" - daa: - type: file - description: File containing hits DAA format - pattern: "*.{daa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.daa": + type: file + description: File containing hits DAA format + pattern: "*.{daa}" - sam: - type: file - description: File containing aligned reads in SAM format - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: File containing aligned reads in SAM format + pattern: "*.{sam}" - tsv: - type: file - description: Tab separated file containing taxonomic classification of hits - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab separated file containing taxonomic classification of hits + pattern: "*.{tsv}" - paf: - type: file - description: File containing aligned reads in pairwise mapping format format - pattern: "*.{paf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: File containing aligned reads in pairwise mapping format format + pattern: "*.{paf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" - "@jfy133" diff --git a/modules/nf-core/diamond/blastx/meta.yml b/modules/nf-core/diamond/blastx/meta.yml index 17106548d6a..a5c05875811 100644 --- a/modules/nf-core/diamond/blastx/meta.yml +++ b/modules/nf-core/diamond/blastx/meta.yml @@ -13,81 +13,126 @@ tools: tool_dev_url: https://github.com/bbuchfink/diamond doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3.0"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: file - description: File of the indexed DIAMOND database - pattern: "*.dmnd" - - out_ext: - type: string - description: | - Specify the type of output file to be generated. `blast` corresponds to - BLAST pairwise format. `xml` corresponds to BLAST xml format. - `txt` corresponds to to BLAST tabular format. `tsv` corresponds to - taxonomic classification format. - pattern: "blast|xml|txt|daa|sam|tsv|paf" - - blast_columns: - type: string - description: | - Optional space separated list of DIAMOND tabular BLAST output keywords - used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: - qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: file + description: File of the indexed DIAMOND database + pattern: "*.dmnd" + - - out_ext: + type: string + description: | + Specify the type of output file to be generated. `blast` corresponds to + BLAST pairwise format. `xml` corresponds to BLAST xml format. + `txt` corresponds to to BLAST tabular format. `tsv` corresponds to + taxonomic classification format. + pattern: "blast|xml|txt|daa|sam|tsv|paf" + - - blast_columns: + type: string + description: | + Optional space separated list of DIAMOND tabular BLAST output keywords + used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: + qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - blast: - type: file - description: File containing blastp hits - pattern: "*.{blast}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.blast": + type: file + description: File containing blastp hits + pattern: "*.{blast}" - xml: - type: file - description: File containing blastp hits - pattern: "*.{xml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xml": + type: file + description: File containing blastp hits + pattern: "*.{xml}" - txt: - type: file - description: File containing hits in tabular BLAST format. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing hits in tabular BLAST format. + pattern: "*.{txt}" - daa: - type: file - description: File containing hits DAA format - pattern: "*.{daa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.daa": + type: file + description: File containing hits DAA format + pattern: "*.{daa}" - sam: - type: file - description: File containing aligned reads in SAM format - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: File containing aligned reads in SAM format + pattern: "*.{sam}" - tsv: - type: file - description: Tab separated file containing taxonomic classification of hits - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab separated file containing taxonomic classification of hits + pattern: "*.{tsv}" - paf: - type: file - description: File containing aligned reads in pairwise mapping format format - pattern: "*.{paf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: File containing aligned reads in pairwise mapping format format + pattern: "*.{paf}" - log: - type: file - description: Log file containing stdout information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stdout information + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" - "@jfy133" diff --git a/modules/nf-core/diamond/cluster/meta.yml b/modules/nf-core/diamond/cluster/meta.yml index 4858b240687..49699cece32 100644 --- a/modules/nf-core/diamond/cluster/meta.yml +++ b/modules/nf-core/diamond/cluster/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "diamond_cluster" description: calculate clusters of highly similar sequences @@ -15,36 +14,36 @@ tools: tool_dev_url: "https://github.com/bbuchfink/diamond" doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3-or-later"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - db: - type: file - description: The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format. - pattern: "*.{dmnd,fa,faa,fasta}(.gz)" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - db: + type: file + description: The input sequence database. Supported formats are FASTA and DIAMOND + (.dmnd) format. + pattern: "*.{dmnd,fa,faa,fasta}(.gz)" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tsv: - type: file - description: a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: a 2-column tabular file with the representative accession as the + first column and the member sequence accession as the second column + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@itrujnara" maintainers: diff --git a/modules/nf-core/diamond/makedb/meta.yml b/modules/nf-core/diamond/makedb/meta.yml index fdcf032dba5..71de32eef86 100644 --- a/modules/nf-core/diamond/makedb/meta.yml +++ b/modules/nf-core/diamond/makedb/meta.yml @@ -13,42 +13,46 @@ tools: tool_dev_url: https://github.com/bbuchfink/diamond doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3.0"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - taxonmap: - type: file - description: Optional mapping file of NCBI protein accession numbers to taxon ids (gzip compressed), required for taxonomy functionality. - pattern: "*.gz" - - taxonnodes: - type: file - description: Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality. - pattern: "*.dmp" - - taxonnames: - type: file - description: Optional NCBI taxonomy names.dmp file, required for taxonomy functionality. - pattern: "*.dmp" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - taxonmap: + type: file + description: Optional mapping file of NCBI protein accession numbers to taxon + ids (gzip compressed), required for taxonomy functionality. + pattern: "*.gz" + - - taxonnodes: + type: file + description: Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality. + pattern: "*.dmp" + - - taxonnames: + type: file + description: Optional NCBI taxonomy names.dmp file, required for taxonomy functionality. + pattern: "*.dmp" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - db: - type: file - description: File of the indexed DIAMOND database - pattern: "*.dmnd" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dmnd": + type: file + description: File of the indexed DIAMOND database + pattern: "*.dmnd" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" maintainers: diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml index 2f1191b2ec6..547e6f24a5f 100644 --- a/modules/nf-core/dragmap/align/environment.yml +++ b/modules/nf-core/dragmap/align/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - dragmap=1.3.0 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.18 - pigz=2.8 + - samtools=1.18 diff --git a/modules/nf-core/dragmap/align/meta.yml b/modules/nf-core/dragmap/align/meta.yml index 2270bd3397d..80f020f58f1 100644 --- a/modules/nf-core/dragmap/align/meta.yml +++ b/modules/nf-core/dragmap/align/meta.yml @@ -13,44 +13,104 @@ tools: documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - hashmap: - type: file - description: DRAGMAP hash table - pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fasta: - type: file - description: Genome fasta reference files - pattern: "*.{fa,fasta,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - hashmap: + type: file + description: DRAGMAP hash table + pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fasta: + type: file + description: Genome fasta reference files + pattern: "*.{fa,fasta,fna}" + - - sort_bam: + type: boolean + description: Sort the BAM file output: + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.{sam}" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Index file for CRAM file + pattern: "*.{crai}" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Index file for CRAM file + pattern: "*.{csi}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/dragmap/hashtable/meta.yml b/modules/nf-core/dragmap/hashtable/meta.yml index 1d1f92f5228..450a1e58e06 100644 --- a/modules/nf-core/dragmap/hashtable/meta.yml +++ b/modules/nf-core/dragmap/hashtable/meta.yml @@ -12,29 +12,32 @@ tools: documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - hashmap: - type: file - description: DRAGMAP hash table - pattern: "*.{cmp,.bin,.txt}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - dragmap: + type: file + description: DRAGMAP hash table + pattern: "*.{cmp,.bin,.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/dragonflye/meta.yml b/modules/nf-core/dragonflye/meta.yml index 60ccad45341..0c5edd88a43 100644 --- a/modules/nf-core/dragonflye/meta.yml +++ b/modules/nf-core/dragonflye/meta.yml @@ -10,51 +10,78 @@ tools: homepage: https://github.com/rpetit3/dragonflye documentation: https://github.com/rpetit3/dragonflye/blob/main/README.md licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - shortreads: - type: file - description: | - Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome. - pattern: "*.fastq.gz" - - longreads: - type: file - description: Input Nanopore FASTQ file - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shortreads: + type: file + description: | + Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome. + pattern: "*.fastq.gz" + - longreads: + type: file + description: Input Nanopore FASTQ file + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - contigs: - type: file - description: The final assembly produced by Dragonflye - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: The final assembly produced by Dragonflye + pattern: "*.fa" - log: - type: file - description: Full log file for bug reporting - pattern: "dragonflye.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dragonflye.log: + type: file + description: Full log file for bug reporting + pattern: "dragonflye.log" - raw_contigs: - type: file - description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven) - pattern: "{flye,miniasm,raven}.fasta" - - txt: - type: file - description: Assembly information output by Flye - pattern: "flye-info.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "{flye,miniasm,raven}.fasta": + type: file + description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven) + pattern: "{flye,miniasm,raven}.fasta" - gfa: - type: file - description: Assembly graph produced by Miniasm, or Raven - pattern: "{flye,miniasm,raven}-unpolished.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "{flye,miniasm,raven}-unpolished.gfa": + type: file + description: Assembly graph produced by Miniasm, or Raven + pattern: "{flye,miniasm,raven}-unpolished.gfa" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - flye-info.txt: + type: file + description: Assembly information output by Flye + pattern: "flye-info.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/dshbio/exportsegments/meta.yml b/modules/nf-core/dshbio/exportsegments/meta.yml index e0e83734205..c5ccac39a84 100644 --- a/modules/nf-core/dshbio/exportsegments/meta.yml +++ b/modules/nf-core/dshbio/exportsegments/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly segments in uncompressed or compressed GFA 1.0 format - pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly segments in uncompressed or compressed GFA 1.0 format + pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Assembly segment sequences in gzipped FASTA format - pattern: "*.{fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa.gz": + type: file + description: Assembly segment sequences in gzipped FASTA format + pattern: "*.{fa.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/filterbed/meta.yml b/modules/nf-core/dshbio/filterbed/meta.yml index 7e8abc8b25a..0669239934d 100644 --- a/modules/nf-core/dshbio/filterbed/meta.yml +++ b/modules/nf-core/dshbio/filterbed/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format - pattern: "*.{bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Features in gzipped BED format + pattern: "*.{bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Features in gzipped BED format - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Features in gzipped BED format + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/filtergff3/meta.yml b/modules/nf-core/dshbio/filtergff3/meta.yml index 5b4da52e787..2a3973a4dd4 100644 --- a/modules/nf-core/dshbio/filtergff3/meta.yml +++ b/modules/nf-core/dshbio/filtergff3/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format - pattern: "*.{gff3.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff3: + type: file + description: Features in gzipped GFF3 format + pattern: "*.{gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gff3: - type: file - description: Features in gzipped GFF3 format - pattern: "*.{gff3.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff3.gz": + type: file + description: Features in gzipped GFF3 format + pattern: "*.{gff3.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/splitbed/meta.yml b/modules/nf-core/dshbio/splitbed/meta.yml index 91d37f0f220..4ef53e7067a 100644 --- a/modules/nf-core/dshbio/splitbed/meta.yml +++ b/modules/nf-core/dshbio/splitbed/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format to split - pattern: "*.{bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Features in gzipped BED format to split + pattern: "*.{bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Features in split gzipped BED formatted files - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Features in split gzipped BED formatted files + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/splitgff3/meta.yml b/modules/nf-core/dshbio/splitgff3/meta.yml index 4de6614e1ff..2e96c20cd6b 100644 --- a/modules/nf-core/dshbio/splitgff3/meta.yml +++ b/modules/nf-core/dshbio/splitgff3/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format to split - pattern: "*.{gff3.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff3: + type: file + description: Features in gzipped GFF3 format to split + pattern: "*.{gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gff3: - type: file - description: Features in split gzipped GFF3 formatted files - pattern: "*.{gff3.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff3.gz": + type: file + description: Features in split gzipped GFF3 formatted files + pattern: "*.{gff3.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/duphold/meta.yml b/modules/nf-core/duphold/meta.yml index 934fe8ed69c..da4d166055f 100644 --- a/modules/nf-core/duphold/meta.yml +++ b/modules/nf-core/duphold/meta.yml @@ -1,5 +1,9 @@ name: "duphold" -description: SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content. +description: SV callers like lumpy look at split-reads and pair distances to find + structural variants. This tool is a fast way to add depth information to those calls. + This can be used as additional information for filtering variants; for example we + will be skeptical of deletion calls that do not have lower than average coverage + compared to regions with similar gc-content. keywords: - sort - duphold @@ -7,52 +11,62 @@ keywords: - depth information tools: - "duphold": - description: "SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls." + description: "SV callers like lumpy look at split-reads and pair distances to + find structural variants. This tool is a fast way to add depth information to + those calls." homepage: "https://github.com/brentp/duphold" documentation: "https://github.com/brentp/duphold" tool_dev_url: "https://github.com/brentp/duphold" doi: "10.1093/gigascience/giz040" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - aligment_file: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - aligment_file_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - sv_variants: - type: file - description: A variants file containing structural variants - pattern: "*.{vcf,bcf}(.gz)?" - - snp_variants: - type: file - description: A variants file containing SNPs - pattern: "*.{vcf,bcf}(.gz)?" - - snp_variants: - type: file - description: The index of the variants file containing SNPs - pattern: "*.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment_file: + type: file + description: file containing alignments + - alignement_index: + type: file + description: index of alignment file + - sv_variants: + type: file + description: A variants file containing structural variants + pattern: "*.{vcf,bcf}(.gz)?" + - snp_variants: + type: file + description: A variants file containing SNPs + pattern: "*.{vcf,bcf}(.gz)?" + - snp_variants_index: + type: file + description: index of snp variants file + - - fasta: + type: file + description: fasta file + pattern: "*.{fa,fasta,fna}" + - - fasta_fai: + type: file + description: Index of fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The output VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The output VCF + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/dupradar/meta.yml b/modules/nf-core/dupradar/meta.yml index 95960ae989d..a532519fea7 100644 --- a/modules/nf-core/dupradar/meta.yml +++ b/modules/nf-core/dupradar/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "dupradar" description: Assessment of duplication rates in RNA-Seq datasets @@ -14,71 +13,109 @@ tools: tool_dev_url: "https://github.com/ssayols/dupRadar" doi: "10.1186/s12859-016-1276-2" licence: ["GPL v3"] + identifier: biotools:dupradar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'human' ] - - gtf: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file containing read alignments + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'human' ] + - gtf: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - scatter2d: - type: file - description: PDF duplication rate against total read count plot - pattern: "*_duprateExpDens.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpDens.pdf": + type: file + description: PDF duplication rate against total read count plot + pattern: "*_duprateExpDens.pdf" - boxplot: - type: file - description: | - PDF duplication rate ~ total reads per kilobase (RPK) boxplot - pattern: "*_duprateExpBoxplot.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpBoxplot.pdf": + type: file + description: | + PDF duplication rate ~ total reads per kilobase (RPK) boxplot + pattern: "*_duprateExpBoxplot.pdf" - hist: - type: file - description: | - PDF expression histogram - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_expressionHist.pdf": + type: file + description: | + PDF expression histogram + pattern: "*.pdf" - dupmatrix: - type: file - description: | - Text file containing tags falling on the features described in the GTF - file - pattern: "*_dupMatrix.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_dupMatrix.txt": + type: file + description: | + Text file containing tags falling on the features described in the GTF + file + pattern: "*_dupMatrix.txt" - intercept_slope: - type: file - description: | - Text file containing intercept and slope from dupRadar modelling - pattern: "*_intercept_slope.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_intercept_slope.txt": + type: file + description: | + Text file containing intercept and slope from dupRadar modelling + pattern: "*_intercept_slope.txt" - multiqc: - type: file - description: | - dupRadar files for passing to MultiQC - pattern: "*_multiqc.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_mqc.txt": + type: file + description: | + dupRadar files for passing to MultiQC + pattern: "*_multiqc.txt" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/dysgu/meta.yml b/modules/nf-core/dysgu/meta.yml index 67c6c70abf8..227a41169db 100644 --- a/modules/nf-core/dysgu/meta.yml +++ b/modules/nf-core/dysgu/meta.yml @@ -1,6 +1,7 @@ name: dysgu -description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations. +description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It + is designed for accurate and efficient detection of structural variations. keywords: - structural variants - sv @@ -13,54 +14,61 @@ tools: tool_dev_url: https://github.com/kcleal/dysgu doi: "10.1093/nar/gkac039" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - input: - type: file - description: Input BAM file - pattern: "*.bam" - - index: - type: file - description: BAM index file - pattern: "*.bai" - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - input: + type: file + description: Input BAM file + pattern: "*.bam" + - index: + type: file + description: BAM index file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample1' ] - vcf: - type: file - description: VCF file with identified structural variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*.vcf.gz": + type: file + description: VCF file with identified structural variants + pattern: "*.{vcf.gz}" - tbi: - type: file - description: The index of the BCF/VCF file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*.vcf.gz.tbi": + type: file + description: The index of the BCF/VCF file + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@famosab" - "@poddarharsh15" diff --git a/modules/nf-core/ectyper/meta.yml b/modules/nf-core/ectyper/meta.yml index 58ae53b687f..97accd7bb62 100644 --- a/modules/nf-core/ectyper/meta.yml +++ b/modules/nf-core/ectyper/meta.yml @@ -11,38 +11,53 @@ tools: documentation: https://github.com/phac-nml/ecoli_serotyping tool_dev_url: https://github.com/phac-nml/ecoli_serotyping licence: ["Apache 2"] + identifier: biotools:ectyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA formatted assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA formatted assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: ectyper log output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: ectyper log output + pattern: "*.log" - tsv: - type: file - description: ectyper serotyping results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: ectyper serotyping results in TSV format + pattern: "*.tsv" - txt: - type: file - description: Allele report generated from BLAST results - pattern: "*.tst" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Allele report generated from BLAST results + pattern: "*.tst" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/eggnogmapper/meta.yml b/modules/nf-core/eggnogmapper/meta.yml index 95090a10c65..8cf836d0874 100644 --- a/modules/nf-core/eggnogmapper/meta.yml +++ b/modules/nf-core/eggnogmapper/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "eggnogmapper" description: Fast genome-wide functional annotation through orthology assignment. @@ -14,55 +13,71 @@ tools: tool_dev_url: "https://github.com/eggnogdb/eggnog-mapper" doi: "10.1093/molbev/msab293" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Database of sequences in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - eggnog_db: - type: file - description: The eggnog database file (e.g. eggnog-mapper/data/eggnog.db) - pattern: "*.db" - - eggnog_data_dir: - type: directory - description: Directory containing eggnog database files (e.g. eggnog-mapper/data) - pattern: "*" - - meta2: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test' ]` - - eggnog_diamond_db: - type: file - description: The eggnog Diamond protein database file (e.g. eggnog-mapper/data/eggnog_proteins.dmnd) - pattern: "*.dmnd" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Database of sequences in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - eggnog_db: + type: file + description: The eggnog database file (e.g. eggnog-mapper/data/eggnog.db) + pattern: "*.db" + - - eggnog_data_dir: + type: directory + description: Directory containing eggnog database files (e.g. eggnog-mapper/data) + pattern: "*" + - - meta2: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test' ]` + - eggnog_diamond_db: + type: file + description: The eggnog Diamond protein database file (e.g. eggnog-mapper/data/eggnog_proteins.dmnd) + pattern: "*.dmnd" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - annotations: - type: file - description: TSV with the results from the annotation phase - pattern: "*.emapper.annotations" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.emapper.annotations": + type: file + description: TSV with the results from the annotation phase + pattern: "*.emapper.annotations" - orthologs: - type: file - description: TSV with the results from parsing the hits, linking queries with seed orthologs (with commented metadata) - pattern: "*.emapper.seed_orthologs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.emapper.seed_orthologs": + type: file + description: TSV with the results from parsing the hits, linking queries with + seed orthologs (with commented metadata) + pattern: "*.emapper.seed_orthologs" - hits: - type: file - description: TSV with the results from the Diamond search phase - pattern: "*.emapper.hits" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.emapper.hits": + type: file + description: TSV with the results from the Diamond search phase + pattern: "*.emapper.hits" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/eido/convert/meta.yml b/modules/nf-core/eido/convert/meta.yml index 9c84140154f..a7c292c6981 100644 --- a/modules/nf-core/eido/convert/meta.yml +++ b/modules/nf-core/eido/convert/meta.yml @@ -13,25 +13,30 @@ tools: documentation: "http://eido.databio.org/en/latest/" doi: "10.1093/gigascience/giab077" licence: ["BSD-2-Clause"] + identifier: biotools:eido-python-package input: - - samplesheet: - type: file - description: Nextflow samplesheet or PEP project - pattern: "*.{yaml,yml,csv}" - - format: - type: string - description: Extension of an output file - - pep_input_base_dir: - type: file - description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory. + - - samplesheet: + type: file + description: Nextflow samplesheet or PEP project + pattern: "*.{yaml,yml,csv}" + - - format: + type: string + description: Extension of an output file + - - pep_input_base_dir: + type: file + description: Optional path to the directory where files specified in a PEP config + file are stored. Any paths specified in the config will need to be relative + to this base directory. output: - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - samplesheet_converted: - type: file - description: PEP project or samplesheet converted to csv file + - ${prefix}.${format}: + type: file + description: PEP project or samplesheet converted to csv file authors: - "@rafalstepien" maintainers: diff --git a/modules/nf-core/eido/validate/meta.yml b/modules/nf-core/eido/validate/meta.yml index 3d895af2903..d5d4016ea01 100644 --- a/modules/nf-core/eido/validate/meta.yml +++ b/modules/nf-core/eido/validate/meta.yml @@ -13,27 +13,32 @@ tools: documentation: "http://eido.databio.org/en/latest/" doi: "10.1093/gigascience/giab077" licence: ["BSD-2-Clause"] + identifier: biotools:eido-python-package input: - - samplesheet: - type: file - description: Samplesheet or PEP file to be validated - pattern: "*.{yaml,yml,csv}" - - schema: - type: file - description: Schema that the samplesheet will be validated against - pattern: "*.{yaml,yml}" - - pep_input_base_dir: - type: file - description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory. + - - samplesheet: + type: file + description: Samplesheet or PEP file to be validated + pattern: "*.{yaml,yml,csv}" + - - schema: + type: file + description: Schema that the samplesheet will be validated against + pattern: "*.{yaml,yml}" + - - pep_input_base_dir: + type: file + description: Optional path to the directory where files specified in a PEP config + file are stored. Any paths specified in the config will need to be relative + to this base directory. output: - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log: - type: file - description: File containing validation log. - pattern: "*.log" + - "*.log": + type: file + description: File containing validation log. + pattern: "*.log" authors: - "@rafalstepien" maintainers: diff --git a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml index bb4c7f84b7f..ac92ca85d3b 100644 --- a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml +++ b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml @@ -1,5 +1,6 @@ name: "eigenstratdatabasetools_eigenstratsnpcoverage" -description: Provide the SNP coverage of each individual in an eigenstrat formatted dataset. +description: Provide the SNP coverage of each individual in an eigenstrat formatted + dataset. keywords: - coverage - eigenstrat @@ -8,46 +9,56 @@ keywords: - snps tools: - "eigenstratdatabasetools": - description: "A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases." + description: "A set of tools to compare and manipulate the contents of EingenStrat + databases, and to calculate SNP coverage statistics in such databases." documentation: "https://github.com/TCLamnidis/EigenStratDatabaseTools/README.md" tool_dev_url: "https://github.com/TCLamnidis/EigenStratDatabaseTools" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - geno: - type: file - description: An Eigenstrat formatted genotype file - pattern: "*.{geno}" - - snp: - type: file - description: An Eigenstrat formatted snp file - pattern: "*.{snp}" - - ind: - type: file - description: An Eigenstrat formatted individual file - pattern: "*.{ind}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - geno: + type: file + description: An Eigenstrat formatted genotype file + pattern: "*.{geno}" + - snp: + type: file + description: An Eigenstrat formatted snp file + pattern: "*.{snp}" + - ind: + type: file + description: An Eigenstrat formatted individual file + pattern: "*.{ind}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV table with the number of covered SNPs per individual. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV table with the number of covered SNPs per individual. + pattern: "*.{tsv}" - json: - type: file - description: A json table with the number of covered SNPs per individual. - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: A json table with the number of covered SNPs per individual. + pattern: "*.{json}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@TCLamnidis" maintainers: diff --git a/modules/nf-core/eklipse/meta.yml b/modules/nf-core/eklipse/meta.yml index 0f5e88a88aa..cf31919594c 100644 --- a/modules/nf-core/eklipse/meta.yml +++ b/modules/nf-core/eklipse/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "eklipse" description: tool for detection and quantification of large mtDNA rearrangements. @@ -17,42 +16,62 @@ tools: tool_dev_url: "https://github.com/dooguypapua/eKLIPse/tree/master" doi: "10.1038/s41436-018-0350-8" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: MT BAM/SAM file - pattern: "*.{bam,sam}" - - bai: - type: file - description: MT BAM/SAM index file - pattern: "*.{bai,sai}" - - ref_gb: - type: file - description: mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used - pattern: "*.{gb}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: MT BAM/SAM file + pattern: "*.{bam,sam}" + - bai: + type: file + description: MT BAM/SAM index file + pattern: "*.{bai,sai}" + - - ref_gb: + type: file + description: mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb + will be used + pattern: "*.{gb}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: csv file containing deletions - pattern: "*.{csv}" + - deletions: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*deletions.csv": + type: file + description: csv file with deletion information + pattern: "*deletions.csv" + - genes: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*genes.csv": + type: file + description: csv file with gene information + pattern: "*genes.csv" - circos: - type: file - description: png file with circos plot of mt - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: png file with circos plot of mt + pattern: "*.{png}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml index 01d76648e91..5ada70e4eb4 100644 --- a/modules/nf-core/elprep/filter/meta.yml +++ b/modules/nf-core/elprep/filter/meta.yml @@ -1,5 +1,6 @@ name: "elprep_filter" -description: "Filter, sort and markdup sam/bam files, with optional BQSR and variant calling." +description: "Filter, sort and markdup sam/bam files, with optional BQSR and variant + calling." keywords: - sort - bam @@ -8,103 +9,156 @@ keywords: - variant calling tools: - "elprep": - description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." homepage: "https://github.com/ExaScience/elprep" documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" licence: ["AGPL v3"] + identifier: biotools:elprep input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input SAM/BAM file - pattern: "*.{bam,sam}" - - run_haplotypecaller: - type: boolean - description: Run variant calling on the input files. Needed to generate gvcf output. - - run_bqsr: - type: boolean - description: Run BQSR on the input files. Needed to generate recall metrics. - - reference_sequences: - type: file - description: Optional SAM header to replace existing header. - pattern: "*.sam" - - filter_regions_bed: - type: file - description: Optional BED file containing regions to filter. - pattern: "*.bed" - - reference_elfasta: - type: file - description: Elfasta file, required for BQSR and variant calling. - pattern: "*.elfasta" - - known_sites_elsites: - type: file - description: Optional elsites file containing known SNPs for BQSR. - pattern: "*.elsites" - - target_regions_bed: - type: file - description: Optional BED file containing target regions for BQSR and variant calling. - pattern: "*.bed" - - intermediate_bqsr_tables: - type: file - description: Optional list of BQSR tables, used when parsing files created by `elprep split` - pattern: "*.table" - - bqsr_tables_only: - type: boolean - description: Write intermediate BQSR tables, used when parsing files created by `elprep split`. - - get_activity_profile: - type: boolean - description: Get the activity profile calculated by the haplotypecaller to the given file in IGV format. - - get_assembly_regions: - type: boolean - description: Get the assembly regions calculated by haplotypecaller to the speficied file in IGV format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input SAM/BAM file + pattern: "*.{bam,sam}" + - - run_haplotypecaller: + type: boolean + description: Run variant calling on the input files. Needed to generate gvcf + output. + - - run_bqsr: + type: boolean + description: Run BQSR on the input files. Needed to generate recall metrics. + - - reference_sequences: + type: file + description: Optional SAM header to replace existing header. + pattern: "*.sam" + - - filter_regions_bed: + type: file + description: Optional BED file containing regions to filter. + pattern: "*.bed" + - - reference_elfasta: + type: file + description: Elfasta file, required for BQSR and variant calling. + pattern: "*.elfasta" + - - known_sites_elsites: + type: file + description: Optional elsites file containing known SNPs for BQSR. + pattern: "*.elsites" + - - target_regions_bed: + type: file + description: Optional BED file containing target regions for BQSR and variant + calling. + pattern: "*.bed" + - - intermediate_bqsr_tables: + type: file + description: Optional list of BQSR tables, used when parsing files created by + `elprep split` + pattern: "*.table" + - - bqsr_tables_only: + type: boolean + description: Write intermediate BQSR tables, used when parsing files created + by `elprep split`. + - - get_activity_profile: + type: boolean + description: Get the activity profile calculated by the haplotypecaller to the + given file in IGV format. + - - get_assembly_regions: + type: boolean + description: Get the assembly regions calculated by haplotypecaller to the speficied + file in IGV format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted, markdup, optionally BQSR BAM/SAM file - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/**.{bam,sam}: + type: file + description: Sorted, markdup, optionally BQSR BAM/SAM file + pattern: "*.{bam,sam}" - logs: - type: list - description: Runtime log files - pattern: "elprep-*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - logs/elprep/elprep*: + type: list + description: Runtime log files + pattern: "elprep-*.log" - metrics: - type: file - description: Optional duplicate metrics file generated by elprep - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Optional duplicate metrics file generated by elprep + pattern: "*.{metrics.txt}" - recall: - type: file - description: Optional recall metrics file generated by elprep - pattern: "*.{recall}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recall": + type: file + description: Optional recall metrics file generated by elprep + pattern: "*.{recall}" - gvcf: - type: file - description: Optional GVCF output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Optional GVCF output file + pattern: "*.{vcf.gz}" - table: - type: file - description: Optional intermediate BQSR table output file - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Optional intermediate BQSR table output file + pattern: "*.{table}" - activity_profile: - type: file - description: Optional activity profile output file - pattern: "*.{activity_profile.igv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.activity_profile.igv": + type: file + description: Optional activity profile output file + pattern: "*.{activity_profile.igv}" - assembly_regions: - type: file - description: Optional activity regions output file - pattern: "*.{assembly_regions.igv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly_regions.igv": + type: file + description: Optional activity regions output file + pattern: "*.{assembly_regions.igv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/elprep/merge/meta.yml b/modules/nf-core/elprep/merge/meta.yml index ec7ec6de292..ffb6b30120f 100644 --- a/modules/nf-core/elprep/merge/meta.yml +++ b/modules/nf-core/elprep/merge/meta.yml @@ -6,37 +6,41 @@ keywords: - merge tools: - "elprep": - description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." homepage: "https://github.com/ExaScience/elprep" documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" licence: ["AGPL v3"] + identifier: biotools:elprep input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM/SAM chunks to merge - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM/SAM chunks to merge + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Merged BAM/SAM file - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/**.{bam,sam}: + type: file + description: Merged BAM/SAM file + pattern: "*.{bam,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/elprep/split/meta.yml b/modules/nf-core/elprep/split/meta.yml index c3854146a95..c3ebc297043 100644 --- a/modules/nf-core/elprep/split/meta.yml +++ b/modules/nf-core/elprep/split/meta.yml @@ -6,37 +6,41 @@ keywords: - chunk tools: - "elprep": - description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." homepage: "https://github.com/ExaScience/elprep" documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" licence: ["AGPL v3"] + identifier: biotools:elprep input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM/SAM files - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM/SAM files + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: List of split BAM/SAM files - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/**.{bam,sam}: + type: file + description: List of split BAM/SAM files + pattern: "*.{bam,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/emboss/cons/meta.yml b/modules/nf-core/emboss/cons/meta.yml index 4be6d581a8c..91e8aff8918 100644 --- a/modules/nf-core/emboss/cons/meta.yml +++ b/modules/nf-core/emboss/cons/meta.yml @@ -1,6 +1,7 @@ ---- name: "emboss_cons" -description: cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment. +description: cons calculates a consensus sequence from a multiple sequence alignment. + To obtain the consensus, the sequence weights and a scoring matrix are used to calculate + a score for each amino acid residue or nucleotide at each position in the alignment. keywords: - emboss - consensus @@ -15,30 +16,33 @@ tools: tool_dev_url: "http://emboss.open-bio.org/" doi: "10.1016/s0168-9525(00)02024-2 " licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Multiple sequence alignment (unzipped) - pattern: "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Multiple sequence alignment (unzipped) + pattern: "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - consensus: - type: file - description: Consensus sequence calculated from multiple sequence alignment - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: Consensus sequence calculated from multiple sequence alignment + pattern: "*.fa" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/emboss/revseq/meta.yml b/modules/nf-core/emboss/revseq/meta.yml index 3019e7be608..1ecdca5dc0f 100644 --- a/modules/nf-core/emboss/revseq/meta.yml +++ b/modules/nf-core/emboss/revseq/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "emboss_revseq" description: the revseq program from emboss reverse complements a nucleotide sequence @@ -14,30 +13,33 @@ tools: tool_dev_url: "http://emboss.open-bio.org/" doi: "10.1016/s0168-9525(00)02024-2 " licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - sequences: - type: file - description: Input sequences - pattern: "*.{fasta,fna,fa,fst,aln,phy}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - sequences: + type: file + description: Input sequences + pattern: "*.{fasta,fna,fa,fst,aln,phy}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - revseq: - type: file - description: File with reverse complemented sequences - pattern: "*.{fasta,fna,fa,fst,aln,phy}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - '*.${sequences.name - ~/.*\./}': + type: file + description: File with reverse complemented sequences + pattern: "*.{fasta,fna,fa,fst,aln,phy}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/emboss/seqret/meta.yml b/modules/nf-core/emboss/seqret/meta.yml index 4af9e11a3d3..dff9a614211 100644 --- a/modules/nf-core/emboss/seqret/meta.yml +++ b/modules/nf-core/emboss/seqret/meta.yml @@ -1,5 +1,6 @@ name: "emboss_seqret" -description: Reads in one or more sequences, converts, filters, or transforms them and writes them out again +description: Reads in one or more sequences, converts, filters, or transforms them + and writes them out again keywords: - emboss - gff @@ -16,33 +17,37 @@ tools: tool_dev_url: "http://emboss.open-bio.org/" doi: "10.1016/s0168-9525(00)02024-2 " licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequence: - type: file - description: Input sequence query - pattern: "*.{gff,em,gb,refseq,pir,swiss,sw,txt}" - - out_ext: - type: string - description: File extension of the output file. Unless otherwise set by a flag in `ext.args`, the extension dictates the output file format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence: + type: file + description: Input sequence query + pattern: "*.{gff,em,gb,refseq,pir,swiss,sw,txt}" + - - out_ext: + type: string + description: File extension of the output file. Unless otherwise set by a flag + in `ext.args`, the extension dictates the output file format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - outseq: - type: file - description: Converted sequence file - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_ext}": + type: file + description: Converted sequence file + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/emmtyper/meta.yml b/modules/nf-core/emmtyper/meta.yml index 9ba56f67987..742498960fa 100644 --- a/modules/nf-core/emmtyper/meta.yml +++ b/modules/nf-core/emmtyper/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/MDU-PHL/emmtyper tool_dev_url: https://github.com/MDU-PHL/emmtyper licence: ["GNU General Public v3 (GPL v3)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/endorspy/meta.yml b/modules/nf-core/endorspy/meta.yml index 4578998425b..0c5490355ae 100644 --- a/modules/nf-core/endorspy/meta.yml +++ b/modules/nf-core/endorspy/meta.yml @@ -1,5 +1,6 @@ name: "endorspy" -description: endorS.py calculates endogenous DNA from samtools flagstat files and print to screen +description: endorS.py calculates endogenous DNA from samtools flagstat files and + print to screen keywords: - endogenous DNA - ancient DNA @@ -7,41 +8,49 @@ keywords: - statistics tools: - "endorspy": - description: "endorS.py calculates percent on target and/or clonality from samtools flagstat files and print to screen" + description: "endorS.py calculates percent on target and/or clonality from samtools + flagstat files and print to screen" homepage: "https://github.com/aidaanva/endorS.py" documentation: "https://github.com/aidaanva/endorS.py" tool_dev_url: "https://github.com/aidaanva/endorS.py" doi: "10.7717/peerj.10947" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats_raw: - type: file - description: output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed - - stats_qualityfiltered: - type: file - description: output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d - - stats_deduplicated: - type: file - description: output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats_raw: + type: file + description: output of samtools flagstat in a txt file, assumes no quality filtering + nor duplicate removal performed + - stats_qualityfiltered: + type: file + description: output of samtools flagstat in a txt file, assumes some form of + quality or length filtering has been performed, must be provided with at least + one of the options -r or -d + - stats_deduplicated: + type: file + description: output of samtools flagstat in a txt file, whereby duplicate removal + has been performed on the input reads output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: file with the endogenous DNA calculation tailored for multiQC - pattern: "*_mqc.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_mqc.json": + type: file + description: file with the endogenous DNA calculation tailored for multiQC + pattern: "*_mqc.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aidaanva" maintainers: diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index a4277ad7a73..8da9621cbf0 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_download -description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. +description: Ensembl Variant Effect Predictor (VEP). The cache downloading options + are controlled through `task.ext.args`. keywords: - annotation - cache @@ -12,33 +13,40 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: string - description: | - Genome assembly - - species: - type: string - description: | - Specie - - cache_version: - type: string - description: | - cache version + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: string + description: | + Genome assembly + - species: + type: string + description: | + Specie + - cache_version: + type: string + description: | + cache version output: - cache: - type: file - description: cache - pattern: "*" + - meta: + type: file + description: cache + pattern: "*" + - prefix: + type: file + description: cache + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index bde3aa16575..a73e3b7a742 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -13,33 +13,37 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input: - type: file - description: VCF/TAB file annotated with vep - pattern: "*.{vcf,tab,tsv,txt}" - - feature_file: - type: file - description: File containing features on separate lines. To be used with --filter option. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: VCF/TAB file annotated with vep + pattern: "*.{vcf,tab,tsv,txt}" + - - feature_file: + type: file + description: File containing features on separate lines. To be used with --filter + option. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: VCF/TAB file - pattern: "*.{vcf,tab,txt,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.${extension}": + type: file + description: VCF/TAB file + pattern: "*.{vcf,tab,txt,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index d8ff8d14435..9288a93849f 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_vep -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled + through `task.ext.args`. keywords: - annotation - vcf @@ -13,75 +14,96 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) - - genome: - type: string - description: | - which genome to annotate with - - species: - type: string - description: | - which species to annotate with - - cache_version: - type: integer - description: | - which version of the cache to annotate with - - cache: - type: file - description: | - path to VEP cache (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" - - extra_files: - type: file - description: | - path to file(s) needed for plugins (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) + - - genome: + type: string + description: | + which genome to annotate with + - - species: + type: string + description: | + which species to annotate with + - - cache_version: + type: integer + description: | + which version of the cache to annotate with + - - cache: + type: file + description: | + path to VEP cache (optional) + - - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" + - - extra_files: + type: file + description: | + path to file(s) needed for plugins (optional) output: - vcf: - type: file - description: | - annotated vcf (optional) - pattern: "*.ann.vcf.gz" + - meta: + type: file + description: | + annotated vcf (optional) + pattern: "*.ann.vcf.gz" + - "*.vcf.gz": + type: file + description: | + annotated vcf (optional) + pattern: "*.ann.vcf.gz" - tab: - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" + - meta: + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + - "*.tab.gz": + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" - json: - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" + - meta: + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + - "*.json.gz": + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" - report: - type: file - description: VEP report file - pattern: "*.html" + - "*.html": + type: file + description: VEP report file + pattern: "*.html" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/entrezdirect/esearch/meta.yml b/modules/nf-core/entrezdirect/esearch/meta.yml index e3e2ffedc90..4a972826f33 100644 --- a/modules/nf-core/entrezdirect/esearch/meta.yml +++ b/modules/nf-core/entrezdirect/esearch/meta.yml @@ -20,34 +20,37 @@ tools: tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/ doi: 10.1016/S0076-6879(96)66012-1 licence: ["PUBLIC DOMAIN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - database: - type: string - description: Value must be a valid Entrez database name. - - term: - type: string - description: | - Entrez text query. All special characters must be URL encoded. - Spaces may be replaced by '+' signs. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - term: + type: string + description: | + Entrez text query. All special characters must be URL encoded. + Spaces may be replaced by '+' signs. + - - database: + type: string + description: Value must be a valid Entrez database name. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + - xml: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xml": + type: file + description: XML file containing search results + pattern: "*.xml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - result_xml: - type: file - description: Query result text in XML format - pattern: "*.xml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/entrezdirect/esummary/meta.yml b/modules/nf-core/entrezdirect/esummary/meta.yml index 8f0dbd589e5..36abbf02fd7 100644 --- a/modules/nf-core/entrezdirect/esummary/meta.yml +++ b/modules/nf-core/entrezdirect/esummary/meta.yml @@ -21,35 +21,40 @@ tools: tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/ doi: 10.1016/S0076-6879(96)66012-1 licence: ["PUBLIC DOMAIN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - database: - type: string - description: Value must be a valid Entrez database name ('assembly', etc). - - uid: - type: string - description: Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file - - uids_file: - type: file - description: Text file containing multiple UIDs. Cannot be used at the same time as uid. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - uid: + type: string + description: Unique Identifier (UID) of record in NCBI database. Cannot be used + at the same time as uids_file + - uids_file: + type: file + description: Text file containing multiple UIDs. Cannot be used at the same + time as uid. + - - database: + type: string + description: Value must be a valid Entrez database name ('assembly', etc). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - xml: - type: file - description: Query result in XML format - pattern: "*.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xml": + type: file + description: Query result in XML format + pattern: "*.xml" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/entrezdirect/xtract/meta.yml b/modules/nf-core/entrezdirect/xtract/meta.yml index 0b3cdd0321c..0b220a5c328 100644 --- a/modules/nf-core/entrezdirect/xtract/meta.yml +++ b/modules/nf-core/entrezdirect/xtract/meta.yml @@ -20,38 +20,41 @@ tools: tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/ doi: 10.1016/S0076-6879(96)66012-1 licence: ["PUBLIC DOMAIN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - xml_input: - type: file - description: XML text file containing query results from database. - - pattern: - type: string - description: String in xml_input that encloses element to search. - - element: - type: string - description: Space-delimited strings that will be converted to columns. - - sep: - type: string - description: Separator/delimiter between columns (for instance "," or "\t"). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - xml_input: + type: file + description: XML text file containing query results from database. + - - pattern: + type: string + description: String in xml_input that encloses element to search. + - - element: + type: string + description: Space-delimited strings that will be converted to columns. + - - sep: + type: string + description: Separator/delimiter between columns (for instance "," or "\t"). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Text file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - xtract_table: - type: file - description: TXT file containing columns searched from element. - pattern: "*.txt" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/epang/place/meta.yml b/modules/nf-core/epang/place/meta.yml index be90ceabfc4..64fc1f59029 100644 --- a/modules/nf-core/epang/place/meta.yml +++ b/modules/nf-core/epang/place/meta.yml @@ -12,53 +12,66 @@ tools: tool_dev_url: "https://github.com/Pbdas/epa-ng" doi: "10.1093/sysbio/syy054" licence: ["GNU Affero General Public License v3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - queryaln: - type: file - description: aligned query sequences in any supported format including phylip and fasta, may be gzipped - pattern: "*" - - referencealn: - type: file - description: reference alignment in any supported format including phylip and fasta, may be gzipped - pattern: "*" - - referencetree: - type: file - description: newick file containing the reference tree in which query sequences will be placed - pattern: "*" - - bfastfile: - type: file - description: file argument to the --bfast parameter - pattern: "*" - - binaryfile: - type: file - description: file argument to the --binary parameter - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - queryaln: + type: file + description: aligned query sequences in any supported format including phylip + and fasta, may be gzipped + pattern: "*" + - referencealn: + type: file + description: reference alignment in any supported format including phylip and + fasta, may be gzipped + pattern: "*" + - referencetree: + type: file + description: newick file containing the reference tree in which query sequences + will be placed + pattern: "*" + - - bfastfile: + type: file + description: file argument to the --bfast parameter + pattern: "*" + - - binaryfile: + type: file + description: file argument to the --binary parameter + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - epang: - type: directory - description: directory in which EPA-NG was run + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ./.: + type: directory + description: directory in which EPA-NG was run - jplace: - type: file - description: gzipped file with placement information - pattern: "*.jplace.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.epa_result.jplace.gz": + type: file + description: gzipped file with placement information + pattern: "*.jplace.gz" - log: - type: file - description: log file from placement - pattern: "*.log" + - "*.epa_info.log": + type: file + description: log file from placement + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/epang/split/meta.yml b/modules/nf-core/epang/split/meta.yml index 21cb81ae217..c91b1de5f53 100644 --- a/modules/nf-core/epang/split/meta.yml +++ b/modules/nf-core/epang/split/meta.yml @@ -12,37 +12,48 @@ tools: tool_dev_url: "https://github.com/Pbdas/epa-ng" doi: "10.1093/sysbio/syy054" licence: ["GNU Affero General Public License v3.0"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - refaln: - type: file - description: reference alignment in any supported format including phylip and fasta, may be gzipped - pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" - - fullaln: - type: file - description: full alignment in any supported format to split into reference and query alignments - pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - refaln: + type: file + description: reference alignment in any supported format including phylip and + fasta, may be gzipped + pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + - fullaln: + type: file + description: full alignment in any supported format to split into reference + and query alignments + pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - query: - type: file - description: query sequence alignment in gzipped fasta format + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*query.fasta.gz": + type: file + description: query sequence alignment in gzipped fasta format - reference: - type: file - description: reference sequence alignment in gzipped fasta format + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*reference.fasta.gz": + type: file + description: reference sequence alignment in gzipped fasta format - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/estsfs/meta.yml b/modules/nf-core/estsfs/meta.yml index 9d3d0d80da1..a1582dc95b6 100644 --- a/modules/nf-core/estsfs/meta.yml +++ b/modules/nf-core/estsfs/meta.yml @@ -1,4 +1,3 @@ ---- name: "estsfs" description: estimation of the unfolded site frequency spectrum keywords: @@ -7,47 +6,64 @@ keywords: - derived alleles tools: - "estsfs": - description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML)." + description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation + of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral + state probabilities by maximum likelihood (ML)." homepage: "https://sourceforge.net/projects/est-usfs/" documentation: "https://sourceforge.net/projects/est-usfs/" tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz" doi: "10.1534/genetics.118.301120" licence: ["Free for Academic Use"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - e_config: - type: file - description: config file for est-sfs - pattern: "*.txt" - - data: - type: file - description: input data file for est-sfs - pattern: "*.txt" - - seed: - type: file - description: text file containing random number seed - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - e_config: + type: file + description: config file for est-sfs + pattern: "*.txt" + - data: + type: file + description: input data file for est-sfs + pattern: "*.txt" + - seed: + type: file + description: text file containing random number seed + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sfs_out: - type: file - description: output file consists of the comma-separated estimated uSFS vector - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - ${prefix}_sfs.txt: + type: file + description: output file consists of the comma-separated estimated uSFS vector + pattern: "*.txt" - pvalues_out: - type: file - description: this file contains the estimated ancestral state probabilities for each site - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - ${prefix}_pvalues.txt: + type: file + description: this file contains the estimated ancestral state probabilities + for each site + pattern: "*.txt" + - ues_out: + type: file + description: this file contains the estimated ancestral state probabilities + for each site + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BioInf2305" diff --git a/modules/nf-core/evigene/tr2aacds/meta.yml b/modules/nf-core/evigene/tr2aacds/meta.yml index 9642ed8bd66..6cc6f579ed3 100644 --- a/modules/nf-core/evigene/tr2aacds/meta.yml +++ b/modules/nf-core/evigene/tr2aacds/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "evigene_tr2aacds" description: Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly @@ -22,34 +21,43 @@ tools: tool_dev_url: "http://arthropods.eugenes.org/EvidentialGene/evigene/" doi: "10.7490/f1000research.1112594.1 " licence: ["Don Gilbert, gilbertd At indiana edu, 2018"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Transcript assembly in fasta format - pattern: "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Transcript assembly in fasta format + pattern: "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - dropset: - type: directory - description: Directory containing dropped transcripts and associated files - pattern: "dropset" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - dropset: + type: directory + description: Directory containing dropped transcripts and associated files + pattern: "dropset" - okayset: - type: directory - description: Directory containing included transcripts and associated files - pattern: "okayset" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - okayset: + type: directory + description: Directory containing included transcripts and associated files + pattern: "okayset" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/expansionhunter/meta.yml b/modules/nf-core/expansionhunter/meta.yml index 698529dcc1b..4d55fe260ed 100644 --- a/modules/nf-core/expansionhunter/meta.yml +++ b/modules/nf-core/expansionhunter/meta.yml @@ -14,69 +14,84 @@ tools: documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md doi: "10.1093/bioinformatics/btz431" licence: ["Apache-2.0"] + identifier: biotools:ExpansionHunter input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index of BAM/CRAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome - pattern: "*.{fna,fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: Reference genome index - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - variant_catalog: - type: file - description: JSON file with repeat expansion sites to genotype - pattern: "*.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index of BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome + pattern: "*.{fna,fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: Reference genome index + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - variant_catalog: + type: file + description: JSON file with repeat expansion sites to genotype + pattern: "*.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', gender:'female' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - vcf: - type: file - description: VCF with repeat expansions - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', gender:'female' ] + - "*.vcf.gz": + type: file + description: VCF with repeat expansions + pattern: "*.vcf.gz" - json: - type: file - description: JSON with repeat expansions - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', gender:'female' ] + - "*.json.gz": + type: file + description: JSON with repeat expansions + pattern: "*.json.gz" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', gender:'female' ] + - "*_realigned.bam": + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jemten" maintainers: diff --git a/modules/nf-core/expansionhunterdenovo/merge/meta.yml b/modules/nf-core/expansionhunterdenovo/merge/meta.yml index a7aa59fb405..3d47ed8d0a2 100644 --- a/modules/nf-core/expansionhunterdenovo/merge/meta.yml +++ b/modules/nf-core/expansionhunterdenovo/merge/meta.yml @@ -6,56 +6,60 @@ keywords: - str tools: - "expansionhunterdenovo": - description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs)." + description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting + novel expansions of short tandem repeats (STRs)." homepage: "https://github.com/Illumina/ExpansionHunterDenovo" documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md" tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo" licence: ["Apache License 2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - manifest: - type: file - description: | - A tab-delimited file containing the sample name, whether it's case or control - and the paths to the corresponding STR profiles. - See here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files - pattern: "*.{tsv,txt}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - manifest: + type: file + description: | + A tab-delimited file containing the sample name, whether it's case or control + and the paths to the corresponding STR profiles. + See here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files + pattern: "*.{tsv,txt}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_profiles: - type: file - description: The merged STR profiles - pattern: "*.multisample_profile.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.multisample_profile.json": + type: file + description: The merged STR profiles + pattern: "*.multisample_profile.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/expansionhunterdenovo/profile/meta.yml b/modules/nf-core/expansionhunterdenovo/profile/meta.yml index 68fac10a2a5..c3a15b9dfbc 100644 --- a/modules/nf-core/expansionhunterdenovo/profile/meta.yml +++ b/modules/nf-core/expansionhunterdenovo/profile/meta.yml @@ -9,65 +9,81 @@ keywords: - cram tools: - "expansionhunterdenovo": - description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs)." + description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting + novel expansions of short tandem repeats (STRs)." homepage: "https://github.com/Illumina/ExpansionHunterDenovo" documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md" tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo" licence: ["Apache License 2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment_file: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - alignment_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The FASTA reference file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the FASTA reference file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment_file: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - alignment_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The FASTA reference file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the FASTA reference file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - locus_tsv: - type: file - description: The locus TSV file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.locus.tsv": + type: file + description: The locus TSV file + pattern: "*.tsv" - motif_tsv: - type: file - description: The motif TSV file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.motif.tsv": + type: file + description: The motif TSV file + pattern: "*.tsv" - str_profile: - type: file - description: The JSON file containing the STR profile - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.str_profile.json": + type: file + description: The JSON file containing the STR profile + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/falco/meta.yml b/modules/nf-core/falco/meta.yml index 6201790ce43..b2405f42432 100644 --- a/modules/nf-core/falco/meta.yml +++ b/modules/nf-core/falco/meta.yml @@ -7,43 +7,49 @@ keywords: - fastq tools: - fastqc: - description: "falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads." + description: "falco is a drop-in C++ implementation of FastQC to assess the quality + of sequence reads." homepage: "https://falco.readthedocs.io/" documentation: "https://falco.readthedocs.io/" licence: ["GPL v3"] + identifier: biotools:falco-rna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC like report - pattern: "*_{fastqc_report.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC like report + pattern: "*_{fastqc_report.html}" - txt: - type: file - description: falco report data - pattern: "*_{data.txt}" - - txt: - type: file - description: falco summary file - pattern: "*_{summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: falco report data + pattern: "*_{data.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucacozzuto" maintainers: diff --git a/modules/nf-core/famsa/align/meta.yml b/modules/nf-core/famsa/align/meta.yml index 6acf3c21010..c12a99dcb3f 100644 --- a/modules/nf-core/famsa/align/meta.yml +++ b/modules/nf-core/famsa/align/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "famsa_align" description: Aligns sequences using FAMSA @@ -14,42 +13,48 @@ tools: tool_dev_url: "https://github.com/refresh-bio/FAMSA" doi: "10.1038/srep33964" licence: ["GPL v3"] + identifier: biotools:famsa input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is handled by passing '-gz' to FAMSA along with any other options specified in task.ext.args. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is handled + by passing '-gz' to FAMSA along with any other options specified in task.ext.args. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed, + depending on if compress is set to true or false + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/famsa/guidetree/meta.yml b/modules/nf-core/famsa/guidetree/meta.yml index 2bd4e798d64..a7b1454fc25 100644 --- a/modules/nf-core/famsa/guidetree/meta.yml +++ b/modules/nf-core/famsa/guidetree/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "famsa_guidetree" description: Renders a guidetree in famsa @@ -14,30 +13,33 @@ tools: tool_dev_url: "https://github.com/refresh-bio/FAMSA" doi: "10.1038/srep33964" licence: ["GPL v3"] + identifier: biotools:famsa input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - tree: - type: file - description: Guide tree file in Newick format - pattern: "*.{dnd}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.dnd": + type: file + description: Guide tree file in Newick format + pattern: "*.{dnd}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/faqcs/meta.yml b/modules/nf-core/faqcs/meta.yml index cc0a8789877..9d8b6711ca1 100644 --- a/modules/nf-core/faqcs/meta.yml +++ b/modules/nf-core/faqcs/meta.yml @@ -14,55 +14,95 @@ tools: tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs doi: "10.1186/s12859-014-0366-2" licence: ["GPLv3 License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*trimmed.fastq.gz" - - reads_fail: - type: file - description: Reads that failed the preprocessing (Optional with --discard args setting) - pattern: "*discard.fastq.gz" - - reads_unpaired: - type: file - description: Reads without matching mates in paired-end files (Optional) - pattern: "*trimmed.unpaired.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trimmed.fastq.gz": + type: file + description: The trimmed/modified fastq reads + pattern: "*trimmed.fastq.gz" - stats: - type: file - description: trimming/qc text stats file - pattern: "*.stats.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats.txt": + type: file + description: trimming/qc text stats file + pattern: "*.stats.txt" - debug: - type: directory - description: trimming/qc files from --debug option - pattern: "./debug" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ./debug: + type: directory + description: trimming/qc files from --debug option + pattern: "./debug" - statspdf: - type: file - description: trimming/qc pdf report file - pattern: "*_qc_report.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_qc_report.pdf": + type: file + description: trimming/qc pdf report file + pattern: "*_qc_report.pdf" + - reads_fail: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.discard.fastq.gz": + type: file + description: Reads that failed the preprocessing (Optional with --discard args + setting) + pattern: "*discard.fastq.gz" + - reads_unpaired: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trimmed.unpaired.fastq.gz": + type: file + description: Reads without matching mates in paired-end files (Optional) + pattern: "*trimmed.unpaired.fastq.gz" - log: - type: file - description: fastq log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" - "@sateeshperi" diff --git a/modules/nf-core/fargene/meta.yml b/modules/nf-core/fargene/meta.yml index 9fc5ce0f8eb..e1bcc5ea18b 100644 --- a/modules/nf-core/fargene/meta.yml +++ b/modules/nf-core/fargene/meta.yml @@ -1,5 +1,6 @@ name: fargene -description: tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. +description: tool that takes either fragmented metagenomic data or longer sequences + as input and predicts and delivers full-length antiobiotic resistance genes as output. keywords: - antibiotic resistance genes - ARGs @@ -8,94 +9,192 @@ keywords: - contigs tools: - fargene: - description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output + description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented + metagenomic data or longer sequences as input and predicts and delivers full-length + antiobiotic resistance genes as output homepage: https://github.com/fannyhb/fargene documentation: https://github.com/fannyhb/fargene tool_dev_url: https://github.com/fannyhb/fargene licence: ["MIT"] + identifier: biotools:fargene input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq) - pattern: "*.{fasta}" - - hmm_model: - type: string - description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: uncompressed fasta file or paired-end fastq files containing either + genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented + metagenomic reads (fastq) + pattern: "*.{fasta}" + - - hmm_model: + type: string + description: name of custom hidden markov model to be used [pre-defined class_a, + class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, + tet_enzyme] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: log file + pattern: "*.{log}" - txt: - type: file - description: analysis summary text file - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/results_summary.txt: + type: file + description: analysis summary text file + pattern: "*.{txt}" - hmm: - type: file - description: output from hmmsearch (both single gene annotations + contigs) - pattern: "*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/hmmsearchresults/*.out: + type: file + description: output from hmmsearch (both single gene annotations + contigs) + pattern: "*.{out}" - hmm_genes: - type: file - description: output from hmmsearch (single gene annotations only) - pattern: "retrieved-*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/hmmsearchresults/retrieved-*.out: + type: file + description: output from hmmsearch (single gene annotations only) + pattern: "retrieved-*.{out}" - orfs: - type: file - description: open reading frames (ORFs) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/predicted-orfs.fasta: + type: file + description: open reading frames (ORFs) + pattern: "*.{fasta}" - orfs_amino: - type: file - description: protein translation of open reading frames (ORFs) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/predicted-orfs-amino.fasta: + type: file + description: protein translation of open reading frames (ORFs) + pattern: "*.{fasta}" - contigs: - type: file - description: (complete) contigs that passed the final full-length classification - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/retrieved-contigs.fasta: + type: file + description: (complete) contigs that passed the final full-length classification + pattern: "*.{fasta}" - contigs_pept: - type: file - description: parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/retrieved-contigs-peptides.fasta: + type: file + description: parts of the contigs that passed the final classification step + that aligned with the HMM, as amino acid sequences + pattern: "*.{fasta}" - filtered: - type: file - description: sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/*filtered.fasta: + type: file + description: sequences that passed the final classification step, but only the + parts that where predicted by the HMM to be part of the gene + pattern: "*.{fasta}" - filtered_pept: - type: file - description: sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/*filtered-peptides.fasta: + type: file + description: sequences from filtered.fasta, translated in the same frame as + the gene is predicted to be located + pattern: "*.{fasta}" - fragments: - type: file - description: All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files - pattern: "*.{fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/retrievedFragments/all_retrieved_*.fastq: + type: file + description: All quality controlled retrieved fragments that were classified + as positive, together with its read-pair, gathered in two files + pattern: "*.{fastq}" - trimmed: - type: file - description: The quality controlled retrieved fragments from each input file. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/retrievedFragments/trimmedReads/*.fasta: + type: file + description: The quality controlled retrieved fragments from each input file. + pattern: "*.{fasta}" - spades: - type: directory - description: The output from the SPAdes assembly - pattern: "spades_assembly" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/spades_assembly/*: + type: directory + description: The output from the SPAdes assembly + pattern: "spades_assembly" - metagenome: - type: file - description: The FASTQ to FASTA converted input files from metagenomic reads. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/tmpdir/*.fasta: + type: file + description: The FASTQ to FASTA converted input files from metagenomic reads. + pattern: "*.{fasta}" - tmp: - type: file - description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/tmpdir/*.out: + type: file + description: The from FASTQ to FASTA converted input files and their translated + input sequences. Are only saved if option --store-peptides is used. + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml index cf505471f92..59a82fc027e 100644 --- a/modules/nf-core/fastani/meta.yml +++ b/modules/nf-core/fastani/meta.yml @@ -6,40 +6,44 @@ keywords: - ANI tools: - fastani: - description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). + description: FastANI is developed for fast alignment-free computation of whole-genome + Average Nucleotide Identity (ANI). homepage: https://github.com/ParBLiSS/FastANI documentation: https://github.com/ParBLiSS/FastANI tool_dev_url: https://github.com/ParBLiSS/FastANI doi: 10.1038/s41467-018-07641-9 licence: ["Apache-2.0"] + identifier: biotools:fastani input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query: - type: file - description: Fasta file(s) to be queried - pattern: "*.fasta" - - reference: - type: file - description: Fasta file(s) to be used as reference for the query - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: Fasta file(s) to be queried + pattern: "*.fasta" + - - reference: + type: file + description: Fasta file(s) to be used as reference for the query + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - ani: - type: file - description: Results of the query - pattern: "*.ani.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ani.txt": + type: file + description: Results of the query + pattern: "*.ani.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/fastavalidator/meta.yml b/modules/nf-core/fastavalidator/meta.yml index c5c4371c629..94198e629d1 100644 --- a/modules/nf-core/fastavalidator/meta.yml +++ b/modules/nf-core/fastavalidator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastavalidator" description: | @@ -19,34 +18,43 @@ tools: tool_dev_url: "https://github.com/linsalrob/py_fasta_validator" doi: "10.5281/zenodo.5002710" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing file information - e.g. [ id:'test' ] - - fasta: - type: file - description: Input fasta file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing file information - e.g. [ id:'test' ] - success_log: - type: file - description: Log file for successful validation - pattern: "*.success.log" + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - "*.success.log": + type: file + description: Log file for successful validation + pattern: "*.success.log" - error_log: - type: file - description: Log file for failed validation - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - "*.error.log": + type: file + description: Log file for failed validation + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gallvp" maintainers: diff --git a/modules/nf-core/fastawindows/meta.yml b/modules/nf-core/fastawindows/meta.yml index 87f1d8b7dcf..f8ee0043203 100644 --- a/modules/nf-core/fastawindows/meta.yml +++ b/modules/nf-core/fastawindows/meta.yml @@ -7,49 +7,78 @@ keywords: - bed tools: - "fastawindows": - description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows" + description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal + level genome assemblies. The executable takes a fasta formatted file and calculates + some statistics of interest in windows" homepage: "https://github.com/tolkit/fasta_windows" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - freq: - type: file - description: TSV file with frequencies and statistics - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_freq_windows.tsv: + type: file + description: TSV file with frequencies and statistics + pattern: "*.{tsv}" - mononuc: - type: file - description: TSV file with mononucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_mononuc_windows.tsv: + type: file + description: TSV file with mononucleotide counts + pattern: "*.{tsv}" - dinuc: - type: file - description: TSV file with dinucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_dinuc_windows.tsv: + type: file + description: TSV file with dinucleotide counts + pattern: "*.{tsv}" - trinuc: - type: file - description: TSV file with trinucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_trinuc_windows.tsv: + type: file + description: TSV file with trinucleotide counts + pattern: "*.{tsv}" - tetranuc: - type: file - description: TSV file with tetranucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_tetranuc_windows.tsv: + type: file + description: TSV file with tetranucleotide counts + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" maintainers: diff --git a/modules/nf-core/fastk/fastk/meta.yml b/modules/nf-core/fastk/fastk/meta.yml index 3086aca51af..4abc1033d32 100644 --- a/modules/nf-core/fastk/fastk/meta.yml +++ b/modules/nf-core/fastk/fastk/meta.yml @@ -10,39 +10,54 @@ tools: homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: Histogram of k-mers - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram of k-mers + pattern: "*.hist" - ktab: - type: file - description: A sorted table of all canonical k‑mers along with their counts. - pattern: "*.ktab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.ktab*", hidden: true': + type: file + description: A sorted table of all canonical k‑mers along with their counts. + pattern: "*.ktab" - prof: - type: file - description: A k‑mer count profile of each sequence in the input data set. - pattern: "*.prof" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.{prof,pidx}*", hidden: true': + type: file + description: A k‑mer count profile of each sequence in the input data set. + pattern: "*.prof" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/fastk/histex/meta.yml b/modules/nf-core/fastk/histex/meta.yml index 6fcd6bd2572..1ce1bd01c1e 100644 --- a/modules/nf-core/fastk/histex/meta.yml +++ b/modules/nf-core/fastk/histex/meta.yml @@ -10,30 +10,33 @@ tools: homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" license: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - histogram: - type: file - description: A FastK histogram file - pattern: "*.hist" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - histogram: + type: file + description: A FastK histogram file + pattern: "*.hist" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: A formatted histogram file - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: A formatted histogram file + pattern: "*.hist" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/fastk/merge/meta.yml b/modules/nf-core/fastk/merge/meta.yml index 2a3c7242983..8bf2eda39d0 100644 --- a/modules/nf-core/fastk/merge/meta.yml +++ b/modules/nf-core/fastk/merge/meta.yml @@ -11,46 +11,58 @@ tools: homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" license: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - fastk_prof: - type: file - description: Histogram profile files from the program FastK (option -p) - pattern: "*.{prof,pidx}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - hist: + type: file + description: FastK histogram file + - ktab: + type: file + description: FastK ktab file + - prof: + type: file + description: FastK prof file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: FastK histogram file + pattern: "*.hist" + - ktab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.ktab*", hidden: true': + type: file + description: FastK ktab file + pattern: "*.ktab" + - prof: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.{prof,pidx}*", hidden: true': + type: file + description: FastK prof file + pattern: "*.{prof,pidx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - fastk_prof: - type: file - description: Histogram profile files from the program FastK (option -p) - pattern: "*.{prof,pidx}*" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/fastme/meta.yml b/modules/nf-core/fastme/meta.yml index 93e1dc671f6..77ce44e6d09 100644 --- a/modules/nf-core/fastme/meta.yml +++ b/modules/nf-core/fastme/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastme" description: "Distance-based phylogeny with FastME" @@ -9,7 +8,8 @@ keywords: - distance-based tools: - "fastme": - description: "A comprehensive, accurate and fast distance-based phylogeny inference program." + description: "A comprehensive, accurate and fast distance-based phylogeny inference + program." homepage: "http://www.atgc-montpellier.fr/fastme" documentation: "http://www.atgc-montpellier.fr/fastme/usersguide.php" tool_dev_url: "https://gite.lirmm.fr/atgc/FastME/" @@ -17,44 +17,70 @@ tools: licence: ["GPL v3"] args_id: "$args" + identifier: biotools:fastme input: - - meta: - type: map - description: | - A Groovy map containing sample information, - e.g. [ id: "test" ] - - infile: - type: file - description: MSA or distance matrix in Phylip format - pattern: "*" - # note: I have omitted any specific extension as it is not standardized for those file types - - topo: - type: file - description: Initial tree topology in Newick format - pattern: "*.{nwk,dnd}" - + - - meta: + type: map + description: | + A Groovy map containing sample information, + e.g. [ id: "test" ] + - infile: + type: file + description: MSA or distance matrix in Phylip format + pattern: "*" + - initial_tree: + type: file + description: Initial tree output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - nwk: - type: file - description: Final phylogeny in Newick format - pattern: "*.nwk" + - meta: + type: file + description: Final phylogeny in Newick format + pattern: "*.nwk" + - "*.nwk": + type: file + description: Final phylogeny in Newick format + pattern: "*.nwk" - stats: - type: file - description: A text file with the statistics of the phylogeny - pattern: "*_stat.txt" + - meta: + type: file + description: A text file with the statistics of the phylogeny + pattern: "*_stat.txt" + - "*_stat.txt": + type: file + description: A text file with the statistics of the phylogeny + pattern: "*_stat.txt" - matrix: - type: file - description: Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten - pattern: "*.matrix.phy" + - meta: + type: file + description: Optional; the distance matrix in Phylip matrix format; it is generated + if the -O option is passed in ext.args, although the provided file name will + be overwritten + pattern: "*.matrix.phy" + - "*.matrix.phy": + type: file + description: Optional; the distance matrix in Phylip matrix format; it is generated + if the -O option is passed in ext.args, although the provided file name will + be overwritten + pattern: "*.matrix.phy" - bootstrap: - type: file - description: A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten - pattern: "*.bootstrap" - + - meta: + type: file + description: A file containing all bootstrap trees in Newick format; it is generated + if the -B option is passed in ext.args (and bootstrap is used), although the + provided file name will be overwritten + pattern: "*.bootstrap" + - "*.bootstrap": + type: file + description: A file containing all bootstrap trees in Newick format; it is generated + if the -B option is passed in ext.args (and bootstrap is used), although the + provided file name will be overwritten + pattern: "*.bootstrap" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@itrujnara" maintainers: diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 8dfecc1848c..159404d08d3 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -11,66 +11,100 @@ tools: documentation: https://github.com/OpenGene/fastp doi: 10.1093/bioinformatics/bty560 licence: ["MIT"] + identifier: biotools:fastp input: - - meta: - type: map - description: | - Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. If you wish to run interleaved paired-end data, supply as single-end data - but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. | - This can be used to use fastp for the output report only. - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + - - meta: + type: map + description: | + Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. If you wish to run interleaved paired-end data, supply as single-end data + but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. + - - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + - - discard_trimmed_pass: + type: boolean + description: Specify true to not write any reads that pass trimming thresholds. + | This can be used to use fastp for the output report only. + - - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified/unmerged fastq reads - pattern: "*fastp.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastp.fastq.gz": + type: file + description: The trimmed/modified/unmerged fastq reads + pattern: "*fastp.fastq.gz" - json: - type: file - description: Results in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.json" - html: - type: file - description: Results in HTML format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format + pattern: "*.html" - log: - type: file - description: fastq log file - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" - reads_fail: - type: file - description: Reads the failed the preprocessing - pattern: "*fail.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fail.fastq.gz": + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" - reads_merged: - type: file - description: Reads that were successfully merged - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Reads that were successfully merged + pattern: "*.{merged.fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e06b6..4827da7af24 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqscan/meta.yml b/modules/nf-core/fastqscan/meta.yml index 6cfe3de361e..6c04aa556e9 100644 --- a/modules/nf-core/fastqscan/meta.yml +++ b/modules/nf-core/fastqscan/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/rpetit3/fastq-scan tool_dev_url: https://github.com/rpetit3/fastq-scan licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file - pattern: "*.{fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file + pattern: "*.{fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON formatted file of summary statistics - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON formatted file of summary statistics + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml index 3d5cb9b12cb..d92817fc13e 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml +++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml @@ -7,28 +7,33 @@ keywords: - reference tools: - "fastqscreen": - description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect." + description: "FastQ Screen allows you to screen a library of sequences in FastQ + format against a set of sequence databases so you can see if the composition + of the library matches with what you expect." homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" documentation: "https://stevenwingett.github.io/FastQ-Screen/" tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip" doi: "10.5281/zenodo.5838377" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - genome_names: - type: string - description: List of names for each index - - indexes: - type: directory - description: Bowtie2 genome directories containing index files + - - genome_names: + type: string + description: List of names for each index + - - indexes: + type: directory + description: Bowtie2 genome directories containing index files output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - database: - type: directory - description: fastq screen database folder containing config file and index folders - pattern: "FastQ_Screen_Genomes" + - FastQ_Screen_Genomes: + type: directory + description: fastq screen database folder containing config file and index folders + pattern: "FastQ_Screen_Genomes" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@snesic" - "@JPejovicApis" diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml index e0b0120df64..39c86b4f586 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml +++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml @@ -9,52 +9,70 @@ keywords: - reference tools: - "fastqscreen": - description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect." + description: "FastQ Screen allows you to screen a library of sequences in FastQ + format against a set of sequence databases so you can see if the composition + of the library matches with what you expect." homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" documentation: "https://stevenwingett.github.io/FastQ-Screen/" tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip" doi: "10.5281/zenodo.5838377" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - database: - type: directory - description: fastq screen database folder containing config file and index folders - pattern: "FastQ_Screen_Genomes" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - database: + type: directory + description: fastq screen database folder containing config file and index folders + pattern: "FastQ_Screen_Genomes" output: - - fastq_screen: - type: directory - description: Output fastq_screen file containing png, html, txt and no_hits_fastq files - pattern: "*.{_fq_screen}" + - txt: + - meta: + type: map + description: Groovy Map containing sample information + - "*.txt": + type: file + description: TXT file containing alignment statistics + pattern: "*.txt" - png: - type: file - description: PNG file with graphical representation of alignments - pattern: "*.png" + - meta: + type: map + description: Groovy Map containing sample information + - "*.png": + type: file + description: PNG file with graphical representation of alignments + pattern: "*.png" - html: - type: file - description: HTML file containing mapping results as a table and graphical representation - pattern: "*.html" - - txt: - type: file - description: TXT file containing alignment statistics - pattern: "*.txt" - - no_hits_fastq: - type: file - description: FastQ file containing reads that did not align to any database (optional) - pattern: "*_nohits.fastq" + - meta: + type: map + description: Groovy Map containing sample information + - "*.html": + type: file + description: HTML file containing mapping results as a table and graphical representation + pattern: "*.html" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: FastQ file containing reads that did not align to any database (optional) + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@snesic" - "@JPejovicApis" diff --git a/modules/nf-core/fasttree/meta.yml b/modules/nf-core/fasttree/meta.yml index 97622e59070..111bbc46afd 100644 --- a/modules/nf-core/fasttree/meta.yml +++ b/modules/nf-core/fasttree/meta.yml @@ -1,29 +1,34 @@ name: fasttree -description: Produces a Newick format phylogeny from a multiple sequence alignment. Capable of bacterial genome size alignments. +description: Produces a Newick format phylogeny from a multiple sequence alignment. + Capable of bacterial genome size alignments. keywords: - phylogeny - newick - alignment tools: - fasttree: - description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences + description: FastTree infers approximately-maximum-likelihood phylogenetic trees + from alignments of nucleotide or protein sequences homepage: http://www.microbesonline.org/fasttree/ documentation: http://www.microbesonline.org/fasttree/#Usage licence: ["GPL v2"] + identifier: biotools:fasttree input: - - alignment: - type: file - description: A FASTA format multiple sequence alignment file - pattern: "*.{fasta,fas,fa,mfa}" + - - alignment: + type: file + description: A FASTA format multiple sequence alignment file + pattern: "*.{fasta,fas,fa,mfa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{tre}" + - "*.tre": + type: file + description: A phylogeny in Newick format + pattern: "*.{tre}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aunderwo" maintainers: diff --git a/modules/nf-core/fastx/collapser/meta.yml b/modules/nf-core/fastx/collapser/meta.yml index ad36701142c..30b774b7de8 100644 --- a/modules/nf-core/fastx/collapser/meta.yml +++ b/modules/nf-core/fastx/collapser/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastx_collapser" -description: Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts) +description: Collapses identical sequences in a FASTQ/A file into a single sequence + (while maintaining reads counts) keywords: - collapse - genomics @@ -9,42 +9,41 @@ keywords: - fastq tools: - "fastx": - description: "A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing" + description: "A collection of command line tools for Short-Reads FASTA/FASTQ files + preprocessing" homepage: "http://hannonlab.cshl.edu/fastx_toolkit/" documentation: "http://hannonlab.cshl.edu/fastx_toolkit/commandline.html" tool_dev_url: "https://github.com/agordon/fastx_toolkit" licence: ["AGPL"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fastx: - type: file - description: Decompressed FASTA/FASTQ input file - pattern: "*.{fastq,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: Decompressed FASTA/FASTQ input file + pattern: "*.{fastq,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: Collapsed FASTA file - pattern: "*.fasta" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.fasta: + type: file + description: Collapsed FASTA file + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvfe" maintainers: diff --git a/modules/nf-core/fcs/fcsadaptor/meta.yml b/modules/nf-core/fcs/fcsadaptor/meta.yml index 54fca1bb7b6..83cae5b7884 100644 --- a/modules/nf-core/fcs/fcsadaptor/meta.yml +++ b/modules/nf-core/fcs/fcsadaptor/meta.yml @@ -18,45 +18,72 @@ tools: documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor" tool_dev_url: "https://github.com/ncbi/fcs" licence: ["United States Government Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: assembly fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: assembly fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cleaned_assembly: - type: file - description: Cleaned assembly in fasta format - pattern: "*.{cleaned_sequences.fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cleaned_sequences.fa.gz": + type: file + description: Cleaned assembly in fasta format + pattern: "*.{cleaned_sequences.fa.gz}" - adaptor_report: - type: file - description: Report of identified adaptors - pattern: "*.{fcs_adaptor_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fcs_adaptor_report.txt": + type: file + description: Report of identified adaptors + pattern: "*.{fcs_adaptor_report.txt}" - log: - type: file - description: Log file - pattern: "*.{fcs_adaptor.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fcs_adaptor.log": + type: file + description: Log file + pattern: "*.{fcs_adaptor.log}" - pipeline_args: - type: file - description: Run arguments - pattern: "*.{pipeline_args.yaml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pipeline_args.yaml": + type: file + description: Run arguments + pattern: "*.{pipeline_args.yaml}" - skipped_trims: - type: file - description: Skipped trim information - pattern: "*.{skipped_trims.jsonl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.skipped_trims.jsonl": + type: file + description: Skipped trim information + pattern: "*.{skipped_trims.jsonl}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d4straub" maintainers: diff --git a/modules/nf-core/fcs/fcsgx/meta.yml b/modules/nf-core/fcs/fcsgx/meta.yml index 0537d97c90d..8e4786f9c31 100644 --- a/modules/nf-core/fcs/fcsgx/meta.yml +++ b/modules/nf-core/fcs/fcsgx/meta.yml @@ -1,5 +1,6 @@ name: "fcs_fcsgx" -description: Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid. +description: Run FCS-GX on assembled genomes. The contigs of the assembly are searched + against a reference database excluding the given taxid. keywords: - assembly - genomics @@ -18,36 +19,47 @@ tools: documentation: "https://github.com/ncbi/fcs/wiki/FCS-GX" tool_dev_url: "https://github.com/ncbi/fcs" license: ["United States Government Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'6973' ] - - assembly: - type: file - description: assembly fasta file - - database: - type: file - description: Files of the database downloaded from the ncbi server, https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/. All files of one db should be downloaded and given to the process as channel.collect(). The link contains 2 databases, test-only and all. Use all for pipeline usage and test-only for tests. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'6973' ] + - assembly: + type: file + description: assembly fasta file + - - gxdb: + type: file + description: The NCBI GenBank database to search against. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'9606' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fcs_gx_report: - type: file - description: Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW) - pattern: "*.fcs_gx_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'9606' ] + - out/*.fcs_gx_report.txt: + type: file + description: Report containing the contig identifier and recommended action + (EXCLUDE, TRIM, FIX, REVIEW) + pattern: "*.fcs_gx_report.txt" - taxonomy_report: - type: file - description: Report containing the contig identifier and mapped contaminant species - pattern: "*.taxonomy.rpt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'9606' ] + - out/*.taxonomy.rpt: + type: file + description: Report containing the contig identifier and mapped contaminant + species + pattern: "*.taxonomy.rpt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tillenglert" maintainers: diff --git a/modules/nf-core/ffq/meta.yml b/modules/nf-core/ffq/meta.yml index d5f17873855..2bd95b86c83 100644 --- a/modules/nf-core/ffq/meta.yml +++ b/modules/nf-core/ffq/meta.yml @@ -1,5 +1,6 @@ name: "ffq" -description: A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA. +description: A command line tool that makes it easier to find sequencing data from + the SRA / GEO / ENA. keywords: - SRA - ENA @@ -10,25 +11,29 @@ keywords: - databases tools: - "ffq": - description: "A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA." + description: "A command line tool that makes it easier to find sequencing data + from the SRA / GEO / ENA." homepage: https://github.com/pachterlab/ffq documentation: https://github.com/pachterlab/ffq#usage tool_dev_url: https://github.com/pachterlab/ffq doi: "10.1101/2022.05.18.492548" licence: ["MIT"] + identifier: "" input: - - ids: - type: list - description: List of supported database ids e.g. SRA / GEO / ENA + - - ids: + type: list + description: List of supported database ids e.g. SRA / GEO / ENA output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON file containing metadata for ids - pattern: "*.{json}" + - "*.json": + type: file + description: JSON file containing metadata for ids + pattern: "*.{json}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml b/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml index 50bc4883907..0b733a5dff9 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml @@ -1,47 +1,53 @@ name: "fgbio_callduplexconsensusreads" -description: Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule. +description: Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences + from reads generated from the same double-stranded source molecule. keywords: - umi - duplex - fgbio tools: - "fgbio": - description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs" + description: "A set of tools for working with genomic and high throughput sequencing + data, including UMIs" homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file, grouped by UMI - pattern: "*.{bam,sam}" - - min_reads: - type: string - description: Minimum number of raw/original reads to build each consensus read. Can be a space delimited list of 1-3 values. See fgbio documentation for more details. - - min_baseq: - type: integer - description: Ignore bases in raw reads that have Q below this value + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - grouped_bam: + type: file + description: Grouped BAM file + pattern: "*.bam" + - - min_reads: + type: string + description: Minimum number of raw/original reads to build each consensus read. Can + be a space delimited list of 1-3 values. See fgbio documentation for more + details. + - - min_baseq: + type: integer + description: Ignore bases in raw reads that have Q below this value output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: consensus BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: consensus BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml index b7246c4296c..846c297b191 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml @@ -10,38 +10,41 @@ tools: homepage: https://github.com/fulcrumgenomics/fgbio documentation: http://fulcrumgenomics.github.io/fgbio/ licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - grouped_bam: - type: file - description: | - The input SAM or BAM file, grouped by UMIs - pattern: "*.{bam,sam}" - - min_reads: - type: integer - description: Minimum number of original reads to build each consensus read. - - min_baseq: - type: integer - description: Ignore bases in raw reads that have Q below this value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - grouped_bam: + type: file + description: | + The input SAM or BAM file, grouped by UMIs + pattern: "*.{bam,sam}" + - - min_reads: + type: integer + description: Minimum number of original reads to build each consensus read. + - - min_baseq: + type: integer + description: Ignore bases in raw reads that have Q below this value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: | - Output SAM or BAM file to write consensus reads. - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: | + Output SAM or BAM file to write consensus reads. + pattern: "*.{bam,sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sruthipsuresh" maintainers: diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml index f7afa4b4101..4ef27fc4f2c 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml @@ -1,4 +1,3 @@ ---- name: "fgbio_collectduplexseqmetrics" description: Collects a suite of metrics to QC duplex sequencing data. keywords: @@ -8,70 +7,112 @@ keywords: - duplex tools: - "fgbio": - description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs" + description: "A set of tools for working with genomic and high throughput sequencing + data, including UMIs" homepage: "http://fulcrumgenomics.github.io/fgbio/" documentation: "http://fulcrumgenomics.github.io/fgbio/" tool_dev_url: "https://github.com/fulcrumgenomics/fgbio" licence: ["MIT"] + identifier: biotools:fgbio - "r-ggplot2": - description: "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. " + description: "ggplot2 is a system for declaratively creating graphics, based on + The Grammar of Graphics. " homepage: "https://ggplot2.tidyverse.org/" documentation: "https://ggplot2.tidyverse.org/" tool_dev_url: "https://github.com/tidyverse/ggplot2" licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - grouped_bam: - type: file - description: It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order. - pattern: "*.bam" - - - interval_list: - type: file - description: Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html - pattern: "*.{tsv|txt|interval_list}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - grouped_bam: + type: file + description: It has to be either 1)The exact BAM output by the GroupReadsByUmi + tool (in the sort-order it was produced in) 2)A BAM file that has MI tags + present on all reads (usually set by GroupReadsByUmi and has been sorted with + SortBam into TemplateCoordinate order. + pattern: "*.bam" + - - interval_list: + type: file + description: Calculation of metrics may be restricted to a set of regions using + the --intervals parameter. The file format is descripted here + https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html + pattern: "*.{tsv|txt|interval_list}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - family_sizes: - type: file - description: Metrics on the frequency of different types of families of different sizes - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.family_sizes.txt": + type: file + description: Metrics on the frequency of different types of families of different + sizes + pattern: "*.txt" - duplex_family_sizes: - type: file - description: Metrics on the frequency of duplex tag families by the number of observations from each strand - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_family_sizes.txt": + type: file + description: Metrics on the frequency of duplex tag families by the number of + observations from each strand + pattern: "*.txt" - duplex_yield_metrics: - type: file - description: Summary QC metrics produced using 5%, 10%, 15%...100% of the data - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_yield_metrics.txt": + type: file + description: Summary QC metrics produced using 5%, 10%, 15%...100% of the data + pattern: "*.txt" - umi_counts: - type: file - description: Metrics on the frequency of observations of UMIs within reads and tag families - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.umi_counts.txt": + type: file + description: Metrics on the frequency of observations of UMIs within reads and + tag families + pattern: "*.txt" - duplex_qc: - type: file - description: A series of plots generated from the preceding metrics files for visualization - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_qc.pdf": + type: file + description: A series of plots generated from the preceding metrics files for + visualization + pattern: "*.pdf" - duplex_umi_counts: - type: file - description: Metrics on the frequency of observations of duplex UMIs within reads and tag families. - pattern: "*.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_umi_counts.txt": + type: file + description: Metrics on the frequency of observations of duplex UMIs within + reads and tag families. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@georgiakes" maintainers: diff --git a/modules/nf-core/fgbio/fastqtobam/meta.yml b/modules/nf-core/fgbio/fastqtobam/meta.yml index f26f29da299..bce76cf8c0a 100644 --- a/modules/nf-core/fgbio/fastqtobam/meta.yml +++ b/modules/nf-core/fgbio/fastqtobam/meta.yml @@ -7,34 +7,49 @@ keywords: - cram tools: - fgbio: - description: A set of tools for working with genomic and high throughput sequencing data, including UMIs + description: A set of tools for working with genomic and high throughput sequencing + data, including UMIs homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - reads: - type: file - description: pair of reads to be converted into BAM file - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: pair of reads to be converted into BAM file + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - version: - type: file - description: File containing software version - pattern: "*.{version.yml}" - bam: - type: file - description: Unaligned, unsorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Unaligned, unsorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Unaligned, unsorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Unaligned, unsorted CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" - "@matthdsm" diff --git a/modules/nf-core/fgbio/filterconsensusreads/meta.yml b/modules/nf-core/fgbio/filterconsensusreads/meta.yml index 0a0d62979b9..e1c04482378 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/filterconsensusreads/meta.yml @@ -1,5 +1,6 @@ name: "fgbio_filterconsensusreads" -description: Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. +description: Uses FGBIO FilterConsensusReads to filter consensus reads generated by + CallMolecularConsensusReads or CallDuplexConsensusReads. keywords: - fgbio - filter @@ -8,54 +9,58 @@ keywords: - duplexumi tools: - "fgbio": - description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs" + description: "A set of tools for working with genomic and high throughput sequencing + data, including UMIs" homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file containing genomic sequence information - pattern: "*.bam" - - min_reads: - type: integer - description: Minimum number of reads required to keep a consensus read - - min_baseq: - type: file - description: Minimum base quality to consider - - max_base_error_rate: - type: file - description: Maximum base error rate for a position before it is replaced with an N. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file containing genomic sequence information + pattern: "*.bam" + - - min_reads: + type: integer + description: Minimum number of reads required to keep a consensus read + - - min_baseq: + type: file + description: Minimum base quality to consider + - - max_base_error_rate: + type: file + description: Maximum base error rate for a position before it is replaced with + an N. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Filtered consensus BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Filtered consensus BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml index c8243f21386..3e525fd647d 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml @@ -12,46 +12,56 @@ keywords: - fgbio tools: - fgbio: - description: A set of tools for working with genomic and high throughput sequencing data, including UMIs + description: A set of tools for working with genomic and high throughput sequencing + data, including UMIs homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file. Note: the MQ tag is required on reads with mapped mates (!) - pattern: "*.bam" - - strategy: - type: string - enum: ["Identity", "Edit", "Adjacency", "Paired"] - description: | - Reguired argument: defines the UMI assignment strategy. - Must be chosen among: Identity, Edit, Adjacency, Paired. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file. Note: the MQ tag is required on reads with mapped mates (!) + pattern: "*.bam" + - - strategy: + type: string + enum: ["Identity", "Edit", "Adjacency", "Paired"] + description: | + Reguired argument: defines the UMI assignment strategy. + Must be chosen among: Identity, Edit, Adjacency, Paired. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: UMI-grouped BAM - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: UMI-grouped BAM + pattern: "*.bam" - histogram: - type: file - description: A text file containing the tag family size counts - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*histogram.txt": + type: file + description: A text file containing the tag family size counts + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/fgbio/sortbam/meta.yml b/modules/nf-core/fgbio/sortbam/meta.yml index 61630d7a597..26cbda22a50 100644 --- a/modules/nf-core/fgbio/sortbam/meta.yml +++ b/modules/nf-core/fgbio/sortbam/meta.yml @@ -1,5 +1,6 @@ name: fgbio_sortbam -description: Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery. +description: Sorts a SAM or BAM file. Several sort orders are available, including + coordinate, queryname, random, and randomquery. keywords: - sort - bam @@ -10,32 +11,35 @@ tools: homepage: https://github.com/fulcrumgenomics/fgbio documentation: http://fulcrumgenomics.github.io/fgbio/ licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - bam: - type: file - description: | - The input SAM or BAM file to be sorted. - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - bam: + type: file + description: | + The input SAM or BAM file to be sorted. + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: | - Output SAM or BAM file. - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: | + Output SAM or BAM file. + pattern: "*.{bam,sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sruthipsuresh" maintainers: diff --git a/modules/nf-core/fgbio/zipperbams/meta.yml b/modules/nf-core/fgbio/zipperbams/meta.yml index 8b7ca634cd5..553e9388f08 100644 --- a/modules/nf-core/fgbio/zipperbams/meta.yml +++ b/modules/nf-core/fgbio/zipperbams/meta.yml @@ -1,5 +1,6 @@ name: "fgbio_zipperbams" -description: FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM +description: FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata + into the output BAM keywords: - fgbio - umi @@ -8,62 +9,66 @@ keywords: - zipperbams tools: - fgbio: - description: A set of tools for working with genomic and high throughput sequencing data, including UMIs + description: A set of tools for working with genomic and high throughput sequencing + data, including UMIs homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mapped_bam: - type: file - description: mapped BAM/SAM file - pattern: "*.{bam,sam}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - unmapped_bam: - type: file - description: unmapped BAM file - pattern: "*.bam" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'GRCh38' ] - - fasta: - type: file - description: fasta file containing genomic sequence information - pattern: "*.{fasta,fa}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'GRCh38' ] - - dict: - type: file - description: dict file containing a sequence dictionary for the fasta file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - unmapped_bam: + type: file + description: unmapped BAM file + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mapped_bam: + type: file + description: mapped BAM/SAM file + pattern: "*.{bam,sam}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'GRCh38' ] + - fasta: + type: file + description: fasta file containing genomic sequence information + pattern: "*.{fasta,fa}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'GRCh38' ] + - dict: + type: file + description: dict file containing a sequence dictionary for the fasta file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Zipped BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Zipped BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/filtlong/meta.yml b/modules/nf-core/filtlong/meta.yml index 4a0f072a1b8..804c1b0d3fc 100644 --- a/modules/nf-core/filtlong/meta.yml +++ b/modules/nf-core/filtlong/meta.yml @@ -9,42 +9,54 @@ keywords: - short reads tools: - filtlong: - description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. + description: Filtlong is a tool for filtering long reads. It can take a set of + long reads and produce a smaller, better subset. It uses both read length (longer + is better) and read identity (higher is better) when choosing which reads pass + the filter. homepage: https://anaconda.org/bioconda/filtlong tool_dev_url: https://github.com/rrwick/Filtlong licence: ["GPL v3"] + identifier: biotools:filtlong input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - shortreads: - type: file - description: fastq file - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - longreads: - type: file - description: fastq file - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shortreads: + type: file + description: fastq file + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - longreads: + type: file + description: fastq file + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Filtered (compressed) fastq file - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Filtered (compressed) fastq file + pattern: "*.fastq.gz" - log: - type: file - description: Standard error logging file containing summary statistics - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Standard error logging file containing summary statistics + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d4straub" - "@sofstam" diff --git a/modules/nf-core/flash/meta.yml b/modules/nf-core/flash/meta.yml index 8253482ebcf..e8d3ac21d96 100644 --- a/modules/nf-core/flash/meta.yml +++ b/modules/nf-core/flash/meta.yml @@ -11,39 +11,54 @@ tools: homepage: https://ccb.jhu.edu/software/FLASH/ doi: 10.1093/bioinformatics/btr507 licence: ["GPL v3+"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 2; i.e., paired-end data. - pattern: "*fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 2; i.e., paired-end data. + pattern: "*fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - merged: - type: file - description: The merged fastq reads - pattern: ".extendedFrags.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.extendedFrags.fastq.gz: + type: file + description: The merged fastq reads + pattern: ".extendedFrags.fastq.gz" - notcombined: - type: file - description: Not combined reads from flash - pattern: ".notCombined_*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.notCombined_*.fastq.gz: + type: file + description: Not combined reads from flash + pattern: ".notCombined_*.fastq.gz" - histogram: - type: file - description: HistogramNumeric histogram of merged read lengths. - pattern: ".hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hist: + type: file + description: HistogramNumeric histogram of merged read lengths. + pattern: ".hist" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Erkison" maintainers: diff --git a/modules/nf-core/flye/meta.yml b/modules/nf-core/flye/meta.yml index 4b030d9ec52..1e33c275de7 100644 --- a/modules/nf-core/flye/meta.yml +++ b/modules/nf-core/flye/meta.yml @@ -8,60 +8,95 @@ keywords: - single molecule tools: - "flye": - description: "Fast and accurate de novo assembler for single molecule sequencing reads" + description: "Fast and accurate de novo assembler for single molecule sequencing + reads" homepage: "https://github.com/fenderglass/Flye" documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md" tool_dev_url: "https://github.com/fenderglass/Flye" doi: "10.1038/s41592-020-00971-x" licence: ["BSD-3-clause"] + identifier: biotools:Flye input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - reads: - type: file - description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format. - pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" - - mode: - type: string - description: Flye mode depending on the input data (source and error rate) - pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - reads: + type: file + description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ + format. + pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" + - - mode: + type: string + description: Flye mode depending on the input data (source and error rate) + pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Assembled FASTA file - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fasta.gz": + type: file + description: Assembled FASTA file + pattern: "*.fasta.gz" - gfa: - type: file - description: Repeat graph in gfa format - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gfa.gz": + type: file + description: Repeat graph in gfa format + pattern: "*.gfa.gz" - gv: - type: file - description: Repeat graph in gv format - pattern: "*.gv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gv.gz": + type: file + description: Repeat graph in gv format + pattern: "*.gv.gz" - txt: - type: file - description: Extra information and statistics about resulting contigs - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.txt": + type: file + description: Extra information and statistics about resulting contigs + pattern: "*.txt" - log: - type: file - description: Flye log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: Flye log file + pattern: "*.log" - json: - type: file - description: Flye parameters - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: Flye parameters + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/foldcomp/compress/meta.yml b/modules/nf-core/foldcomp/compress/meta.yml index e924039651a..cd45099ff08 100644 --- a/modules/nf-core/foldcomp/compress/meta.yml +++ b/modules/nf-core/foldcomp/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "foldcomp_compress" description: Efficient compression tool for protein structures @@ -8,37 +7,42 @@ keywords: - compression tools: - "foldcomp": - description: "Foldcomp: a library and format for compressing and indexing large protein structure sets" + description: "Foldcomp: a library and format for compressing and indexing large + protein structure sets" homepage: "https://github.com/steineggerlab/foldcomp" documentation: "https://github.com/steineggerlab/foldcomp" tool_dev_url: "https://github.com/steineggerlab/foldcomp" doi: "10.1093/bioinformatics/btad153" licence: ["GPL v3-or-later"] + identifier: biotools:foldcomp input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - pdb: - type: file - description: Protein structure(s) in PDB or CIF format to compress (also works with folder input) - pattern: "*.{pdb,cif}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pdb: + type: file + description: Protein structure(s) in PDB or CIF format to compress (also works + with folder input) + pattern: "*.{pdb,cif}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - fcz: - type: file - description: | - Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory) - pattern: "{*_fcz,*.fcz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*fcz": + type: file + description: | + Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory) + pattern: "{*_fcz,*.fcz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/foldcomp/decompress/meta.yml b/modules/nf-core/foldcomp/decompress/meta.yml index 81800f0fd7d..6084220d3da 100644 --- a/modules/nf-core/foldcomp/decompress/meta.yml +++ b/modules/nf-core/foldcomp/decompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "foldcomp_decompress" description: Decompression tool for foldcomp compressed structures @@ -8,36 +7,41 @@ keywords: - compression tools: - "foldcomp": - description: "Foldcomp: a library and format for compressing and indexing large protein structure sets" + description: "Foldcomp: a library and format for compressing and indexing large + protein structure sets" homepage: "https://github.com/steineggerlab/foldcomp" documentation: "https://github.com/steineggerlab/foldcomp" tool_dev_url: "https://github.com/steineggerlab/foldcomp" doi: "10.1093/bioinformatics/btad153" licence: ["GPL v3-or-later"] + identifier: biotools:foldcomp input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - fcz: - type: file - description: Foldcomp compressed protein structure(s) (also works with folder input) - pattern: "*{*,*.fcz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fcz: + type: file + description: Foldcomp compressed protein structure(s) (also works with folder + input) + pattern: "*{*,*.fcz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - pdb: - type: file - description: | - Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory) - pattern: "{*_pdb,*.pdb,*.cif}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "{*pdb,*.cif}": + type: file + description: | + Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory) + pattern: "{*_pdb,*.pdb,*.cif}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" diff --git a/modules/nf-core/foldmason/easymsa/meta.yml b/modules/nf-core/foldmason/easymsa/meta.yml index e1b807888db..cc00f44c58b 100644 --- a/modules/nf-core/foldmason/easymsa/meta.yml +++ b/modules/nf-core/foldmason/easymsa/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "foldmason_easymsa" description: Aligns protein structures using foldmason @@ -15,40 +14,51 @@ tools: tool_dev_url: "https://github.com/steineggerlab/foldmason" doi: "10.1101/2024.08.01.606130" licence: ["GPL v3"] + identifier: biotools:foldmason input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - pdbs: - type: file - description: Input protein structures in PDB format. - pattern: "*.{pdb,mmcif}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pdbs: + type: file + description: Input protein structures in PDB format. + pattern: "*.{pdb,mmcif}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - msa_3di: - type: file - description: Fasta file containing the multiple sequence alignment with 3Di alphabet - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "${prefix}_3di.fa${compress ? '.gz' : ''}": + type: file + description: Fasta file containing the multiple sequence alignment with 3Di + alphabet + pattern: "*.{fa}" - msa_aa: - type: file - description: Fasta file containing the multiple sequence alignment with Amino Acid alphabet - pattern: "*.{fa}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "${prefix}_aa.fa${compress ? '.gz' : ''}": + type: file + description: Fasta file containing the multiple sequence alignment with Amino + Acid alphabet + pattern: "*.{fa}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/foldseek/createdb/environment.yml b/modules/nf-core/foldseek/createdb/environment.yml index 5467561cf93..c59ddfe54d7 100644 --- a/modules/nf-core/foldseek/createdb/environment.yml +++ b/modules/nf-core/foldseek/createdb/environment.yml @@ -1,3 +1,4 @@ +name: foldseek_createdb channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldseek/createdb/meta.yml b/modules/nf-core/foldseek/createdb/meta.yml index 27d0a43f057..f11e24c96ee 100644 --- a/modules/nf-core/foldseek/createdb/meta.yml +++ b/modules/nf-core/foldseek/createdb/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "foldseek_createdb" description: Create a database from protein structures @@ -14,29 +13,33 @@ tools: tool_dev_url: "https://github.com/steineggerlab/foldseek" doi: "10.1038/s41587-023-01773-0" licence: ["GPL v3"] + identifier: biotools:foldseek input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - pdb: - type: file - description: Protein structure(s) in PDB, mmCIF or mmJSON format (also works with folder input) - pattern: "*.{pdb,mmcif,mmjson}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - pdb: + type: file + description: Protein structure(s) in PDB, mmCIF or mmJSON format (also works + with folder input) + pattern: "*.{pdb,mmcif,mmjson}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db: - type: directory - description: Directory containing pdb database files - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${meta.id}: + type: directory + description: Directory containing pdb database files + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" diff --git a/modules/nf-core/foldseek/easysearch/environment.yml b/modules/nf-core/foldseek/easysearch/environment.yml index 5467561cf93..c38d477d0c4 100644 --- a/modules/nf-core/foldseek/easysearch/environment.yml +++ b/modules/nf-core/foldseek/easysearch/environment.yml @@ -1,3 +1,4 @@ +name: foldseek_easysearch channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldseek/easysearch/meta.yml b/modules/nf-core/foldseek/easysearch/meta.yml index d18cc01dbed..c548213705c 100644 --- a/modules/nf-core/foldseek/easysearch/meta.yml +++ b/modules/nf-core/foldseek/easysearch/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "foldseek_easysearch" -description: Search for protein structural hits against a foldseek database of protein structures +description: Search for protein structural hits against a foldseek database of protein + structures keywords: - protein - structure @@ -14,41 +14,45 @@ tools: tool_dev_url: "https://github.com/steineggerlab/foldseek" doi: "10.1038/s41587-023-01773-0" licence: ["GPL v3"] + identifier: biotools:foldseek input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - pdb: - type: file - description: Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input) - pattern: "*.{pdb,mmcif,mmjson}" - - meta_db: - type: map - description: | - Groovy Map containing sample information for the foldseek db - e.g. `[ id:'test', single_end:false ]` - - db: - type: directory - description: foldseek database from protein structures - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - pdb: + type: file + description: Protein structure(s) in PDB, mmCIF or mmJSON format to compare + against a foldseek database (also works with folder input) + pattern: "*.{pdb,mmcif,mmjson}" + - - meta_db: + type: map + description: | + Groovy Map containing sample information for the foldseek db + e.g. `[ id:'test', single_end:false ]` + - db: + type: directory + description: foldseek database from protein structures + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - aln: - type: file - description: | - Structural comparisons file output - Query, Target, Identity, Alignment length, Mismatches, Gap openings, - Query start, Query end, Target start, Target end, E-value, Bit score - pattern: "*.{m8}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${meta.id}.m8: + type: file + description: | + Structural comparisons file output + Query, Target, Identity, Alignment length, Mismatches, Gap openings, + Query start, Query end, Target start, Target end, E-value, Bit score + pattern: "*.{m8}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" diff --git a/modules/nf-core/fq/generate/meta.yml b/modules/nf-core/fq/generate/meta.yml index e8fcfce7294..10e6cc0fa2f 100644 --- a/modules/nf-core/fq/generate/meta.yml +++ b/modules/nf-core/fq/generate/meta.yml @@ -13,26 +13,29 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Random generated FASTQ files. - pattern: "*_R[12].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Random generated FASTQ files. + pattern: "*_R[12].fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fq/lint/meta.yml b/modules/nf-core/fq/lint/meta.yml index 96223bd0589..7240fb5796e 100644 --- a/modules/nf-core/fq/lint/meta.yml +++ b/modules/nf-core/fq/lint/meta.yml @@ -11,25 +11,32 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file list - pattern: "*.fastq{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file list + pattern: "*.fastq{,.gz}" output: - lint: - type: file - description: Lint output - pattern: "*.fq_lint.txt" + - meta: + type: file + description: Lint output + pattern: "*.fq_lint.txt" + - "*.fq_lint.txt": + type: file + description: Lint output + pattern: "*.fq_lint.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fq/subsample/meta.yml b/modules/nf-core/fq/subsample/meta.yml index 6c5e87f3e85..7d91b0d9ada 100644 --- a/modules/nf-core/fq/subsample/meta.yml +++ b/modules/nf-core/fq/subsample/meta.yml @@ -1,5 +1,6 @@ name: "fq_subsample" -description: fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args. +description: fq subsample outputs a subset of records from single or paired FASTQ + files. This requires a seed (--seed) to be set in ext.args. keywords: - fastq - fq @@ -11,30 +12,33 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file - pattern: "*.{fq,fastq}{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file + pattern: "*.{fq,fastq}{,.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Randomly sampled FASTQ files. - pattern: "*_R[12].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Randomly sampled FASTQ files. + pattern: "*_R[12].fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fqtk/meta.yml b/modules/nf-core/fqtk/meta.yml index 357b23ca22b..db8063e71f1 100644 --- a/modules/nf-core/fqtk/meta.yml +++ b/modules/nf-core/fqtk/meta.yml @@ -10,43 +10,59 @@ tools: homepage: "https://github.com/fulcrumgenomics/fqtk" documentation: "https://github.com/fulcrumgenomics/fqtk" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sample_sheet: - type: file - description: Tsv file, with two columns sample_id and barcode - pattern: "*.{tsv}" - - fastq_readstructure_pairs: - type: map - description: List of lists i.e. [[, , ],...] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sample_sheet: + type: file + description: Tsv file, with two columns sample_id and barcode + pattern: "*.{tsv}" + - fastq_readstructure_pairs: + type: map + description: List of lists i.e. [[, , ],...] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_fastq: - type: file - description: Demultiplexed per-sample FASTQ files - pattern: "output/*R*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/*.fq.gz: + type: file + description: Demultiplexed per-sample FASTQ files + pattern: "output/*R*.fastq.gz" - metrics: - type: file - description: | - Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best - pattern: "output/demux-metrics.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/demux-metrics.txt: + type: file + description: | + Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best + pattern: "output/demux-metrics.txt" - most_frequent_unmatched: - type: file - description: | - File containing unmatched fastq records - pattern: "output/unmatched*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/unmatched*.fq.gz: + type: file + description: | + File containing unmatched fastq records + pattern: "output/unmatched*.fq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nh13" - "@sam-white04" diff --git a/modules/nf-core/freebayes/meta.yml b/modules/nf-core/freebayes/meta.yml index 1803b2b3195..45fc61d5bd7 100644 --- a/modules/nf-core/freebayes/meta.yml +++ b/modules/nf-core/freebayes/meta.yml @@ -16,95 +16,101 @@ tools: tool_dev_url: https://github.com/freebayes/freebayes doi: "10.48550/arXiv.1207.3907" licence: ["MIT"] + identifier: biotools:freebayes input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_1: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_1_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai}" - - input_2: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_2_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai}" - - target_bed: - type: file - description: Optional - Limit analysis to targets listed in this BED-format FILE. - pattern: "*.bed" - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: reference fasta file - pattern: ".{fa,fa.gz,fasta,fasta.gz}" - - ref_idx_meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test_reference' ] - - fasta_fai: - type: file - description: reference fasta file index - pattern: "*.{fa,fasta}.fai" - - samples_meta: - type: map - description: | - Groovy Map containing meta information for the samples file. - e.g. [ id:'test_samples' ] - - samples: - type: file - description: Optional - Limit analysis to samples listed (one per line) in the FILE. - pattern: "*.txt" - - populations_meta: - type: map - description: | - Groovy Map containing meta information for the populations file. - e.g. [ id:'test_populations' ] - - populations: - type: file - description: Optional - Each line of FILE should list a sample and a population which it is part of. - pattern: "*.txt" - - cnv_meta: - type: map - description: | - Groovy Map containing meta information for the cnv file. - e.g. [ id:'test_cnv' ] - - cnv: - type: file - description: | - A copy number map BED file, which has either a sample-level ploidy: - sample_name copy_number - or a region-specific format: - seq_name start end sample_name copy_number - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_1: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_1_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - input_2: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_2_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - target_bed: + type: file + description: Optional - Limit analysis to targets listed in this BED-format + FILE. + pattern: "*.bed" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: reference fasta file + pattern: ".{fa,fa.gz,fasta,fasta.gz}" + - - ref_idx_meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test_reference' ] + - fasta_fai: + type: file + description: reference fasta file index + pattern: "*.{fa,fasta}.fai" + - - samples_meta: + type: map + description: | + Groovy Map containing meta information for the samples file. + e.g. [ id:'test_samples' ] + - samples: + type: file + description: Optional - Limit analysis to samples listed (one per line) in the + FILE. + pattern: "*.txt" + - - populations_meta: + type: map + description: | + Groovy Map containing meta information for the populations file. + e.g. [ id:'test_populations' ] + - populations: + type: file + description: Optional - Each line of FILE should list a sample and a population + which it is part of. + pattern: "*.txt" + - - cnv_meta: + type: map + description: | + Groovy Map containing meta information for the cnv file. + e.g. [ id:'test_cnv' ] + - cnv: + type: file + description: | + A copy number map BED file, which has either a sample-level ploidy: + sample_name copy_number + or a region-specific format: + seq_name start end sample_name copy_number + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@maxibor" - "@FriederikeHanssen" diff --git a/modules/nf-core/freyja/boot/meta.yml b/modules/nf-core/freyja/boot/meta.yml index f3d91b52de4..3095a1f268d 100644 --- a/modules/nf-core/freyja/boot/meta.yml +++ b/modules/nf-core/freyja/boot/meta.yml @@ -1,5 +1,11 @@ name: "freyja_boot" -description: Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth. +description: Bootstrap sample demixing by resampling each site based on a multinomial + distribution of read depth across all sites, where the event probabilities were + determined by the fraction of the total sample reads found at each site, followed + by a secondary resampling at each site according to a multinomial distribution (that + is, binomial when there was only one SNV at a site), where event probabilities were + determined by the frequencies of each base at the site, and the number of trials + is given by the sequencing depth. keywords: - variants - fasta @@ -8,55 +14,67 @@ keywords: - bootstrapping tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variants: - type: file - description: File containing identified variants in a gff-like format - pattern: "*.variants.tsv" - - depths: - type: file - description: File containing depth of the variants - pattern: "*.depth.tsv" - - repeats: - type: integer - description: Number of bootstrap repeats to perform - - barcodes: - type: file - description: File containing lineage defining barcodes - pattern: "*barcodes.csv" - - lineages_meta: - type: file - description: File containing lineage metadata that correspond to barcodes - pattern: "*lineages.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variants: + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" + - depths: + type: file + description: File containing depth of the variants + pattern: "*.depth.tsv" + - - repeats: + type: integer + description: Number of bootstrap repeats to perform + - - barcodes: + type: file + description: File containing lineage defining barcodes + pattern: "*barcodes.csv" + - - lineages_meta: + type: file + description: File containing lineage metadata that correspond to barcodes + pattern: "*lineages.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - lineages: - type: file - description: a csv file that includes the lineages present and their corresponding abundances - pattern: "*lineages.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*lineages.csv": + type: file + description: a csv file that includes the lineages present and their corresponding + abundances + pattern: "*lineages.csv" - summarized: - type: file - description: a csv file that includes the lineages present but summarized by constellation and their corresponding abundances - pattern: "*summarized.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summarized.csv": + type: file + description: a csv file that includes the lineages present but summarized by + constellation and their corresponding abundances + pattern: "*summarized.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/freyja/demix/meta.yml b/modules/nf-core/freyja/demix/meta.yml index 141a155fd82..6b95e2e614c 100644 --- a/modules/nf-core/freyja/demix/meta.yml +++ b/modules/nf-core/freyja/demix/meta.yml @@ -7,48 +7,53 @@ keywords: - wastewater tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variants: - type: file - description: File containing identified variants in a gff-like format - pattern: "*.variants.tsv" - - depths: - type: file - description: File containing depth of the variants - pattern: "*.depth.tsv" - - barcodes: - type: file - description: File containing lineage defining barcodes - pattern: "*barcodes.csv" - - lineages_meta: - type: file - description: File containing lineage metadata that correspond to barcodes - pattern: "*lineages.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variants: + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" + - depths: + type: file + description: File containing depth of the variants + pattern: "*.depth.tsv" + - - barcodes: + type: file + description: File containing lineage defining barcodes + pattern: "*barcodes.csv" + - - lineages_meta: + type: file + description: File containing lineage metadata that correspond to barcodes + pattern: "*lineages.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - demix: - type: file - description: a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation - pattern: "*.demix.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: a tsv file that includes the lineages present, their corresponding + abundances, and summarization by constellation + pattern: "*.demix.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/freyja/update/meta.yml b/modules/nf-core/freyja/update/meta.yml index 1f5fc3c633e..a61b0676f2c 100644 --- a/modules/nf-core/freyja/update/meta.yml +++ b/modules/nf-core/freyja/update/meta.yml @@ -6,33 +6,39 @@ keywords: - UShER tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - db_name: - type: string - description: "The name of the database directory" + - - db_name: + type: string + description: "The name of the database directory" output: - barcodes: - type: file - description: File containing lineage defining barcodes - pattern: "*barcodes.csv" + - ${db_name}/usher_barcodes.csv: + type: file + description: File containing lineage defining barcodes + pattern: "*barcodes.csv" - lineages_topology: - type: file - description: File containing the lineage topology - pattern: "*lineages.yml" + - ${db_name}/lineages.yml: + type: file + description: File containing the lineage topology + pattern: "*lineages.yml" - lineages_meta: - type: file - description: File containing lineage metadata that correspond to barcodes - pattern: "*lineages.json" + - ${db_name}/curated_lineages.json: + type: file + description: File containing lineage metadata that correspond to barcodes + pattern: "*lineages.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/freyja/variants/meta.yml b/modules/nf-core/freyja/variants/meta.yml index 24f8d6936a3..bccfb36fed0 100644 --- a/modules/nf-core/freyja/variants/meta.yml +++ b/modules/nf-core/freyja/variants/meta.yml @@ -6,44 +6,49 @@ keywords: - wastewater tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM + file + pattern: "*.fa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - variants: - type: file - description: File containing identified variants in a gff-like format - pattern: "*.variants.tsv" - - depths: - type: file - description: File containing depth of the variants - pattern: "*.depth.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.variants.tsv": + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" + - "*.depth.tsv": + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/galah/meta.yml b/modules/nf-core/galah/meta.yml index 1a14d8a9f2b..efadae5822a 100644 --- a/modules/nf-core/galah/meta.yml +++ b/modules/nf-core/galah/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "galah" description: Cluster genome FASTA files by average nucleotide identity @@ -9,54 +8,64 @@ keywords: - metagenomics tools: - "galah": - description: "Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method." + description: "Galah aims to be a more scalable metagenome assembled genome (MAG) + dereplication method." homepage: "https://github.com/wwood/galah" documentation: "https://github.com/wwood/galah" tool_dev_url: "https://github.com/wwood/galah" doi: "10.1111/NODOI" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bins: - type: file - description: A list of fasta-formatted genomes for dereplication - pattern: "*.{fa,fna,fa.gz, etc}" - - qc_table: - type: file - description: | - (optional) Either a (CheckM)[https://nf-co.re/modules/checkm_lineagewf] summary TSV containing - information on the completeness and contamination of the input genomes (13 columns), - or a 3-column csv with the header `genome,completeness,contamination`. - In both cases the first column should contain the names of the input genome files, - minus the last file extension - (i.e. if the genome is gzipped, the genome name should retain the .fasta extension). - pattern: "*.{csv,tsv}" - - qc_format: - type: string - description: Defines the type if input table in `qc_table`, if specified. - pattern: "checkm|genome_info" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bins: + type: file + description: A list of fasta-formatted genomes for dereplication + pattern: "*.{fa,fna,fa.gz, etc}" + - qc_table: + type: file + description: | + (optional) Either a (CheckM)[https://nf-co.re/modules/checkm_lineagewf] summary TSV containing + information on the completeness and contamination of the input genomes (13 columns), + or a 3-column csv with the header `genome,completeness,contamination`. + In both cases the first column should contain the names of the input genome files, + minus the last file extension + (i.e. if the genome is gzipped, the genome name should retain the .fasta extension). + pattern: "*.{csv,tsv}" + - qc_format: + type: string + description: Defines the type if input table in `qc_table`, if specified. + pattern: "checkm|genome_info" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - tsv: - type: file - description: TSV file in the format `representative_genome` \t `member_genome` - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tsv": + type: file + description: TSV file in the format `representative_genome` \t `member_genome` + pattern: "*.tsv" - dereplicated_bins: - type: file - description: The representative genomes following dereplication by galah. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}-dereplicated/*: + type: file + description: The representative genomes following dereplication by galah. + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/gamma/gamma/meta.yml b/modules/nf-core/gamma/gamma/meta.yml index 7eb3287359e..f8c5f92e827 100644 --- a/modules/nf-core/gamma/gamma/meta.yml +++ b/modules/nf-core/gamma/gamma/meta.yml @@ -13,46 +13,67 @@ tools: tool_dev_url: "https://github.com/rastanton/GAMMA" doi: "10.1093/bioinformatics/btab607" licence: ["Apache License 2.0"] + identifier: biotools:gamma input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - db: - type: file - description: Database in FASTA format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - db: + type: file + description: Database in FASTA format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gamma: - type: file - description: GAMMA file with annotated gene matches - pattern: "*.{gamma}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gamma": + type: file + description: GAMMA file with annotated gene matches + pattern: "*.{gamma}" - psl: - type: file - description: PSL file with all gene matches found - pattern: "*.{psl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.psl": + type: file + description: PSL file with all gene matches found + pattern: "*.{psl}" - gff: - type: file - description: GFF file - pattern: "*.{gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff": + type: file + description: GFF file + pattern: "*.{gff}" - fasta: - type: file - description: multifasta file of the gene matches - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: multifasta file of the gene matches + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@rastanton" diff --git a/modules/nf-core/gangstr/meta.yml b/modules/nf-core/gangstr/meta.yml index 96339533729..0d091925784 100644 --- a/modules/nf-core/gangstr/meta.yml +++ b/modules/nf-core/gangstr/meta.yml @@ -1,5 +1,6 @@ name: "gangstr" -description: GangSTR is a tool for genome-wide profiling tandem repeats from short reads. +description: GangSTR is a tool for genome-wide profiling tandem repeats from short + reads. keywords: - gangstr - STR @@ -8,62 +9,71 @@ keywords: - vcf tools: - "gangstr": - description: "GangSTR is a tool for genome-wide profiling tandem repeats from short reads." + description: "GangSTR is a tool for genome-wide profiling tandem repeats from + short reads." homepage: "https://github.com/gymreklab/GangSTR" documentation: "https://github.com/gymreklab/GangSTR" tool_dev_url: "https://github.com/gymreklab/GangSTR" doi: "10.1093/nar/gkz501" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - aligment_files: - type: file - description: One or more sorted BAM/CRAM file(s) - pattern: "*.{bam,cram}" - - alignment_indices: - type: file - description: The index/indices of the BAM/CRAM file(s) - pattern: "*.{bai,crai}" - - ref_regions: - type: file - description: | - A reference set of regions to genotype in a BED-like format. The file should have following columns: - 1. The name of the chromosome on which the STR is located - 2. The start position of the STR on its chromosome - 3. The end position of the STR on its chromosome - 4. The motif length - 5. The repeat motif - pattern: "*.bed" - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment_files: + type: file + description: Alignment files + - alignment_indices: + type: file + description: The index/indices of the BAM/CRAM file(s) + pattern: "*.{bai,crai}" + - ref_regions: + type: file + description: | + A reference set of regions to genotype in a BED-like format. The file should have following columns: + 1. The name of the chromosome on which the STR is located + 2. The start position of the STR on its chromosome + 3. The end position of the STR on its chromosome + 4. The motif length + 5. The repeat motif + pattern: "*.bed" + - - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The resulting VCF file containing the genotypes - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: The resulting VCF file containing the genotypes + pattern: "*.vcf" - samplestats: - type: file - description: A tab-delimited file containing statistics for each sample - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.samplestats.tab": + type: file + description: A tab-delimited file containing statistics for each sample + pattern: "*.tab" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ganon/buildcustom/meta.yml b/modules/nf-core/ganon/buildcustom/meta.yml index 7ddae1211bd..538fd21306d 100644 --- a/modules/nf-core/ganon/buildcustom/meta.yml +++ b/modules/nf-core/ganon/buildcustom/meta.yml @@ -9,49 +9,61 @@ keywords: - database tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - List of input FASTA files, or a directory containing input FASTA files. - Note you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`. - pattern: "*" - - taxonomy_files: - type: file - description: Pre-downloaded taxonomy files of input sequences. See ganon docs for formats - - genome_size_files: - type: file - description: Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats - pattern: "{species_genome_size.txt.gz,*_metadata.tar.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + List of input FASTA files, or a directory containing input FASTA files. + Note you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`. + pattern: "*" + - - taxonomy_files: + type: file + description: Pre-downloaded taxonomy files of input sequences. See ganon docs + for formats + - - genome_size_files: + type: file + description: Pre-downloaded NCBI or GTDB genome size files of input sequences. + See ganon docs for formats + pattern: "{species_genome_size.txt.gz,*_metadata.tar.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: ganon database files - pattern: "*.{ibf,tax}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{hibf,ibf,tax}": + type: file + description: ganon database files + pattern: "*.{ibf,tax}" - info: - type: file - description: Copy of target info generated. Can be used for updating database. - pattern: "*info.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.info.tsv": + type: file + description: Copy of target info generated. Can be used for updating database. + pattern: "*info.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/ganon/classify/meta.yml b/modules/nf-core/ganon/classify/meta.yml index 55a8eae6d05..49f0572bc01 100644 --- a/modules/nf-core/ganon/classify/meta.yml +++ b/modules/nf-core/ganon/classify/meta.yml @@ -10,60 +10,95 @@ keywords: - classify tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastqs: - type: file - description: Single or paired FASTQ files, optionally gzipped - pattern: "*.{fq,fq.gz,fastq,fastq.gz}" - - db: - type: file - description: Ganon database files from build or build-custom - pattern: "*.{ibf,tax}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastqs: + type: file + description: Single or paired FASTQ files, optionally gzipped + pattern: "*.{fq,fq.gz,fastq,fastq.gz}" + - - db: + type: file + description: Ganon database files from build or build-custom + pattern: "*.{ibf,tax}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tre: - type: file - description: Full ganon report file - pattern: "*.tre" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tre": + type: file + description: Full ganon report file + pattern: "*.tre" - report: - type: file - description: Plain ganon report file with only targets with match - pattern: "*.rep" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rep": + type: file + description: Plain ganon report file with only targets with match + pattern: "*.rep" - one: - type: file - description: Information about a single (best) match of a given read after EM or LCA algorithms - pattern: "*.one" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.one": + type: file + description: Information about a single (best) match of a given read after EM + or LCA algorithms + pattern: "*.one" - all: - type: file - description: Information of all matches to a given read - pattern: "*.all" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.all": + type: file + description: Information of all matches to a given read + pattern: "*.all" - unc: - type: file - description: List of all reads without a hit - pattern: "*.unc" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unc": + type: file + description: List of all reads without a hit + pattern: "*.unc" - log: - type: file - description: Text file containing console output from ganon classify - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Text file containing console output from ganon classify + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/ganon/report/meta.yml b/modules/nf-core/ganon/report/meta.yml index c820e9c430a..e282c82014a 100644 --- a/modules/nf-core/ganon/report/meta.yml +++ b/modules/nf-core/ganon/report/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ganon_report" description: Generate a ganon report file from the output of ganon classify @@ -12,40 +11,45 @@ keywords: - report tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rep: - type: file - description: Input 'repo' files from ganon classify - pattern: "*.rep" - - db: - type: file - description: Ganon database files from build or build-custom - pattern: "*.{ibf,tax}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rep: + type: file + description: Input 'repo' files from ganon classify + pattern: "*.rep" + - - db: + type: file + description: Ganon database files from build or build-custom + pattern: "*.{ibf,tax}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tre: - type: file - description: Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format. - pattern: "*.tre" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tre": + type: file + description: Output ganon report containing taxonomic profile information. Formatting + of contents depends on --output-format. + pattern: "*.tre" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/ganon/table/meta.yml b/modules/nf-core/ganon/table/meta.yml index bf15f083591..23abe6bdb19 100644 --- a/modules/nf-core/ganon/table/meta.yml +++ b/modules/nf-core/ganon/table/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ganon_table" description: Generate a multi-sample report file from the output of ganon report runs @@ -13,36 +12,41 @@ keywords: - table tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tre: - type: file - description: A list of 'tre' files from ganon report - pattern: "*.tre" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tre: + type: file + description: A list of 'tre' files from ganon report + pattern: "*.tre" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Output ganon table containing taxonomic profile information of multiple samples. Formatting of contents depends on --output-format. - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Output ganon table containing taxonomic profile information of + multiple samples. Formatting of contents depends on --output-format. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gappa/examineassign/meta.yml b/modules/nf-core/gappa/examineassign/meta.yml index e70489e6265..12c1bfe6297 100644 --- a/modules/nf-core/gappa/examineassign/meta.yml +++ b/modules/nf-core/gappa/examineassign/meta.yml @@ -13,41 +13,86 @@ tools: tool_dev_url: "https://github.com/lczech/gappa" doi: "10.1093/bioinformatics/btaa070" licence: ["GPL v3"] + identifier: biotools:GAPPA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - jplace: - type: file - description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not - pattern: "*.{jplace,jplace.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - jplace: + type: file + description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped + or not + pattern: "*.{jplace,jplace.gz}" + - taxonomy: + type: file + description: taxonomy file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - examineassign: - type: directory - description: Execution directory + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ./.: + type: directory + description: Execution directory - profile: - type: file - description: profile tsv file - pattern: "*profile.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*profile.tsv": + type: file + description: profile tsv file + pattern: "*profile.tsv" - labelled_tree: - type: file - description: labelled tree in newick format - pattern: "*labelled_tree.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*labelled_tree.newick": + type: file + description: labelled tree in newick format + pattern: "*labelled_tree.newick" - per_query: - type: file - description: per query taxonomy assignments in tsv format - pattern: "*per_query.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*per_query.tsv": + type: file + description: per query taxonomy assignments in tsv format + pattern: "*per_query.tsv" + - krona: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*krona.profile": + type: file + description: krona profile file + pattern: "*krona.profile" + - sativa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*sativa.tsv": + type: file + description: sativa output file + pattern: "*sativa.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/gappa/examinegraft/meta.yml b/modules/nf-core/gappa/examinegraft/meta.yml index 195c3e44047..f24b732e01c 100644 --- a/modules/nf-core/gappa/examinegraft/meta.yml +++ b/modules/nf-core/gappa/examinegraft/meta.yml @@ -12,30 +12,34 @@ tools: tool_dev_url: "https://github.com/lczech/gappa" doi: "10.1093/bioinformatics/btaa070" licence: ["GPL v3"] + identifier: biotools:GAPPA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - jplace: - type: file - description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not - pattern: "*.{jplace,jplace.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - jplace: + type: file + description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped + or not + pattern: "*.{jplace,jplace.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - newick: - type: file - description: phylogenetic tree file in newick format - pattern: "*.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.newick": + type: file + description: phylogenetic tree file in newick format + pattern: "*.newick" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/gappa/examineheattree/meta.yml b/modules/nf-core/gappa/examineheattree/meta.yml index 4e59d029e78..2e533d36764 100644 --- a/modules/nf-core/gappa/examineheattree/meta.yml +++ b/modules/nf-core/gappa/examineheattree/meta.yml @@ -13,50 +13,84 @@ tools: tool_dev_url: "https://github.com/lczech/gappa" doi: "10.1093/bioinformatics/btaa070" licence: ["GPL v3"] + identifier: biotools:GAPPA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - jplace: - type: file - description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not - pattern: "*.{jplace,jplace.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - jplace: + type: file + description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped + or not + pattern: "*.{jplace,jplace.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - newick: - type: file - description: phylogenetic tree file in newick format - pattern: "*.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.newick": + type: file + description: phylogenetic tree file in newick format + pattern: "*.newick" - nexus: - type: file - description: coloured phylogenetic tree file in nexus format - pattern: "*.nexus" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.nexus": + type: file + description: coloured phylogenetic tree file in nexus format + pattern: "*.nexus" - phyloxml: - type: file - description: coloured phylogenetic tree file in phyloxml format - pattern: "*.phyloxml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.phyloxml": + type: file + description: coloured phylogenetic tree file in phyloxml format + pattern: "*.phyloxml" - svg: - type: file - description: coloured phylogenetic tree file in svg format - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svg": + type: file + description: coloured phylogenetic tree file in svg format + pattern: "*.svg" - colours: - type: file - description: colours used in plot - pattern: "*.colours.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.colours.txt": + type: file + description: colours used in plot + pattern: "*.colours.txt" - log: - type: file - description: log file from the run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: log file from the run + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/gatk/indelrealigner/meta.yml b/modules/nf-core/gatk/indelrealigner/meta.yml index 31806e175f0..75639de1b63 100644 --- a/modules/nf-core/gatk/indelrealigner/meta.yml +++ b/modules/nf-core/gatk/indelrealigner/meta.yml @@ -17,78 +17,81 @@ tools: "BSD", "https://www.broadinstitute.org/gatk/about/#licensing", ] + identifier: biotools:gatk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted and indexed BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - intervals: - type: file - description: Intervals file created by gatk3 RealignerTargetCreator - pattern: "*.{intervals,list}" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference file used to generate BAM file - pattern: ".{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference file used to generate BAM file - pattern: ".fai" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: GATK dict file for reference - pattern: ".dict" - - meta5: - type: map - description: | - Groovy Map containing file meta-information for known_vcf. - e.g. [ id:'test', single_end:false ] - - known_vcf: - type: file - description: Optional input VCF file(s) with known indels - pattern: ".vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted and indexed BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - intervals: + type: file + description: Intervals file created by gatk3 RealignerTargetCreator + pattern: "*.{intervals,list}" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file used to generate BAM file + pattern: ".{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference file used to generate BAM file + pattern: ".fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: GATK dict file for reference + pattern: ".dict" + - - meta5: + type: map + description: | + Groovy Map containing file meta-information for known_vcf. + e.g. [ id:'test', single_end:false ] + - known_vcf: + type: file + description: Optional input VCF file(s) with known indels + pattern: ".vcf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted and indexed BAM file with local realignment around variants - pattern: "*.bam" - - bai: - type: file - description: Output BAM Index file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted and indexed BAM file with local realignment around variants + pattern: "*.bam" + - "*.bai": + type: file + description: Sorted and indexed BAM file with local realignment around variants + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gatk/realignertargetcreator/meta.yml b/modules/nf-core/gatk/realignertargetcreator/meta.yml index 038b0007274..789f0b2bf69 100644 --- a/modules/nf-core/gatk/realignertargetcreator/meta.yml +++ b/modules/nf-core/gatk/realignertargetcreator/meta.yml @@ -1,5 +1,6 @@ name: "gatk_realignertargetcreator" -description: Generates a list of locations that should be considered for local realignment prior genotyping. +description: Generates a list of locations that should be considered for local realignment + prior genotyping. keywords: - bam - vcf @@ -18,70 +19,79 @@ tools: "BSD", "https://www.broadinstitute.org/gatk/about/#licensing", ] + identifier: biotools:gatk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted and indexed BAM/CRAM/SAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference file used to generate BAM file - pattern: ".{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference file used to generate BAM file - pattern: ".fai" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: GATK dict file for reference - pattern: ".dict" - - meta5: - type: map - description: | - Groovy Map containing file meta-information for known_vcf. - e.g. [ id:'test', single_end:false ] - - known_vcf: - type: file - description: Optional input VCF file(s) with known indels - pattern: ".vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted and indexed BAM/CRAM/SAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file used to generate BAM file + pattern: ".{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference file used to generate BAM file + pattern: ".fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: GATK dict file for reference + pattern: ".dict" + - - meta5: + type: map + description: | + Groovy Map containing file meta-information for known_vcf. + e.g. [ id:'test', single_end:false ] + - known_vcf: + type: file + description: Optional input VCF file(s) with known indels + pattern: ".vcf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - intervals: - type: file - description: File containg intervals that represent sites of extant and potential indels. - pattern: "*.intervals" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.intervals": + type: file + description: File containg intervals that represent sites of extant and potential + indels. + pattern: "*.intervals" + - s: + type: file + description: File containg intervals that represent sites of extant and potential + indels. + pattern: "*.intervals" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gatk/unifiedgenotyper/meta.yml b/modules/nf-core/gatk/unifiedgenotyper/meta.yml index 95ac33375dd..27b95a0aaa4 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/meta.yml +++ b/modules/nf-core/gatk/unifiedgenotyper/meta.yml @@ -15,97 +15,101 @@ tools: "BSD", "https://www.broadinstitute.org/gatk/about/#licensing", ] + identifier: biotools:gatk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted and indexed BAM/CRAM/SAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference file used to generate BAM file - pattern: ".{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference file used to generate BAM file - pattern: ".fai" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: GATK dict file for reference - pattern: ".dict" - - meta5: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - pattern: "*.intervals" - - meta6: - type: map - description: | - Groovy Map containing file meta-information for the contamination file. - e.g. [ id:'test', single_end:false ] - - contamination: - type: file - description: Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove - pattern: "*" - - meta7: - type: map - description: | - Groovy Map containing file meta-information for the dbsnps file. - e.g. [ id:'test', single_end:false ] - - dbsnp: - type: file - description: VCF file containing known sites (optional) - pattern: "*" - - meta8: - type: map - description: | - Groovy Map containing file meta-information for the VCF comparison file. - e.g. [ id:'test', single_end:false ] - - comp: - type: file - description: Comparison VCF file (optional) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted and indexed BAM/CRAM/SAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file used to generate BAM file + pattern: ".{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference file used to generate BAM file + pattern: ".fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: GATK dict file for reference + pattern: ".dict" + - - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + pattern: "*.intervals" + - - meta6: + type: map + description: | + Groovy Map containing file meta-information for the contamination file. + e.g. [ id:'test', single_end:false ] + - contamination: + type: file + description: Tab-separated file containing fraction of contamination in sequencing + data (per sample) to aggressively remove + pattern: "*" + - - meta7: + type: map + description: | + Groovy Map containing file meta-information for the dbsnps file. + e.g. [ id:'test', single_end:false ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + pattern: "*" + - - meta8: + type: map + description: | + Groovy Map containing file meta-information for the VCF comparison file. + e.g. [ id:'test', single_end:false ] + - comp: + type: file + description: Comparison VCF file (optional) + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file containing called variants - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file containing called variants + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ilight1542" - "@jfy133" diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml b/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml index d78081d5db9..2f1f022320e 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml @@ -16,56 +16,71 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - fasta_index: - type: file - description: Reference genome index file - pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_index: + type: file + description: Reference genome index file + pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Output BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/gatk4/annotateintervals/meta.yml b/modules/nf-core/gatk4/annotateintervals/meta.yml index 1c8e77ff138..ee644c97b1d 100644 --- a/modules/nf-core/gatk4/annotateintervals/meta.yml +++ b/modules/nf-core/gatk4/annotateintervals/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_annotateintervals" -description: Annotates intervals with GC content, mappability, and segmental-duplication content +description: Annotates intervals with GC content, mappability, and segmental-duplication + content keywords: - annotateintervals - annotation @@ -16,95 +17,105 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: One or more interval files to annotate - pattern: "*.{interval_list,list,bed}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - dict: - type: file - description: The sequence dictionary reference FASTA file - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - mappable_regions: - type: file - description: | - Optional - Umap single-read mappability track - The track should correspond to the appropriate read length and overlapping intervals must be merged - pattern: "*.bed(.gz)?" - - meta6: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - mappable_regions_tbi: - type: file - description: Optional - The index of the gzipped umap single-read mappability track - pattern: "*.bed.gz.tbi" - - meta7: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - segmental_duplication_regions: - type: file - description: Optional - Segmental-duplication track - pattern: "*.bed(.gz)?" - - meta8: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - segmental_duplication_regions_tbi: - type: file - description: Optional - The index of the gzipped segmental-duplication track - pattern: "*.bed.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: One or more interval files to annotate + pattern: "*.{interval_list,list,bed}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: The sequence dictionary reference FASTA file + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - mappable_regions: + type: file + description: | + Optional - Umap single-read mappability track + The track should correspond to the appropriate read length and overlapping intervals must be merged + pattern: "*.bed(.gz)?" + - - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - mappable_regions_tbi: + type: file + description: Optional - The index of the gzipped umap single-read mappability + track + pattern: "*.bed.gz.tbi" + - - meta7: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - segmental_duplication_regions: + type: file + description: Optional - Segmental-duplication track + pattern: "*.bed(.gz)?" + - - meta8: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - segmental_duplication_regions_tbi: + type: file + description: Optional - The index of the gzipped segmental-duplication track + pattern: "*.bed.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotated_intervals: - type: file - description: The output TSV file with a SAM-style header containing the annotated intervals - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The output TSV file with a SAM-style header containing the annotated + intervals + pattern: "*.tsv" + - s: + type: file + description: The output TSV file with a SAM-style header containing the annotated + intervals + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml index ab9efea3f4b..65d9c9e9a89 100644 --- a/modules/nf-core/gatk4/applybqsr/meta.yml +++ b/modules/nf-core/gatk4/applybqsr/meta.yml @@ -16,56 +16,65 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - bqsr_table: - type: file - description: Recalibration table from gatk4_baserecalibrator - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - bqsr_table: + type: file + description: Recalibration table from gatk4_baserecalibrator + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Recalibrated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Recalibrated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Recalibrated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Recalibrated CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/applyvqsr/meta.yml b/modules/nf-core/gatk4/applyvqsr/meta.yml index de5d6d067af..ceedff621ed 100644 --- a/modules/nf-core/gatk4/applyvqsr/meta.yml +++ b/modules/nf-core/gatk4/applyvqsr/meta.yml @@ -19,57 +19,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: file - description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator. - pattern: "*.vcf" - - vcf_tbi: - type: file - description: tabix index for the input vcf file. - pattern: "*.vcf.tbi" - - recal: - type: file - description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: "*.recal" - - recal_index: - type: file - description: Index file for the recalibration file. - pattern: ".recal.idx" - - tranches: - type: file - description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: ".tranches" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to be recalibrated, this should be the same file as used + for the first stage VariantRecalibrator. + pattern: "*.vcf" + - vcf_tbi: + type: file + description: tabix index for the input vcf file. + pattern: "*.vcf.tbi" + - recal: + type: file + description: Recalibration file produced when the input vcf was run through + VariantRecalibrator in stage 1. + pattern: "*.recal" + - recal_index: + type: file + description: Index file for the recalibration file. + pattern: ".recal.idx" + - tranches: + type: file + description: Tranches file produced when the input vcf was run through VariantRecalibrator + in stage 1. + pattern: ".tranches" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - vcf: - type: file - description: compressed vcf file containing the recalibrated variants. - pattern: "*.vcf.gz" + - meta: + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of recalibrated vcf file. - pattern: "*vcf.gz.tbi" + - meta: + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/asereadcounter/meta.yml b/modules/nf-core/gatk4/asereadcounter/meta.yml index 1adfaa813ae..799f9cbed94 100644 --- a/modules/nf-core/gatk4/asereadcounter/meta.yml +++ b/modules/nf-core/gatk4/asereadcounter/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_asereadcounter" -description: Calculates the allele-specific read counts for alle-specific expression analysis of RNAseq data +description: Calculates the allele-specific read counts for alle-specific expression + analysis of RNAseq data keywords: - allele-specific - asereadcounter @@ -15,72 +16,71 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: index file for input file - pattern: "*.{bai,crai}" - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" - - tbi: - type: file - description: index file for VCF file - pattern: "*.{vcf.gz.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - fasta: - type: file - description: fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - fai: - type: file - description: fasta index file - pattern: "*.{fai}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - dict: - type: file - description: dictionary file - pattern: "*.{dict}" - - intervals: - type: file - description: interval file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: index file for BAM file + pattern: "*.{bai}" + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" + - tbi: + type: file + description: index file for VCF file + pattern: "*.{vcf.gz.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - fasta: + type: file + description: fasta file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - fai: + type: file + description: fasta index file + pattern: "*.{fai}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - dict: + type: file + description: dictionary file + pattern: "*.{dict}" + - - intervals: + type: file + description: interval file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: output file - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml index 8252b8c290d..876b7960398 100644 --- a/modules/nf-core/gatk4/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4/baserecalibrator/meta.yml @@ -16,57 +16,60 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Recalibration table from BaseRecalibrator - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Recalibration table from BaseRecalibrator + pattern: "*.{table}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 187da8850c7..25348e16214 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -15,34 +15,45 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bed: - type: file - description: Input bed file - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bed: + type: file + description: Input bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary + pattern: "*.dict" output: - interval_list: - type: file - description: gatk interval list file - pattern: "*.interval_list" + - meta: + type: file + description: gatk interval list file + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: gatk interval list file + pattern: "*.interval_list" + - _list: + type: file + description: gatk interval list file + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/calculatecontamination/meta.yml b/modules/nf-core/gatk4/calculatecontamination/meta.yml index b0ffe814c54..ee90a482529 100644 --- a/modules/nf-core/gatk4/calculatecontamination/meta.yml +++ b/modules/nf-core/gatk4/calculatecontamination/meta.yml @@ -17,33 +17,50 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pileup: - type: file - description: File containing the pileups summary table of a tumor sample to be used to calculate contamination. - pattern: "*.pileups.table" - - matched: - type: file - description: File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input. - pattern: "*.pileups.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pileup: + type: file + description: File containing the pileups summary table of a tumor sample to + be used to calculate contamination. + pattern: "*.pileups.table" + - matched: + type: file + description: File containing the pileups summary table of a normal sample that + matches with the tumor sample specified in pileup argument. This is an optional + input. + pattern: "*.pileups.table" output: - contamination: - type: file - description: File containing the contamination table. - pattern: "*.contamination.table" + - meta: + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" + - "*.contamination.table": + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" - segmentation: - type: file - description: output table containing segmentation of tumor minor allele fractions (optional) - pattern: "*.segmentation.table" + - meta: + type: file + description: output table containing segmentation of tumor minor allele fractions + (optional) + pattern: "*.segmentation.table" + - "*.segmentation.table": + type: file + description: output table containing segmentation of tumor minor allele fractions + (optional) + pattern: "*.segmentation.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@maxulysse" diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml b/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml index bf2ca2d7389..cc19131b70b 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml @@ -8,62 +8,65 @@ keywords: - calibratedragstrmodel tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bam_index: - type: file - description: index of the BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - intervals: - type: file - description: BED file or interval list containing regions (optional) - pattern: "*.{bed,interval_list}" - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" - - dict: - type: file - description: The sequence dictionary of the reference FASTA file - pattern: "*.dict" - - strtablefile: - type: file - description: The StrTableFile zip folder of the reference FASTA file - pattern: "*.zip" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bam_index: + type: file + description: index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" + - - dict: + type: file + description: The sequence dictionary of the reference FASTA file + pattern: "*.dict" + - - strtablefile: + type: file + description: The StrTableFile zip folder of the reference FASTA file + pattern: "*.zip" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - dragstr_model: - type: file - description: The DragSTR model - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: The DragSTR model + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/cnnscorevariants/meta.yml b/modules/nf-core/gatk4/cnnscorevariants/meta.yml index 8a9d0f51c2a..b55c9d99953 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/meta.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/meta.yml @@ -14,65 +14,74 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: VCF index file - pattern: "*.vcf.gz.tbi" - - aligned_input: - type: file - description: BAM/CRAM file from alignment (optional) - pattern: "*.{bam,cram}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - architecture: - type: file - description: Neural Net architecture configuration json file (optional) - pattern: "*.json" - - weights: - type: file - description: Keras model HD5 file with neural net weights. (optional) - pattern: "*.hd5" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.vcf.gz" + - tbi: + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + - aligned_input: + type: file + description: BAM/CRAM file from alignment (optional) + pattern: "*.{bam,cram}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - architecture: + type: file + description: Neural Net architecture configuration json file (optional) + pattern: "*.json" + - - weights: + type: file + description: Keras model HD5 file with neural net weights. (optional) + pattern: "*.hd5" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Annotated VCF file - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cnn.vcf.gz": + type: file + description: Annotated VCF file + pattern: "*.vcf" - tbi: - type: file - description: VCF index file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cnn.vcf.gz.tbi": + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/collectreadcounts/meta.yml b/modules/nf-core/gatk4/collectreadcounts/meta.yml index 25fb8b8cf15..cf8c7731d34 100644 --- a/modules/nf-core/gatk4/collectreadcounts/meta.yml +++ b/modules/nf-core/gatk4/collectreadcounts/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_collectreadcounts" -description: Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. +description: Collects read counts at specified intervals. The count for each interval + is calculated by counting the number of read starts that lie in the interval. keywords: - collectreadcounts - bam @@ -7,75 +8,88 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - intervals: - type: file - description: A file containing the specified intervals - pattern: "*.{bed,intervals}" - - fasta: - type: file - description: Optional - Reference FASTA - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Optional - Index of the reference FASTA file - pattern: "*.fai" - - dict: - type: file - description: Optional - Sequence dictionary of the reference FASTA file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - intervals: + type: file + description: A file containing the specified intervals + pattern: "*.{bed,intervals}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Optional - Reference FASTA + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: Optional - Index of the reference FASTA file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: Optional - Sequence dictionary of the reference FASTA file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hdf5: - type: file - description: The read counts in hdf5 format - pattern: "*.hdf5" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hdf5": + type: file + description: The read counts in hdf5 format + pattern: "*.hdf5" - tsv: - type: file - description: The read counts in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The read counts in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/collectsvevidence/meta.yml b/modules/nf-core/gatk4/collectsvevidence/meta.yml index 264a58922d0..2a8b6fc4643 100644 --- a/modules/nf-core/gatk4/collectsvevidence/meta.yml +++ b/modules/nf-core/gatk4/collectsvevidence/meta.yml @@ -1,5 +1,8 @@ name: "gatk4_collectsvevidence" -description: Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. +description: Gathers paired-end and split read evidence files for use in the GATK-SV + pipeline. Output files are a file containing the location of and orientation of + read pairs marked as discordant, and a file containing the clipping location of + all soft clipped reads and the orientation of the clipping. keywords: - gatk4 - collectsvevidence @@ -12,74 +15,112 @@ tools: tool_dev_url: "https://github.com/broadinstitute/gatk" doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: Index of the BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - site_depth_vcf: - type: file - description: Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output - pattern: "*.vcf.gz" - - site_depth_vcf_index: - type: file - description: Optional - index of the VCF file, needed for the site depths output - pattern: "*.tbi" - - fasta: - type: file - description: Optional - reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Optional - index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: Index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - site_depth_vcf: + type: file + description: Optional - input VCF of SNPs marking loci for site depths, needed + for the site depths output + pattern: "*.vcf.gz" + - site_depth_vcf_tbi: + type: file + description: tbi index of the input VCF of SNPs marking loci for site + depths + pattern: "*.vcf.gz.tbi" + - - fasta: + type: file + description: Optional - reference FASTA file needed when the input is a CRAM + file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Optional - index of the reference FASTA file needed when the input + is a CRAM file + pattern: "*.fai" + - - dict: + type: file + description: Optional - sequence dictionary of the reference FASTA file needed + when the input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_read_evidence: - type: file - description: Output file for split read evidence - pattern: "*.sr.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sr.txt.gz": + type: file + description: Output file for split read evidence + pattern: "*.sr.txt.gz" - split_read_evidence_index: - type: file - description: Index of the output file for split read evidence - pattern: "*.sr.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sr.txt.gz.tbi": + type: file + description: Index of the output file for split read evidence + pattern: "*.sr.txt.gz.tbi" - paired_end_evidence: - type: file - description: Output file for paired end evidence - pattern: "*.pe.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pe.txt.gz": + type: file + description: Output file for paired end evidence + pattern: "*.pe.txt.gz" - paired_end_evidence_index: - type: file - description: Index of the output file for paired end evidence - pattern: "*.pe.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pe.txt.gz.tbi": + type: file + description: Index of the output file for paired end evidence + pattern: "*.pe.txt.gz.tbi" - site_depths: - type: file - description: Output file for site depths - pattern: "*.sd.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sd.txt.gz": + type: file + description: Output file for site depths + pattern: "*.sd.txt.gz" - site_depths_index: - type: file - description: Index of the output file for site depths - pattern: "*.sd.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sd.txt.gz.tbi": + type: file + description: Index of the output file for site depths + pattern: "*.sd.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/combinegvcfs/meta.yml b/modules/nf-core/gatk4/combinegvcfs/meta.yml index f13ddde7f6e..c4fd646cf15 100644 --- a/modules/nf-core/gatk4/combinegvcfs/meta.yml +++ b/modules/nf-core/gatk4/combinegvcfs/meta.yml @@ -1,5 +1,6 @@ name: gatk4_combinegvcfs -description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file +description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample + gVCF file keywords: - gvcf - gatk4 @@ -8,47 +9,58 @@ keywords: - short variant discovery tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: Compressed VCF files - pattern: "*.vcf.gz" - - vcf_idx: - type: file - description: VCF Index file - pattern: "*.vcf.gz.idx" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: FASTA index file - pattern: "*.fasta.fai" - - dict: - type: file - description: FASTA dictionary file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: Compressed VCF files + pattern: "*.vcf.gz" + - vcf_idx: + type: file + description: VCF Index file + pattern: "*.vcf.gz.idx" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: FASTA index file + pattern: "*.fasta.fai" + - - dict: + type: file + description: FASTA dictionary file + pattern: "*.dict" output: - combined_gvcf: - type: file - description: Compressed Combined GVCF file - pattern: "*.combined.g.vcf.gz" + - meta: + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" + - "*.combined.g.vcf.gz": + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/gatk4/composestrtablefile/meta.yml b/modules/nf-core/gatk4/composestrtablefile/meta.yml index 249aed2448e..fd56c797cc8 100644 --- a/modules/nf-core/gatk4/composestrtablefile/meta.yml +++ b/modules/nf-core/gatk4/composestrtablefile/meta.yml @@ -1,5 +1,7 @@ name: "gatk4_composestrtablefile" -description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel. +description: This tool looks for low-complexity STR sequences along the reference + that are later used to estimate the Dragstr model during single sample auto calibration + CalibrateDragstrModel. keywords: - composestrtablefile - dragstr @@ -14,28 +16,31 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: index of the FASTA reference file - pattern: "*.fai" - - dict: - type: file - description: Sequence dictionary of the FASTA reference file - pattern: "*.dict" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: index of the FASTA reference file + pattern: "*.fai" + - - dict: + type: file + description: Sequence dictionary of the FASTA reference file + pattern: "*.dict" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - str_table: - type: file - description: A zipped folder containing the STR table files - pattern: "*.zip" + - "*.zip": + type: file + description: A zipped folder containing the STR table files + pattern: "*.zip" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/condensedepthevidence/meta.yml b/modules/nf-core/gatk4/condensedepthevidence/meta.yml index dffb414bf46..b5c0207d83f 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/meta.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/meta.yml @@ -11,50 +11,61 @@ tools: tool_dev_url: "https://github.com/broadinstitute/gatk" doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - depth_evidence: - type: file - description: The depth evidence file - pattern: "*.rd.txt.gz" - - depth_evidence_index: - type: file - description: The index of the depth evidence file - pattern: "*.rd.txt.gz.tbi" - - fasta: - type: file - description: Reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - depth_evidence: + type: file + description: The depth evidence file + pattern: "*.rd.txt.gz" + - depth_evidence_index: + type: file + description: The index of the depth evidence file + pattern: "*.rd.txt.gz.tbi" + - - fasta: + type: file + description: Reference FASTA file needed when the input is a CRAM file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference FASTA file needed when the input is a CRAM + file + pattern: "*.fai" + - - dict: + type: file + description: Sequence dictionary of the reference FASTA file needed when the + input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - condensed_evidence: - type: file - description: The condensed depth evidence - pattern: "*.rd.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rd.txt.gz": + type: file + description: The condensed depth evidence + pattern: "*.rd.txt.gz" - condensed_evidence_index: - type: file - description: The condensed depth evidence - pattern: "*.rd.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rd.txt.gz.tbi": + type: file + description: The condensed depth evidence + pattern: "*.rd.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml index ba01f630302..cbbed8c0a15 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_createreadcountpanelofnormals" -description: Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel. +description: Creates a panel of normals (PoN) for read-count denoising given the read + counts for samples in the panel. keywords: - createreadcountpanelofnormals - gatk4 @@ -15,30 +16,33 @@ tools: doi: 10.1158/1538-7445.AM2017-3590 tool_dev_url: "https://github.com/broadinstitute/gatk" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - counts: - type: file - description: Read counts in hdf5 or tsv format. - pattern: "*.{hdf5,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - counts: + type: file + description: Read counts in hdf5 or tsv format. + pattern: "*.{hdf5,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pon: - type: file - description: Panel-of-normals file. - pattern: "*.{hdf5}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.hdf5": + type: file + description: Panel-of-normals file. + pattern: "*.{hdf5}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index f9d70be0982..7b5156bb3d4 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -15,25 +15,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fasta,fa}" output: - dict: - type: file - description: gatk dictionary file - pattern: "*.{dict}" + - meta: + type: file + description: gatk dictionary file + pattern: "*.{dict}" + - "*.dict": + type: file + description: gatk dictionary file + pattern: "*.{dict}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml index 9c3ee192cc4..45d88c16a08 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml @@ -1,5 +1,6 @@ name: gatk4_createsomaticpanelofnormals -description: Create a panel of normals contraining germline and artifactual sites for use with mutect2. +description: Create a panel of normals contraining germline and artifactual sites + for use with mutect2. keywords: - createsomaticpanelofnormals - gatk4 @@ -13,56 +14,67 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - genoomicsdb: - type: directory - description: genomicsDB workspace that contains the samples to create the somatic panel of normals with. - pattern: "*_genomicsDBworkspace" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - genomicsdb: + type: file + description: GenomicsDB database + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - vcf: - type: file - description: panel of normal as compressed vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: panel of normal as compressed vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: panel of normal as compressed vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: Tabix index of vcf file - pattern: "*vcf.gz.tbi" + - meta: + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" + - "*.tbi": + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/denoisereadcounts/meta.yml b/modules/nf-core/gatk4/denoisereadcounts/meta.yml index f2bd853f52c..367321ba209 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/meta.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/meta.yml @@ -15,43 +15,52 @@ tools: doi: 10.1158/1538-7445.AM2017-3590 tool_dev_url: "https://github.com/broadinstitute/gatk" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - counts: - type: file - description: Read counts in hdf5 or tsv format. - pattern: "*.{hdf5,tsv}" - - pon: - type: file - description: Panel of normals file hdf5 or tsv format. - pattern: "*.{hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - counts: + type: file + description: Read counts in hdf5 or tsv format. + pattern: "*.{hdf5,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - pon: + type: file + description: Panel of normals file hdf5 or tsv format. + pattern: "*.{hdf5}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - standardized: - type: file - description: Standardized copy ratios file. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_standardizedCR.tsv": + type: file + description: Standardized copy ratios file. + pattern: "*.{tsv}" - denoised: - type: file - description: Denoised copy ratios file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_denoisedCR.tsv": + type: file + description: Denoised copy ratios file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index 56eb4089064..828628b2834 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_determinegermlinecontigploidy" -description: Determines the baseline contig ploidy for germline samples given counts data +description: Determines the baseline contig ploidy for germline samples given counts + data keywords: - copy number - counts @@ -15,59 +16,70 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - counts: - type: file - description: One or more count TSV files created with gatk/collectreadcounts - pattern: "*.tsv" - - bed: - type: file - description: Optional - A bed file containing the intervals to include in the process - pattern: "*.bed" - - exclude_beds: - type: file - description: Optional - One or more bed files containing intervals to exclude from the process - pattern: "*.bed" - - contig_ploidy_table: - type: file - description: The contig ploidy priors table - pattern: "*.tsv" - - ploidy_model: - type: directory - description: | - Optional - A folder containing the ploidy model. - When a model is supplied to tool will run in CASE mode. - pattern: '*-model/' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - counts: + type: file + description: One or more count TSV files created with gatk/collectreadcounts + pattern: "*.tsv" + - bed: + type: file + description: Optional - A bed file containing the intervals to include in the + process + pattern: "*.bed" + - exclude_beds: + type: file + description: Optional - One or more bed files containing intervals to exclude + from the process + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ploidy_model: + type: directory + description: | + Optional - A folder containing the ploidy model. + When a model is supplied to tool will run in CASE mode. + pattern: '*-model/' + - - contig_ploidy_table: + type: file + description: The contig ploidy priors table + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - calls: - type: directory - description: A folder containing the calls from the input files - pattern: "*-calls/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-calls: + type: directory + description: A folder containing the calls from the input files + pattern: "*-calls/" - model: - type: directory - description: | - A folder containing the model from the input files. - This will only be created in COHORT mode (when no model is supplied to the process). - pattern: "*-model/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-model: + type: directory + description: | + A folder containing the model from the input files. + This will only be created in COHORT mode (when no model is supplied to the process). + pattern: "*-model/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml index 2d5bddf6c9e..4fb06a3a2e0 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml @@ -13,42 +13,45 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - metrics: - type: file - description: File containing metrics on the input files - pattern: "*.{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: File containing metrics on the input files + pattern: "*.{metrics}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/gatk4/fastqtosam/meta.yml b/modules/nf-core/gatk4/fastqtosam/meta.yml index 60658df0031..6d3e9078615 100644 --- a/modules/nf-core/gatk4/fastqtosam/meta.yml +++ b/modules/nf-core/gatk4/fastqtosam/meta.yml @@ -7,36 +7,44 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Converted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Converted BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/gatk4/filterintervals/meta.yml b/modules/nf-core/gatk4/filterintervals/meta.yml index 425c0015a10..87376ed6bcb 100644 --- a/modules/nf-core/gatk4/filterintervals/meta.yml +++ b/modules/nf-core/gatk4/filterintervals/meta.yml @@ -6,53 +6,63 @@ keywords: - interval_list tools: - "gatk4": - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - intervals: - type: file - description: Processed interval list file (processed_intervals.interval_list) - pattern: "*.interval_list" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - read_counts: - type: file - description: Read counts input file - pattern: "*.{tsv, hdf5}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - annotated_intervals: - type: file - description: Annotated intervals TSV file (annotated_intervals.tsv). - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - intervals: + type: file + description: Processed interval list file (processed_intervals.interval_list) + pattern: "*.interval_list" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - read_counts: + type: file + description: Read counts input file + pattern: "*.{tsv, hdf5}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - annotated_intervals: + type: file + description: Annotated intervals TSV file (annotated_intervals.tsv). + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Filtered interval list file - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interval_list": + type: file + description: Filtered interval list file + pattern: "*.interval_list" + - _list: + type: file + description: Filtered interval list file + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/filtermutectcalls/meta.yml b/modules/nf-core/gatk4/filtermutectcalls/meta.yml index 736c8386255..9287277eb7a 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/meta.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/meta.yml @@ -16,83 +16,103 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: compressed vcf file of mutect2calls - pattern: "*.vcf.gz" - - vcf_tbi: - type: file - description: Tabix index of vcf file - pattern: "*vcf.gz.tbi" - - stats: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" - - orientationbias: - type: file - description: files containing artifact priors for input vcf. Optional input. - pattern: "*.artifact-prior.tar.gz" - - segmentation: - type: file - description: tables containing segmentation information for input vcf. Optional input. - pattern: "*.segmentation.table" - - table: - type: file - description: table(s) containing contamination data for input vcf. Optional input, takes priority over estimate. - pattern: "*.contamination.table" - - estimate: - type: float - description: estimation of contamination value as a double. Optional input, will only be used if table is not specified. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: compressed vcf file of mutect2calls + pattern: "*.vcf.gz" + - vcf_tbi: + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" + - stats: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - orientationbias: + type: file + description: files containing artifact priors for input vcf. Optional input. + pattern: "*.artifact-prior.tar.gz" + - segmentation: + type: file + description: tables containing segmentation information for input vcf. Optional + input. + pattern: "*.segmentation.table" + - table: + type: file + description: table(s) containing contamination data for input vcf. Optional + input, takes priority over estimate. + pattern: "*.contamination.table" + - estimate: + type: float + description: estimation of contamination value as a double. Optional input, + will only be used if table is not specified. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - vcf: - type: file - description: file containing filtered mutect2 calls. - pattern: "*.vcf.gz" + - meta: + type: file + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" - tbi: - type: file - description: tbi file that pairs with vcf. - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" + - "*.vcf.gz.tbi": + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" - stats: - type: file - description: file containing statistics of the filtermutectcalls run. - pattern: "*.filteringStats.tsv" + - meta: + type: file + description: file containing statistics of the filtermutectcalls run. + pattern: "*.filteringStats.tsv" + - "*.filteringStats.tsv": + type: file + description: file containing statistics of the filtermutectcalls run. + pattern: "*.filteringStats.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@maxulysse" diff --git a/modules/nf-core/gatk4/filtervarianttranches/meta.yml b/modules/nf-core/gatk4/filtervarianttranches/meta.yml index 9346d2b4a43..398bbb07c1d 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/meta.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/meta.yml @@ -14,58 +14,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: a VCF file containing variants, must have info key:CNN_2D - pattern: "*.vcf.gz" - - tbi: - type: file - description: tbi file matching with -vcf - pattern: "*.vcf.gz.tbi" - - resources: - type: list - description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary - pattern: "*.vcf.gz" - - resources_index: - type: list - description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary - pattern: "*.vcf.gz" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: ".dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: a VCF file containing variants, must have info key:CNN_2D + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - intervals: + type: file + description: Intervals + - - resources: + type: list + description: resource A VCF containing known SNP and or INDEL sites. Can be + supplied as many times as necessary + pattern: "*.vcf.gz" + - - resources_index: + type: list + description: Index of resource VCF containing known SNP and or INDEL sites. + Can be supplied as many times as necessary + pattern: "*.vcf.gz" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: ".dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: VCF index file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/gatherbqsrreports/meta.yml b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml index b9f5bf5f8ba..587175b3a43 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/meta.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - table: - type: file - description: File(s) containing BQSR table(s) - pattern: "*.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - table: + type: file + description: File(s) containing BQSR table(s) + pattern: "*.table" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - table: - type: file - description: File containing joined BQSR table - pattern: "*.table" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: File containing joined BQSR table + pattern: "*.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml index 35381a3b514..d8b29d21006 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml @@ -12,30 +12,36 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pileup: - type: file - description: Pileup files from gatk4/getpileupsummaries - pattern: "*.pileups.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pileup: + type: file + description: Pileup files from gatk4/getpileupsummaries + pattern: "*.pileups.table" + - - dict: + type: file + description: dictionary output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - table: - type: file - description: pileup summaries table file - pattern: "*.pileups.table" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pileups.table": + type: file + description: pileup summaries table file + pattern: "*.pileups.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/gatk4/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml index 11e565b1046..174ae2eb0a8 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/meta.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/meta.yml @@ -1,5 +1,6 @@ name: gatk4_genomicsdbimport -description: merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation. +description: merge GVCFs from multiple samples. For use in joint genotyping or somatic + panel of normal creation. keywords: - gatk4 - genomicsdb @@ -15,61 +16,99 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used. - pattern: "*.vcf.gz" - - tbi: - type: list - description: list of tbi files that match with the input vcf files - pattern: "*.vcf.gz_tbi" - - wspace: - type: file - description: path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode. - pattern: "/path/to/existing/gendb" - - interval_file: - type: file - description: file containing the intervals to be used when creating the genomicsdb - pattern: "*.interval_list" - - interval_value: - type: string - description: if an intervals file has not been spcified, the value enetered here will be used as an interval via the "-L" argument - pattern: "example: chr1:1000-10000" - - run_intlist: - type: boolean - description: Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace. - pattern: "true/false" - - run_updatewspace: - type: boolean - description: Specify whether to run update genomicsdb mode, this option takes priority over run_intlist. - pattern: "true/false" - - input_map: - type: boolean - description: Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb. - pattern: "*.sample_map" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: either a list of vcf files to be used to create or update a genomicsdb, + or a file that contains a map to vcf files to be used. + pattern: "*.vcf.gz" + - tbi: + type: list + description: list of tbi files that match with the input vcf files + pattern: "*.vcf.gz_tbi" + - interval_file: + type: file + description: file containing the intervals to be used when creating the genomicsdb + pattern: "*.interval_list" + - interval_value: + type: string + description: if an intervals file has not been spcified, the value enetered + here will be used as an interval via the "-L" argument + pattern: "example: chr1:1000-10000" + - wspace: + type: file + description: path to an existing genomicsdb to be used in update db mode or + get intervals mode. This WILL NOT specify name of a new genomicsdb in create + db mode. + pattern: "/path/to/existing/gendb" + - - run_intlist: + type: boolean + description: Specify whether to run get interval list mode, this option cannot + be specified at the same time as run_updatewspace. + pattern: "true/false" + - - run_updatewspace: + type: boolean + description: Specify whether to run update genomicsdb mode, this option takes + priority over run_intlist. + pattern: "true/false" + - - input_map: + type: boolean + description: Specify whether the vcf input is providing a list of vcf file(s) + or a single file containing a map of paths to vcf files to be used to create + or update a genomicsdb. + pattern: "*.sample_map" output: - genomicsdb: - type: directory - description: Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db - pattern: "*/$prefix" + - meta: + type: directory + description: Directory containing the files that compose the genomicsdb workspace, + this is only output for create mode, as update changes an existing db + pattern: "*/$prefix" + - $prefix: + type: directory + description: Directory containing the files that compose the genomicsdb workspace, + this is only output for create mode, as update changes an existing db + pattern: "*/$prefix" - updatedb: - type: directory - description: Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace. - pattern: "same/path/as/wspace" + - meta: + type: directory + description: Directory containing the files that compose the updated genomicsdb + workspace, this is only output for update mode, and should be the same path + as the input wspace. + pattern: "same/path/as/wspace" + - $updated_db: + type: directory + description: Directory containing the files that compose the updated genomicsdb + workspace, this is only output for update mode, and should be the same path + as the input wspace. + pattern: "same/path/as/wspace" - intervallist: - type: file - description: File containing the intervals used to generate the genomicsdb, only created by get intervals mode. - pattern: "*.interval_list" + - meta: + type: file + description: File containing the intervals used to generate the genomicsdb, + only created by get intervals mode. + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: File containing the intervals used to generate the genomicsdb, + only created by get intervals mode. + pattern: "*.interval_list" + - list: + type: file + description: File containing the intervals used to generate the genomicsdb, + only created by get intervals mode. + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml index eb704364b48..0c1fe491fe0 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/meta.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml @@ -14,91 +14,101 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - gVCF(.gz) file or a GenomicsDB - pattern: "*.{vcf,vcf.gz}" - - gvcf_index: - type: file - description: | - index of gvcf file, or empty when providing GenomicsDB - pattern: "*.{idx,tbi}" - - intervals: - type: file - description: Interval file with the genomic regions included in the library (optional) - - intervals_index: - type: file - description: Interval index file (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing fai information - e.g. [ id:'test' ] - - fai: - type: file - description: Reference fasta index file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing dict information - e.g. [ id:'test' ] - - dict: - type: file - description: Reference fasta sequence dict file - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test' ] - - dbsnp: - type: file - description: dbSNP VCF file - pattern: "*.vcf.gz" - - meta6: - type: map - description: | - Groovy Map containing dbsnp tbi information - e.g. [ id:'test' ] - - dbsnp_tbi: - type: file - description: dbSNP VCF index file - pattern: "*.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + gVCF(.gz) file or a GenomicsDB + pattern: "*.{vcf,vcf.gz}" + - gvcf_index: + type: file + description: | + index of gvcf file, or empty when providing GenomicsDB + pattern: "*.{idx,tbi}" + - intervals: + type: file + description: Interval file with the genomic regions included in the library + (optional) + - intervals_index: + type: file + description: Interval index file (optional) + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test' ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing dict information + e.g. [ id:'test' ] + - dict: + type: file + description: Reference fasta sequence dict file + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test' ] + - dbsnp: + type: file + description: dbSNP VCF file + pattern: "*.vcf.gz" + - - meta6: + type: map + description: | + Groovy Map containing dbsnp tbi information + e.g. [ id:'test' ] + - dbsnp_tbi: + type: file + description: dbSNP VCF index file + pattern: "*.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Genotyped VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Genotyped VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Tbi index for VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Tbi index for VCF file + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@santiagorevale" - "@maxulysse" diff --git a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml index d4715ff0f77..a185d9d1091 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml @@ -1,60 +1,85 @@ name: "gatk4_germlinecnvcaller" -description: Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy. +description: Calls copy-number variants in germline samples given their counts and + the output of DetermineGermlineContigPloidy. keywords: - gatk - germline contig ploidy - germlinecnvcaller tools: - "gatk4": - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tsv: - type: file - description: One or more count TSV files created with gatk/collectreadcounts - pattern: "*.tsv" - - intervals: - type: file - description: Optional - A bed file containing the intervals to include in the process - pattern: "*.bed" - - model: - type: directory - description: Optional - directory containing the model produced by germlinecnvcaller cohort mode - pattern: "*-cnv-model/*-model" - - ploidy: - type: directory - description: Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode - pattern: "*-calls" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tsv: + type: file + description: One or more count TSV files created with gatk/collectreadcounts + pattern: "*.tsv" + - intervals: + type: file + description: Optional - A bed file containing the intervals to include in the + process + pattern: "*.bed" + - ploidy: + type: directory + description: Directory containing ploidy calls produced by determinegermlinecontigploidy + case or cohort mode + pattern: "*-calls" + - model: + type: directory + description: Optional - directory containing the model produced by germlinecnvcaller + cohort mode + pattern: "*-cnv-model/*-model" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cohortcalls: - type: directory - description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode - pattern: "*-cnv-model/*-calls" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cnv-model/*-calls": + type: directory + description: Tar gzipped directory containing calls produced by germlinecnvcaller + case mode + pattern: "*-cnv-model/*-calls" - cohortmodel: - type: directory - description: Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode - pattern: "*-cnv-model/*-model" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cnv-model/*-model": + type: directory + description: Optional - Tar gzipped directory containing the model produced + by germlinecnvcaller cohort mode + pattern: "*-cnv-model/*-model" - casecalls: - type: directory - description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode - pattern: "*-cnv-calls/*-calls" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cnv-calls/*-calls": + type: directory + description: Tar gzipped directory containing calls produced by germlinecnvcaller + case mode + pattern: "*-cnv-calls/*-calls" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/getpileupsummaries/meta.yml b/modules/nf-core/gatk4/getpileupsummaries/meta.yml index fab3c1435e5..86b851e13a4 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/meta.yml @@ -16,68 +16,78 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM file to be summarised. - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAM file index. - pattern: "*.{bai,crai}" - - intervals: - type: file - description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. - pattern: "*.interval_list" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - variants: - type: file - description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified. - pattern: "*.vcf.gz" - - variants_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input: + type: file + description: BAM/CRAM file to be summarised. + pattern: "*.{bam,cram}" + - index: + type: file + description: Index file for the input BAM/CRAM file. + pattern: "*.{bam.bai,cram.crai}" + - intervals: + type: file + description: File containing specified sites to be used for the summary. If + this option is not specified, variants file is used instead automatically. + pattern: "*.interval_list" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - variants: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + Is also used as sites file if no separate sites file is specified. + pattern: "*.vcf.gz" + - - variants_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" output: - - pileup: - type: file - description: File containing the pileup summary table. - pattern: "*.pileups.table" + - table: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.pileups.table": + type: file + description: Table containing read counts for each site. + pattern: "*.pileups.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 703b99a0985..9d4a05e9144 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -14,92 +14,108 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - dragstr_model: - type: file - description: Text file containing the DragSTR model of the used BAM/CRAM file (optional) - pattern: "*.txt" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test_dbsnp' ] - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - meta6: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test_dbsnp' ] - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - dragstr_model: + type: file + description: Text file containing the DragSTR model of the used BAM/CRAM file + (optional) + pattern: "*.txt" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test_dbsnp' ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - meta6: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test_dbsnp' ] + - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - bam: - type: file - description: Assembled haplotypes and locally realigned reads - pattern: "*.realigned.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.realigned.bam": + type: file + description: Assembled haplotypes and locally realigned reads + pattern: "*.realigned.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/indexfeaturefile/meta.yml b/modules/nf-core/gatk4/indexfeaturefile/meta.yml index 575c6038b3f..cfc717d227b 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/meta.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - feature_file: - type: file - description: VCF/BED file - pattern: "*.{vcf,vcf.gz,bed,bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - feature_file: + type: file + description: VCF/BED file + pattern: "*.{vcf,vcf.gz,bed,bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Index for VCF/BED file - pattern: "*.{tbi,idx}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tbi,idx}": + type: file + description: Index for VCF/BED file + pattern: "*.{tbi,idx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@santiagorevale" maintainers: diff --git a/modules/nf-core/gatk4/intervallisttobed/meta.yml b/modules/nf-core/gatk4/intervallisttobed/meta.yml index 28d264dfef5..0779fa18223 100644 --- a/modules/nf-core/gatk4/intervallisttobed/meta.yml +++ b/modules/nf-core/gatk4/intervallisttobed/meta.yml @@ -13,30 +13,32 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - interval: - type: file - description: Interval list - pattern: "*.{interval,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: IntervalList file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/intervallisttools/meta.yml b/modules/nf-core/gatk4/intervallisttools/meta.yml index 748dccfc56b..8ee15a2975f 100644 --- a/modules/nf-core/gatk4/intervallisttools/meta.yml +++ b/modules/nf-core/gatk4/intervallisttools/meta.yml @@ -1,5 +1,6 @@ name: gatk4_intervallisttools -description: Splits the interval list file into unique, equally-sized interval files and place it under a directory +description: Splits the interval list file into unique, equally-sized interval files + and place it under a directory keywords: - bed - gatk4 @@ -15,30 +16,36 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - interval_list: - type: file - description: Interval list file - pattern: "*.interval_list" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: Interval file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Interval list files - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_split/*/*.interval_list": + type: file + description: Interval list files + pattern: "*.interval_list" + - _list: + type: file + description: Interval list files + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@praveenraj2018" maintainers: diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml index 4b73a51adba..fde7829c8d9 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml @@ -16,25 +16,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - f1r2: - type: list - description: list of f1r2 files to be used as input. - pattern: "*.f1r2.tar.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - f1r2: + type: list + description: list of f1r2 files to be used as input. + pattern: "*.f1r2.tar.gz" output: - artifactprior: - type: file - description: file containing artifact-priors to be used by filtermutectcalls - pattern: "*.tar.gz" + - meta: + type: file + description: file containing artifact-priors to be used by filtermutectcalls + pattern: "*.tar.gz" + - "*.tar.gz": + type: file + description: file containing artifact-priors to be used by filtermutectcalls + pattern: "*.tar.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml index ace4d5031e7..176cc902f25 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml @@ -16,55 +16,64 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be normalized - e.g. 'file1.vcf.gz' - - tbi: - type: file - description: | - Index of the vcf file to be normalized - e.g. 'file1.vcf.gz.tbi' - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf.gz' + - tbi: + type: file + description: | + Index of the vcf file to be normalized + e.g. 'file1.vcf.gz.tbi' + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Tbi index for VCF file - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Tbi index for VCF file + pattern: "*.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 9fe34eb36c8..3c73c17e433 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,7 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - bioconda::gatk4=4.5.0.0 - - bioconda::samtools=1.19.2 - bioconda::htslib=1.19.1 + - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml index b0f09d4b843..4772c5f39aa 100644 --- a/modules/nf-core/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/gatk4/markduplicates/meta.yml @@ -1,5 +1,6 @@ name: gatk4_markduplicates -description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. +description: This tool locates and tags duplicate reads in a BAM or SAM file, where + duplicate reads are defined as originating from a single fragment of DNA. keywords: - bam - gatk4 @@ -7,60 +8,90 @@ keywords: - sort tools: - gatk4: - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta}" - - fasta_fai: - type: file - description: Fasta index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - - fasta: + type: file + description: Fasta file + pattern: "*.{fasta}" + - - fasta_fai: + type: file + description: Fasta index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Marked duplicates BAM file - pattern: "*.{bam}" - cram: - type: file - description: Marked duplicates CRAM file - pattern: "*.{cram}" - - bai: - type: file - description: BAM index file - pattern: "*.{bam.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cram": + type: file + description: Marked duplicates CRAM file + pattern: "*.{cram}" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*bam": + type: file + description: Marked duplicates BAM file + pattern: "*.{bam}" - crai: - type: file - description: CRAM index file - pattern: "*.{cram.crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file + pattern: "*.{cram.crai}" + - bai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM index file + pattern: "*.{bam.bai}" - metrics: - type: file - description: Duplicate metrics file generated by GATK - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Duplicate metrics file generated by GATK + pattern: "*.{metrics.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ajodeh-juma" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/mergebamalignment/meta.yml b/modules/nf-core/gatk4/mergebamalignment/meta.yml index af4a3f18b0a..7bde9345947 100644 --- a/modules/nf-core/gatk4/mergebamalignment/meta.yml +++ b/modules/nf-core/gatk4/mergebamalignment/meta.yml @@ -16,45 +16,52 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - aligned: - type: file - description: The aligned bam file - pattern: "*.{bam}" - - unaligned: - type: file - description: The unmaped bam file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - aligned: + type: file + description: The aligned bam file + pattern: "*.{bam}" + - unmapped: + type: file + description: The unmapped bam file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary output: - bam: - type: file - description: The merged bam file - pattern: "*.bam" + - meta: + type: file + description: The merged bam file + pattern: "*.bam" + - "*.bam": + type: file + description: The merged bam file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/mergemutectstats/meta.yml b/modules/nf-core/gatk4/mergemutectstats/meta.yml index 12695256576..09c8a547209 100644 --- a/modules/nf-core/gatk4/mergemutectstats/meta.yml +++ b/modules/nf-core/gatk4/mergemutectstats/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: Stats file - pattern: "*.{stats}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats: + type: file + description: Stats file + pattern: "*.{stats}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Stats file - pattern: "*.vcf.gz.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.stats": + type: file + description: Stats file + pattern: "*.vcf.gz.stats" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml index 996053fcc61..b4f61d780d9 100644 --- a/modules/nf-core/gatk4/mergevcfs/meta.yml +++ b/modules/nf-core/gatk4/mergevcfs/meta.yml @@ -14,38 +14,50 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: Two or more VCF files - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - dict: - type: file - description: Optional Sequence Dictionary as input - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: Two or more VCF files + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: + type: file + description: Optional Sequence Dictionary as input + pattern: "*.dict" output: - vcf: - type: file - description: merged vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: merged vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: merged vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: index files for the merged vcf files - pattern: "*.tbi" + - meta: + type: file + description: index files for the merged vcf files + pattern: "*.tbi" + - "*.tbi": + type: file + description: index files for the merged vcf files + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/mutect2/meta.yml b/modules/nf-core/gatk4/mutect2/meta.yml index 21c928ed96b..27fd63a243a 100644 --- a/modules/nf-core/gatk4/mutect2/meta.yml +++ b/modules/nf-core/gatk4/mutect2/meta.yml @@ -17,88 +17,113 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - input: - type: list - description: list of BAM files, also able to take CRAM as an input - pattern: "*.{bam/cram}" - - input_index: - type: list - description: list of BAM file indexes, also able to take CRAM indexes as an input - pattern: "*.{bam.bai/cram.crai}" - - intervals: - type: file - description: Specify region the tools is run on. - pattern: ".{bed,interval_list}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - germline_resource: - type: file - description: Population vcf of germline sequencing, containing allele fractions. - pattern: "*.vcf.gz" - - germline_resource_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" - - panel_of_normals: - type: file - description: vcf file to be used as a panel of normals. - pattern: "*.vcf.gz" - - panel_of_normals_tbi: - type: file - description: Index for the panel of normals. - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - input: + type: list + description: list of BAM files, also able to take CRAM as an input + pattern: "*.{bam/cram}" + - input_index: + type: list + description: list of BAM file indexes, also able to take CRAM indexes as an + input + pattern: "*.{bam.bai/cram.crai}" + - intervals: + type: file + description: Specify region the tools is run on. + pattern: ".{bed,interval_list}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - germline_resource: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + pattern: "*.vcf.gz" + - - germline_resource_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" + - - panel_of_normals: + type: file + description: vcf file to be used as a panel of normals. + pattern: "*.vcf.gz" + - - panel_of_normals_tbi: + type: file + description: Index for the panel of normals. + pattern: "*.vcf.gz.tbi" output: - vcf: - type: file - description: compressed vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: compressed vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: compressed vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of vcf file - pattern: "*vcf.gz.tbi" + - meta: + type: file + description: Index of vcf file + pattern: "*vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of vcf file + pattern: "*vcf.gz.tbi" - stats: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" + - meta: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - "*.stats": + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" - f1r2: - type: file - description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run) - pattern: "*.f1r2.tar.gz" + - meta: + type: file + description: file containing information to be passed to LearnReadOrientationModel + (only outputted when tumor_normal_pair mode is run) + pattern: "*.f1r2.tar.gz" + - "*.f1r2.tar.gz": + type: file + description: file containing information to be passed to LearnReadOrientationModel + (only outputted when tumor_normal_pair mode is run) + pattern: "*.f1r2.tar.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml index a724da11c1a..d090169ab07 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_postprocessgermlinecnvcalls" -description: Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios +description: Postprocesses the output of GermlineCNVCaller and generates VCFs and + denoised copy ratios keywords: - copy number - gatk4 @@ -14,50 +15,69 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593411-PostprocessGermlineCNVCalls doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ploidy: - type: directory - description: | - Optional - A folder containing the ploidy model. - When a model is supplied to tool will run in CASE mode. - pattern: "*-calls/" - - calls: - type: directory - description: A folder containing the calls from the input files - pattern: "*-cnv-calls/*-calls" - - model: - type: directory - description: | - A folder containing the model from the input files. - This will only be created in COHORT mode (when no model is supplied to the process). - pattern: "*-cnv-model/*-model" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - calls: + type: directory + description: A folder containing the calls from the input files + pattern: "*-cnv-calls/*-calls" + - model: + type: directory + description: | + A folder containing the model from the input files. + This will only be created in COHORT mode (when no model is supplied to the process). + pattern: "*-cnv-model/*-model" + - ploidy: + type: directory + description: | + Optional - A folder containing the ploidy model. + When a model is supplied to tool will run in CASE mode. + pattern: "*-calls/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - denoised: - type: file - description: Denoised copy ratio file - pattern: "*.vcf.gz" - - segments: - type: file - description: Segments VCF file - pattern: "*.vcf.gz" - intervals: - type: file - description: Intervals VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genotyped_intervals.vcf.gz": + type: file + description: Intervals VCF file + pattern: "*.vcf.gz" + - s: + type: file + description: Intervals VCF file + pattern: "*.vcf.gz" + - segments: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genotyped_segments.vcf.gz": + type: file + description: Segments VCF file + pattern: "*.vcf.gz" + - denoised: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_denoised.vcf.gz": + type: file + description: Denoised copy ratio file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" maintainers: diff --git a/modules/nf-core/gatk4/preprocessintervals/meta.yml b/modules/nf-core/gatk4/preprocessintervals/meta.yml index cf3f6ac43a0..0e136748799 100644 --- a/modules/nf-core/gatk4/preprocessintervals/meta.yml +++ b/modules/nf-core/gatk4/preprocessintervals/meta.yml @@ -7,71 +7,83 @@ keywords: - preprocessintervals tools: - "gatk4": - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - intervals: - type: file - description: Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional) - pattern: "*.{bed,interval_list}" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - exclude_intervals: - type: file - description: Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional) - pattern: "*.{bed,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - intervals: + type: file + description: Interval file (bed or interval_list) with the genomic regions to + be included from the analysis (optional) + pattern: "*.{bed,interval_list}" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - exclude_intervals: + type: file + description: Interval file (bed or interval_list) with the genomic regions to + be excluded from the analysis (optional) + pattern: "*.{bed,interval_list}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Processed interval list file - pattern: "*.{bed,interval_list}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - "*.interval_list": + type: file + description: Processed interval list file + pattern: "*.{bed,interval_list}" + - _list: + type: file + description: Processed interval list file + pattern: "*.{bed,interval_list}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/printreads/meta.yml b/modules/nf-core/gatk4/printreads/meta.yml index aca7e18878a..de8da7c56a3 100644 --- a/modules/nf-core/gatk4/printreads/meta.yml +++ b/modules/nf-core/gatk4/printreads/meta.yml @@ -16,69 +16,84 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: reference fasta file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: reference fasta index file - pattern: "*.{fai}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: reference fasta dictionary file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: reference fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: reference fasta index file + pattern: "*.{fai}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: reference fasta dictionary file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - sam: - type: file - description: Sorted SAM file - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sam: + type: file + description: Sorted SAM file + pattern: "*.{sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/printsvevidence/meta.yml b/modules/nf-core/gatk4/printsvevidence/meta.yml index 6d24fe19027..3e3ad72d58e 100644 --- a/modules/nf-core/gatk4/printsvevidence/meta.yml +++ b/modules/nf-core/gatk4/printsvevidence/meta.yml @@ -1,5 +1,9 @@ name: "gatk4_printsvevidence" -description: WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. +description: WARNING - this tool is still experimental and shouldn't be used in a + production setting. Gathers paired-end and split read evidence files for use in + the GATK-SV pipeline. Output files are a file containing the location of and orientation + of read pairs marked as discordant, and a file containing the clipping location + of all soft clipped reads and the orientation of the clipping. keywords: - gatk4 - printsvevidence @@ -14,54 +18,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - evidence_files: - type: file - description: The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence. - pattern: "*.{pe,sr,baf,rd}.txt(.gz)" - - evidence_indices: - type: file - description: The indices of the evidence files created by CollectSVEvidence - pattern: "*.{pe,sr,baf,rd}.txt(.gz).tbi" - - bed: - type: file - description: An optional BED file - pattern: "*.bed" - - fasta: - type: file - description: An optional reference FASTA file - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: An optional reference FASTA file index - pattern: "*.fai" - - dict: - type: file - description: The mandatory sequence dictionary file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - evidence_files: + type: file + description: The evidence files created by CollectSVEvidence. They all need + to be of the same type to print the SV evidence. + pattern: "*.{pe,sr,baf,rd}.txt(.gz)" + - evidence_indices: + type: file + description: The indices of the evidence files created by CollectSVEvidence + pattern: "*.{pe,sr,baf,rd}.txt(.gz).tbi" + - - bed: + type: file + description: An optional BED file + pattern: "*.bed" + - - fasta: + type: file + description: An optional reference FASTA file + pattern: "*.{fa,fasta}" + - - fasta_fai: + type: file + description: An optional reference FASTA file index + pattern: "*.fai" + - - dict: + type: file + description: The mandatory sequence dictionary file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - printed_evidence: - type: file - description: The output file containing the discordant read pairs or the soft clipped reads - pattern: "*.{pe,sr,baf,rd}.txt.gz" - - printed_evidence: - type: file - description: The index of the output file containing the discordant read pairs or the soft clipped reads - pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: The output file containing the discordant read pairs or the soft + clipped reads + pattern: "*.{pe,sr,baf,rd}.txt.gz" + - printed_evidence_index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz.tbi": + type: file + description: The index file of the output compressed text file containing the discordant read + pairs or the soft clipped reads + pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/reblockgvcf/meta.yml b/modules/nf-core/gatk4/reblockgvcf/meta.yml index 5a93f0f072f..d02c24e7774 100644 --- a/modules/nf-core/gatk4/reblockgvcf/meta.yml +++ b/modules/nf-core/gatk4/reblockgvcf/meta.yml @@ -14,59 +14,63 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gvcf: - type: file - description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode - pattern: "*.{vcf,gvcf}.gz" - - tbi: - type: file - description: Index of the GVCF file - pattern: "*.tbi" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gvcf: + type: file + description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or + '-ERC BP_RESOLUTION' mode + pattern: "*.{vcf,gvcf}.gz" + - tbi: + type: file + description: Index of the GVCF file + pattern: "*.tbi" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rb.g.vcf.gz": + type: file + description: The reblocked GVCF file + pattern: "*.rb.g.vcf.gz" + - "*.tbi": + type: file + description: Index of the reblocked GVCF file + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - gvcf: - type: file - description: Filtered GVCF - pattern: "*rb.g.vcf.gz" - - tbi: - type: file - description: Index of the filtered GVCF - pattern: "*rb.g.vcf.gz.tbi" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/revertsam/meta.yml b/modules/nf-core/gatk4/revertsam/meta.yml index ac6c0d0f0e8..fb73b13f747 100644 --- a/modules/nf-core/gatk4/revertsam/meta.yml +++ b/modules/nf-core/gatk4/revertsam/meta.yml @@ -14,25 +14,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: file - description: The input bam/sam file - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: The input bam/sam file + pattern: "*.{bam,sam}" output: - bam: - type: file - description: The reverted bam/sam file - pattern: "*.reverted.bam" + - meta: + type: file + description: The reverted bam/sam file + pattern: "*.reverted.bam" + - "*.bam": + type: file + description: The reverted bam/sam file + pattern: "*.reverted.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/samtofastq/meta.yml b/modules/nf-core/gatk4/samtofastq/meta.yml index b61ef4fc956..91a8e503f50 100644 --- a/modules/nf-core/gatk4/samtofastq/meta.yml +++ b/modules/nf-core/gatk4/samtofastq/meta.yml @@ -14,25 +14,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: file - description: Input SAM/BAM file - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: Input SAM/BAM file + pattern: "*.{bam,sam}" output: - fastq: - type: file - description: converted fastq file - pattern: "*.fastq" + - meta: + type: file + description: converted fastq file + pattern: "*.fastq" + - "*.fastq.gz": + type: file + description: converted fastq file + pattern: "*.fastq" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/selectvariants/meta.yml b/modules/nf-core/gatk4/selectvariants/meta.yml index 5bd0fc69aba..5fd9c6f39a9 100644 --- a/modules/nf-core/gatk4/selectvariants/meta.yml +++ b/modules/nf-core/gatk4/selectvariants/meta.yml @@ -15,42 +15,51 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: VCF(.gz) file - pattern: "*.{vcf,vcf.gz}" - - vcf_idx: - type: list - description: VCF file index - pattern: "*.{idx,tbi}" - - intervals: - type: file - description: One or more genomic intervals over which to operate - pattern: ".intervals" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: VCF(.gz) file + pattern: "*.{vcf,vcf.gz}" + - vcf_idx: + type: list + description: VCF file index + pattern: "*.{idx,tbi}" + - intervals: + type: file + description: One or more genomic intervals over which to operate + pattern: ".intervals" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.selectvariants.vcf.gz" - - vcf_tbi: - type: list - description: VCF file index - pattern: "*.{idx,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.selectvariants.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Tabix index file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/shiftfasta/meta.yml b/modules/nf-core/gatk4/shiftfasta/meta.yml index c1ab0c2f1c8..28b2ac555b7 100644 --- a/modules/nf-core/gatk4/shiftfasta/meta.yml +++ b/modules/nf-core/gatk4/shiftfasta/meta.yml @@ -17,64 +17,109 @@ tools: tool_dev_url: "https://github.com/broadinstitute/gatk" doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: fasta file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: index for fasta file - pattern: "*.{fai}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - dict: - type: file - description: sequence dictionary file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: fasta file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: index for fasta file + pattern: "*.{fai}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: sequence dictionary file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - shift_fa: + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.fasta": + type: file + description: Shifted fasta file + pattern: "*.{fa,fasta}" + - shift_fai: + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.fasta.fai": + type: file + description: Index file for the shifted fasta file + pattern: "*.{fai}" + - shift_back_chain: + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.back_chain": + type: file + description: The shiftback chain file to use when lifting over + pattern: "*.{back_chain}" - dict: - type: file - description: sequence dictionary file - pattern: "*.{dict}" + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.dict": + type: file + description: sequence dictionary file + pattern: "*.{dict}" - intervals: - type: file - description: Intervals file for the fasta file - pattern: "*.{intervals}" - - shift_back_chain: - type: file - description: The shiftback chain file to use when lifting over - pattern: "*.{back_chain}" - - shift_fa: - type: file - description: Shifted fasta file - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*.intervals": + type: file + description: Intervals file for the fasta file + pattern: "*.{intervals}" + - s: + type: file + description: Intervals file for the fasta file + pattern: "*.{intervals}" - shift_intervals: - type: file - description: Intervals file for the shifted fasta file - pattern: "*.{shifted.intervals}" + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*.shifted.intervals": + type: file + description: Intervals file for the shifted fasta file + pattern: "*.{shifted.intervals}" + - s: + type: file + description: Intervals file for the shifted fasta file + pattern: "*.{shifted.intervals}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/sitedepthtobaf/meta.yml b/modules/nf-core/gatk4/sitedepthtobaf/meta.yml index 2876fb9e2d1..fee4b33f97e 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/meta.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/meta.yml @@ -12,58 +12,67 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - site_depths: - type: file - description: Files containing site depths - pattern: "*.sd.txt.gz" - - site_depths_indices: - type: file - description: The indices of the site depth files - pattern: "*.sd.txt.gz.tbi" - - vcf: - type: file - description: Input VCF of SNPs marking loci for site depths - pattern: "*.vcf.gz" - - tbi: - type: file - description: Index of the input VCF of SNPs marking loci for site depths - pattern: "*.vcf.gz.tbi" - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" - - dict: - type: file - description: The sequence dictionary of the reference FASTA file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - site_depths: + type: file + description: Files containing site depths + pattern: "*.sd.txt.gz" + - site_depths_indices: + type: file + description: The indices of the site depth files + pattern: "*.sd.txt.gz.tbi" + - - vcf: + type: file + description: Input VCF of SNPs marking loci for site depths + pattern: "*.vcf.gz" + - tbi: + type: file + description: Index of the input VCF of SNPs marking loci for site depths + pattern: "*.vcf.gz.tbi" + - - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" + - - dict: + type: file + description: The sequence dictionary of the reference FASTA file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - baf: - type: file - description: The created BAF file - pattern: "*.baf.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.baf.txt.gz": + type: file + description: The created BAF file + pattern: "*.baf.txt.gz" - baf_tbi: - type: file - description: The index of the created BAF file - pattern: "*.baf.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.baf.txt.gz.tbi": + type: file + description: The index of the created BAF file + pattern: "*.baf.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/splitcram/meta.yml b/modules/nf-core/gatk4/splitcram/meta.yml index cb3005ee71b..56b81b63702 100644 --- a/modules/nf-core/gatk4/splitcram/meta.yml +++ b/modules/nf-core/gatk4/splitcram/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_splitcram" -description: Splits CRAM files efficiently by taking advantage of their container based structure +description: Splits CRAM files efficiently by taking advantage of their container + based structure keywords: - cram - gatk4 @@ -15,30 +16,33 @@ tools: documentation: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cram: - type: file - description: The CRAM file to split - pattern: "*.cram" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: The CRAM file to split + pattern: "*.cram" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_crams: - type: file - description: A list of split CRAM files - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: A list of split CRAM files + pattern: "*.cram" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/splitintervals/meta.yml b/modules/nf-core/gatk4/splitintervals/meta.yml index c92bad8b531..6a1b869b0d1 100644 --- a/modules/nf-core/gatk4/splitintervals/meta.yml +++ b/modules/nf-core/gatk4/splitintervals/meta.yml @@ -13,57 +13,59 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - interval: - type: file - description: Interval list or BED - pattern: "*.{interval,interval_list,bed}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference FASTA - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference FASTA index - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Reference sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - intervals: + type: file + description: Interval file + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference FASTA + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference FASTA index + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Reference sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bed: - type: file - description: A list of scattered interval lists - pattern: "*.interval_list" + - split_intervals: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "**.interval_list": + type: file + description: interval files + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/splitncigarreads/meta.yml b/modules/nf-core/gatk4/splitncigarreads/meta.yml index f813274671e..6b05bef10b9 100644 --- a/modules/nf-core/gatk4/splitncigarreads/meta.yml +++ b/modules/nf-core/gatk4/splitncigarreads/meta.yml @@ -14,59 +14,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: list - description: BAM/SAM/CRAM file containing reads - pattern: "*.{bam,sam,cram}" - - bai: - type: list - description: BAI/SAI/CRAI index file (optional) - pattern: "*.{bai,sai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: list + description: BAM/SAM/CRAM file containing reads + pattern: "*.{bam,sam,cram}" + - bai: + type: list + description: BAI/SAI/CRAI index file (optional) + pattern: "*.{bai,sai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - bam: - type: file - description: Output file with split reads (BAM/SAM/CRAM) - pattern: "*.{bam,sam,cram}" + - meta: + type: file + description: Output file with split reads (BAM/SAM/CRAM) + pattern: "*.{bam,sam,cram}" + - "*.bam": + type: file + description: Output file with split reads (BAM/SAM/CRAM) + pattern: "*.{bam,sam,cram}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/svannotate/meta.yml b/modules/nf-core/gatk4/svannotate/meta.yml index 30a56f6fcb2..8f398a8372a 100644 --- a/modules/nf-core/gatk4/svannotate/meta.yml +++ b/modules/nf-core/gatk4/svannotate/meta.yml @@ -1,5 +1,8 @@ name: "gatk4_svannotate" -description: Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF. +description: Adds predicted functional consequence, gene overlap, and noncoding element + overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, + a GTF file containing primary or canonical transcripts, and a BED file containing + noncoding elements. Output file is an annotated SV VCF. keywords: - annotate - gatk4 @@ -14,54 +17,66 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A VCF file created with a structural variant caller - pattern: "*.vcf.gz" - - tbi: - type: file - description: The index file of the VCF - pattern: "*.vcf.gz.tbi" - - bed: - type: file - description: Regions to limit the analysis to - pattern: "*.bed" - - fasta: - type: file - description: Optional - reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Optional - index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: A VCF file created with a structural variant caller + pattern: "*.vcf.gz" + - tbi: + type: file + description: The index file of the VCF + pattern: "*.vcf.gz.tbi" + - bed: + type: file + description: Regions to limit the analysis to + pattern: "*.bed" + - - fasta: + type: file + description: Optional - reference FASTA file needed when the input is a CRAM + file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Optional - index of the reference FASTA file needed when the input + is a CRAM file + pattern: "*.fai" + - - dict: + type: file + description: Optional - sequence dictionary of the reference FASTA file needed + when the input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotated_vcf: - type: file - description: The annotated structural variant VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The annotated structural variant VCF + pattern: "*.vcf.gz" - index: - type: file - description: The index of the VCF - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: The index of the VCF + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/svcluster/meta.yml b/modules/nf-core/gatk4/svcluster/meta.yml index 8a772058e3e..39d3e887673 100644 --- a/modules/nf-core/gatk4/svcluster/meta.yml +++ b/modules/nf-core/gatk4/svcluster/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_svcluster" -description: Clusters structural variants based on coordinates, event type, and supporting algorithms +description: Clusters structural variants based on coordinates, event type, and supporting + algorithms keywords: - gatk4 - structural variants @@ -15,54 +16,65 @@ tools: documentation: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: file - description: One or more VCF files created with a structural variant caller - pattern: "*.vcf.gz" - - indices: - type: file - description: Index files for the VCFs - pattern: "*.vcf.gz.tbi" - - ploidy_table: - type: file - description: The sample ploidy table - pattern: "*.tsv" - - fasta: - type: file - description: Reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: One or more VCF files created with a structural variant caller + pattern: "*.vcf.gz" + - indices: + type: file + description: Index files for the VCFs + pattern: "*.vcf.gz.tbi" + - - ploidy_table: + type: file + description: The sample ploidy table + pattern: "*.tsv" + - - fasta: + type: file + description: Reference FASTA file needed when the input is a CRAM file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference FASTA file needed when the input is a CRAM + file + pattern: "*.fai" + - - dict: + type: file + description: Sequence dictionary of the reference FASTA file needed when the + input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - clustered_vcf: - type: file - description: The VCF containing the clustered VCFs - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The VCF containing the clustered VCFs + pattern: "*.vcf.gz" - clustered_vcf_index: - type: file - description: The index of the VCF containing the clustered VCFs - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: The index of the VCF containing the clustered VCFs + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/variantfiltration/meta.yml b/modules/nf-core/gatk4/variantfiltration/meta.yml index 11915a94ff1..8e23e205b07 100644 --- a/modules/nf-core/gatk4/variantfiltration/meta.yml +++ b/modules/nf-core/gatk4/variantfiltration/meta.yml @@ -15,60 +15,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: List of VCF(.gz) files - pattern: "*.{vcf,vcf.gz}" - - vcf_tbi: - type: list - description: List of VCF file indexes - pattern: "*.{idx,tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of fastea file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: List of VCF(.gz) files + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: list + description: List of VCF file indexes + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of fastea file + pattern: "*.dict" output: - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/variantrecalibrator/meta.yml b/modules/nf-core/gatk4/variantrecalibrator/meta.yml index 39a415b61c7..72fcfd601c5 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/meta.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/meta.yml @@ -18,64 +18,92 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: input vcf file containing the variants to be recalibrated - pattern: "*.vcf.gz" - - tbi: - type: file - description: tbi file matching with -vcf - pattern: "*.vcf.gz.tbi" - - resource_vcf: - type: file - description: all resource vcf files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz" - - resource_tbi: - type: file - description: all resource tbi files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz.tbi" - - labels: - type: string - description: necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: input vcf file containing the variants to be recalibrated + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - - resource_vcf: + type: file + description: all resource vcf files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz" + - - resource_tbi: + type: file + description: all resource tbi files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz.tbi" + - - labels: + type: string + description: necessary arguments for GATK VariantRecalibrator. Specified to + directly match the resources provided. More information can be found at + https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - recal: - type: file - description: Output recal file used by ApplyVQSR - pattern: "*.recal" + - meta: + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" + - "*.recal": + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" - idx: - type: file - description: Index file for the recal output file - pattern: "*.idx" + - meta: + type: file + description: Index file for the recal output file + pattern: "*.idx" + - "*.idx": + type: file + description: Index file for the recal output file + pattern: "*.idx" - tranches: - type: file - description: Output tranches file used by ApplyVQSR - pattern: "*.tranches" + - meta: + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" + - "*.tranches": + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" - plots: - type: file - description: Optional output rscript file to aid in visualization of the input data and learned model. - pattern: "*plots.R" - - version: - type: file - description: File containing software versions - pattern: "*.versions.yml" + - meta: + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - "*plots.R": + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@nickhsmith" diff --git a/modules/nf-core/gatk4/variantstotable/meta.yml b/modules/nf-core/gatk4/variantstotable/meta.yml index 80d31265c4f..28ee57083f4 100644 --- a/modules/nf-core/gatk4/variantstotable/meta.yml +++ b/modules/nf-core/gatk4/variantstotable/meta.yml @@ -15,68 +15,75 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk. - e.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD'] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: Index of VCF file. - pattern: "*.{idx,tbi}" - - arguments_file: - type: file - description: "optional GATK arguments file" - pattern: "*.{txt,list,args,arguments}" - - include_intervals: - type: file - description: "optional GATK region file" - pattern: "*.{bed,bed.gz,interval,interval_list}" - - exclude_intervals: - type: file - description: "optional GATK exclude region file" - pattern: "*.{bed,bed.gz,interval,interval_list}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of fastea file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk. + e.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD'] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: Index of VCF file. + pattern: "*.{idx,tbi}" + - arguments_file: + type: file + description: "optional GATK arguments file" + pattern: "*.{txt,list,args,arguments}" + - include_intervals: + type: file + description: "optional GATK region file" + pattern: "*.{bed,bed.gz,interval,interval_list}" + - exclude_intervals: + type: file + description: "optional GATK exclude region file" + pattern: "*.{bed,bed.gz,interval,interval_list}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of fastea file + pattern: "*.dict" output: - table: - type: file - description: GATK output - pattern: "*.tsv" + - meta: + type: file + description: GATK output + pattern: "*.tsv" + - "*.tsv": + type: file + description: GATK output + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/gatk4spark/applybqsr/meta.yml b/modules/nf-core/gatk4spark/applybqsr/meta.yml index 4904568d2e7..609af2f4503 100644 --- a/modules/nf-core/gatk4spark/applybqsr/meta.yml +++ b/modules/nf-core/gatk4spark/applybqsr/meta.yml @@ -16,56 +16,65 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - bqsr_table: - type: file - description: Recalibration table from gatk4_baserecalibrator - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - bqsr_table: + type: file + description: Recalibration table from gatk4_baserecalibrator + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Recalibrated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Recalibrated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Recalibrated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Recalibrated CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4spark/baserecalibrator/meta.yml b/modules/nf-core/gatk4spark/baserecalibrator/meta.yml index dd334a225f2..abb0e1a65e1 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/meta.yml @@ -16,57 +16,60 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Recalibration table from BaseRecalibrator - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Recalibration table from BaseRecalibrator + pattern: "*.{table}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4spark/markduplicates/meta.yml b/modules/nf-core/gatk4spark/markduplicates/meta.yml index 016a215b259..fc8dee3dffb 100644 --- a/modules/nf-core/gatk4spark/markduplicates/meta.yml +++ b/modules/nf-core/gatk4spark/markduplicates/meta.yml @@ -1,5 +1,6 @@ name: gatk4spark_markduplicates -description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. +description: This tool locates and tags duplicate reads in a BAM or SAM file, where + duplicate reads are defined as originating from a single fragment of DNA. keywords: - bam - gatk4spark @@ -7,52 +8,74 @@ keywords: - sort tools: - gatk4: - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fasta_fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Marked duplicates BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Marked duplicates BAM/CRAM file + pattern: "*.{bam,cram}" - bam_index: - type: file - description: Optional BAM index file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bai: + type: file + description: Optional BAM index file + pattern: "*.bai" + - metrics: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Metrics file + pattern: "*.metrics" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ajodeh-juma" - "@FriederikeHanssen" diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 2b6033b0b5e..051700820de 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -16,34 +16,40 @@ tools: documentation: "https://www.gnu.org/software/gawk/manual/" tool_dev_url: "https://www.gnu.org/prep/ftp.html" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file - pattern: "*" - - program_file: - type: file - description: Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file - Specify the logic that needs to be executed on + this file on the `ext.args2` or in the program file + pattern: "*" + - - program_file: + type: file + description: Optional file containing logic for awk to execute. If you don't + wish to use a file, you can use `ext.args2` to specify the logic. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix` - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${suffix}: + type: file + description: The output file - specify the name of this file using `ext.prefix` + and the extension using `ext.suffix` + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gecco/run/meta.yml b/modules/nf-core/gecco/run/meta.yml index a2f4a7266bb..6a557ceaf55 100644 --- a/modules/nf-core/gecco/run/meta.yml +++ b/modules/nf-core/gecco/run/meta.yml @@ -1,5 +1,7 @@ name: "gecco_run" -description: GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs). +description: GECCO is a fast and scalable method for identifying putative novel Biosynthetic + Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields + (CRFs). keywords: - bgc - detection @@ -13,53 +15,86 @@ tools: tool_dev_url: "https://github.com/zellerlab/GECCO" doi: "10.1101/2021.05.03.442509" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.) - pattern: "*" - - hmm: - type: file - description: Alternative HMM file(s) to use in HMMER format - pattern: "*.hmm" - - model_dir: - type: directory - description: Path to an alternative CRF (Conditional Random Fields) module to use + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: A genomic file containing one or more sequences as input. Input + type is any supported by Biopython (fasta, gbk, etc.) + pattern: "*" + - hmm: + type: file + description: Alternative HMM file(s) to use in HMMER format + pattern: "*.hmm" + - - model_dir: + type: directory + description: Path to an alternative CRF (Conditional Random Fields) module to + use output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - genes: - type: file - description: TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found. - pattern: "*.genes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.genes.tsv": + type: file + description: TSV file containing detected/predicted genes with BGC probability + scores. Will not be generated if no hits are found. + pattern: "*.genes.tsv" - features: - type: file - description: TSV file containing identified domains - pattern: "*.features.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.features.tsv": + type: file + description: TSV file containing identified domains + pattern: "*.features.tsv" - clusters: - type: file - description: TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found. - pattern: "*.clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clusters.tsv": + type: file + description: TSV file containing coordinates of predicted clusters and BGC types. Will + not be generated if no hits are found. + pattern: "*.clusters.tsv" - gbk: - type: file - description: Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found. - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_cluster_*.gbk": + type: file + description: Per cluster GenBank file (if found) containing sequence with annotations. + Will not be generated if no hits are found. + pattern: "*.gbk" - json: - type: file - description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found. - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. + Will not be generated if no hits are found. + pattern: "*.gbk" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gem2/gem2bedmappability/meta.yml b/modules/nf-core/gem2/gem2bedmappability/meta.yml index a625c9e87ad..6cc486a7c77 100644 --- a/modules/nf-core/gem2/gem2bedmappability/meta.yml +++ b/modules/nf-core/gem2/gem2bedmappability/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem2_gem2bedmappability" description: Convert a mappability file to bedgraph format @@ -9,46 +8,57 @@ keywords: - gem tools: - "gem2": - description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." - homepage: "https://paoloribeca.science/gem" - # This is not a valid link because all documentation is gone for this tool (it's here because the linter isn't happy otherwise) + description: "GEM2 is a high-performance mapping tool. It also provide a unique + tool to evaluate mappability." + homepage: + "https://paoloribeca.science/gem" + # This is not a valid link because all documentation is gone for this tool (it's here because the linter isn't happy otherwise) licence: ["Custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - map: - type: file - description: The mappability file created from the index - pattern: "*.mappability" - - meta2: - type: map - description: | - Groovy Map containing index information - - index: - type: file - description: The index of the reference FASTA - pattern: "*.gem" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - map: + type: file + description: The mappability file created from the index + pattern: "*.mappability" + - - meta2: + type: map + description: | + Groovy Map containing index information + - index: + type: file + description: The index of the reference FASTA + pattern: "*.gem" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: The resulting bedgraph file - pattern: "*.bg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bg": + type: file + description: The resulting bedgraph file + pattern: "*.bg" - sizes: - type: file - description: The chromosome sizes - pattern: "*.sizes" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: The chromosome sizes + pattern: "*.sizes" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gem2/gemindexer/meta.yml b/modules/nf-core/gem2/gemindexer/meta.yml index 00152b05649..c0bb6a56f4b 100644 --- a/modules/nf-core/gem2/gemindexer/meta.yml +++ b/modules/nf-core/gem2/gemindexer/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem2_gemindexer" description: Create a GEM index from a FASTA file @@ -9,37 +8,47 @@ keywords: - mappability tools: - "gem2": - description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." + description: "GEM2 is a high-performance mapping tool. It also provide a unique + tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" licence: ["Custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A reference FASTA file to index - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A reference FASTA file to index + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - gem: - type: file - description: The created index - pattern: "*.gem" + - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gem": + type: file + description: The GEM index file + pattern: "*.gem" - log: - type: file - description: The execution log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: The execution log + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gem2/gemmappability/meta.yml b/modules/nf-core/gem2/gemmappability/meta.yml index 8157a85a609..cf388545863 100644 --- a/modules/nf-core/gem2/gemmappability/meta.yml +++ b/modules/nf-core/gem2/gemmappability/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem2_gemmappability" description: Define the mappability of a reference @@ -9,36 +8,40 @@ keywords: - reference tools: - "gem2": - description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." + description: "GEM2 is a high-performance mapping tool. It also provide a unique + tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" licence: ["Custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: The index created with gem-indexer from the reference FASTA - pattern: "*.gem" - - read_length: - type: integer - description: The read length to define the mappability of + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: The index created with gem-indexer from the reference FASTA + pattern: "*.gem" + - - read_length: + type: integer + description: The read length to define the mappability of output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - map: - type: file - description: The resulting mappability file - pattern: "*.mappability" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mappability": + type: file + description: The resulting mappability file + pattern: "*.mappability" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gem3/gem3indexer/meta.yml b/modules/nf-core/gem3/gem3indexer/meta.yml index b1c66350234..61ef661aa16 100644 --- a/modules/nf-core/gem3/gem3indexer/meta.yml +++ b/modules/nf-core/gem3/gem3indexer/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem3_gem3indexer" description: Create a GEM index from a FASTA file @@ -11,34 +10,43 @@ tools: description: "The GEM indexer (v3)." homepage: "https://github.com/miqalvarez/gem3/tree/gem3-indexer" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information about the fasta file - e.g. [ id:'test' ] - - fasta: - type: file - description: A reference FASTA file to index - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing information about the fasta file + e.g. [ id:'test' ] + - fasta: + type: file + description: A reference FASTA file to index + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - gem: - type: file - description: The created index - pattern: "*.gem" + - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gem": + type: file + description: The GEM index file + pattern: "*.gem" - info: - type: file - description: The execution log - pattern: "*.info" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.info": + type: file + description: The execution log + pattern: "*.info" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@miqalvarez" maintainers: diff --git a/modules/nf-core/gem3/gem3mapper/meta.yml b/modules/nf-core/gem3/gem3mapper/meta.yml index 8ef2f16dc98..63e430bac9d 100644 --- a/modules/nf-core/gem3/gem3mapper/meta.yml +++ b/modules/nf-core/gem3/gem3mapper/meta.yml @@ -9,42 +9,46 @@ tools: description: "The GEM indexer (v3)." homepage: "https://github.com/smarco/gem3-mapper" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference/index information - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fastq: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - - gem: - type: file - description: GEM3 genome index files - pattern: "*.{gem}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - gem: + type: file + description: GEM3 genome index files + pattern: "*.{gem}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fastq: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@miqalvarez" diff --git a/modules/nf-core/genescopefk/meta.yml b/modules/nf-core/genescopefk/meta.yml index b54cfbcd976..7bba21a793e 100644 --- a/modules/nf-core/genescopefk/meta.yml +++ b/modules/nf-core/genescopefk/meta.yml @@ -10,54 +10,94 @@ tools: homepage: "https://github.com/thegenemyers/GENESCOPE.FK" tool_dev_url: "https://github.com/thegenemyers/GENESCOPE.FK" licence: ["https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_histex_histogram: - type: file - description: A histogram formatted for GeneScope using the -G parameter from Fastk Histex - pattern: "*.hist" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_histex_histogram: + type: file + description: A histogram formatted for GeneScope using the -G parameter from + Fastk Histex + pattern: "*.hist" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - linear_plot: - type: file - description: A GeneScope linear plot in PNG format - pattern: "*_linear_plot.png" - - transformed_linear_plot: - type: file - description: A GeneScope transformed linear plot in PNG format - pattern: "*_transformed_linear_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_linear_plot.png": + type: file + description: A GeneScope linear plot in PNG format + pattern: "*_linear_plot.png" - log_plot: - type: file - description: A GeneScope log plot in PNG format - pattern: "*_log_plot.png" - - transformed_log_plot: - type: file - description: A GeneScope transformed log plot in PNG format - pattern: "*_transformed_log_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_log_plot.png": + type: file + description: A GeneScope log plot in PNG format + pattern: "*_log_plot.png" - model: - type: file - description: GeneScope model fit summary - pattern: "*_model.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_model.txt": + type: file + description: GeneScope model fit summary + pattern: "*_model.txt" - summary: - type: file - description: GeneScope histogram summary - pattern: "*_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary.txt": + type: file + description: GeneScope histogram summary + pattern: "*_summary.txt" + - transformed_linear_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_transformed_linear_plot.png": + type: file + description: A GeneScope transformed linear plot in PNG format + pattern: "*_transformed_linear_plot.png" + - transformed_log_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_transformed_log_plot.png": + type: file + description: A GeneScope transformed log plot in PNG format + pattern: "*_transformed_log_plot.png" - kmer_cov: - type: float - description: Average kmer coverage value extracted from summary file - pattern: "[0-9.]+" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - KMERCOV: + type: float + description: Average kmer coverage value extracted from summary file + pattern: "[0-9.]+" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/genmap/index/meta.yml b/modules/nf-core/genmap/index/meta.yml index 8441333f3bf..064a8a33dc1 100644 --- a/modules/nf-core/genmap/index/meta.yml +++ b/modules/nf-core/genmap/index/meta.yml @@ -12,29 +12,32 @@ tools: tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file to index - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file to index + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Genmap index directory + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Genmap index directory + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@nvnieuwk" diff --git a/modules/nf-core/genmap/map/meta.yml b/modules/nf-core/genmap/map/meta.yml index 394fadb7d4d..9026744905a 100644 --- a/modules/nf-core/genmap/map/meta.yml +++ b/modules/nf-core/genmap/map/meta.yml @@ -15,50 +15,71 @@ tools: tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - index: - type: directory - description: index directory - - meta2: - type: map - description: | - Groovy Map containing regions information - e.g. [ id:'test', single_end:false ] - - regions: - type: file - description: optional - a bed file with regions to define the mappability off - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: index directory + - - meta2: + type: map + description: | + Groovy Map containing regions information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: optional - a bed file with regions to define the mappability off + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: genmap wig mappability file - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: genmap wig mappability file + pattern: "*.wig" - bedgraph: - type: file - description: genmap bedgraph mappability file - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedgraph": + type: file + description: genmap bedgraph mappability file + pattern: "*.bedgraph" - txt: - type: file - description: genmap text mappability file - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: genmap text mappability file + pattern: "*.txt" - csv: - type: file - description: genmap csv mappability file - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: genmap csv mappability file + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@nvnieuwk" diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml index 3c876ac588e..bb4afb6b407 100644 --- a/modules/nf-core/genmod/annotate/meta.yml +++ b/modules/nf-core/genmod/annotate/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: VCF file - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Annotated VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_annotate.vcf": + type: file + description: Annotated VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/compound/meta.yml b/modules/nf-core/genmod/compound/meta.yml index aa5f7da52cd..ebd6a110c8e 100644 --- a/modules/nf-core/genmod/compound/meta.yml +++ b/modules/nf-core/genmod/compound/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: VCF file - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] # + - "*_compound.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml index dd9001e0451..dca74095080 100644 --- a/modules/nf-core/genmod/models/meta.yml +++ b/modules/nf-core/genmod/models/meta.yml @@ -11,38 +11,40 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: vcf file - pattern: "*.{vcf}" - - reduced_penetrance: - type: file - description: file with gene ids that have reduced penetrance - pattern: "*.{tsv}" - - family_file: - type: file - description: ped file - pattern: "*.{ped}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: vcf file + pattern: "*.{vcf}" + - - fam: + type: file + description: file with family information + - - reduced_penetrance: + type: file + description: file with gene ids that have reduced penetrance + pattern: "*.{tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_models.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml index 8998b00c9c6..32da6468d2c 100644 --- a/modules/nf-core/genmod/score/meta.yml +++ b/modules/nf-core/genmod/score/meta.yml @@ -11,38 +11,40 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: vcf file - pattern: "*.{vcf}" - - family_file: - type: file - description: ped file - pattern: "*.{ped}" - - score_config: - type: file - description: rank model config file - pattern: "*.{ini}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: vcf file + pattern: "*.{vcf}" + - - fam: + type: file + description: file with family information + - - score_config: + type: file + description: rank model config file + pattern: "*.{ini}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_score.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genomad/download/meta.yml b/modules/nf-core/genomad/download/meta.yml index 5df21ee6a80..7bb2f3bc55a 100644 --- a/modules/nf-core/genomad/download/meta.yml +++ b/modules/nf-core/genomad/download/meta.yml @@ -16,15 +16,19 @@ tools: tool_dev_url: https://github.com/apcamargo/genomad/ doi: 10.1101/2023.03.05.531206 licence: ["Lawrence Berkeley National Labs BSD variant license"] + identifier: biotools:genomad output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - genomad_db: - type: directory - description: Directory containing downloaded data with directory being named "genomad_db" - pattern: "genomad_db" + - genomad_db/: + type: directory + description: Directory containing downloaded data with directory being named + "genomad_db" + pattern: "genomad_db" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/genomad/endtoend/meta.yml b/modules/nf-core/genomad/endtoend/meta.yml index 0b70dde77a8..085aeb9f489 100644 --- a/modules/nf-core/genomad/endtoend/meta.yml +++ b/modules/nf-core/genomad/endtoend/meta.yml @@ -16,81 +16,159 @@ tools: tool_dev_url: https://github.com/apcamargo/genomad/ doi: 10.1101/2023.03.05.531206 licence: ["Lawrence Berkeley National Labs BSD variant license"] + identifier: biotools:genomad input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing contigs/scaffolds/chromosomes - pattern: "*.{fasta,fna,fa}" - - genomad_db: - type: directory - description: Directory pointing to geNomad database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing contigs/scaffolds/chromosomes + pattern: "*.{fasta,fna,fa}" + - - genomad_db: + type: directory + description: Directory pointing to geNomad database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - aggregated_classification: - type: file - description: Combined classification scores for each contig/scaffold/chromosome - pattern: "*_aggregated_classification.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_aggregated_classification/*_aggregated_classification.tsv": + type: file + description: Combined classification scores for each contig/scaffold/chromosome + pattern: "*_aggregated_classification.tsv" - taxonomy: - type: file - description: Detailed output of geNomad's marker gene taxonomy analysis - pattern: "*_taxonomy.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_annotate/*_taxonomy.tsv": + type: file + description: Detailed output of geNomad's marker gene taxonomy analysis + pattern: "*_taxonomy.tsv" - provirus: - type: file - description: Detailed output of each provirus identified by geNomad's find_proviruses module - pattern: "*_provirus.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_find_proviruses/*_provirus.tsv": + type: file + description: Detailed output of each provirus identified by geNomad's find_proviruses + module + pattern: "*_provirus.tsv" - compositions: - type: file - description: OPTIONAL - Predicted sample composition when `--enable-score-calibration` is used - pattern: "*_compositions.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_score_calibration/*_compositions.tsv": + type: file + description: OPTIONAL - Predicted sample composition when `--enable-score-calibration` + is used + pattern: "*_compositions.tsv" - calibrated_classification: - type: file - description: OPTIONAL - Classification scores that have been adjusted based on sample composition when `--enable-score-calibration` is used` - pattern: "*_calibrated_aggregated_classification.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_score_calibration/*_calibrated_aggregated_classification.tsv": + type: file + description: OPTIONAL - Classification scores that have been adjusted based + on sample composition when `--enable-score-calibration` is used` + pattern: "*_calibrated_aggregated_classification.tsv" - plasmid_fasta: - type: file - description: FASTA file containing predicted plasmid sequences - pattern: "*_plasmid.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid.fna.gz": + type: file + description: FASTA file containing predicted plasmid sequences + pattern: "*_plasmid.fna" - plasmid_genes: - type: file - description: TSV file containing predicted plasmid genes and their annotations - pattern: "*_plasmid_genes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid_genes.tsv": + type: file + description: TSV file containing predicted plasmid genes and their annotations + pattern: "*_plasmid_genes.tsv" - plasmid_proteins: - type: file - description: FASTA file containing predicted plasmid protein sequences - pattern: "*_plasmid_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid_proteins.faa.gz": + type: file + description: FASTA file containing predicted plasmid protein sequences + pattern: "*_plasmid_proteins.faa" - plasmid_summary: - type: file - description: TSV file containing a summary of geNomad's plasmid predictions - pattern: "*_plasmid_summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid_summary.tsv": + type: file + description: TSV file containing a summary of geNomad's plasmid predictions + pattern: "*_plasmid_summary.tsv" - virus_fasta: - type: file - description: FASTA file containing predicted virus sequences - pattern: "*_virus.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus.fna.gz": + type: file + description: FASTA file containing predicted virus sequences + pattern: "*_virus.fna" - virus_genes: - type: file - description: TSV file containing predicted virus genes and their annotations - pattern: "*_virus_genes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus_genes.tsv": + type: file + description: TSV file containing predicted virus genes and their annotations + pattern: "*_virus_genes.tsv" - virus_proteins: - type: file - description: FASTA file containing predicted virus protein sequences - pattern: "*_virus_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus_proteins.faa.gz": + type: file + description: FASTA file containing predicted virus protein sequences + pattern: "*_virus_proteins.faa" - virus_summary: - type: file - description: TSV file containing a summary of geNomad's virus predictions - pattern: "*_virus_summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus_summary.tsv": + type: file + description: TSV file containing a summary of geNomad's virus predictions + pattern: "*_virus_summary.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/genomescope2/meta.yml b/modules/nf-core/genomescope2/meta.yml index 928bb812d0c..5076abf1838 100644 --- a/modules/nf-core/genomescope2/meta.yml +++ b/modules/nf-core/genomescope2/meta.yml @@ -1,5 +1,6 @@ name: "genomescope2" -description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach +description: Estimate genome heterozygosity, repeat content, and size from sequencing + reads using a kmer-based statistical approach keywords: - "genome size" - "genome heterozygosity" @@ -12,62 +13,103 @@ tools: tool_dev_url: "https://github.com/tbenavi1/genomescope2.0" doi: "10.1038/s41467-020-14998-3" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - histogram: - type: file - description: A K-mer histogram file - pattern: "*.hist" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - histogram: + type: file + description: A K-mer histogram file + pattern: "*.hist" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - linear_plot_png: - type: file - description: A genomescope2 linear plot in PNG format - pattern: "*_linear_plot.png" - linear_plot_png: - type: file - description: A genomescope2 linear plot in PNG format - pattern: "*_linear_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_linear_plot.png: + type: file + description: A genomescope2 linear plot in PNG format + pattern: "*_linear_plot.png" - transformed_linear_plot_png: - type: file - description: A genomescope2 transformed linear plot in PNG format - pattern: "*_transformed_linear_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_transformed_linear_plot.png: + type: file + description: A genomescope2 transformed linear plot in PNG format + pattern: "*_transformed_linear_plot.png" - log_plot_png: - type: file - description: A genomescope2 log plot in PNG format - pattern: "*_log_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_log_plot.png: + type: file + description: A genomescope2 log plot in PNG format + pattern: "*_log_plot.png" - transformed_log_plot_png: - type: file - description: A genomescope2 transformed log plot in PNG format - pattern: "*_transformed_log_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_transformed_log_plot.png: + type: file + description: A genomescope2 transformed log plot in PNG format + pattern: "*_transformed_log_plot.png" - model: - type: file - description: Genomescope2 model fit summary - pattern: "*_model.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_model.txt: + type: file + description: Genomescope2 model fit summary + pattern: "*_model.txt" - summary: - type: file - description: Genomescope2 histogram summary - pattern: "*_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_summary.txt: + type: file + description: Genomescope2 histogram summary + pattern: "*_summary.txt" - lookup_table: - type: file - description: Fitted histogram lookup table - pattern: "*_lookup_table.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_lookup_table.txt: + type: file + description: Fitted histogram lookup table + pattern: "*_lookup_table.txt" - fitted_histogram_png: - type: file - description: A genomescope2 fitted histogram plot in PNG format - pattern: "*_fitted_hist.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_fitted_hist.png: + type: file + description: A genomescope2 fitted histogram plot in PNG format + pattern: "*_fitted_hist.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/genotyphi/parse/meta.yml b/modules/nf-core/genotyphi/parse/meta.yml index 8648761e0fd..4190b501d9c 100644 --- a/modules/nf-core/genotyphi/parse/meta.yml +++ b/modules/nf-core/genotyphi/parse/meta.yml @@ -6,35 +6,39 @@ keywords: - Mykrobe tools: - "genotyphi": - description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)" + description: "Assign genotypes to Salmonella Typhi genomes based on VCF files + (mapped to Typhi CT18 reference genome)" homepage: "https://github.com/katholt/genotyphi" documentation: "https://github.com/katholt/genotyphi" tool_dev_url: "https://github.com/katholt/genotyphi" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - json: - type: file - description: JSON formatted file of Mykrobe results - pattern: "*.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - json: + type: file + description: JSON formatted file of Mykrobe results + pattern: "*.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file of predicted genotypes - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A tab-delimited file of predicted genotypes + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/genrich/meta.yml b/modules/nf-core/genrich/meta.yml index 11c1466e441..56f242f772b 100644 --- a/modules/nf-core/genrich/meta.yml +++ b/modules/nf-core/genrich/meta.yml @@ -14,66 +14,91 @@ tools: documentation: https://github.com/jsh58/Genrich#readme tool_dev_url: https://github.com/jsh58/Genrich licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - treatment_bam: - type: file - description: Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates - pattern: "*.{bam,sam}" - - control_bam: - type: file - description: Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples - pattern: "*.{bam,sam}" - - blacklist_bed: - type: file - description: Bed file containing genomic intervals to exclude from the analysis - pattern: "*.{bed}" - - save_pvalues: - type: boolean - description: Create bedgraph-ish file for p/q-values file - - save_pileup: - type: boolean - description: Create bedgraph-ish file for pileups and p-values - - save_bed: - type: boolean - description: Create BED file for reads/fragments/intervals - - save_duplicates: - type: boolean - description: Create PCR duplicates file (only works if -r option is set) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - treatment_bam: + type: file + description: Coordinate sorted BAM/SAM file from treatment sample or list of + BAM/SAM files from biological replicates + pattern: "*.{bam,sam}" + - control_bam: + type: file + description: Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM + files from control samples + pattern: "*.{bam,sam}" + - - blacklist_bed: + type: file + description: Bed file containing genomic intervals to exclude from the analysis + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: Output file is in ENCODE narrowPeak format - pattern: "*.{narrowPeak}" + - peak: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.narrowPeak": + type: file + description: Narrow peak file containing genomic intervals of significant enrichment + pattern: "*.{narrowPeak}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - bedgraph_pvalues: - type: file - description: bedGraph file containing p/q values - pattern: "*.{pvalues.bedGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvalues.bedGraph": + type: file + description: bedGraph file containing p/q values + pattern: "*.{pvalues.bedGraph}" + - ues: + type: file + description: bedGraph file containing p/q values + pattern: "*.{pvalues.bedGraph}" - bedgraph_pileup: - type: file - description: bedGraph file containing pileups and p-values - pattern: "*.{pileup.bedGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pileup.bedGraph": + type: file + description: bedGraph file containing pileups and p-values + pattern: "*.{pileup.bedGraph}" - bed_intervals: - type: file - description: Bed file containing annotated intervals - pattern: "*.{intervals.bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.intervals.bed": + type: file + description: Bed file containing annotated intervals + pattern: "*.{intervals.bed}" + - s: + type: file + description: Bed file containing annotated intervals + pattern: "*.{intervals.bed}" - duplicates: - type: file - description: Text output file containing intervals corresponding to PCR duplicates - pattern: "*.{intervals.txt}" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.duplicates.txt": + type: file + description: Text output file containing intervals corresponding to PCR duplicates + pattern: "*.{intervals.txt}" authors: - "@JoseEspinosa" - "@samuelruizperez" diff --git a/modules/nf-core/geofetch/meta.yml b/modules/nf-core/geofetch/meta.yml index b7ef89e13ed..a4377a4d224 100644 --- a/modules/nf-core/geofetch/meta.yml +++ b/modules/nf-core/geofetch/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "geofetch" -description: geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA +description: geofetch is a command-line tool that downloads and organizes data and + metadata from GEO and SRA keywords: - GEO - expression @@ -9,31 +9,34 @@ keywords: - sequencing tools: - "geofetch": - description: "Downloads data and metadata from GEO and SRA and creates standard PEPs." + description: "Downloads data and metadata from GEO and SRA and creates standard + PEPs." homepage: "http://geofetch.databio.org/" documentation: "http://geofetch.databio.org/" tool_dev_url: "https://github.com/pepkit/geofetch" licence: ["BSD-2-clause"] args_id: "$args" + identifier: "" input: - - geo_accession: - type: string - description: GEO accession ID - + - - geo_accession: + type: string + description: GEO accession ID output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - geo_accession: - type: string - description: String with the GEO accession - samples: - type: file - description: List of sample files fetched - pattern: "${geo_accession}/*.CEL.gz" - + - ${geo_accession}: + type: file + description: List of sample files fetched + pattern: "${geo_accession}/*.CEL.gz" + - ${geo_accession}/*.CEL.gz: + type: file + description: List of sample files fetched + pattern: "${geo_accession}/*.CEL.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mribeirodantas" maintainers: diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml index b8000288415..ceade89a64d 100644 --- a/modules/nf-core/geoquery/getgeo/meta.yml +++ b/modules/nf-core/geoquery/getgeo/meta.yml @@ -12,32 +12,49 @@ tools: tool_dev_url: "https://github.com/seandavi/GEOquery" doi: "10.1093/bioinformatics/btm254" licence: ["MIT"] + identifier: biotools:geoquery input: - - meta: - type: map - description: | - Groovy Map containing metadata about the GEO dataset, minimally 'id'. - - querygse: - type: string - description: | - GSE identifier to pass to getGEO() + - - meta: + type: map + description: | + Groovy Map containing metadata about the GEO dataset, minimally 'id'. + - querygse: + type: string + description: | + GSE identifier to pass to getGEO() output: - rds: - type: file - description: R object containing GEO data - pattern: "*.rds" + - meta: + type: file + description: R object containing GEO data + pattern: "*.rds" + - "*.rds": + type: file + description: R object containing GEO data + pattern: "*.rds" - expression: - type: file - description: TSV-format expression matrix - pattern: "*matrix.tsv" + - meta: + type: file + description: TSV-format expression matrix + pattern: "*matrix.tsv" + - "*matrix.tsv": + type: file + description: TSV-format expression matrix + pattern: "*matrix.tsv" - annotation: - type: file - description: TSV-format annotation file - pattern: "*annotation.tsv" + - meta: + type: file + description: TSV-format annotation file + pattern: "*annotation.tsv" + - "*annotation.tsv": + type: file + description: TSV-format annotation file + pattern: "*annotation.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@azedinez" - "@pinin4fjords" diff --git a/modules/nf-core/getorganelle/config/meta.yml b/modules/nf-core/getorganelle/config/meta.yml index 832761d3bc5..5ca86baad75 100644 --- a/modules/nf-core/getorganelle/config/meta.yml +++ b/modules/nf-core/getorganelle/config/meta.yml @@ -14,27 +14,26 @@ tools: tool_dev_url: "https://github.com/Kinggerm/GetOrganelle" doi: "10.1186/s13059-020-02154-5" licence: ["GPL v3"] + identifier: biotools:getorganelle input: - - organelle_type: - type: string - description: | - Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) - + - - organelle_type: + type: string + description: | + Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - - organelle_type: - type: string - description: | - Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) - - db: - type: directory - description: Downloaded database for GetOrganelle - + - organelle_type: + type: string + description: | + Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) + - getorganelle: + type: directory + description: Downloaded database for GetOrganelle + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erinyoung" diff --git a/modules/nf-core/getorganelle/fromreads/meta.yml b/modules/nf-core/getorganelle/fromreads/meta.yml index 193df60b220..ba5b9176515 100644 --- a/modules/nf-core/getorganelle/fromreads/meta.yml +++ b/modules/nf-core/getorganelle/fromreads/meta.yml @@ -13,48 +13,44 @@ tools: tool_dev_url: "https://github.com/Kinggerm/GetOrganelle" doi: "10.1186/s13059-020-02154-5" licence: ["GPL v3"] + identifier: biotools:getorganelle input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - fastq: - type: file - description: Input fastq files - pattern: "*.{fastq.gz}" - - - organelle_type: - type: string - description: | - Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) - - - db: - type: directory - description: GetOrganelle database - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fastq: + type: file + description: Input fastq files + pattern: "*.{fastq.gz}" + - - organelle_type: + type: string + description: | + Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) + - db: + type: directory + description: GetOrganelle database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: Complete or partial organelle sequences - pattern: "*.fasta.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - results/${prefix}.${organelle_type}.fasta.gz: + type: file + description: Complete or partial organelle sequences + pattern: "*.fasta.gz" - etc: - type: file - description: Other output files - + - results/*: + type: file + description: Other output files + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erinyoung" diff --git a/modules/nf-core/gfaffix/meta.yml b/modules/nf-core/gfaffix/meta.yml index 384696cf0b0..f1f2966f2ac 100644 --- a/modules/nf-core/gfaffix/meta.yml +++ b/modules/nf-core/gfaffix/meta.yml @@ -13,34 +13,43 @@ tools: homepage: https://github.com/marschall-lab/GFAffix documentation: https://github.com/marschall-lab/GFAffix licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA format - pattern: "*.{gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA format + pattern: "*.{gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gfa: - type: file - description: Non-redundant variation graph in GFA 1.0 format - pattern: "*.{gfa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa": + type: file + description: Non-redundant variation graph in GFA 1.0 format + pattern: "*.{gfa}" - affixes: - type: file - description: Shared affixes in tab-separated values (TSV) text format - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Shared affixes in tab-separated values (TSV) text format + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml index aaaf47caeb8..a621343388d 100644 --- a/modules/nf-core/gfastats/meta.yml +++ b/modules/nf-core/gfastats/meta.yml @@ -17,55 +17,66 @@ tools: tool_dev_url: "https://github.com/vgl-hub/gfastats" doi: "10.1093/bioinformatics/btac460" licence: ["MIT"] + identifier: biotools:gfastats input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly file - pattern: "*.{fasta,fastq,gfa}(.gz)?" - - out_fmt: - type: string - description: Output format (fasta, fastq, gfa) - - genome_size: - type: integer - description: estimated genome size (bp) for NG* statistics (optional). - - target: - type: string - description: target specific sequence by header, optionally with coordinates (optional). - - agpfile: - type: file - description: converts input agp to path and replaces existing paths. - - include_bed: - type: file - description: generates output on a subset list of headers or coordinates in 0-based bed format. - - exclude_bed: - type: file - description: opposite of --include-bed. They can be combined (no coordinates). - - instructions: - type: file - description: set of instructions provided as an ordered list. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly file + pattern: "*.{fasta,fastq,gfa}(.gz)?" + - - out_fmt: + type: string + description: Output format (fasta, fastq, gfa) + - - genome_size: + type: integer + description: estimated genome size (bp) for NG* statistics (optional). + - - target: + type: string + description: target specific sequence by header, optionally with coordinates + (optional). + - - agpfile: + type: file + description: converts input agp to path and replaces existing paths. + - - include_bed: + type: file + description: generates output on a subset list of headers or coordinates in + 0-based bed format. + - - exclude_bed: + type: file + description: opposite of --include-bed. They can be combined (no coordinates). + - - instructions: + type: file + description: set of instructions provided as an ordered list. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly_summary: - type: file - description: Assembly summary statistics file - pattern: "*.assembly_summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly_summary": + type: file + description: Assembly summary statistics file + pattern: "*.assembly_summary" - assembly: - type: file - description: The assembly as modified by gfastats - pattern: "*.{fasta,fastq,gfa}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_fmt}.gz": + type: file + description: The assembly as modified by gfastats + pattern: "*.{fasta,fastq,gfa}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/gfatools/gfa2fa/meta.yml b/modules/nf-core/gfatools/gfa2fa/meta.yml index a22d50a0e39..1554218f0bc 100644 --- a/modules/nf-core/gfatools/gfa2fa/meta.yml +++ b/modules/nf-core/gfatools/gfa2fa/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gfatools_gfa2fa" description: Converts GFA or rGFA files to FASTA @@ -17,30 +16,33 @@ tools: tool_dev_url: "https://github.com/lh3/gfatools" doi: "no DOI available" licence: ["Unknown"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - gfa: - type: file - description: GFA or rGFA file - pattern: "*.gfa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - gfa: + type: file + description: GFA or rGFA file + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: FASTA file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta.gz": + type: file + description: FASTA file + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/gfatools/stat/meta.yml b/modules/nf-core/gfatools/stat/meta.yml index 58503165c47..29c53078cd3 100644 --- a/modules/nf-core/gfatools/stat/meta.yml +++ b/modules/nf-core/gfatools/stat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gfatools_stat" description: Summary statistics for GFA files @@ -17,30 +16,33 @@ tools: tool_dev_url: "https://github.com/lh3/gfatools" doi: "no DOI available" licence: ["Unknown"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - gfa: - type: file - description: GFA or rGFA file - pattern: "*.gfa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - gfa: + type: file + description: GFA or rGFA file + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Summary statistics of the GFA file - pattern: "*.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.stats": + type: file + description: Summary statistics of the GFA file + pattern: "*.stats" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/gffcompare/meta.yml b/modules/nf-core/gffcompare/meta.yml index dd944f2f25b..7c3a91e39d2 100644 --- a/modules/nf-core/gffcompare/meta.yml +++ b/modules/nf-core/gffcompare/meta.yml @@ -13,78 +13,127 @@ tools: tool_dev_url: "https://github.com/gpertea/gffcompare" doi: "10.12688/f1000research.23297.1" licence: ["MIT"] + identifier: biotools:gffcompare input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test', single_end:false ] - - gtfs: - type: file - description: | - GTF/GFF files - e.g. [ 'file_1.gtf', 'file_2.gtf' ] - pattern: "*.{gtf,gff}" - - fasta: - type: file - description: Genome reference fasta file (optional) - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Index for fasta file - pattern: "*.fai" - - reference_gtf: - type: file - description: Reference annotation in gtf/gff format (optional) - pattern: "*.{gtf,gff}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - gtfs: + type: file + description: | + GTF/GFF files + e.g. [ 'file_1.gtf', 'file_2.gtf' ] + pattern: "*.{gtf,gff}" + - - meta2: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome reference fasta file (optional) + pattern: "*.{fasta,fa}" + - fai: + type: file + description: Index for fasta file + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - reference_gtf: + type: file + description: Reference annotation in gtf/gff format (optional) + pattern: "*.{gtf,gff}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test', single_end:false ] - annotated_gtf: - type: file - description: | - Annotated gtf file when reference gtf is provided (optional) - pattern: "*.annotated.gtf" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.annotated.gtf": + type: file + description: | + Annotated gtf file when reference gtf is provided (optional) + pattern: "*.annotated.gtf" - combined_gtf: - type: file - description: | - Combined gtf file when multiple input files are - provided (optional) - pattern: "*.annotated.gtf" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.combined.gtf": + type: file + description: | + Combined gtf file when multiple input files are + provided (optional) + pattern: "*.annotated.gtf" - tmap: - type: file - description: | - File listing the most closely matching reference transcript - for each query transcript (optional) - pattern: "*.tmap" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.tmap": + type: file + description: | + File listing the most closely matching reference transcript + for each query transcript (optional) + pattern: "*.tmap" - refmap: - type: file - description: | - File listing the reference transcripts with overlapping - query transcripts (optional) - pattern: "*.refmap" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.refmap": + type: file + description: | + File listing the reference transcripts with overlapping + query transcripts (optional) + pattern: "*.refmap" - loci: - type: file - description: File with loci - pattern: "*.loci" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.loci": + type: file + description: File with loci + pattern: "*.loci" - stats: - type: file - description: | - File with stats for input transcripts as compared to - reference alternatively stats for the combined gtf - pattern: "*.stats" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: | + File with stats for input transcripts as compared to + reference alternatively stats for the combined gtf + pattern: "*.stats" - tracking: - type: file - description: | - This file matches transcripts up between samples - pattern: "*.tracking" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.tracking": + type: file + description: | + This file matches transcripts up between samples + pattern: "*.tracking" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jemten" maintainers: diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index c060282084b..bebe7f575c2 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -1,53 +1,73 @@ name: gffread -description: Validate, filter, convert and perform various other operations on GFF files +description: Validate, filter, convert and perform various other operations on GFF + files keywords: - gff - conversion - validation tools: - gffread: - description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more. + description: GFF/GTF utility providing format conversions, region filtering, FASTA + sequence extraction and more. homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] + identifier: biotools:gffread input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - gff: + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" + - - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - gtf: - type: file - description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present - pattern: "*.{gtf}" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gtf": + type: file + description: GTF file resulting from the conversion of the GFF input file if + '-T' argument is present + pattern: "*.{gtf}" - gffread_gff: - type: file - description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gff3": + type: file + description: GFF3 file resulting from the conversion of the GFF input file if + '-T' argument is absent + pattern: "*.gff3" - gffread_fasta: - type: file - description: Fasta file produced when either of '-w', '-x', '-y' parameters is present - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.fasta": + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters + is present + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/gget/gget/meta.yml b/modules/nf-core/gget/gget/meta.yml index 103fd70653f..6d0acec13a4 100644 --- a/modules/nf-core/gget/gget/meta.yml +++ b/modules/nf-core/gget/gget/meta.yml @@ -1,5 +1,8 @@ name: "gget_gget" -description: gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code. +description: gget is a free, open-source command-line tool and Python package that + enables efficient querying of genomic databases. gget consists of a collection of + separate but interoperable modules, each designed to facilitate one type of database + querying in a single line of code. keywords: - gget - reference @@ -14,34 +17,42 @@ tools: tool_dev_url: "https://github.com/pachterlab/gget" doi: "10.1093/bioinformatics/btac836" licence: ["BSD-2-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - files: - type: file - description: | - Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - files: + type: file + description: | + Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*[!versions.yml][!${prefix}.${extension}]*": + type: file + description: File containing output of gget command. - output: - type: file - description: File containing output of gget command (-o for most gget tools). - pattern: "*.{json,csv}" - - file: - type: file - description: Path to any file downloaded by gget - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}: + type: file + description: File containing output of gget command (-o for most gget tools). + pattern: "*.{json,csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml index e500d9e9715..e8ff401990a 100644 --- a/modules/nf-core/glimpse/chunk/meta.yml +++ b/modules/nf-core/glimpse/chunk/meta.yml @@ -6,43 +6,50 @@ keywords: - low coverage tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - Target dataset in VCF/BCF format defined at all variable positions. - The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - region: - type: string - description: | - Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + Target dataset in VCF/BCF format defined at all variable positions. + The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file for the input VCF/BCF file. + - region: + type: string + description: | + Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - chunk_chr: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab delimited output txt file containing buffer and imputation regions. + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: Tab delimited output txt file containing buffer and imputation regions. - pattern: "*.{txt}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/concordance/meta.yml b/modules/nf-core/glimpse/concordance/meta.yml index 2b2d7195df8..ea4c26087c5 100644 --- a/modules/nf-core/glimpse/concordance/meta.yml +++ b/modules/nf-core/glimpse/concordance/meta.yml @@ -1,5 +1,6 @@ name: "glimpse_concordance" -description: Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset. +description: Compute the r2 correlation between imputed dosages (in MAF bins) and + highly-confident genotype calls from the high-coverage dataset. keywords: - concordance - low-coverage @@ -7,78 +8,120 @@ keywords: - imputation tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - freq: - type: file - description: File containing allele frequencies at each site. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - truth: - type: file - description: Validation dataset called at the same positions as the imputed file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - estimate: - type: file - description: Imputed data. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - min_prob: - type: float - description: Minimum posterior probability P(G|R) in validation data - - min_dp: - type: integer - description: | - Minimum coverage in validation data. - If FORMAT/DP is missing and --minDP > 0, the program exits with an error. - - bins: - type: string - description: | - Allele frequency bins used for rsquared computations. - By default they should as MAF bins [0-0.5], while - they should take the full range [0-1] if --use-ref-alt is used. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - estimate: + type: file + description: Imputed data. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - estimate_index: + type: file + description: Index file for the imputed data. + - freq: + type: file + description: File containing allele frequencies at each site. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - freq_index: + type: file + description: Index file for the allele frequencies file. + - truth: + type: file + description: Validation dataset called at the same positions as the imputed + file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - truth_index: + type: file + description: Index file for the truth file. + - region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - min_prob: + type: float + description: Minimum posterior probability P(G|R) in validation data + - - min_dp: + type: integer + description: | + Minimum coverage in validation data. + If FORMAT/DP is missing and --minDP > 0, the program exits with an error. + - - bins: + type: string + description: | + Allele frequency bins used for rsquared computations. + By default they should as MAF bins [0-0.5], while + they should take the full range [0-1] if --use-ref-alt is used. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - errors_cal: - type: file - description: Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.cal.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.cal.txt.gz": + type: file + description: Calibration correlation errors between imputed dosages (in MAF + bins) and highly-confident genotype. + pattern: "*.errors.cal.txt.gz" - errors_grp: - type: file - description: Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.grp.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.grp.txt.gz": + type: file + description: Groups correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.grp.txt.gz" - errors_spl: - type: file - description: Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.spl.txt.gz" - - rsquared_grp: - type: file - description: Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.grp.txt.gz" - - rsquared_spl: - type: file - description: Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.spl.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.spl.txt.gz": + type: file + description: Samples correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.spl.txt.gz" + - rsquare_grp: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.grp.txt.gz": + type: file + description: Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. + pattern: "*.rsquare.grp.txt.gz" + - rsquare_spl: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.spl.txt.gz": + type: file + description: Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. + pattern: "*.rsquare.spl.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml index c3b1485c436..c1ed67ee67b 100644 --- a/modules/nf-core/glimpse/ligate/meta.yml +++ b/modules/nf-core/glimpse/ligate/meta.yml @@ -1,5 +1,6 @@ name: "glimpse_ligate" -description: Concatenates imputation chunks in a single VCF/BCF file ligating phased information. +description: Concatenates imputation chunks in a single VCF/BCF file ligating phased + information. keywords: - ligate - low-coverage @@ -7,42 +8,46 @@ keywords: - imputation tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_list: - type: file - description: VCF/BCF file containing genotype probabilities (GP field). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_list: + type: file + description: VCF/BCF file containing genotype probabilities (GP field). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_variants: - type: file - description: | - Output VCF/BCF file for the merged regions. - Phased information (HS field) is updated accordingly for the full region. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: | + Output VCF/BCF file for the merged regions. + Phased information (HS field) is updated accordingly for the full region. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/phase/meta.yml b/modules/nf-core/glimpse/phase/meta.yml index 862033b7f83..e905b7581c8 100644 --- a/modules/nf-core/glimpse/phase/meta.yml +++ b/modules/nf-core/glimpse/phase/meta.yml @@ -1,5 +1,6 @@ name: "glimpse_phase" -description: main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods +description: main GLIMPSE algorithm, performs phasing and imputation refining genotype + likelihoods keywords: - phase - imputation @@ -7,71 +8,76 @@ keywords: - glimpse tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - samples_file: - type: file - description: | - File with sample names and ploidy information. - One sample per line with a mandatory second column indicating ploidy (1 or 2). - Sample names that are not present are assumed to have ploidy 2 (diploids). - GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. - pattern: "*.{txt,tsv}" - - input_region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - output_region: - type: string - description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - samples_file: + type: file + description: | + File with sample names and ploidy information. + One sample per line with a mandatory second column indicating ploidy (1 or 2). + Sample names that are not present are assumed to have ploidy 2 (diploids). + GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. + pattern: "*.{txt,tsv}" + - input_region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - output_region: + type: string + description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phased_variants: - type: file - description: | - Output VCF/BCF file containing genotype probabilities (GP field), - imputed dosages (DS field), best guess genotypes (GT field), - sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: | + Output VCF/BCF file containing genotype probabilities (GP field), + imputed dosages (DS field), best guess genotypes (GT field), + sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/sample/meta.yml b/modules/nf-core/glimpse/sample/meta.yml index 36937ec0c26..483f0c59777 100644 --- a/modules/nf-core/glimpse/sample/meta.yml +++ b/modules/nf-core/glimpse/sample/meta.yml @@ -6,36 +6,40 @@ keywords: - Imputation tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: VCF/BCF file generated using GLIMPSE ligate - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: VCF/BCF file generated using GLIMPSE ligate + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - haplo_sampled: - type: file - description: Output VCF/BCF file containing phased genotypes. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Output VCF/BCF file containing phased genotypes. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/chunk/meta.yml b/modules/nf-core/glimpse2/chunk/meta.yml index 759ee0249be..7757a7a445e 100644 --- a/modules/nf-core/glimpse2/chunk/meta.yml +++ b/modules/nf-core/glimpse2/chunk/meta.yml @@ -7,66 +7,71 @@ keywords: - glimpse tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 requirements: - AVX2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - Target dataset in VCF/BCF format defined at all variable positions. - The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - region: - type: string - description: | - Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. - - meta2: - type: map - description: | - Groovy Map containing genomic map information - e.g. [ map:'GRCh38' ] - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" - - model: - type: string - description: | - Algorithm model to use: - "recursive": Recursive algorithm - "sequential": Sequential algorithm (Recommended) - "uniform-number-variants": Experimental. Uniform the number of variants in the sequential algorithm - pattern: "{recursive,sequential,uniform-number-variants}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + Target dataset in VCF/BCF format defined at all variable positions. + The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - region: + type: string + description: | + Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + - - meta2: + type: map + description: | + Groovy Map containing genomic map information + e.g. [ map:'GRCh38' ] + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" + - - model: + type: string + description: | + Algorithm model to use: + "recursive": Recursive algorithm + "sequential": Sequential algorithm (Recommended) + "uniform-number-variants": Experimental. Uniform the number of variants in the sequential algorithm + pattern: "{recursive,sequential,uniform-number-variants}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - chunk_chr: - type: file - description: Tab delimited output txt file containing buffer and imputation regions. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab delimited output txt file containing buffer and imputation + regions. + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/concordance/meta.yml b/modules/nf-core/glimpse2/concordance/meta.yml index 7d145d2b4b1..f286f6e929d 100644 --- a/modules/nf-core/glimpse2/concordance/meta.yml +++ b/modules/nf-core/glimpse2/concordance/meta.yml @@ -1,5 +1,6 @@ name: "glimpse2_concordance" -description: Program to compute the genotyping error rate at the sample or marker level. +description: Program to compute the genotyping error rate at the sample or marker + level. keywords: - concordance - low-coverage @@ -7,103 +8,160 @@ keywords: - imputation tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - freq: - type: file - description: File containing allele frequencies at each site. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - truth: - type: file - description: Validation dataset called at the same positions as the imputed file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - estimate: - type: file - description: Imputed dataset file obtain after phasing. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - samples: - type: file - description: List of samples to process, one sample ID per line. - pattern: "*.{txt,tsv}" - - groups: - type: file - description: Alternative to frequency bins, group bins are user defined, provided in a file. - pattern: "*.{txt,tsv}" - - bins: - type: string - description: | - Allele frequency bins used for rsquared computations. - By default they should as MAF bins [0-0.5], while - they should take the full range [0-1] if --use-ref-alt is used. - pattern: "0 0.01 0.05 ... 0.5" - - ac_bins: - type: string - description: User-defined allele count bins used for rsquared computations. - pattern: "1 2 5 10 20 ... 100000" - - allele_counts: - type: string - description: | - Default allele count bins used for rsquared computations. - AN field must be defined in the frequency file. - - min_val_gl: - type: float - description: | - Minimum genotype likelihood probability P(G|R) in validation data. - Set to zero to have no filter of if using –gt-validation - - min_val_dp: - type: integer - description: | - Minimum coverage in validation data. - If FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error. - Set to zero to have no filter of if using –gt-validation + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - estimate: + type: file + description: Imputed dataset file obtain after phasing. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - estimate_index: + type: file + description: Index file for the imputed dataset file. + - truth: + type: file + description: Validation dataset called at the same positions as the imputed + file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - truth_index: + type: file + description: Index file for the truth file. + - freq: + type: file + description: File containing allele frequencies at each site. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - freq_index: + type: file + description: Index file for the allele frequencies file. + - samples: + type: file + description: List of samples to process, one sample ID per line. + pattern: "*.{txt,tsv}" + - region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). Can also be a list of such regions. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - groups: + type: file + description: Alternative to frequency bins, group bins are user defined, provided + in a file. + pattern: "*.{txt,tsv}" + - bins: + type: string + description: | + Allele frequency bins used for rsquared computations. + By default they should as MAF bins [0-0.5], while + they should take the full range [0-1] if --use-ref-alt is used. + pattern: "0 0.01 0.05 ... 0.5" + - ac_bins: + type: string + description: User-defined allele count bins used for rsquared computations. + pattern: "1 2 5 10 20 ... 100000" + - allele_counts: + type: string + description: | + Default allele count bins used for rsquared computations. + AN field must be defined in the frequency file. + - - min_val_gl: + type: float + description: | + Minimum genotype likelihood probability P(G|R) in validation data. + Set to zero to have no filter of if using –gt-validation + - - min_val_dp: + type: integer + description: | + Minimum coverage in validation data. + If FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error. + Set to zero to have no filter of if using –gt-validation output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - errors_cal: - type: file - description: Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.cal.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.cal.txt.gz": + type: file + description: Calibration correlation errors between imputed dosages (in MAF + bins) and highly-confident genotype. + pattern: "*.errors.cal.txt.gz" - errors_grp: - type: file - description: Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.grp.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.grp.txt.gz": + type: file + description: Groups correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.grp.txt.gz" - errors_spl: - type: file - description: Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.spl.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.spl.txt.gz": + type: file + description: Samples correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.spl.txt.gz" - rsquare_grp: - type: file - description: Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.grp.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.grp.txt.gz": + type: file + description: Groups r-squared correlation between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.rsquare.grp.txt.gz" - rsquare_spl: - type: file - description: Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.spl.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.spl.txt.gz": + type: file + description: Samples r-squared correlation between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.rsquare.spl.txt.gz" - rsquare_per_site: - type: file - description: Variant r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "_r2_sites.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_r2_sites.txt.gz": + type: file + description: Variant r-squared correlation between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "_r2_sites.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/ligate/meta.yml b/modules/nf-core/glimpse2/ligate/meta.yml index 7c07973f75b..14fc8dac578 100644 --- a/modules/nf-core/glimpse2/ligate/meta.yml +++ b/modules/nf-core/glimpse2/ligate/meta.yml @@ -9,40 +9,44 @@ keywords: - imputation tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_list: - type: file - description: VCF/BCF file containing genotype probabilities (GP field). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{csi,tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_list: + type: file + description: VCF/BCF file containing genotype probabilities (GP field). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{csi,tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_variants: - type: file - description: Output ligated (phased) file in VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Output ligated (phased) file in VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/phase/meta.yml b/modules/nf-core/glimpse2/phase/meta.yml index 700b6204fe5..11d0860b745 100644 --- a/modules/nf-core/glimpse2/phase/meta.yml +++ b/modules/nf-core/glimpse2/phase/meta.yml @@ -7,98 +7,109 @@ keywords: - glimpse tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input: - type: file - description: | - Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods. - When using BAM/CRAM the name of the file is used as samples name. - pattern: "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}" - - input_index: - type: file - description: Index file of the input BAM/CRAM/VCF/BCF file. - pattern: "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}" - - samples_file: - type: file - description: | - File with sample names and ploidy information. - One sample per line with a mandatory second column indicating ploidy (1 or 2). - Sample names that are not present are assumed to have ploidy 2 (diploids). - GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. - pattern: "*.{txt,tsv}" - - input_region: - type: string - description: | - Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - Optional if reference panel is in bin format. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - output_region: - type: string - description: | - Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). - Optional if reference panel is in bin format. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - meta2: - type: map - description: | - Groovy Map containing genomic map information - e.g. `[ map:'GRCh38' ]` - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - map: - type: file - description: | - File containing the genetic map. - Optional if reference panel is in bin format. - pattern: "*.gmap" - - fasta_reference: - type: file - description: | - Faidx-indexed reference sequence file in the appropriate genome build. - Necessary for CRAM files. - pattern: "*.fasta" - - fasta_reference_index: - type: file - description: | - Faidx index of the reference sequence file in the appropriate genome build. - Necessary for CRAM files. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: | + Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods. + When using BAM/CRAM the name of the file is used as samples name. + pattern: "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}" + - input_index: + type: file + description: Index file of the input BAM/CRAM/VCF/BCF file. + pattern: "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}" + - samples_file: + type: file + description: | + File with sample names and ploidy information. + One sample per line with a mandatory second column indicating ploidy (1 or 2). + Sample names that are not present are assumed to have ploidy 2 (diploids). + GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. + pattern: "*.{txt,tsv}" + - input_region: + type: string + description: | + Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). + Optional if reference panel is in bin format. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - output_region: + type: string + description: | + Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). + Optional if reference panel is in bin format. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - map: + type: file + description: | + File containing the genetic map. + Optional if reference panel is in bin format. + pattern: "*.gmap" + - - meta2: + type: map + description: | + Groovy Map containing genomic map information + e.g. `[ map:'GRCh38' ]` + - fasta_reference: + type: file + description: | + Faidx-indexed reference sequence file in the appropriate genome build. + Necessary for CRAM files. + pattern: "*.fasta" + - fasta_reference_index: + type: file + description: | + Faidx index of the reference sequence file in the appropriate genome build. + Necessary for CRAM files. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phased_variants: - type: file - description: | - Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{vcf,vcf.gz,bcf,bgen}": + type: file + description: | + Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - stats_coverage: - type: file - description: Optional coverage statistic file created when BAM/CRAM files are used as inputs. - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt.gz": + type: file + description: Optional coverage statistic file created when BAM/CRAM files are + used as inputs. + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/glimpse2/splitreference/meta.yml b/modules/nf-core/glimpse2/splitreference/meta.yml index c70ec024f76..192e6d659c4 100644 --- a/modules/nf-core/glimpse2/splitreference/meta.yml +++ b/modules/nf-core/glimpse2/splitreference/meta.yml @@ -7,59 +7,64 @@ keywords: - imputation tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 requirements: - AVX2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - input_region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - output_region: - type: string - description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - meta2: - type: map - description: | - Groovy Map containing genomic map information - e.g. `[ map:'GRCh38' ]` - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - input_region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - output_region: + type: string + description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing genomic map information + e.g. `[ map:'GRCh38' ]` + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bin_ref: - type: file - description: binary reference panel - pattern: "*.bin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bin": + type: file + description: binary reference panel + pattern: "*.bin" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml index 416829cbf63..a79fc63cff3 100644 --- a/modules/nf-core/glnexus/meta.yml +++ b/modules/nf-core/glnexus/meta.yml @@ -6,30 +6,38 @@ keywords: - joint-variant-calling tools: - glnexus: - description: scalable gVCF merging and joint variant calling for population sequencing projects. + description: scalable gVCF merging and joint variant calling for population sequencing + projects. homepage: https://github.com/dnanexus-rnd/GLnexus documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started doi: 10.1101/343970 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - gvcfs: - type: list - description: Input genomic vcf files - pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - gvcfs: + type: list + description: Input genomic vcf files + pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bcf: - type: file - description: merged BCF file - pattern: "*.bcf" + - meta: + type: file + description: merged BCF file + pattern: "*.bcf" + - "*.bcf": + type: file + description: merged BCF file + pattern: "*.bcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gmmdemux/meta.yml b/modules/nf-core/gmmdemux/meta.yml index 5b53c9abf42..cca6932649f 100644 --- a/modules/nf-core/gmmdemux/meta.yml +++ b/modules/nf-core/gmmdemux/meta.yml @@ -1,90 +1,125 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gmmdemux" -description: GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq). +description: GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample + barcoding data (cell hashing and MULTI-seq). keywords: - demultiplexing - hashing-based deconvolution - single-cell tools: - "gmmdemux": - description: "GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq)." + description: "GMM-Demux is a Gaussian-Mixture-Model-based software for processing + sample barcoding data (cell hashing and MULTI-seq)." homepage: "https://pypi.org/project/GMM-Demux/" documentation: "https://github.com/CHPGenetics/GMM-Demux" tool_dev_url: "https://github.com/CHPGenetics/GMM-demux" doi: "10.1186/s13059-020-02084-2" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - hto_matrix: - type: file - description: path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters - - hto_names: - type: string - description: | - Comma separated list of HTO names, without whitespace - - type_report: - type: boolean - description: | - If true, full classification report is generated, otherwise the simplified classification report. - - summary_report: - type: boolean - description: | - If true, summary report is generated. - - skip: - type: file - description: | - Load a full classification report and skip the mtx folder as input. Require a path argument. - - examine: - type: file - description: | - Provide the cell list. Requires a file argument. Only executes if -u is set. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - hto_matrix: + type: file + description: path to matrix from cell hashing data, the tool receives either + CSV files or TSV, type must be specified using parameters + - hto_names: + type: string + description: | + Comma separated list of HTO names, without whitespace + - - type_report: + type: boolean + description: | + If true, full classification report is generated, otherwise the simplified classification report. + - - summary_report: + type: boolean + description: | + If true, summary report is generated. + - - skip: + type: file + description: | + Load a full classification report and skip the mtx folder as input. Require a path argument. + - - examine: + type: file + description: | + Provide the cell list. Requires a file argument. Only executes if -u is set. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - barcodes: - type: file - description: | - barcodes tsv file with removed cell-hashing-identifiable multiplets - pattern: "barcodes.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'barcodes.tsv.gz" ': + type: file + description: | + barcodes tsv file with removed cell-hashing-identifiable multiplets + pattern: "barcodes.tsv.gz" - matrix: - type: file - description: | - matrix mtx.tsv file with removed cell-hashing-identifiable multiplets - pattern: "matrix.mtx.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'matrix.mtx.gz" ': + type: file + description: | + matrix mtx.tsv file with removed cell-hashing-identifiable multiplets + pattern: "matrix.mtx.gz" - features: - type: file - description: | - features tsv file with removed cell-hashing-identifiable multiplets - pattern: "features.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'features.tsv.gz" ': + type: file + description: | + features tsv file with removed cell-hashing-identifiable multiplets + pattern: "features.tsv.gz" - classification_report: - type: file - description: | - full or simplified classification report - pattern: "GMM_*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'GMM_*.csv" ': + type: file + description: | + full or simplified classification report + pattern: "GMM_*.csv" - config_report: - type: file - description: | - Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report. - pattern: "GMM_*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'GMM_*.config" ': + type: file + description: | + Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report. + pattern: "GMM_*.csv" - summary_report: - type: file - description: | - summary report, optional output - pattern: "test/summary_report_*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - summary_report_*.txt: + type: file + description: | + summary report, optional output + pattern: "test/summary_report_*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/gnu/sort/meta.yml b/modules/nf-core/gnu/sort/meta.yml index 9d961750c64..c555dbb5c4b 100644 --- a/modules/nf-core/gnu/sort/meta.yml +++ b/modules/nf-core/gnu/sort/meta.yml @@ -11,30 +11,29 @@ tools: homepage: "https://github.com/vgl-hub/gfastats" documentation: "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Draft assembly file - pattern: "*.{txt,bed,interval,genome,bins}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Draft assembly file + pattern: "*.{txt,bed,interval,genome,bins}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: The sorted txt file generated by sort - pattern: "*.{txt,bed,interval,genome,bins}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/gnu/split/meta.yml b/modules/nf-core/gnu/split/meta.yml index da705b8f595..da3bb380014 100644 --- a/modules/nf-core/gnu/split/meta.yml +++ b/modules/nf-core/gnu/split/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gnu_split" description: Split a file into consecutive or interleaved sections @@ -9,35 +8,39 @@ keywords: - generic tools: - "gnu": - description: "The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system." + description: "The GNU Core Utilities are the basic file, shell and text manipulation + utilities of the GNU operating system. These are the core utilities which are + expected to exist on every operating system." homepage: "https://www.gnu.org/software/coreutils/" documentation: "https://www.gnu.org/software/coreutils/manual/html_node/index.html" tool_dev_url: "https://git.savannah.gnu.org/cgit/coreutils.git" doi: "10.5281/zenodo.581670" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - input: - type: file - description: Text file, possibly gzip file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: Text file, possibly gzip file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - split: - type: file - description: Split files - pattern: "*split*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ' "*split*" ': + type: file + description: Split files + pattern: "*split*" - versions: - type: file - description: The split files - + - versions.yml: + type: file + description: The split files authors: - "@k1sauce" maintainers: diff --git a/modules/nf-core/goat/taxonsearch/meta.yml b/modules/nf-core/goat/taxonsearch/meta.yml index 1bb19e30d7b..db8b8adc03e 100644 --- a/modules/nf-core/goat/taxonsearch/meta.yml +++ b/modules/nf-core/goat/taxonsearch/meta.yml @@ -13,36 +13,39 @@ tools: documentation: https://github.com/genomehubs/goat-cli/wiki tool_dev_url: https://genomehubs.github.io/goat-cli/goat_cli/ licence: ["MIT"] + identifier: biotools:goat input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - taxon: - type: string - description: | - The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank. - - taxa_file: - type: file - description: | - A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line - should contain a single entry.File size is limited to 500 entries. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - taxon: + type: string + description: | + The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank. + - taxa_file: + type: file + description: | + A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line + should contain a single entry.File size is limited to 500 entries. + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - taxonsearch: - type: file - description: TSV file containing search results. - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file containing search results. + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/goleft/indexcov/meta.yml b/modules/nf-core/goleft/indexcov/meta.yml index dd0cd655fbe..1619caf32d8 100644 --- a/modules/nf-core/goleft/indexcov/meta.yml +++ b/modules/nf-core/goleft/indexcov/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "goleft_indexcov" -description: Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome. +description: Quickly estimate coverage from a whole-genome bam or cram index. A bam + index has 16KB resolution so that's what this gives, but it provides what appears + to be a high-quality coverage estimate in seconds per genome. keywords: - coverage - cnv @@ -9,43 +10,112 @@ keywords: - depth tools: - "goleft": - description: "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary" + description: "goleft is a collection of bioinformatics tools distributed under + MIT license in a single static binary" homepage: "https://github.com/brentp/goleft" documentation: "https://github.com/brentp/goleft" tool_dev_url: "https://github.com/brentp/goleft" doi: "10.1093/gigascience/gix090" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false] - - bams: - type: file - description: Sorted BAM/CRAM/SAM files - pattern: "*.{bam,cram,sam}" - - indexes: - type: file - description: BAI/CRAI files - pattern: "*.{bai,crai}" - - fai: - type: file - description: FASTA index - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false] + - bams: + type: file + description: Sorted BAM/CRAM/SAM files + pattern: "*.{bam,cram,sam}" + - indexes: + type: file + description: BAI/CRAI files + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false] + - fai: + type: file + description: FASTA index + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Files generated by indexcov - - bams: - type: file - description: Sorted ans indexed BAM or CRAM index (.crai) files - pattern: "*.{bam,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*: + type: file + description: Files generated by indexcov + - ped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*ped: + type: file + description: ped files + pattern: "*ped" + - bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*bed.gz: + type: file + description: bed files + pattern: "*bed.gz" + - bed_index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*bed.gz.tbi: + type: file + description: bed index files + pattern: "*bed.gz.tbi" + - roc: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*roc: + type: file + description: roc files + pattern: "*roc" + - html: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*html: + type: file + description: html files + pattern: "*html" + - png: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*png: + type: file + description: png files + pattern: "*png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/goleft/indexsplit/meta.yml b/modules/nf-core/goleft/indexsplit/meta.yml index 49ee3b4f4eb..e27840a2f48 100644 --- a/modules/nf-core/goleft/indexsplit/meta.yml +++ b/modules/nf-core/goleft/indexsplit/meta.yml @@ -1,5 +1,6 @@ name: "goleft_indexsplit" -description: Quickly generate evenly sized (by amount of data) regions across a number of bam/cram files +description: Quickly generate evenly sized (by amount of data) regions across a number + of bam/cram files keywords: - bam - bed @@ -8,45 +9,52 @@ keywords: - split tools: - "goleft": - description: "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary" + description: "goleft is a collection of bioinformatics tools distributed under + MIT license in a single static binary" homepage: "https://github.com/brentp/goleft" documentation: "https://github.com/brentp/goleft" tool_dev_url: "https://github.com/brentp/goleft" doi: "10.1093/gigascience/gix090" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bai: - type: file - description: BAI/CRAI file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference fasta index file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bai: + type: file + description: BAI/CRAI file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - split: + type: boolean + description: Split the regions output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file containing split regions - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file containing split regions + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/gprofiler2/gost/meta.yml b/modules/nf-core/gprofiler2/gost/meta.yml index a2789f27ae4..33c9bff24b3 100644 --- a/modules/nf-core/gprofiler2/gost/meta.yml +++ b/modules/nf-core/gprofiler2/gost/meta.yml @@ -8,95 +8,120 @@ keywords: - gene set tools: - "gprofiler2": - description: "An R interface corresponding to the 2019 update of g:Profiler web tool." + description: "An R interface corresponding to the 2019 update of g:Profiler web + tool." homepage: "https://biit.cs.ut.ee/gprofiler/page/r" documentation: "https://rdrr.io/cran/gprofiler2/" tool_dev_url: "https://gl.cs.ut.ee/biit/r-gprofiler2" doi: "10.1093/nar/gkad347" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - de_file: - type: file - pattern: "*.{csv,tsv}" - description: | - CSV or TSV-format tabular file with differential analysis outputs - - contrast_variable: - type: string - description: | - The contrast variable that is being investigated in DE analysis, e.g. "treatment". - - reference: - type: string - description: | - The contrast level of the reference samples, e.g. "control" - - target: - type: string - description: | - The contrast level of the target samples, e.g. "treated" - - background_file: - type: file - pattern: "*.{csv,tsv,txt}" - description: | - Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs. - - gmt_file: - type: file - pattern: "*.gmt" - description: | - Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases - + - - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - de_file: + type: file + pattern: "*.{csv,tsv}" + description: | + CSV or TSV-format tabular file with differential analysis outputs + - - gmt_file: + type: file + pattern: "*.gmt" + description: | + Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases + - - background_file: + type: file + pattern: "*.{csv,tsv,txt}" + description: | + Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs. output: - - meta: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - all_enrich: - type: file - description: | - TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found - pattern: "*gprofiler2.*all_enriched_pathways.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.all_enriched_pathways.tsv": + type: file + description: | + TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found + pattern: "*gprofiler2.*all_enriched_pathways.tsv" - rds: - type: file - description: | - RDS file; R object containing the results of the gost query - pattern: "*gprofiler2.*gost_results.rds" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.gost_results.rds": + type: file + description: | + RDS file; R object containing the results of the gost query + pattern: "*gprofiler2.*gost_results.rds" - plot_png: - type: file - description: | - PNG file; Manhattan plot of all enriched pathways - pattern: "*gprofiler2.*gostplot.png" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.gostplot.png": + type: file + description: | + PNG file; Manhattan plot of all enriched pathways + pattern: "*gprofiler2.*gostplot.png" - plot_html: - type: file - description: | - HTML file; interactive Manhattan plot of all enriched pathways - pattern: "*gprofiler2.*gostplot.html" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.gostplot.html": + type: file + description: | + HTML file; interactive Manhattan plot of all enriched pathways + pattern: "*gprofiler2.*gostplot.html" - sub_enrich: - type: file - description: | - TSV file; table listing enriched pathways that were found from one particular source - pattern: "*gprofiler2.*sub_enriched_pathways.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.*.sub_enriched_pathways.tsv": + type: file + description: | + TSV file; table listing enriched pathways that were found from one particular source + pattern: "*gprofiler2.*sub_enriched_pathways.tsv" - sub_plot: - type: file - description: | - PNG file; bar plot showing the fraction of genes that were found enriched in each pathway - pattern: "*gprofiler2.*sub_enriched_pathways.png" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.*.sub_enriched_pathways.png": + type: file + description: | + PNG file; bar plot showing the fraction of genes that were found enriched in each pathway + pattern: "*gprofiler2.*sub_enriched_pathways.png" - filtered_gmt: - type: file - description: | - GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources - pattern: "*ENSG_filtered.gmt" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*ENSG_filtered.gmt": + type: file + description: | + GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources + pattern: "*ENSG_filtered.gmt" - session_info: - type: file - description: | - Log file containing information about the R session that was run for this module - pattern: "*R_sessionInfo.log" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*R_sessionInfo.log": + type: file + description: | + Log file containing information about the R session that was run for this module + pattern: "*R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@WackerO" diff --git a/modules/nf-core/grabix/check/meta.yml b/modules/nf-core/grabix/check/meta.yml index 7997cdd6a12..cd65ea9525d 100644 --- a/modules/nf-core/grabix/check/meta.yml +++ b/modules/nf-core/grabix/check/meta.yml @@ -1,4 +1,3 @@ ---- name: "grabix_check" description: Checks if the input file is bgzip compressed or not keywords: @@ -11,21 +10,27 @@ tools: homepage: "https://github.com/arq5x/grabix" documentation: "https://github.com/arq5x/grabix" + identifier: "" input: - - input: - type: file - pattern: "*.gz" - description: file to check compression - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + pattern: "*.gz" + description: file to check compression output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - compress_bgzip: - type: string - description: environmental variable with value "yes" or "no" - + - meta: + type: string + description: environmental variable with value "yes" or "no" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MartaSantanaSilva" maintainers: diff --git a/modules/nf-core/graphmap2/align/meta.yml b/modules/nf-core/graphmap2/align/meta.yml index b5e0f8ce417..40087840a24 100644 --- a/modules/nf-core/graphmap2/align/meta.yml +++ b/modules/nf-core/graphmap2/align/meta.yml @@ -13,39 +13,40 @@ tools: homepage: https://github.com/lbcb-sci/graphmap2 documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads licence: ["MIT"] + identifier: biotools:Graphmap2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input FASTQ files - and paired-end data, respectively. - - fasta: - type: file - description: | - Reference database in FASTA format. - - index: - type: file - description: | - FASTA index in gmidx. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: file containing reads to be aligned. + - - fasta: + type: file + description: | + Reference database in FASTA format. + - - index: + type: file + description: | + FASTA index in gmidx. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: Alignment in SAM format - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Alignment in SAM format + pattern: "*.sam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/graphmap2/index/meta.yml b/modules/nf-core/graphmap2/index/meta.yml index 303f248945c..6719574d353 100644 --- a/modules/nf-core/graphmap2/index/meta.yml +++ b/modules/nf-core/graphmap2/index/meta.yml @@ -11,20 +11,23 @@ tools: homepage: https://github.com/lbcb-sci/graphmap2 documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads licence: ["MIT"] + identifier: biotools:Graphmap2 input: - - fasta: - type: file - description: | - Reference database in FASTA format. + - - fasta: + type: file + description: | + Reference database in FASTA format. output: - - gmidx: - type: file - description: Graphmap2 fasta index in gmidx format - pattern: "*.gmidx" + - index: + - "*.gmidx": + type: file + description: Index file in gmidx format + pattern: "*.gmidx" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/graphtyper/genotype/meta.yml b/modules/nf-core/graphtyper/genotype/meta.yml index b440dce4928..8e109be90a8 100644 --- a/modules/nf-core/graphtyper/genotype/meta.yml +++ b/modules/nf-core/graphtyper/genotype/meta.yml @@ -8,56 +8,80 @@ keywords: - pangenome tools: - "graphtyper": - description: A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants. + description: A graph-based variant caller capable of genotyping population-scale + short read data sets while incoperating previously discovered variants. homepage: "https://github.com/DecodeGenetics/graphtyper" documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" licence: ["MIT"] + identifier: biotools:Graphtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM index file. This is automatically found base on BAM input file name - pattern: "*.{bai}" - - ref: - type: file - description: Reference fasta file - pattern: "*.{fa, fasta, fas}" - - ref_fai: - type: file - description: Reference index file. This is automatically found based on referece input file name. - pattern: "*.{.fai}" - - region_file: - type: file - description: File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM index file. This is automatically found base on BAM input file + name + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - ref: + type: file + description: Reference fasta file + pattern: "*.{fa, fasta, fas}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - ref_fai: + type: file + description: Reference index file. This is automatically found based on referece + input file name. + pattern: "*.{.fai}" + - - region_file: + type: file + description: File with a list of chromosome/locations in reference genome to + genotype. One region per line in the format :-. This or + `--region` (in ext.args) must be specified. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with genotyped variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/*/*.vcf.gz: + type: file + description: VCF file with genotyped variants + pattern: "*.{vcf.gz}" - tbi: - type: file - description: VCF index file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/*/*.vcf.gz.tbi: + type: file + description: VCF index file + pattern: "*.{vcf.gz.tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zachary-foster" maintainers: diff --git a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml index a34a83e83fc..f2512a33616 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml @@ -7,40 +7,50 @@ keywords: - vcf tools: - "graphtyper": - description: A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants. + description: A graph-based variant caller capable of genotyping population-scale + short read data sets while incoperating previously discovered variants. homepage: "https://github.com/DecodeGenetics/graphtyper" documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" licence: ["MIT"] + identifier: biotools:Graphtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: VCF files - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: VCF files + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Concatenated VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Concatenated VCF file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Concatenated VCF file index - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.tbi": + type: file + description: Concatenated VCF file index + pattern: "*.{tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zachary-foster" maintainers: diff --git a/modules/nf-core/gridss/gridss/meta.yml b/modules/nf-core/gridss/gridss/meta.yml index a75bb46df9d..7b26734b11e 100644 --- a/modules/nf-core/gridss/gridss/meta.yml +++ b/modules/nf-core/gridss/gridss/meta.yml @@ -1,5 +1,6 @@ name: "gridss_gridss" -description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. +description: GRIDSS is a module software suite containing tools useful for the detection + of genomic rearrangements. keywords: - gridss - structural variants @@ -13,41 +14,57 @@ tools: tool_dev_url: "https://github.com/PapenfussLab/gridss" doi: "10.1186/s13059-021-02423-x" licence: ["GPL v3"] + identifier: biotools:gridss input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - inputs: - type: file - description: One or more input BAM/CRAM file(s) - pattern: "*.{bam,cram}" - - fasta: - type: file - description: The reference fasta - pattern: "*.{fa,fna,fasta}" - - fasta_fai: - type: file - description: The index of the reference fasta - pattern: "*.fai" - - bwa_index: - type: directory - description: OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - inputs: + type: file + description: One or more input BAM/CRAM file(s) + pattern: "*.{bam,cram}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + - fasta: + type: file + description: The reference fasta + pattern: "*.{fa,fna,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + - fasta_fai: + type: file + description: The index of the reference fasta + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + - bwa_index: + type: directory + description: OPTIONAL - The BWA index created from the reference fasta, will + be generated by Gridss in the setupreference step output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The called VCF file created by Gridss' call step - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: The called VCF file created by Gridss' call step + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml index 852e5ea402b..fda9054e820 100644 --- a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml +++ b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml @@ -1,5 +1,6 @@ name: "gridss_gridssgenerateponbedpe" -description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. +description: GRIDSS is a module software suite containing tools useful for the detection + of genomic rearrangements. keywords: - gridss - structural variants @@ -15,69 +16,77 @@ tools: doi: "10.1186/s13059-021-02423-x" licence: ["GPL v3"] + identifier: biotools:gridss input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - meta3: - type: map - description: | - Groovy Map containing reference fai information - e.g. [ id:'test'] - - meta4: - type: map - description: | - Groovy Map containing bwa generated index information - e.g. [ id:'test'] - - vcf: - type: file - description: GRIDSS generated vcf file - pattern: "*.vcf" - - bedpe: - type: file - description: GRIDSS generated bedpe file - pattern: "*.bedpe" - - bed: - type: file - description: GRIDSS generated bed file - pattern: "*.bed" - - fasta: - type: file - description: The reference fasta - pattern: "*.{fa,fna,fasta}" - - fasta_fai: - type: file - description: The index of the reference fasta - pattern: "*.fai" - - bwa_index: - type: directory - description: OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: GRIDSS generated vcf file + pattern: "*.vcf" + - bedpe: + type: file + description: GRIDSS generated bedpe file + pattern: "*.bedpe" + - bed: + type: file + description: GRIDSS generated bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - fasta: + type: file + description: The reference fasta + pattern: "*.{fa,fna,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference fai information + e.g. [ id:'test'] + - fai: + type: file + description: The index of the reference fasta + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bwa generated index information + e.g. [ id:'test'] + - bwa_index: + type: directory + description: OPTIONAL - The BWA index created from the reference fasta, will + be generated by Gridss in the setupreference step output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedpe: - type: file - description: GRIDSS generated breakpoint pon bedpe file - pattern: "*.bedpe" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bedpe": + type: file + description: GRIDSS generated breakpoint pon bedpe file + pattern: "*.bedpe" - bed: - type: file - description: GRIDSS generated breakpoint pon bed file - pattern: "*.bed" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bed": + type: file + description: GRIDSS generated breakpoint pon bed file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml index 3aea9b8cdd1..cc54ea9ef4f 100644 --- a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml +++ b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml @@ -1,5 +1,6 @@ name: "gridss_gridsssomaticfilter" -description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. +description: GRIDSS is a module software suite containing tools useful for the detection + of genomic rearrangements. keywords: - gridss - structural variants @@ -13,41 +14,51 @@ tools: doi: "10.1186/s13059-021-02423-x" licence: ["GPL v3"] + identifier: biotools:gridss input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing information for PONDIR - e.g. [ id:'test'] - - vcf: - type: file - description: Input VCF file, must be generated with GRIDSS - pattern: "*.{vcf,vcf.gz}" - - pondir: - type: directory - description: Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: Input VCF file, must be generated with GRIDSS + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing information for PONDIR + e.g. [ id:'test'] + - pondir: + type: directory + description: Directory containing Panel Of Normal bed/bedpe used to filter FP + somatic events. Use gridss.GeneratePonBedpe to generate the PON. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - high_conf_sv: - type: file - description: VCF file including high confidence somatic SVs - pattern: "*.vcf.bgz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.high_confidence_somatic.vcf.bgz": + type: file + description: VCF file including high confidence somatic SVs + pattern: "*.vcf.bgz" - all_sv: - type: file - description: VCF file including all somatic SVs - pattern: "*.vcf.bgz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.all_somatic.vcf.bgz": + type: file + description: VCF file including all somatic SVs + pattern: "*.vcf.bgz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/gsea/gsea/meta.yml b/modules/nf-core/gsea/gsea/meta.yml index fe2d4c95692..f3ce403fd04 100644 --- a/modules/nf-core/gsea/gsea/meta.yml +++ b/modules/nf-core/gsea/gsea/meta.yml @@ -12,132 +12,245 @@ tools: documentation: "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page" doi: "10.1073/pnas.0506580102" licence: ["BSD-3-clause"] + identifier: biotools:gsea input: - - meta: - type: map - description: | - Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]. - - gct: - type: file - description: GCT file with expression values - pattern: "*.{gct}" - - cls: - type: file - description: CL file with the classes of the samples in the GCT file - pattern: "*.{gct}" - - gene_sets: - type: file - description: GMX or GMT file with gene sets - pattern: "*.{gmx,gmt}" - - reference: - type: string - description: | - String indicating which of the classes in the cls file should be used - as the reference level of the comparison. - - target: - type: string - description: | - String indicating which of the classes in the cls file should be used - as the target level of the comparison. - - chip: - type: file - description: | - optional Broad-style chip file mapping identifiers in gct to - those in gene_sets - pattern: "*.{chip}" + - - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]. + - gct: + type: file + description: GCT file with expression values + pattern: "*.{gct}" + - cls: + type: file + description: CL file with the classes of the samples in the GCT file + pattern: "*.{gct}" + - gene_sets: + type: file + description: GMX or GMT file with gene sets + pattern: "*.{gmx,gmt}" + - - reference: + type: string + description: | + String indicating which of the classes in the cls file should be used + as the reference level of the comparison. + - target: + type: string + description: | + String indicating which of the classes in the cls file should be used + as the target level of the comparison. + - - chip: + type: file + description: | + optional Broad-style chip file mapping identifiers in gct to + those in gene_sets + pattern: "*.{chip}" output: - - meta: - type: map - description: | - Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] - rpt: - type: file - description: File containing parameter settings used - pattern: "*.rpt" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*.rpt": + type: file + description: File containing parameter settings used + pattern: "*.rpt" - index_html: - type: file - description: Top level report HTML file - pattern: "index.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*index.html": + type: file + description: Top level report HTML file + pattern: "index.html" - heat_map_corr_plot: - type: file - description: HTML file combining heatmap and rank correlation plot - pattern: "heat_map_corr_plot.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*heat_map_corr_plot.html": + type: file + description: HTML file combining heatmap and rank correlation plot + pattern: "heat_map_corr_plot.html" - report_tsvs_ref: - type: file - description: Main TSV results report file for the reference group. - pattern: "gsea_report_for_reference*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${reference}.tsv": + type: file + description: Main TSV results report file for the reference group. + pattern: "gsea_report_for_reference*.tsv" - report_htmls_ref: - type: file - description: Main HTML results report file for the reference group. sample groups - pattern: "gsea_report_for_reference*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${reference}.html": + type: file + description: Main HTML results report file for the reference group. sample groups + pattern: "gsea_report_for_reference*.html" - report_tsvs_target: - type: file - description: Main TSV results report file for the target group. - pattern: "gsea_report_for_target*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${target}.tsv": + type: file + description: Main TSV results report file for the target group. + pattern: "gsea_report_for_target*.tsv" - report_htmls_target: - type: file - description: Main HTML results report file for the target group. - pattern: "gsea_report_for_target*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${target}.html": + type: file + description: Main HTML results report file for the target group. + pattern: "gsea_report_for_target*.html" - ranked_gene_list: - type: file - description: TSV file with ranked gene list and scores - pattern: "ranked_gene_list*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*ranked_gene_list*.tsv": + type: file + description: TSV file with ranked gene list and scores + pattern: "ranked_gene_list*.tsv" - gene_set_sizes: - type: file - description: TSV file with gene set sizes - pattern: "gene_set_sizes.tsv" - - butterfly_plot: - type: file - description: Butterfly plot with gene rank plotted against score - pattern: "butterfly_plot.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gene_set_sizes.tsv": + type: file + description: TSV file with gene set sizes + pattern: "gene_set_sizes.tsv" - histogram: - type: file - description: Plot showing number of gene sets by enrichment score - pattern: "global_es_histogram.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*global_es_histogram.png": + type: file + description: Plot showing number of gene sets by enrichment score + pattern: "global_es_histogram.png" - heatmap: - type: file - description: Heat Map of the top 50 features for each phenotype in test - pattern: "heat_map_1.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*heat_map_1.png": + type: file + description: Heat Map of the top 50 features for each phenotype in test + pattern: "heat_map_1.png" - pvalues_vs_nes_plot: - type: file - description: Plot showing FDR q-value by normalised enrichment score - pattern: "pvalues_vs_nes_plot" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*pvalues_vs_nes_plot.png": + type: file + description: Plot showing FDR q-value by normalised enrichment score + pattern: "pvalues_vs_nes_plot" + - ues_vs_nes_plot: + type: file + description: Plot showing FDR q-value by normalised enrichment score + pattern: "pvalues_vs_nes_plot" - ranked_list_corr: - type: file - description: Ranked Gene List Correlation Profile - pattern: "ranked_list_corr_2.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*ranked_list_corr_2.png": + type: file + description: Ranked Gene List Correlation Profile + pattern: "ranked_list_corr_2.png" + - butterfly_plot: + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*butterfly_plot.png": + type: file + description: Butterfly plot with gene rank plotted against score + pattern: "butterfly_plot.png" - gene_set_tsv: - type: list - description: Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene - pattern: "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv": + type: list + description: Where -make_sets is not set to false, TSV files, one file for each + gene set, with detail on enrichment for each gene + pattern: "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" - gene_set_html: - type: list - description: Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene - pattern: "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html": + type: list + description: Where -make_sets is not set to false, HTML files, one file for + each gene set, with detail on enrichment for each gene + pattern: "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" - gene_set_heatmap: - type: list - description: Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene - pattern: "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png": + type: list + description: Where -make_sets is not set to false, PNG-format heatmaps, one + file for each gene set, showing expression for each gene + pattern: "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" - snapshot: - type: list - description: HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot - pattern: "*_snapshot*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*_snapshot*.html": + type: list + description: HTML files, one each for positive and negative enrichment, collecting + elements of gene_set_enplot + pattern: "*_snapshot*.html" - gene_set_enplot: - type: list - description: Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one file for each gene set, showing how genes contribute to enrichment. - pattern: "enplot*.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*enplot*.png": + type: list + description: Where -make_sets is not set to false, PNG-format enrichment (barcode) + plots, one file for each gene set, showing how genes contribute to enrichment. + pattern: "enplot*.png" - gene_set_dist: - type: list - description: Where -make_sets is not set to false, PNG-format enrichment score distributions plots, one file for each gene set. - pattern: "gset_rnd_es_dist*.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gset_rnd_es_dist*.png": + type: list + description: Where -make_sets is not set to false, PNG-format enrichment score + distributions plots, one file for each gene set. + pattern: "gset_rnd_es_dist*.png" - archive: - type: file - description: Where -zip_report is set, a zip archive containing all outputs - pattern: "*.zip" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*.zip": + type: file + description: Where -zip_report is set, a zip archive containing all outputs + pattern: "*.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/gstama/collapse/meta.yml b/modules/nf-core/gstama/collapse/meta.yml index c9bca15bee4..0166dc24d6d 100644 --- a/modules/nf-core/gstama/collapse/meta.yml +++ b/modules/nf-core/gstama/collapse/meta.yml @@ -16,66 +16,132 @@ tools: tool_dev_url: https://github.com/sguizard/gs-tama doi: 10.1186/s12864-020-07123-7 licence: ["GNU GPL3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: A sorted BAM or sam file of aligned reads - pattern: "*.{bam,sam}" - - fasta: - type: file - description: A fasta file of the genome used for the mapping - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: A sorted BAM or sam file of aligned reads + pattern: "*.{bam,sam}" + - - fasta: + type: file + description: A fasta file of the genome used for the mapping + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: a bed12 format file containing the final collapsed version of your transcriptome - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_collapsed.bed": + type: file + description: a bed12 format file containing the final collapsed version of your + transcriptome + pattern: "*.bed" - bed_trans_reads: - type: file - description: This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models. - pattern: "*_trans_read.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_read.bed": + type: file + description: This file uses bed12 format to show the transcript model for each + read based on the mapping prior to collapsing. This only contains the reads + which were accepted according to the defined thresholds. You can use this + file to see if there were any strange occurrences during collapsing. It also + contains the relationships between reads and collapsed transcript models. + The 1st subfield in the 4th column shows the final transcript ID and the 2nd + subfield in the 4th column shows the read ID. If you used no_cap mode for + collapsing there may be multiple lines for a single read. This happens when + a 5' degraded read can match to multiple 5' longer transcript models. + pattern: "*_trans_read.bed" - local_density_error: - type: file - description: This file contains the log of filtering for local density error around the splice junctions ("-lde") - pattern: "*_local_density_error.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_local_density_error.txt": + type: file + description: This file contains the log of filtering for local density error + around the splice junctions ("-lde") + pattern: "*_local_density_error.txt" - polya: - type: file - description: This file contains the reads with potential poly A truncation. - pattern: "*_polya.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_polya.txt": + type: file + description: This file contains the reads with potential poly A truncation. + pattern: "*_polya.txt" - read: - type: file - description: This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file - pattern: "*_read.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_read.txt": + type: file + description: This file contains information for all mapped reads from the input + SAM/BAM file. It shows both accepted and discarded reads and should match + the number of mapped reads in your SAM/BAM file + pattern: "*_read.txt" - strand_check: - type: file - description: This file shows instances where the sam flag strand information contrasted the GMAP strand information. - pattern: "*_strand_check.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_strand_check.txt": + type: file + description: This file shows instances where the sam flag strand information + contrasted the GMAP strand information. + pattern: "*_strand_check.txt" - trans_report: - type: file - description: This file contains collapsing information for each transcript. - pattern: "*_trans_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_report.txt": + type: file + description: This file contains collapsing information for each transcript. + pattern: "*_trans_report.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - varcov: - type: file - description: This file contains the coverage information for each variant detected. - pattern: "*_varcov.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_varcov.txt": + type: file + description: This file contains the coverage information for each variant detected. + pattern: "*_varcov.txt" - variants: - type: file - description: This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo. - pattern: "*_variants.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_variants.txt": + type: file + description: This file contains the variants called. Variants are only called + if 5 or more reads show the variant at a specific locus. If you would like + to change the threshold, please make an issue about this in the Github repo. + pattern: "*_variants.txt" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/merge/meta.yml b/modules/nf-core/gstama/merge/meta.yml index adb2b32dd3d..81cbc87b5af 100644 --- a/modules/nf-core/gstama/merge/meta.yml +++ b/modules/nf-core/gstama/merge/meta.yml @@ -17,42 +17,79 @@ tools: tool_dev_url: https://github.com/sguizard/gs-tama doi: "10.1186/s12864-020-07123-7" licence: ["GPL v3 License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: bed12 file generated by TAMA collapse - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed12 file generated by TAMA collapse + pattern: "*.bed" + - - filelist: + type: file + description: list of files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - bed: - type: file - description: This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bed": + type: file + description: This is the main merged annotation file. Transcripts are coloured + according to the source support for each model. Sources are numbered based + on the order supplied in the input filelist file. For example the first file + named in the filelist file would have its transcripts coloured in red. If + a transcript has multiple sources the colour is shown as magenta. + pattern: "*.bed" - gene_report: - type: file - description: This contains a report of the genes from the merged file. "num_clusters" refers to the number of source transcripts that were used to make this gene model. "num_final_trans" refers to the number of transcripts in the final gene model. - pattern: "*_gene_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_gene_report.txt": + type: file + description: This contains a report of the genes from the merged file. "num_clusters" + refers to the number of source transcripts that were used to make this gene + model. "num_final_trans" refers to the number of transcripts in the final + gene model. + pattern: "*_gene_report.txt" - merge: - type: file - description: This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the "txt" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix. - pattern: "*_merge.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_merge.txt": + type: file + description: This contains a bed12 format file which shows the coordinates of + each input transcript matched to the merged transcript ID. I used the "txt" + extension even though it is a bed file just to avoid confusion with the main + bed file. You can use this file to map the final merged transcript models + to their pre-merged supporting transcripts. The 1st subfield in the 4th column + shows the final merged transcript ID while the 2nd subfield shows the pre-merged + transcript ID with source prefix. + pattern: "*_merge.txt" - trans_report: - type: file - description: This contains the source information for each merged transcript. - pattern: "*_trans_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_report.txt": + type: file + description: This contains the source information for each merged transcript. + pattern: "*_trans_report.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/polyacleanup/meta.yml b/modules/nf-core/gstama/polyacleanup/meta.yml index d8d17543bb7..7f7284a7c6e 100644 --- a/modules/nf-core/gstama/polyacleanup/meta.yml +++ b/modules/nf-core/gstama/polyacleanup/meta.yml @@ -1,5 +1,6 @@ name: gstama_polyacleanup -description: Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3) +description: Helper script, remove remaining polyA sequences from Full Length Non + Chimeric reads (Pacbio isoseq3) keywords: - gstama - gstama/polyacleanup @@ -16,38 +17,55 @@ tools: tool_dev_url: https://github.com/sguizard/gs-tama doi: "10.1186/s12864-020-07123-7" licence: ["GPL v3 License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Full Length Non Chimeric reads in fasta format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Full Length Non Chimeric reads in fasta format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip. - pattern: "*_tama.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tama.fa.gz": + type: file + description: The Full Length Non Chimeric reads clened from remaining polyA + tails. The sequences are in FASTA format compressed with gzip. + pattern: "*_tama.fa.gz" - report: - type: file - description: A text file describing the number of polyA tails removed and their length. Compressed with gzip. - pattern: "*_tama_polya_flnc_report.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tama_polya_flnc_report.txt.gz": + type: file + description: A text file describing the number of polyA tails removed and their + length. Compressed with gzip. + pattern: "*_tama_polya_flnc_report.txt.gz" - tails: - type: file - description: A gzip compressed FASTA file of trimmed polyA tails. - pattern: "*_tama_tails.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tama_tails.fa.gz": + type: file + description: A gzip compressed FASTA file of trimmed polyA tails. + pattern: "*_tama_tails.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gt/gff3/meta.yml b/modules/nf-core/gt/gff3/meta.yml index 5cecd8d0f18..62c4cbc6a01 100644 --- a/modules/nf-core/gt/gff3/meta.yml +++ b/modules/nf-core/gt/gff3/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_gff3" -description: "GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files" +description: "GenomeTools gt-gff3 utility to parse, possibly transform, and output + GFF3 files" keywords: - genome - gff3 @@ -14,34 +14,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - gt_gff3: - type: file - description: Parsed gff3 file produced only if there is no parsing error - pattern: "*.gt.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.gt.gff3": + type: file + description: Parsed gff3 file produced only if there is no parsing error + pattern: "*.gt.gff3" - error_log: - type: file - description: Error log if gt-gff3 failed to parse the input gff3 file - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.error.log": + type: file + description: Error log if gt-gff3 failed to parse the input gff3 file + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gallvp" maintainers: diff --git a/modules/nf-core/gt/gff3validator/meta.yml b/modules/nf-core/gt/gff3validator/meta.yml index 3322faf90cf..98ff256d15a 100644 --- a/modules/nf-core/gt/gff3validator/meta.yml +++ b/modules/nf-core/gt/gff3validator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_gff3validator" description: "GenomeTools gt-gff3validator utility to strictly validate a GFF3 file" @@ -15,34 +14,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - success_log: - type: file - description: Log file for successful validation - pattern: "*.success.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.success.log": + type: file + description: Log file for successful validation + pattern: "*.success.log" - error_log: - type: file - description: Log file for failed validation - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.error.log": + type: file + description: Log file for failed validation + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gt/ltrharvest/meta.yml b/modules/nf-core/gt/ltrharvest/meta.yml index a4181308522..a57501eaef1 100644 --- a/modules/nf-core/gt/ltrharvest/meta.yml +++ b/modules/nf-core/gt/ltrharvest/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_ltrharvest" description: Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility @@ -17,42 +16,64 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - index: - type: directory - description: Folder containing the suffixerator index files - pattern: "suffixerator" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - index: + type: directory + description: Folder containing the suffixerator index files + pattern: "suffixerator" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - tabout: - type: file - description: Old tabular output by default or when `-tabout yes` argument is present - pattern: "*.tabout" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tabout": + type: file + description: Old tabular output by default or when `-tabout yes` argument is + present + pattern: "*.tabout" - gff3: - type: file - description: GFF3 output when `-tabout no` argument is present - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: GFF3 output when `-tabout no` argument is present + pattern: "*.gff3" - fasta: - type: file - description: FASTA output when `-out` argument is present - pattern: "*.{fa,fsa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $out_name: + type: file + description: FASTA output when `-out` argument is present + pattern: "*.{fa,fsa,fasta}" - inner_fasta: - type: file - description: FASTA output for inner regions when `-outinner` argument is present - pattern: "*.{fa,fsa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $outinner_name: + type: file + description: FASTA output for inner regions when `-outinner` argument is present + pattern: "*.{fa,fsa,fasta}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gt/stat/meta.yml b/modules/nf-core/gt/stat/meta.yml index fa477f340a4..3f62f8eba26 100644 --- a/modules/nf-core/gt/stat/meta.yml +++ b/modules/nf-core/gt/stat/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_stat" -description: "GenomeTools gt-stat utility to show statistics about features contained in GFF3 files" +description: "GenomeTools gt-stat utility to show statistics about features contained + in GFF3 files" keywords: - genome - gff3 @@ -16,30 +16,33 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - stats: - type: file - description: Stats file in yaml format - pattern: "*.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.yml: + type: file + description: Stats file in yaml format + pattern: "*.yml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gt/suffixerator/meta.yml b/modules/nf-core/gt/suffixerator/meta.yml index 8fa39f1c890..74e02f4ed0b 100644 --- a/modules/nf-core/gt/suffixerator/meta.yml +++ b/modules/nf-core/gt/suffixerator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_suffixerator" description: Computes enhanced suffix array using GenomeTools gt-suffixerator utility @@ -15,33 +14,36 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Input fasta file to index - pattern: "*.{fsa,fa,fasta}" - - mode: - type: string - description: Mode must be one of 'dna', or 'protein' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input fasta file to index + pattern: "*.{fsa,fa,fasta}" + - - mode: + type: string + description: Mode must be one of 'dna', or 'protein' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - index: - type: directory - description: Folder containing the suffixerator index files - pattern: "suffixerator" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $prefix: + type: directory + description: Folder containing the suffixerator index files + pattern: "suffixerator" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml index 0667dcd6d73..fc081897d80 100644 --- a/modules/nf-core/gtdbtk/classifywf/meta.yml +++ b/modules/nf-core/gtdbtk/classifywf/meta.yml @@ -1,5 +1,6 @@ name: gtdbtk_classifywf -description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. +description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications + to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. keywords: - GTDB taxonomy - taxonomic classification @@ -10,79 +11,135 @@ keywords: - archaea tools: - gtdbtk: - description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. + description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications + to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. homepage: https://ecogenomics.github.io/GTDBTk/ documentation: https://ecogenomics.github.io/GTDBTk/ tool_dev_url: https://github.com/Ecogenomics/GTDBTk doi: "10.1093/bioinformatics/btz848" licence: ["GNU General Public v3 (GPL v3)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, assembler:'spades' ] - - bins: - type: file - description: The binned fasta files from the assembler - pattern: "*.{fasta,fa}" - - database: - type: file - description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy) - pattern: "*" - - use_pplacer_scratch_dir: - type: boolean - description: Set to true to reduce pplacer memory usage by writing to disk (slower) - - mash_db: - type: file - description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional) - pattern: "*.msh" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, assembler:'spades' ] + - '"bins/*"': + type: file + description: bins + - - db_name: + type: string + description: The name of the GTDB database to use. + - '"database/*"': + type: file + description: GTDB database + - - use_pplacer_scratch_dir: + type: boolean + description: Set to true to reduce pplacer memory usage by writing to disk (slower) + - - mash_db: + type: file + description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` + mode is used (optional) + pattern: "*.msh" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - summary: - type: file - description: A TSV summary file for the classification - pattern: "*.{summary.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.summary.tsv: + type: file + description: A TSV summary file for the classification + pattern: "*.{summary.tsv}" - tree: - type: file - description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment - pattern: "*.{classify.tree.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.classify.tree.gz: + type: file + description: NJ or UPGMA tree in Newick format produced from a multiple sequence + alignment + pattern: "*.{classify.tree.gz}" - markers: - type: file - description: A TSV summary file lineage markers used for the classification. - pattern: "*.{markers_summary.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.markers_summary.tsv: + type: file + description: A TSV summary file lineage markers used for the classification. + pattern: "*.{markers_summary.tsv}" - msa: - type: file - description: Multiple sequence alignments file. - pattern: "*.{msa.fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.msa.fasta.gz: + type: file + description: Multiple sequence alignments file. + pattern: "*.{msa.fasta.gz}" - user_msa: - type: file - description: Multiple sequence alignments file for the user-provided files. - pattern: "*.{user_msa.fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.user_msa.fasta.gz: + type: file + description: Multiple sequence alignments file for the user-provided files. + pattern: "*.{user_msa.fasta.gz}" - filtered: - type: file - description: A list of genomes with an insufficient number of amino acids in MSA.. - pattern: "*.{filtered.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.filtered.tsv: + type: file + description: A list of genomes with an insufficient number of amino acids in + MSA.. + pattern: "*.{filtered.tsv}" + - failed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.failed_genomes.tsv: + type: file + description: A TSV summary of the genomes which GTDB-tk failed to classify. + pattern: "*.{failed_genomes.tsv}" - log: - type: file - description: GTDB-tk log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.log: + type: file + description: GTDB-tk log file + pattern: "*.{log}" - warnings: - type: file - description: GTDB-tk warnings log file - pattern: "*.{warnings.log}" - - failed: - type: file - description: A TSV summary of the genomes which GTDB-tk failed to classify. - pattern: "*.{failed_genomes.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.warnings.log: + type: file + description: GTDB-tk warnings log file + pattern: "*.{warnings.log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@skrakau" - "@abhi18av" diff --git a/modules/nf-core/gtfsort/meta.yml b/modules/nf-core/gtfsort/meta.yml index 836b72e03d8..bc9842bab23 100644 --- a/modules/nf-core/gtfsort/meta.yml +++ b/modules/nf-core/gtfsort/meta.yml @@ -1,4 +1,3 @@ ---- name: "gtfsort" description: Sort GTF files in chr/pos/feature order keywords: @@ -7,27 +6,30 @@ keywords: - genomics tools: - "gtfsort": - description: "A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm." + description: "A chr/pos/feature GTF sorter that uses a lexicographically-based + index ordering algorithm." homepage: "https://github.com/alejandrogzi/gtfsort" documentation: "https://github.com/alejandrogzi/gtfsort" tool_dev_url: "https://github.com/alejandrogzi/gtfsort" licence: ["MIT"] + identifier: "" input: - - gtf: - type: file - description: Unsorted GTF/GFF file. - pattern: "*.gtf" - + - - gtf: + type: file + description: Unsorted GTF/GFF file. + pattern: "*.gtf" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gtf: - type: file - description: Sorted GTF file - pattern: "*.gtf" + - "*.sorted.gtf": + type: file + description: Sorted GTF file + pattern: "*.gtf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@georgiakes" maintainers: diff --git a/modules/nf-core/gubbins/meta.yml b/modules/nf-core/gubbins/meta.yml index 191660b82ae..2bb4f24c784 100644 --- a/modules/nf-core/gubbins/meta.yml +++ b/modules/nf-core/gubbins/meta.yml @@ -1,5 +1,8 @@ name: gubbins -description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. +description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) + is an algorithm that iteratively identifies loci containing elevated densities of + base substitutions while concurrently constructing a phylogeny based on the putative + point mutations outside of these regions. licence: ["GPL-2.0-only"] keywords: - recombination @@ -7,55 +10,67 @@ keywords: - phylogeny tools: - gubbins: - description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. + description: Rapid phylogenetic analysis of large samples of recombinant bacterial + whole genome sequences using Gubbins. homepage: https://sanger-pathogens.github.io/gubbins/ documentation: https://sanger-pathogens.github.io/gubbins/ + identifier: biotools:gubbins input: - - alignment: - type: file - description: fasta alignment file - pattern: "*.{fasta,fas,fa,aln}" + - - alignment: + type: file + description: fasta alignment file + pattern: "*.{fasta,fas,fa,aln}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Filtered variant alignment in fasta format - pattern: "*.{fasta}" - - embl_predicted: - type: file - description: Recombination predictions in embl format - pattern: "*.{recombination_predictions.embl}" + - "*.fasta": + type: file + description: Filtered variant alignment in fasta format + pattern: "*.{fasta}" - gff: - type: file - description: Recombination predictions in gff format - pattern: "*.{gff}" - - embl_branch: - type: file - description: Branch base reconstruction - pattern: "*.{branch_base_reconstruction.embl}" + - "*.gff": + type: file + description: Recombination predictions in gff format + pattern: "*.{gff}" - vcf: - type: file - description: SNP distribution - pattern: "*.{vcf}" + - "*.vcf": + type: file + description: SNP distribution + pattern: "*.{vcf}" - stats: - type: file - description: Per branch statistics - pattern: "*.{csv}" + - "*.csv": + type: file + description: Per branch statistics + pattern: "*.{csv}" - phylip: - type: file - description: Filtered variant alignment in phylip format - pattern: "*.{phylip}" + - "*.phylip": + type: file + description: Filtered variant alignment in phylip format + pattern: "*.{phylip}" + - embl_predicted: + - "*.recombination_predictions.embl": + type: file + description: Recombination predictions in embl format + pattern: "*.{recombination_predictions.embl}" + - embl_branch: + - "*.branch_base_reconstruction.embl": + type: file + description: Branch base reconstruction + pattern: "*.{branch_base_reconstruction.embl}" - tree: - type: file - description: Recombination removed RAxML phylogenetic tree - pattern: "*.{final_tree.tre}" + - "*.final_tree.tre": + type: file + description: Recombination removed RAxML phylogenetic tree + pattern: "*.{final_tree.tre}" - tree_labelled: - type: file - description: Recombination removed RAxML phylogenetic tree (nodes labelled) - pattern: "*.{node_labelled.final_tree.tre}" + - "*.node_labelled.final_tree.tre": + type: file + description: Recombination removed RAxML phylogenetic tree (nodes labelled) + pattern: "*.{node_labelled.final_tree.tre}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/gunc/downloaddb/meta.yml b/modules/nf-core/gunc/downloaddb/meta.yml index ac280236b39..41fa20e0f6c 100644 --- a/modules/nf-core/gunc/downloaddb/meta.yml +++ b/modules/nf-core/gunc/downloaddb/meta.yml @@ -1,5 +1,6 @@ name: gunc_downloaddb -description: Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes +description: Download database for GUNC detection of Chimerism and Contamination in + Prokaryotic Genomes keywords: - download - prokaryote @@ -9,26 +10,30 @@ keywords: - chimeras tools: - gunc: - description: Python package for detection of chimerism and contamination in prokaryotic genomes. + description: Python package for detection of chimerism and contamination in prokaryotic + genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: biotools:gunc input: - - db_name: - type: string - description: "Which database to download. Options: progenomes or gtdb" - pattern: "progenomes|gtdb" + - - db_name: + type: string + description: "Which database to download. Options: progenomes or gtdb" + pattern: "progenomes|gtdb" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: GUNC database file - pattern: "*.dmnd" + - "*.dmnd": + type: file + description: GUNC database file + pattern: "*.dmnd" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gunc/mergecheckm/meta.yml b/modules/nf-core/gunc/mergecheckm/meta.yml index c7746b2eabb..4a7a2c1ce1a 100644 --- a/modules/nf-core/gunc/mergecheckm/meta.yml +++ b/modules/nf-core/gunc/mergecheckm/meta.yml @@ -11,40 +11,44 @@ keywords: - chimeras tools: - gunc: - description: Python package for detection of chimerism and contamination in prokaryotic genomes. + description: Python package for detection of chimerism and contamination in prokaryotic + genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: biotools:gunc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gunc_file: - type: file - description: Path of a gunc_scores.tsv file (mandatory) - pattern: "*.{bam,cram,sam}" - - checkm_file: - type: file - description: Output TSV from CheckM qa (ideally with -o 2 extended format) (mandatory) - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gunc_file: + type: file + description: Path of a gunc_scores.tsv file (mandatory) + pattern: "*.{bam,cram,sam}" + - checkm_file: + type: file + description: Output TSV from CheckM qa (ideally with -o 2 extended format) (mandatory) + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Merged checkm/gunc results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Merged checkm/gunc results in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gunc/run/meta.yml b/modules/nf-core/gunc/run/meta.yml index 7809b494fc5..63f437f363b 100644 --- a/modules/nf-core/gunc/run/meta.yml +++ b/modules/nf-core/gunc/run/meta.yml @@ -8,44 +8,54 @@ keywords: - chimeras tools: - gunc: - description: Python package for detection of chimerism and contamination in prokaryotic genomes. + description: Python package for detection of chimerism and contamination in prokaryotic + genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: biotools:gunc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing contig (bins) - pattern: "*.fa" - - db: - type: file - description: GUNC database file - pattern: "*.dmnd" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing contig (bins) + pattern: "*.fa" + - - db: + type: file + description: GUNC database file + pattern: "*.dmnd" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - maxcss_levels_tsv: - type: file - description: Output file with scores for a taxonomic level with the highest CSS score - pattern: "*.tsv" + - maxcss_level_tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*maxCSS_level.tsv": + type: file + description: Output file with results for the maximum CSS level + pattern: "*.tsv" - all_levels_tsv: - type: file - description: Optional output file with results for each taxonomic level - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*all_levels.tsv": + type: file + description: Optional output file with results for each taxonomic level + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a0a56..9066c0353b1 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/gvcftools/extractvariants/meta.yml b/modules/nf-core/gvcftools/extractvariants/meta.yml index da2b7d884dd..2075496cb5e 100644 --- a/modules/nf-core/gvcftools/extractvariants/meta.yml +++ b/modules/nf-core/gvcftools/extractvariants/meta.yml @@ -1,5 +1,6 @@ name: "gvcftools_extractvariants" -description: Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file. +description: Removes all non-variant blocks from a gVCF file to produce a smaller + variant-only VCF file. keywords: - gvcftools - extract_variants @@ -8,35 +9,39 @@ keywords: - vcf tools: - "gvcftools": - description: "gvcftools is a package of small utilities for creating and analyzing gVCF files" + description: "gvcftools is a package of small utilities for creating and analyzing + gVCF files" homepage: "https://sites.google.com/site/gvcftools/home" documentation: "https://sites.google.com/site/gvcftools/home/configuration-and-analysis" tool_dev_url: "https://github.com/sequencing/gvcftools" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gvcf: - type: file - description: GVCF file - pattern: "*.{g.vcf,gvcf}.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gvcf: + type: file + description: GVCF file + pattern: "*.{g.vcf,gvcf}.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Converted variant-only VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Converted variant-only VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/hamronization/abricate/meta.yml b/modules/nf-core/hamronization/abricate/meta.yml index 4a0867d6ce5..b1346892e59 100644 --- a/modules/nf-core/hamronization/abricate/meta.yml +++ b/modules/nf-core/hamronization/abricate/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_abricate" -description: Tool to convert and summarize ABRicate outputs using the hAMRonization specification +description: Tool to convert and summarize ABRicate outputs using the hAMRonization + specification keywords: - amr - antimicrobial resistance @@ -7,51 +8,61 @@ keywords: - abricate tools: - "hamronization": - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output TSV or CSV file from ABRicate - pattern: "*.{csv,tsv}" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of ABRicate used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of ABRicate used - pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output TSV or CSV file from ABRicate + pattern: "*.{csv,tsv}" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of ABRicate used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of ABRicate used + pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/hamronization/amrfinderplus/meta.yml b/modules/nf-core/hamronization/amrfinderplus/meta.yml index c0997150582..aba55b1f652 100644 --- a/modules/nf-core/hamronization/amrfinderplus/meta.yml +++ b/modules/nf-core/hamronization/amrfinderplus/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_amrfinderplus" -description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification. +description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization + specification. keywords: - amr - antimicrobial resistance @@ -9,51 +10,61 @@ keywords: - amrfinderplus tools: - "hamronization": - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .tsv file from AMRfinderPlus - pattern: "*.tsv" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of AMRfinder used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of ncbi_AMRfinder used - pattern: "[0-9]-[0-9]-[0-9].[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .tsv file from AMRfinderPlus + pattern: "*.tsv" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of AMRfinder used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of ncbi_AMRfinder used + pattern: "[0-9]-[0-9]-[0-9].[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/hamronization/deeparg/meta.yml b/modules/nf-core/hamronization/deeparg/meta.yml index de01196e9d7..39149a346a0 100644 --- a/modules/nf-core/hamronization/deeparg/meta.yml +++ b/modules/nf-core/hamronization/deeparg/meta.yml @@ -1,5 +1,6 @@ name: hamronization_deeparg -description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification +description: Tool to convert and summarize DeepARG outputs using the hAMRonization + specification keywords: - amr - antimicrobial resistance @@ -7,51 +8,61 @@ keywords: - deeparg tools: - hamronization: - description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification + description: Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/ documentation: https://github.com/pha4ge/hAMRonization/ tool_dev_url: https://github.com/pha4ge/hAMRonization licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .mapping.ARG file from DeepARG - pattern: "*.mapping.ARG" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of DeepARG used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: integer - description: Database version of DeepARG used - pattern: "[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .mapping.ARG file from DeepARG + pattern: "*.mapping.ARG" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of DeepARG used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: integer + description: Database version of DeepARG used + pattern: "[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hamronization/fargene/meta.yml b/modules/nf-core/hamronization/fargene/meta.yml index 45a3811de7d..efd3de36806 100644 --- a/modules/nf-core/hamronization/fargene/meta.yml +++ b/modules/nf-core/hamronization/fargene/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_fargene" -description: Tool to convert and summarize fARGene outputs using the hAMRonization specification +description: Tool to convert and summarize fARGene outputs using the hAMRonization + specification keywords: - amr - antimicrobial resistance @@ -9,51 +10,61 @@ keywords: - fARGene tools: - hamronization: - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .txt file from fARGene - pattern: "*.txt" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of fARGene used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of fARGene used - pattern: "[0-9].[0-9].[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .txt file from fARGene + pattern: "*.txt" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of fARGene used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of fARGene used + pattern: "[0-9].[0-9].[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hamronization/rgi/meta.yml b/modules/nf-core/hamronization/rgi/meta.yml index 0cca850261c..525148e5bfd 100644 --- a/modules/nf-core/hamronization/rgi/meta.yml +++ b/modules/nf-core/hamronization/rgi/meta.yml @@ -9,51 +9,61 @@ keywords: - rgi tools: - hamronization: - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .txt file from RGI - pattern: "*.txt" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of DeepARG used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of DeepARG used - pattern: "[0-9].[0-9].[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .txt file from RGI + pattern: "*.txt" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of DeepARG used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of DeepARG used + pattern: "[0-9].[0-9].[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/hamronization/summarize/meta.yml b/modules/nf-core/hamronization/summarize/meta.yml index 7d4c7b688ba..54ceeff36d9 100644 --- a/modules/nf-core/hamronization/summarize/meta.yml +++ b/modules/nf-core/hamronization/summarize/meta.yml @@ -1,42 +1,49 @@ name: hamronization_summarize -description: Tool to summarize and combine all hAMRonization reports into a single file +description: Tool to summarize and combine all hAMRonization reports into a single + file keywords: - amr - antimicrobial resistance - reporting tools: - hamronization: - description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification + description: Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/ documentation: https://github.com/pha4ge/hAMRonization/ tool_dev_url: https://github.com/pha4ge/hAMRonization licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - reports: - type: file - description: List of multiple hAMRonization reports in either JSON or TSV format - pattern: "*.{json,tsv}" - - format: - type: string - description: Type of final combined report file to be produced - pattern: "tsv|json|interactive" + - - reports: + type: file + description: List of multiple hAMRonization reports in either JSON or TSV format + pattern: "*.{json,tsv}" + - - format: + type: string + description: Type of final combined report file to be produced + pattern: "tsv|json|interactive" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised summary in JSON format - pattern: "*.json" + - hamronization_combined_report.json: + type: file + description: hAMRonised summary in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised summary in TSV format - pattern: "*.json" + - hamronization_combined_report.tsv: + type: file + description: hAMRonised summary in TSV format + pattern: "*.json" - html: - type: file - description: hAMRonised summary in HTML format - pattern: "*.html" + - hamronization_combined_report.html: + type: file + description: hAMRonised summary in HTML format + pattern: "*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hapibd/meta.yml b/modules/nf-core/hapibd/meta.yml index 8def0c8d662..6b27fc42a74 100644 --- a/modules/nf-core/hapibd/meta.yml +++ b/modules/nf-core/hapibd/meta.yml @@ -1,56 +1,77 @@ name: "hapibd" -description: The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples. +description: The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent + (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets + with hundreds of thousands of samples. keywords: - ibd - hbd - beagle tools: - "hapibd": - description: "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data." + description: "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent + (HBD) segments in phased genotype data." homepage: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" documentation: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" doi: "10.1016/j.ajhg.2020.02.010" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing cohort information - e.g. [ id:'test' ] - - vcf: - type: file - description: phased VCF file with a GT FORMAT subfield with no missing alleles - pattern: "*.{vcf,vcf.gz}" - - map: - type: file - description: genetic map with cM units in PLINK format - pattern: "*.{map,map.gz,map.zip}" - - exclude: - type: file - description: text file containing samples one sample per line to be excluded from the analysis - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - vcf: + type: file + description: phased VCF file with a GT FORMAT subfield with no missing alleles + pattern: "*.{vcf,vcf.gz}" + - - map: + type: file + description: genetic map with cM units in PLINK format + pattern: "*.{map,map.gz,map.zip}" + - - exclude: + type: file + description: text file containing samples one sample per line to be excluded + from the analysis + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing cohort information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hbd: - type: file - description: contains HBD segments within individuals - pattern: "*.hbd.gz" + - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - "*.hbd.gz": + type: file + description: contains HBD segments within individuals + pattern: "*.hbd.gz" - ibd: - type: file - description: contains IBD segments shared between individuals - pattern: "*.ibd.gz" + - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - "*.ibd.gz": + type: file + description: contains IBD segments shared between individuals + pattern: "*.ibd.gz" - log: - type: file - description: contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - "*.log": + type: file + description: contains a summary of the analysis which includes the analysis + parameters the number of markers the number of samples the number of output + HBD and IBD segments and the mean number of HBD and IBD segments per sample + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" maintainers: diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml index abf636f00f9..25e6127a7f4 100644 --- a/modules/nf-core/haplocheck/meta.yml +++ b/modules/nf-core/haplocheck/meta.yml @@ -10,40 +10,50 @@ keywords: - contamination tools: - "haplocheck": - description: "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content." + description: "Detects in-sample contamination in mtDNA or WGS sequencing studies + by analyzing the mitochondrial content." homepage: "https://github.com/genepi/haplocheck" documentation: "https://github.com/genepi/haplocheck" tool_dev_url: "https://github.com/genepi/haplocheck" doi: 10.1101/gr.256545.119 licence: ["MIT"] + identifier: biotools:haplocheck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Raw report in txt format - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Raw report in txt format + pattern: "*.{txt}" - html: - type: file - description: Haplocheck HTML report - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Haplocheck HTML report + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lmtani" maintainers: diff --git a/modules/nf-core/haplogrep2/classify/meta.yml b/modules/nf-core/haplogrep2/classify/meta.yml index c5399f5c00d..5f11335ba85 100644 --- a/modules/nf-core/haplogrep2/classify/meta.yml +++ b/modules/nf-core/haplogrep2/classify/meta.yml @@ -11,33 +11,36 @@ tools: documentation: "https://github.com/seppinho/haplogrep-cmd" tool_dev_url: "https://github.com/seppinho/haplogrep-cmd" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputfile: - type: file - description: valid options are hsd, vcf, or fasta files - pattern: "*.{vcf,vcf.gz,fasta,hsd}" - - format: - type: string - description: either "vcf", "fasta" or "hsd" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputfile: + type: file + description: valid options are hsd, vcf, or fasta files + pattern: "*.{vcf,vcf.gz,fasta,hsd}" + - - format: + type: string + description: either "vcf", "fasta" or "hsd" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: text file with classification information - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: text file with classification information + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/happy/ftxpy/meta.yml b/modules/nf-core/happy/ftxpy/meta.yml index 266b6235fec..15a67325266 100644 --- a/modules/nf-core/happy/ftxpy/meta.yml +++ b/modules/nf-core/happy/ftxpy/meta.yml @@ -12,61 +12,63 @@ tools: documentation: "https://github.com/Illumina/hap.py" tool_dev_url: "https://github.com/Illumina/hap.py" licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing sample information for reference fasta - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing sample information for reference fai - e.g. [ id:'test3' ] - - vcf: - type: file - description: VCF file to process - pattern: "*.{vcf,vcf.gz}" - - regions_bed: - type: file - description: BED file. Restrict analysis to given (sparse) regions. - pattern: "*.bed" - - targets_bed: - type: file - description: Restrict analysis to given (dense) regions. - pattern: "*.bed" - - bam: - type: file - description: Pass one or more BAM files for feature table extraction - pattern: "*.bam" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to process + pattern: "*.{vcf,vcf.gz}" + - regions_bed: + type: file + description: BED file. Restrict analysis to given (sparse) regions. + pattern: "*.bed" + - targets_bed: + type: file + description: Restrict analysis to given (dense) regions. + pattern: "*.bed" + - bam: + type: file + description: Pass one or more BAM files for feature table extraction + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing sample information for reference fasta + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information for reference fai + e.g. [ id:'test3' ] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - features: - type: file - description: Fuature table - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Fuature table + pattern: "*.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/happy/happy/meta.yml b/modules/nf-core/happy/happy/meta.yml index dc8ebf25a31..3582adef1f4 100644 --- a/modules/nf-core/happy/happy/meta.yml +++ b/modules/nf-core/happy/happy/meta.yml @@ -1,5 +1,8 @@ name: "happy_happy" -description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants. +description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather + than comparing VCF records row by row, hap.py will generate and match alternate + sequences in a superlocus. A superlocus is a small region of the genome (sized between + 1 and around 1000 bp) that contains one or more variants. keywords: - happy - benchmark @@ -12,127 +15,193 @@ tools: documentation: "https://github.com/Illumina/hap.py" tool_dev_url: "https://github.com/Illumina/hap.py" licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing fasta file information - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing fai file information - e.g. [ id:'test3'] - - meta4: - type: map - description: | - Groovy Map containing false_positives_bed file information - e.g. [ id:'test4'] - - meta5: - type: map - description: | - Groovy Map containing stratification_tsv file information - e.g. [ id:'test5'] - - meta6: - type: map - description: | - Groovy Map containing stratification_beds file information - e.g. [ id:'test6'] - - query_vcf: - type: file - description: VCF/GVCF file to query - pattern: "*.{gvcf,vcf}.gz" - - truth_vcf: - type: file - description: gold standard VCF file - pattern: "*.{gvcf,vcf}.gz" - - regions_bed: - type: file - description: Sparse regions to restrict the analysis to - pattern: "*.bed" - - targets_bed: - type: file - description: Dense regions to restrict the analysis to - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" - - false_positives_bed: - type: file - description: False positive / confident call regions. Calls outside these regions will be labelled as UNK. - pattern: "*.{bed,bed.gz}" - - stratification_tsv: - type: file - description: Stratification file list in TSV format - pattern: "*.tsv" - - stratification_beds: - type: file - description: One or more BED files used for stratification (these should be referenced in the stratification TSV) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_vcf: + type: file + description: VCF/GVCF file to query + pattern: "*.{gvcf,vcf}.gz" + - truth_vcf: + type: file + description: gold standard VCF file + pattern: "*.{gvcf,vcf}.gz" + - regions_bed: + type: file + description: Sparse regions to restrict the analysis to + pattern: "*.bed" + - targets_bed: + type: file + description: Dense regions to restrict the analysis to + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta file information + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing fai file information + e.g. [ id:'test3'] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing false_positives_bed file information + e.g. [ id:'test4'] + - false_positives_bed: + type: file + description: False positive / confident call regions. Calls outside these regions + will be labelled as UNK. + pattern: "*.{bed,bed.gz}" + - - meta5: + type: map + description: | + Groovy Map containing stratification_tsv file information + e.g. [ id:'test5'] + - stratification_tsv: + type: file + description: Stratification file list in TSV format + pattern: "*.tsv" + - - meta6: + type: map + description: | + Groovy Map containing stratification_beds file information + e.g. [ id:'test6'] + - stratification_beds: + type: file + description: One or more BED files used for stratification (these should be + referenced in the stratification TSV) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - summary_csv: - type: file - description: A CSV file containing the summary of the benchmarking - pattern: "*.summary.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.csv": + type: file + description: A CSV file containing the summary of the benchmarking + pattern: "*.summary.csv" - roc_all_csv: - type: file - description: A CSV file containing ROC values for all variants - pattern: "*.roc.all.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.all.csv.gz": + type: file + description: A CSV file containing ROC values for all variants + pattern: "*.roc.all.csv.gz" - roc_indel_locations_csv: - type: file - description: A CSV file containing ROC values for all indels - pattern: "*.roc.Locations.INDEL.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.INDEL.csv.gz": + type: file + description: A CSV file containing ROC values for all indels + pattern: "*.roc.Locations.INDEL.csv.gz" - roc_indel_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all indels that passed all filters - pattern: "*.roc.Locations.INDEL.PASS.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.INDEL.PASS.csv.gz": + type: file + description: A CSV file containing ROC values for all indels that passed all + filters + pattern: "*.roc.Locations.INDEL.PASS.csv.gz" - roc_snp_locations_csv: - type: file - description: A CSV file containing ROC values for all SNPs - pattern: "*.roc.Locations.SNP.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.SNP.csv.gz": + type: file + description: A CSV file containing ROC values for all SNPs + pattern: "*.roc.Locations.SNP.csv.gz" - roc_snp_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all SNPs that passed all filters - pattern: "*.roc.Locations.SNP.PASS.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.SNP.PASS.csv.gz": + type: file + description: A CSV file containing ROC values for all SNPs that passed all filters + pattern: "*.roc.Locations.SNP.PASS.csv.gz" - extended_csv: - type: file - description: A CSV file containing extended info of the benchmarking - pattern: "*.extended.csv" - - metrics_json: - type: file - description: A JSON file containing the run info - pattern: "*.runinfo.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.extended.csv": + type: file + description: A CSV file containing extended info of the benchmarking + pattern: "*.extended.csv" - runinfo: - type: file - description: A JSON file containing the benchmarking metrics - pattern: "*.metrics.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.runinfo.json": + type: file + description: A JSON file containing the benchmarking metrics + pattern: "*.metrics.json.gz" + - metrics_json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json.gz": + type: file + description: A JSON file containing the run info + pattern: "*.runinfo.json" - vcf: - type: file - description: An annotated VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: An annotated VCF + pattern: "*.vcf.gz" - tbi: - type: file - description: The index of the annotated VCF - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: The index of the annotated VCF + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/happy/prepy/meta.yml b/modules/nf-core/happy/prepy/meta.yml index 3e8898fcd68..f308cc889b1 100644 --- a/modules/nf-core/happy/prepy/meta.yml +++ b/modules/nf-core/happy/prepy/meta.yml @@ -11,52 +11,55 @@ tools: documentation: https://github.com/Illumina/hap.py tool_dev_url: https://github.com/Illumina/hap.py licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information for reference fasta - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing sample information for reference fai - e.g. [ id:'test3' ] - - vcf: - type: file - description: VCF file to preprocess - pattern: "*.{vcf,vcf.gz}" - - bed: - type: file - description: BED file - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file to preprocess + pattern: "*.{vcf,vcf.gz}" + - bed: + type: file + description: BED file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information for reference fasta + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information for reference fai + e.g. [ id:'test3' ] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A preprocessed VCF file - pattern: "*.vcf.gz" + - preprocessed_vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Preprocessed VCF file + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/happy/sompy/meta.yml b/modules/nf-core/happy/sompy/meta.yml index 8a04a601739..f7847c4a286 100644 --- a/modules/nf-core/happy/sompy/meta.yml +++ b/modules/nf-core/happy/sompy/meta.yml @@ -1,5 +1,6 @@ name: "happy_sompy" -description: Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations. +description: Hap.py is a tool to compare diploid genotypes at haplotype level. som.py + is a part of hap.py compares somatic variations. keywords: - happy - sompy @@ -14,97 +15,113 @@ tools: documentation: "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md" tool_dev_url: "https://github.com/Illumina/hap.py" licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing fasta file information - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing fai file information - e.g. [ id:'test3'] - - meta4: - type: map - description: | - Groovy Map containing false_positives_bed file information - e.g. [ id:'test4'] - - meta5: - type: map - description: | - Groovy Map containing ambiguous_beds file information - e.g. [ id:'test5'] - - meta6: - type: map - description: | - Groovy Map containing bam file information - e.g. [ id:'test6'] - - query_vcf: - type: file - description: VCF/GVCF file to query - pattern: "*.{gvcf,vcf}.gz" - - truth_vcf: - type: file - description: gold standard VCF file - pattern: "*.{gvcf,vcf}.gz" - - regions_bed: - type: file - description: Sparse regions to restrict the analysis to - pattern: "*.bed" - - targets_bed: - type: file - description: Dense regions to restrict the analysis to - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" - - false_positives_bed: - type: file - description: False positive / confident call regions. Calls outside these regions will be labelled as UNK. - pattern: "*.{bed,bed.gz}" - - stratification_tsv: - type: file - description: Ambiguous region bed file(s) - pattern: "*.bed" - - bams: - type: file - description: one or more BAM files for feature table extraction - pattern: "*.bam" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_vcf: + type: file + description: VCF/GVCF file to query + pattern: "*.{gvcf,vcf}.gz" + - truth_vcf: + type: file + description: gold standard VCF file + pattern: "*.{gvcf,vcf}.gz" + - regions_bed: + type: file + description: Sparse regions to restrict the analysis to + pattern: "*.bed" + - targets_bed: + type: file + description: Dense regions to restrict the analysis to + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta file information + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing fai file information + e.g. [ id:'test3'] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing false_positives_bed file information + e.g. [ id:'test4'] + - false_positives_bed: + type: file + description: False positive / confident call regions. Calls outside these regions + will be labelled as UNK. + pattern: "*.{bed,bed.gz}" + - - meta5: + type: map + description: | + Groovy Map containing ambiguous_beds file information + e.g. [ id:'test5'] + - ambiguous_beds: + type: file + description: Ambiguous regions + pattern: "*.{bed,bed.gz}" + - - meta6: + type: map + description: | + Groovy Map containing bam file information + e.g. [ id:'test6'] + - bams: + type: file + description: one or more BAM files for feature table extraction + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - features: - type: file - description: One or more than one (if AF count is on ) CSV file containing feature information - pattern: "*.features.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.features.csv": + type: file + description: One or more than one (if AF count is on ) CSV file containing feature + information + pattern: "*.features.csv" - metrics: - type: file - description: One or more than one (if AF count is on ) JSON file with metrics - pattern: "*.metrics.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json": + type: file + description: One or more than one (if AF count is on ) JSON file with metrics + pattern: "*.metrics.json" - stats: - type: file - description: One or more than one (if AF count is on ) CSV file with benchmark stats - pattern: "*.stats.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats.csv": + type: file + description: One or more than one (if AF count is on ) CSV file with benchmark + stats + pattern: "*.stats.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/hicap/meta.yml b/modules/nf-core/hicap/meta.yml index 6cc19b0f2d0..2d4245fecc5 100644 --- a/modules/nf-core/hicap/meta.yml +++ b/modules/nf-core/hicap/meta.yml @@ -1,5 +1,6 @@ name: hicap -description: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies +description: Identify cap locus serotype and structure in your Haemophilus influenzae + assemblies keywords: - fasta - serotype @@ -12,46 +13,61 @@ tools: tool_dev_url: https://github.com/scwatts/hicap doi: "10.1128/JCM.00190-19" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA formatted assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - database_dir: - type: directory - description: Optional - Directory containing locus database - pattern: "*/*" - - model_fp: - type: file - description: Optional - Prodigal model to use for gene prediction - pattern: "*.{bin}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA formatted assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - database_dir: + type: directory + description: Optional - Directory containing locus database + pattern: "*/*" + - - model_fp: + type: file + description: Optional - Prodigal model to use for gene prediction + pattern: "*.{bin}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gbk: - type: file - description: GenBank file and cap locus annotations - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gbk": + type: file + description: GenBank file and cap locus annotations + pattern: "*.gbk" - svg: - type: file - description: Visualization of annotated cap locus - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: Visualization of annotated cap locus + pattern: "*.svg" - tsv: - type: file - description: Detailed summary of cap locus annotations - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Detailed summary of cap locus annotations + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/hicexplorer/hicpca/meta.yml b/modules/nf-core/hicexplorer/hicpca/meta.yml index 742b6514851..4fd39addc04 100644 --- a/modules/nf-core/hicexplorer/hicpca/meta.yml +++ b/modules/nf-core/hicexplorer/hicpca/meta.yml @@ -6,40 +6,56 @@ keywords: - hicPCA tools: - "hicexplorer": - description: "Set of programs to process, analyze and visualize Hi-C and capture Hi-C data" + description: "Set of programs to process, analyze and visualize Hi-C and capture + Hi-C data" homepage: "https://hicexplorer.readthedocs.io" documentation: "https://hicexplorer.readthedocs.io" tool_dev_url: "https://github.com/deeptools/HiCExplorer" doi: "10.1038/s41467-017-02525-w" licence: ["GPL v3"] + identifier: biotools:hicexplorer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', bin:50000 ] - - matrix: - type: file - description: HiCExplorer matrix in h5 format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - matrix: + type: file + description: HiCExplorer matrix in h5 format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', bin:50000 ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: Outputs of hicPCA + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - ${prefix}_*: + type: file + description: Outputs of hicPCA - pca1: - type: file - description: PCA1 file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - ${prefix}_pca1.$format: + type: file + description: PCA1 file - pca2: - type: file - description: PCA2 file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - ${prefix}_pca2.$format: + type: file + description: PCA2 file + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/hifiasm/meta.yml b/modules/nf-core/hifiasm/meta.yml index d07c0828174..5f948b798a9 100644 --- a/modules/nf-core/hifiasm/meta.yml +++ b/modules/nf-core/hifiasm/meta.yml @@ -15,81 +15,147 @@ tools: tool_dev_url: https://github.com/chhylp123/hifiasm doi: "10.1038/s41592-020-01056-5" licence: ["MIT"] + identifier: biotools:hifiasm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file with PacBio HiFi reads - pattern: "*.{fastq}" - - paternal_kmer_dump: - type: file - description: Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension. - - maternal_kmer_dump: - type: file - description: Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension. - - use_parental_kmers: - type: boolean - description: A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps. - - hic_read1: - type: file - description: Hi-C data Forward reads. - - hic_read2: - type: file - description: Hi-C data Reverse reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file with PacBio HiFi reads + pattern: "*.{fastq}" + - - paternal_kmer_dump: + type: file + description: Yak kmer dump file for paternal reads (can be used for haplotype + resolution). It can have an arbitrary extension. + - - maternal_kmer_dump: + type: file + description: Yak kmer dump file for maternal reads (can be used for haplotype + resolution). It can have an arbitrary extension. + - - hic_read1: + type: file + description: Hi-C data Forward reads. + - - hic_read2: + type: file + description: Hi-C data Reverse reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - raw_unitigs: - type: file - description: Raw unitigs - pattern: "*.r_utg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.r_utg.gfa": + type: file + description: Raw unitigs + pattern: "*.r_utg.gfa" + - corrected_reads: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ec.bin": + type: file + description: Corrected reads + pattern: "*.ec.bin" + - source_overlaps: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ovlp.source.bin": + type: file + description: Source overlaps + pattern: "*.ovlp.source.bin" + - reverse_overlaps: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ovlp.reverse.bin": + type: file + description: Reverse overlaps + pattern: "*.ovlp.reverse.bin" + - processed_contigs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bp.p_ctg.gfa": + type: file + description: Processed contigs + pattern: "*.bp.p_ctg.gfa" - processed_unitigs: - type: file - description: Processed unitigs - pattern: "*.p_utg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.p_utg.gfa": + type: file + description: Processed unitigs + pattern: "*.p_utg.gfa" - primary_contigs: - type: file - description: Primary contigs - pattern: "*.asm.p_ctg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.asm.p_ctg.gfa": + type: file + description: Primary contigs + pattern: "*.asm.p_ctg.gfa" - alternate_contigs: - type: file - description: Alternative contigs - pattern: "*.asm.a_ctg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.asm.a_ctg.gfa": + type: file + description: Alternative contigs + pattern: "*.asm.a_ctg.gfa" - paternal_contigs: - type: file - description: Paternal contigs - pattern: "*.hap1.p_ctg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap1.p_ctg.gfa": + type: file + description: Paternal contigs + pattern: "*.hap1.p_ctg.gfa" - maternal_contigs: - type: file - description: Maternal contigs - pattern: "*.hap2.p_ctg.gfa" - - corrected_reads: - type: file - description: Corrected reads - pattern: "*.ec.bin" - - source_overlaps: - type: file - description: Source overlaps - pattern: "*.ovlp.source.bin" - - reverse_overlaps: - type: file - description: Reverse overlaps - pattern: "*.ovlp.reverse.bin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap2.p_ctg.gfa": + type: file + description: Maternal contigs + pattern: "*.hap2.p_ctg.gfa" - log: - type: file - description: Stderr log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Stderr log + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sidorov-si" - "@scorreard" diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml index b23eab75b98..d869c5d567b 100644 --- a/modules/nf-core/hisat2/align/meta.yml +++ b/modules/nf-core/hisat2/align/meta.yml @@ -7,58 +7,79 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - index: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - summary: - type: file - description: Aligment log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Aligment log + pattern: "*.log" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Output FastQ file + pattern: "*fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml index 6c28eb21ca6..3272f8e05c0 100644 --- a/modules/nf-core/hisat2/build/meta.yml +++ b/modules/nf-core/hisat2/build/meta.yml @@ -8,53 +8,58 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fa,fasta,fna}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fa,fasta,fna}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - hisat2: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml index 40d77ce0015..c1bdc9e65f8 100644 --- a/modules/nf-core/hisat2/extractsplicesites/meta.yml +++ b/modules/nf-core/hisat2/extractsplicesites/meta.yml @@ -7,35 +7,40 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] + - txt: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - "*.splice_sites.txt": + type: file + description: Splice sites in txt file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{splice_sites.txt}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/hlala/preparegraph/meta.yml b/modules/nf-core/hlala/preparegraph/meta.yml index a2a2fbf9dad..6d3bdce9169 100644 --- a/modules/nf-core/hlala/preparegraph/meta.yml +++ b/modules/nf-core/hlala/preparegraph/meta.yml @@ -13,18 +13,31 @@ tools: tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" licence: ["GPL"] + identifier: "" input: - - graph: - type: directory - description: PRG graph directory + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: directory + description: PRG graph directory output: + - graph: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${graph}: + type: directory + description: PRG graph directory - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - folder: - type: directory - description: Directory containing indexed graph + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mapo9" maintainers: diff --git a/modules/nf-core/hlala/typing/meta.yml b/modules/nf-core/hlala/typing/meta.yml index 20c0844aa1d..e2765acc471 100644 --- a/modules/nf-core/hlala/typing/meta.yml +++ b/modules/nf-core/hlala/typing/meta.yml @@ -1,5 +1,6 @@ name: "hlala_typing" -description: Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph. +description: Performs HLA typing based on a population reference graph and employs + a new linear projection method to align reads to the graph. keywords: - hla - hlala @@ -13,32 +14,108 @@ tools: tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - graph: - type: directory - description: Path to prepared graph with hla-la --acton prepareGraph + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - graph: + type: directory + description: Path to prepared graph with hla-la --acton prepareGraph output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}: + type: file + description: results file + - extraction: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/extraction.bam*: + type: file + description: Extraction BAM file + pattern: "*.bam*" + - extraction_mapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/extraction_mapped.bam: + type: file + description: Extraction mapped BAM file + pattern: "*.bam" + - extraction_unmpapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/extraction_unmapped.bam: + type: file + description: Extraction unmapped BAM file + pattern: "*.bam" + - hla: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/hla/*: + type: file + description: HLA results + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*.fastq: + type: file + description: Fastq file + pattern: "*.fastq" + - reads_per_level: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/reads_per_level.txt: + type: file + description: Reads per level + pattern: "*.txt" + - remapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/remapped_with_a.bam*: + type: file + description: Remapped BAM file + pattern: "*.bam*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - folder: - type: directory - description: Folder containing the HLA typing output + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mapo9" maintainers: diff --git a/modules/nf-core/hmmcopy/gccounter/meta.yml b/modules/nf-core/hmmcopy/gccounter/meta.yml index 7fb6990136c..031a4127d1d 100644 --- a/modules/nf-core/hmmcopy/gccounter/meta.yml +++ b/modules/nf-core/hmmcopy/gccounter/meta.yml @@ -1,39 +1,44 @@ name: hmmcopy_gccounter -description: gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference +description: gcCounter function from HMMcopy utilities, used to generate GC content + in non-overlapping windows from a fasta reference keywords: - hmmcopy - gccounter - cnv tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: wig file containing gc content of each window of the genome - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: wig file containing gc content of each window of the genome + pattern: "*.wig" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" - "@adamrtalbot" diff --git a/modules/nf-core/hmmcopy/generatemap/meta.yml b/modules/nf-core/hmmcopy/generatemap/meta.yml index 89c77360076..cb648763d5e 100644 --- a/modules/nf-core/hmmcopy/generatemap/meta.yml +++ b/modules/nf-core/hmmcopy/generatemap/meta.yml @@ -1,39 +1,45 @@ name: hmmcopy_generatemap -description: Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all. +description: Perl script (generateMap.pl) generates the mappability of a genome given + a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time + on large genomes, is not parallelised at all. keywords: - hmmcopy - mapcounter - mappability tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigwig: - type: file - description: bigwig file containing the mappability of the genome - pattern: "*.bw" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bw": + type: file + description: bigwig file containing the mappability of the genome + pattern: "*.bw" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" - "@adamrtalbot" diff --git a/modules/nf-core/hmmcopy/mapcounter/meta.yml b/modules/nf-core/hmmcopy/mapcounter/meta.yml index 4345d51fc60..8a8132ee0ea 100644 --- a/modules/nf-core/hmmcopy/mapcounter/meta.yml +++ b/modules/nf-core/hmmcopy/mapcounter/meta.yml @@ -1,40 +1,46 @@ name: hmmcopy_mapcounter -description: mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file +description: mapCounter function from HMMcopy utilities, used to generate mappability + in non-overlapping windows from a bigwig file keywords: - hmmcopy - mapcounter - cnv tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bigwig: - type: file - description: BigWig file with the mappability score of the genome, for instance made with generateMap function. - pattern: "*.wig" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bigwig: + type: file + description: BigWig file with the mappability score of the genome, for instance + made with generateMap function. + pattern: "*.wig" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: wig file containing mappability of each window of the genome - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: wig file containing mappability of each window of the genome + pattern: "*.wig" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/hmmcopy/readcounter/meta.yml b/modules/nf-core/hmmcopy/readcounter/meta.yml index 511a0987f2d..a55f05edf41 100644 --- a/modules/nf-core/hmmcopy/readcounter/meta.yml +++ b/modules/nf-core/hmmcopy/readcounter/meta.yml @@ -1,40 +1,50 @@ name: hmmcopy_readcounter -description: readCounter function from HMMcopy utilities, used to generate read in windows +description: readCounter function from HMMcopy utilities, used to generate read in + windows keywords: - hmmcopy - readcounter - cnv tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: A wig file with the number of reads lying within each window in each chromosome - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: A wig file with the number of reads lying within each window in + each chromosome + pattern: "*.wig" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/hmmer/eslalimask/meta.yml b/modules/nf-core/hmmer/eslalimask/meta.yml index 4a3d84e1bd7..4d16ca5de09 100644 --- a/modules/nf-core/hmmer/eslalimask/meta.yml +++ b/modules/nf-core/hmmer/eslalimask/meta.yml @@ -11,76 +11,87 @@ tools: documentation: http://hmmer.org/documentation.html doi: "10.1371/journal.pcbi.1002195" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - unmaskedaln: - type: file - description: multiple sequence alignment, Stockholm or other formats - pattern: "*" - - fmask_rf: - type: boolean - description: Flag to output optional file with final mask of non-gap RF len - - fmask_all: - type: boolean - description: Flag to output optional file with final mask of full aln len - - gmask_rf: - type: boolean - description: Flag to output optional file gap-based 0/1 mask of non-gap RF len - - gmask_all: - type: boolean - description: Flag to output optional file gap-based 0/1 mask of full aln len - - pmask_rf: - type: boolean - description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len - - pmask_all: - type: boolean - description: Flag to output optional file with PP-based 0/1 mask of full aln len - - maskfile: - type: file - description: mask file, see program documentation - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - unmaskedaln: + type: file + description: multiple sequence alignment, Stockholm or other formats + pattern: "*" + - fmask_rf: + type: boolean + description: Flag to output optional file with final mask of non-gap RF len + - fmask_all: + type: boolean + description: Flag to output optional file with final mask of full aln len + - gmask_rf: + type: boolean + description: Flag to output optional file gap-based 0/1 mask of non-gap RF len + - gmask_all: + type: boolean + description: Flag to output optional file gap-based 0/1 mask of full aln len + - pmask_rf: + type: boolean + description: Flag to output optional file with PP-based 0/1 mask of non-gap + RF len + - pmask_all: + type: boolean + description: Flag to output optional file with PP-based 0/1 mask of full aln + len + - - maskfile: + type: file + description: mask file, see program documentation + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maskedaln: - type: file - description: Masked alignment in gzipped Stockholm format - pattern: "*.sthlm.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.masked.sthlm.gz": + type: file + description: Masked alignment in gzipped Stockholm format + pattern: "*.sthlm.gz" - fmask_rf: - type: file - description: File with final mask of non-gap RF len - pattern: "*.fmask-rf.gz" + - "*.fmask-rf.gz": + type: file + description: File with final mask of non-gap RF len + pattern: "*.fmask-rf.gz" - fmask_all: - type: file - description: File with final mask of full aln len - pattern: "*.fmask-all.gz" + - "*.fmask-all.gz": + type: file + description: File with final mask of full aln len + pattern: "*.fmask-all.gz" - gmask_rf: - type: file - description: File with gap-based 0/1 mask of non-gap RF len - pattern: "*.gmask-rf.gz" + - "*.gmask-rf.gz": + type: file + description: File with gap-based 0/1 mask of non-gap RF len + pattern: "*.gmask-rf.gz" - gmask_all: - type: file - description: File with gap-based 0/1 mask of full aln len - pattern: "*.gmask-all.gz" + - "*.gmask-all.gz": + type: file + description: File with gap-based 0/1 mask of full aln len + pattern: "*.gmask-all.gz" - pmask_rf: - type: file - description: File with PP-based 0/1 mask of non-gap RF len - pattern: "*.pmask-rf.gz" + - "*.pmask-rf.gz": + type: file + description: File with PP-based 0/1 mask of non-gap RF len + pattern: "*.pmask-rf.gz" - pmask_all: - type: file - description: File with PP-based 0/1 mask of full aln len - pattern: "*.pmask-all.gz" + - "*.pmask-all.gz": + type: file + description: File with PP-based 0/1 mask of full aln len + pattern: "*.pmask-all.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/eslreformat/meta.yml b/modules/nf-core/hmmer/eslreformat/meta.yml index 009e35873a7..e2104034948 100644 --- a/modules/nf-core/hmmer/eslreformat/meta.yml +++ b/modules/nf-core/hmmer/eslreformat/meta.yml @@ -1,5 +1,7 @@ name: "hmmer_eslreformat" -description: reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values. +description: reformats sequence files, see HMMER documentation for details. The module + requires that the format is specified in ext.args in a config file, and that this + comes last. See the tools help for possible values. keywords: - sort - hmmer @@ -11,30 +13,33 @@ tools: documentation: http://hmmer.org/documentation.html doi: "10.1371/journal.pcbi.1002195" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - seqfile: - type: file - description: Sequences, aligned or not, in any supported format - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - seqfile: + type: file + description: Sequences, aligned or not, in any supported format + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - seqreformated: - type: file - description: Reformated sequence file - pattern: "*.*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.*.gz": + type: file + description: Reformated sequence file + pattern: "*.*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml index df6a7b3c4fe..366cf4f5a58 100644 --- a/modules/nf-core/hmmer/hmmalign/meta.yml +++ b/modules/nf-core/hmmer/hmmalign/meta.yml @@ -1,5 +1,6 @@ name: hmmer_hmmalign -description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile +description: hmmalign from the HMMER suite aligns a number of sequences to an HMM + profile keywords: - alignment - HMMER @@ -13,34 +14,37 @@ tools: documentation: http://hmmer.org/documentation.html doi: "10.1371/journal.pcbi.1002195" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fasta: - type: file - description: Amino acid or nucleotide gzipped compressed fasta file - pattern: "*.{fna.gz,faa.gz,fasta.gz,fa.gz}" - - hmm: - type: file - description: A gzipped HMM file - pattern: "*.hmm.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fasta: + type: file + description: Amino acid or nucleotide gzipped compressed fasta file + pattern: "*.{fna.gz,faa.gz,fasta.gz,fa.gz}" + - - hmm: + type: file + description: A gzipped HMM file + pattern: "*.hmm.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sthlm: - type: file - description: Multiple alignment in gzipped Stockholm format - pattern: "*.sthlm.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sthlm.gz": + type: file + description: Multiple alignment in gzipped Stockholm format + pattern: "*.sthlm.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" - "@jfy133" diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml index fb9d5083001..9be14fe9a8a 100644 --- a/modules/nf-core/hmmer/hmmbuild/meta.yml +++ b/modules/nf-core/hmmer/hmmbuild/meta.yml @@ -14,29 +14,42 @@ tools: tool_dev_url: "https://github.com/EddyRivasLab/hmmer" doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment: - type: file - description: multiple sequence alignment in fasta, clustal, stockholm or phylip format - pattern: "*" - - mxfile: - type: file - description: read substitution score matrix, for use when building profiles from single sequences (--singlemx option) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: multiple sequence alignment in fasta, clustal, stockholm or phylip + format + pattern: "*" + - - mxfile: + type: file + description: read substitution score matrix, for use when building profiles + from single sequences (--singlemx option) + pattern: "*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hmm: - type: file - description: Gzipped HMM file - pattern: "*.{hmm.gz}" + - meta: + type: file + description: Gzipped HMM file + pattern: "*.{hmm.gz}" + - "*.hmm.gz": + type: file + description: Gzipped HMM file + pattern: "*.{hmm.gz}" + - hmmbuildout: + - "*.hmmbuild.txt": + type: file + description: HMM build output + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmfetch/meta.yml b/modules/nf-core/hmmer/hmmfetch/meta.yml index 82668f68eb5..20616210dd4 100644 --- a/modules/nf-core/hmmer/hmmfetch/meta.yml +++ b/modules/nf-core/hmmer/hmmfetch/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "hmmer_hmmfetch" description: extract hmm from hmm database file or create index for hmm database @@ -15,41 +14,55 @@ tools: tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - hmm: - type: file - description: HMM file with multiple HMM models - pattern: "*.hmm" - - key: - type: string - description: Name of HMM to extract. Specify either this or keyfile. If none is specified, an index will be built. - - keyfile: - type: file - description: File containing list of HMM models to extract. Specify either this or key. If none is specified, an index will be built. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - hmm: + type: file + description: HMM file with multiple HMM models + pattern: "*.hmm" + - - key: + type: string + description: Name of HMM to extract. Specify either this or keyfile. If none + is specified, an index will be built. + - - keyfile: + type: file + description: File containing list of HMM models to extract. Specify either this + or key. If none is specified, an index will be built. + pattern: "*.txt" + - - index: + type: file + description: Index file from another run. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hmm: - type: file - description: File with one or more HMM models - pattern: "selection.hmm" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hmm": + type: file + description: File with one or more HMM models + pattern: "selection.hmm" - index: - type: file - description: Index for HMM database. Created if neither key nor keyfile is specified. - pattern: "*.ssi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ssi": + type: file + description: Index for HMM database. Created if neither key nor keyfile is specified. + pattern: "*.ssi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmrank/environment.yml b/modules/nf-core/hmmer/hmmrank/environment.yml index 653e9ea1d51..fbce96e2508 100644 --- a/modules/nf-core/hmmer/hmmrank/environment.yml +++ b/modules/nf-core/hmmer/hmmrank/environment.yml @@ -4,8 +4,8 @@ channels: dependencies: - conda-forge::r-base=4.2.3 - - conda-forge::r-stringi=1.8.4 - - conda-forge::r-stringr=1.5.1 - conda-forge::r-data.table=1.14.8 - conda-forge::r-dtplyr=1.3.1 + - conda-forge::r-stringi=1.8.4 + - conda-forge::r-stringr=1.5.1 - conda-forge::r-tidyverse=2.0.0 diff --git a/modules/nf-core/hmmer/hmmrank/meta.yml b/modules/nf-core/hmmer/hmmrank/meta.yml index 428b280b8cb..96f9536187c 100644 --- a/modules/nf-core/hmmer/hmmrank/meta.yml +++ b/modules/nf-core/hmmer/hmmrank/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "hmmer_hmmrank" description: R script that scores output from multiple runs of hmmer/hmmsearch @@ -14,11 +13,13 @@ tools: tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" - "R": description: "A Language and Environment for Statistical Computing" homepage: https://www.r-project.org/ documentation: https://www.r-project.org/ licence: ["GPL v2"] + identifier: "" - "Tidyverse": description: "Tidyverse: R packages for data science" homepage: https://www.tidyverse.org/ @@ -26,37 +27,36 @@ tools: tool_dev_url: https://github.com/tidyverse doi: "10.21105/joss.01686" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - tblouts: - type: file - description: table outputs from hmmsearch - pattern: "*.tsv.gz" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tblouts: + type: file + description: table outputs from hmmsearch + pattern: "*.tsv.gz" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - hmmrank: - type: file - description: TSV file with ranked hmmer results - pattern: "*.hmmrank.tsv.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.hmmrank.tsv.gz": + type: file + description: TSV file with ranked hmmer results + pattern: "*.hmmrank.tsv.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmsearch/meta.yml b/modules/nf-core/hmmer/hmmsearch/meta.yml index 39893c3bef4..0e0786591d3 100644 --- a/modules/nf-core/hmmer/hmmsearch/meta.yml +++ b/modules/nf-core/hmmer/hmmsearch/meta.yml @@ -13,55 +13,79 @@ tools: tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - hmmfile: - type: file - description: One or more HMM profiles created with hmmbuild - pattern: "*.{hmm,hmm.gz}" - - seqdb: - type: file - description: Database of sequences in FASTA format - pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" - - write_align: - type: boolean - description: Flag to save optional alignment output. Specify with 'true' to save. - - write_target: - type: boolean - description: Flag to save optional per target summary. Specify with 'true' to save. - - write_domain: - type: boolean - description: Flag to save optional per domain summary. Specify with 'true' to save. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - hmmfile: + type: file + description: One or more HMM profiles created with hmmbuild + pattern: "*.{hmm,hmm.gz}" + - seqdb: + type: file + description: Database of sequences in FASTA format + pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" + - write_align: + type: boolean + description: Flag to save optional alignment output. Specify with 'true' to + save. + - write_target: + type: boolean + description: Flag to save optional per target summary. Specify with 'true' to + save. + - write_domain: + type: boolean + description: Flag to save optional per domain summary. Specify with 'true' to + save. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Human readable output summarizing hmmsearch results - pattern: "*.{txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Human readable output summarizing hmmsearch results + pattern: "*.{txt.gz}" - alignments: - type: file - description: Optional multiple sequence alignment (MSA) in Stockholm format - pattern: "*.{sto.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sto.gz": + type: file + description: Optional multiple sequence alignment (MSA) in Stockholm format + pattern: "*.{sto.gz}" - target_summary: - type: file - description: Optional tabular (space-delimited) summary of per-target output - pattern: "*.{tbl.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbl.gz": + type: file + description: Optional tabular (space-delimited) summary of per-target output + pattern: "*.{tbl.gz}" - domain_summary: - type: file - description: Optional tabular (space-delimited) summary of per-domain output - pattern: "*.{domtbl.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.domtbl.gz": + type: file + description: Optional tabular (space-delimited) summary of per-domain output + pattern: "*.{domtbl.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/hmtnote/annotate/meta.yml b/modules/nf-core/hmtnote/annotate/meta.yml index 4ab41831359..661d5cde094 100644 --- a/modules/nf-core/hmtnote/annotate/meta.yml +++ b/modules/nf-core/hmtnote/annotate/meta.yml @@ -1,5 +1,6 @@ name: hmtnote_annotate -description: Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline +description: Human mitochondrial variants annotation using HmtVar. Contains .plk file + with annotation, so can be run offline keywords: - hmtnote - mitochondria @@ -11,28 +12,31 @@ tools: documentation: https://hmtnote.readthedocs.io/en/latest/usage.html doi: "10.1101/600619" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - - vcf: - type: file - description: vcf file - pattern: "*.vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + - vcf: + type: file + description: vcf file + pattern: "*.vcf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: annotated vcf - pattern: "*_annotated.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + - "*_annotated.vcf": + type: file + description: annotated vcf + pattern: "*_annotated.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sysbiocoder" maintainers: diff --git a/modules/nf-core/homer/annotatepeaks/meta.yml b/modules/nf-core/homer/annotatepeaks/meta.yml index 0d76caba8d6..37a8ea09597 100644 --- a/modules/nf-core/homer/annotatepeaks/meta.yml +++ b/modules/nf-core/homer/annotatepeaks/meta.yml @@ -11,42 +11,50 @@ tools: documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: The peak files in bed format - pattern: "*.bed" - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - gtf: - type: file - description: GTF file of reference genome - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peak: + type: file + description: Peak file to annotate + - - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - gtf: + type: file + description: GTF file of reference genome + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - annotated_peaks: - type: file - description: The annotated peaks - pattern: "*annotatePeaks.txt" - - annotation_stats: - type: file - description: the annStats file output from -annStats parameter - pattern: "*annStats.txt" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annotatePeaks.txt": + type: file + description: Annotated peaks in txt file + pattern: "*annotatePeaks.txt" + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annStats.txt": + type: file + description: Annotation statistics in txt file + pattern: "*annStats.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/homer/findpeaks/meta.yml b/modules/nf-core/homer/findpeaks/meta.yml index 286032c3090..fdcc1055703 100644 --- a/modules/nf-core/homer/findpeaks/meta.yml +++ b/modules/nf-core/homer/findpeaks/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "http://homer.ucsd.edu/homer/ngs/peaks.html" doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tagDir: - type: directory - description: "The 'Tag Directory'" - pattern: "tagDir" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tagDir: + type: directory + description: "The 'Tag Directory'" + pattern: "tagDir" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: The found peaks - pattern: "*.peaks.txt" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.peaks.txt": + type: file + description: "Peaks in txt file" + pattern: "*.peaks.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/homer/maketagdirectory/environment.yml b/modules/nf-core/homer/maketagdirectory/environment.yml index e1a60845799..9864257f102 100644 --- a/modules/nf-core/homer/maketagdirectory/environment.yml +++ b/modules/nf-core/homer/maketagdirectory/environment.yml @@ -1,10 +1,11 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::homer=4.11 - - bioconda::samtools=1.11 - - conda-forge::r-base=4.0.2 - bioconda::bioconductor-deseq2=1.30.0 - bioconda::bioconductor-edger=3.32.0 + - bioconda::homer=4.11 + - bioconda::samtools=1.11 - conda-forge::perl=5.26.2 + - conda-forge::r-base=4.0.2 diff --git a/modules/nf-core/homer/maketagdirectory/meta.yml b/modules/nf-core/homer/maketagdirectory/meta.yml index 8b240411b81..1e3b9c45bdb 100644 --- a/modules/nf-core/homer/maketagdirectory/meta.yml +++ b/modules/nf-core/homer/maketagdirectory/meta.yml @@ -12,6 +12,7 @@ tools: documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer - samtools: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -21,6 +22,7 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:homer - DESeq2: description: | Differential gene expression analysis based on the negative binomial distribution @@ -29,6 +31,7 @@ tools: tool_dev_url: "https://github.com/mikelove/DESeq2" doi: 10.18129/B9.bioc.DESeq2 licence: ["LGPL-3.0-or-later"] + identifier: biotools:homer - edgeR: description: | Empirical Analysis of Digital Gene Expression Data in R @@ -37,38 +40,47 @@ tools: tool_dev_url: "https://git.bioconductor.org/packages/edgeR" doi: 10.18129/B9.bioc.edgeR licence: ["GPL >=2"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/BED/SAM file - pattern: "*.{bam,bed,sam}" - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/BED/SAM file + pattern: "*.{bam,bed,sam}" + - - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tagdir: - type: directory - description: The "Tag Directory" - pattern: "*_tagdir" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tagdir": + type: directory + description: The "Tag Directory" + pattern: "*_tagdir" - taginfo: - type: directory - description: The tagInfo.txt included to ensure there's proper output - pattern: "*_tagdir/tagInfo.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tagdir/tagInfo.txt": + type: directory + description: The tagInfo.txt included to ensure there's proper output + pattern: "*_tagdir/tagInfo.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/homer/makeucscfile/meta.yml b/modules/nf-core/homer/makeucscfile/meta.yml index 808c310f131..6271f46618a 100644 --- a/modules/nf-core/homer/makeucscfile/meta.yml +++ b/modules/nf-core/homer/makeucscfile/meta.yml @@ -11,30 +11,33 @@ tools: documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tagDir: - type: directory - description: "The 'Tag Directory'" - pattern: "tagDir" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tagDir: + type: directory + description: "The 'Tag Directory'" + pattern: "tagDir" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedGraph: - type: file - description: The UCSC bed graph - pattern: "*.bedGraph.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph.gz": + type: file + description: The UCSC bed graph + pattern: "*.bedGraph.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/homer/pos2bed/meta.yml b/modules/nf-core/homer/pos2bed/meta.yml index f870fa7175a..5fc5f9b1db4 100644 --- a/modules/nf-core/homer/pos2bed/meta.yml +++ b/modules/nf-core/homer/pos2bed/meta.yml @@ -13,30 +13,32 @@ tools: tool_dev_url: "http://homer.ucsd.edu/homer/ngs/miscellaneous.html" doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tagDir: - type: directory - description: "The 'Tag Directory'" - pattern: "tagDir" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peaks: + type: file + description: Peak file to convert to BED format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/hpsuissero/meta.yml b/modules/nf-core/hpsuissero/meta.yml index a171da1477c..28f919cb2e6 100644 --- a/modules/nf-core/hpsuissero/meta.yml +++ b/modules/nf-core/hpsuissero/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/jimmyliu1326/HpsuisSero tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited serotype prediction - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited serotype prediction + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/htseq/count/meta.yml b/modules/nf-core/htseq/count/meta.yml index 9373e680e02..7e30fe0063e 100644 --- a/modules/nf-core/htseq/count/meta.yml +++ b/modules/nf-core/htseq/count/meta.yml @@ -1,4 +1,3 @@ ---- name: "htseq_count" description: count how many reads map to each feature keywords: @@ -8,44 +7,52 @@ keywords: - annotation tools: - "htseq/count": - description: "HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments." + description: "HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments." homepage: "https://htseq.readthedocs.io/en/latest/" documentation: "https://htseq.readthedocs.io/en/latest/index.html" doi: "10.1093/bioinformatics/btu638" licence: ["GPL v3"] + identifier: biotools:htseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - .gtf file information - e.g. `[ id:'test' ]` - - input: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: Contains indexed bam file - pattern: "*.bai" - - gtf: - type: file - description: Contains the features in the GTF format - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: Contains indexed bam file + pattern: "*.bai" + - - meta2: + type: map + description: | + .gtf file information + e.g. `[ id:'test' ]` + - gtf: + type: file + description: Contains the features in the GTF format + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - txt: - type: file - description: File containing feature counts output - pattern: ".txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: File containing feature counts output + pattern: ".txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zehrahazalsezer" maintainers: diff --git a/modules/nf-core/htsnimtools/vcfcheck/meta.yml b/modules/nf-core/htsnimtools/vcfcheck/meta.yml index 19304f7a1a2..c34ecaa9057 100644 --- a/modules/nf-core/htsnimtools/vcfcheck/meta.yml +++ b/modules/nf-core/htsnimtools/vcfcheck/meta.yml @@ -1,6 +1,7 @@ ---- name: "htsnimtools_vcfcheck" -description: This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants. +description: This tools takes a background VCF, such as gnomad, that has full genome + (though in some cases, users will instead want whole exome) coverage and uses that + as an expectation of variants. keywords: - validation - check @@ -12,50 +13,52 @@ tools: documentation: "https://github.com/brentp/hts-nim-tools" tool_dev_url: "https://github.com/brentp/hts-nim-tools" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: The query VCF file - pattern: "*.{vcf,vcf.gz,bcf}" - - tbi: - type: file - description: The index of the query VCF file - pattern: "*.{tbi}" - - meta2: - type: map - description: | - Groovy Map containing background VCF information - e.g. `[ id:'sample1', single_end:false ]` - - background_vcf: - type: file - description: The background VCF file - pattern: "*.{vcf,vcf.gz,bcf}" - - background_tbi: - type: file - description: The index of the background VCF file - pattern: "*.{tbi}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: The query VCF file + pattern: "*.{vcf,vcf.gz,bcf}" + - tbi: + type: file + description: The index of the query VCF file + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing background VCF information + e.g. `[ id:'sample1', single_end:false ]` + - background_vcf: + type: file + description: The background VCF file + pattern: "*.{vcf,vcf.gz,bcf}" + - background_tbi: + type: file + description: The index of the background VCF file + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file comparing the variant count of each region in the query VCF and background VCF - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: A tab-delimited file comparing the variant count of each region + in the query VCF and background VCF + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/humid/meta.yml b/modules/nf-core/humid/meta.yml index c8548ea3a7a..e5fa28df0b8 100644 --- a/modules/nf-core/humid/meta.yml +++ b/modules/nf-core/humid/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "humid" -description: HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs. +description: HUMID is a tool to quickly and easily remove duplicate reads from FastQ + files, with or without UMIs. keywords: - umi - fastq @@ -15,59 +15,72 @@ tools: documentation: "https://humid.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/jfjlaros/HUMID" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - reads: - type: file - description: Fastq file(s) to deduplicate - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - umis: - type: file - description: Fastq file(s) containing UMIs - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Fastq file(s) to deduplicate + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - umi_file: + type: file + description: UMI file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.log: + type: file + description: Log file of humid, containing progress and errors + pattern: "*.log" - dedup: - type: file - description: Deduplicated Fastq file(s) - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_dedup*.fastq.gz": + type: file + description: Deduplicated Fastq file(s) + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - annotated: - type: file - description: Annotated Fastq file(s) - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_annotated*.fastq.gz": + type: file + description: Annotated Fastq file(s) + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - stats: - type: directory - description: Directory containg statistics file, use for multiqc. - pattern: "${prefix}/" - - - log: - type: file - description: Log file of humid, containing progress and errors - pattern: "*.log" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}: + type: directory + description: Directory containg statistics file, use for multiqc. + pattern: "${prefix}/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/hypo/meta.yml b/modules/nf-core/hypo/meta.yml index 002b418f5c8..f9887f08c43 100644 --- a/modules/nf-core/hypo/meta.yml +++ b/modules/nf-core/hypo/meta.yml @@ -13,47 +13,51 @@ tools: tool_dev_url: "https://github.com/kensung-lab/hypo" doi: "10.1101/2019.12.19.882506" licence: ["GPL v3"] + identifier: biotools:hypo input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Short reads file(s). In fastq or fasta, compressed or uncompressed - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sr_bam: - type: file - description: Aligned short-read BAM/SAM file. Must have CIGAR information. - pattern: "*.{bam,sam}" - - draft: - type: file - description: Input (fasta) file containing draft contig assembly - - genome_size: - type: string - description: Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g - - reads_coverage: - type: integer - description: Appprimate depth of coverage of short reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sr_bam: + type: file + description: Aligned short-read BAM/SAM file. Must have CIGAR information. + pattern: "*.{bam,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Short reads file(s). In fastq or fasta, compressed or uncompressed + - - draft: + type: file + description: Input (fasta) file containing draft contig assembly + - - genome_size: + type: string + description: Estimated size of the genome. Number or nts or use suffixes k/m/g, + e.g. 5m, 3.2g + - - reads_coverage: + type: integer + description: Appprimate depth of coverage of short reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Polished assembly fasta file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Polished assembly fasta file + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@remiolsen" maintainers: diff --git a/modules/nf-core/ichorcna/createpon/meta.yml b/modules/nf-core/ichorcna/createpon/meta.yml index d5fa233e39e..9d0cb18c187 100644 --- a/modules/nf-core/ichorcna/createpon/meta.yml +++ b/modules/nf-core/ichorcna/createpon/meta.yml @@ -1,5 +1,7 @@ name: ichorcna_createpon -description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals +description: ichorCNA is an R package for calculating copy number alteration from + (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This + module generates a panel of normals keywords: - ichorcna - cnv @@ -9,51 +11,61 @@ keywords: - panel_of_normals tools: - ichorcna: - description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. + description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole + genome sequencing. homepage: https://github.com/broadinstitute/ichorCNA documentation: https://github.com/broadinstitute/ichorCNA/wiki tool_dev_url: https://github.com/broadinstitute/ichorCNA doi: "10.1038/s41467-017-00965-y" licence: ["GPL v3"] + identifier: "" input: - - wigs: - type: file - description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals. - pattern: "*.{wig}" - - gc_wig: - type: file - description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window - pattern: "*.{wig}" - - map_wig: - type: file - description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window - pattern: "*.{wig}" - - centromere: - type: file - description: Text file giving centromere locations of each genome, to exclude these windows - pattern: "*.{txt}" - - rep_time_wig: - type: file - description: Replication/timing .wig file. - pattern: "*.{wig}" - - exons: - type: file - description: BED file for exon regions to annotate CNA regions. - pattern: "*.{bed}" - + - - wigs: + type: file + description: Any number of hmmcopy/readCounter processed .wig files giving the + number of reads in the sample, in each genomic window. These will be averaged + over to generate the panel of normals. + pattern: "*.{wig}" + - - gc_wig: + type: file + description: hmmcopy/gcCounter processed .wig file giving the gc content in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - map_wig: + type: file + description: hmmcopy/mapCounter processed .wig file giving the mapability in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - centromere: + type: file + description: Text file giving centromere locations of each genome, to exclude + these windows + pattern: "*.{txt}" + - - rep_time_wig: + type: file + description: Replication/timing .wig file. + pattern: "*.{wig}" + - - exons: + type: file + description: BED file for exon regions to annotate CNA regions. + pattern: "*.{bed}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rds: - type: file - description: R data file (.rds) containing panel of normals data, medians of each bin. - pattern: "*.rds" + - ${prefix}*.rds: + type: file + description: R data file (.rds) containing panel of normals data, medians of + each bin. + pattern: "*.rds" - txt: - type: file - description: Text file containing panel of normals data, medians of each bin. - pattern: "*.txt" + - ${prefix}*.txt: + type: file + description: Text file containing panel of normals data, medians of each bin. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ichorcna/run/meta.yml b/modules/nf-core/ichorcna/run/meta.yml index ef4a31c889b..aeca09df6cb 100644 --- a/modules/nf-core/ichorcna/run/meta.yml +++ b/modules/nf-core/ichorcna/run/meta.yml @@ -1,5 +1,6 @@ name: ichorcna_run -description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA +description: ichorCNA is an R package for calculating copy number alteration from + (low-pass) whole genome sequencing, particularly for use in cell-free DNA keywords: - ichorcna - cnv @@ -8,111 +9,146 @@ keywords: - wgs tools: - ichorcna: - description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. + description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole + genome sequencing. homepage: https://github.com/broadinstitute/ichorCNA documentation: https://github.com/broadinstitute/ichorCNA/wiki tool_dev_url: https://github.com/broadinstitute/ichorCNA doi: "10.1038/s41467-017-00965-y" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - - wig: - type: file - description: hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window - pattern: "*.{wig}" - - - gc_wig: - type: file - description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window - pattern: "*.{wig}" - - - map_wig: - type: file - description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window - pattern: "*.{wig}" - - - normal_wig: - type: file - description: hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window - pattern: "*.{wig}" - - - normal_background: - type: file - description: Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc. - pattern: "*.{rds}" - - - centromere: - type: file - description: Text file giving centromere locations of each genome, to exclude these windows - pattern: "*.{txt}" - - - rep_time_wig: - type: file - description: Replication/timing .wig file. - pattern: "*.{wig}" - - - exons: - type: file - description: BED file for exon regions to annotate CNA regions. - pattern: "*.{bed}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - wig: + type: file + description: hmmcopy/readCounter processed .wig file giving the number of reads + in the sample, in each genomic window + pattern: "*.{wig}" + - - gc_wig: + type: file + description: hmmcopy/gcCounter processed .wig file giving the gc content in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - map_wig: + type: file + description: hmmcopy/mapCounter processed .wig file giving the mapability in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - normal_wig: + type: file + description: hmmcopy/readCounter processed .wig file giving the number of reads + in the normal sample, in each genomic window + pattern: "*.{wig}" + - - normal_background: + type: file + description: Panel of normals data, generated by calling ichorCNA on a set of + normal samples with the same window size etc. + pattern: "*.{rds}" + - - centromere: + type: file + description: Text file giving centromere locations of each genome, to exclude + these windows + pattern: "*.{txt}" + - - rep_time_wig: + type: file + description: Replication/timing .wig file. + pattern: "*.{wig}" + - - exons: + type: file + description: BED file for exon regions to annotate CNA regions. + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - + - rdata: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.RData: + type: file + description: RData file containing all the intermediate R objects + pattern: "*.{cng.seg}" - seg: - type: file - description: Predicted copy number variation per segment - pattern: "*.{seg}" - - - seg_txt: - type: file - description: Predicted copy number variation per segment - pattern: "*.{seg.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.seg: + type: file + description: Predicted copy number variation per segment + pattern: "*.{seg}" - cna_seg: - type: file - description: Predicted copy number variation per segment - pattern: "*.{cng.seg}" - - - ichorcna_params: - type: file - description: A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc - pattern: "*.{params.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.cna.seg: + type: file + description: Predicted copy number variation per segment + pattern: "*.{cng.seg}" + - seg_txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.seg.txt: + type: file + description: Predicted copy number variation per segment + pattern: "*.{seg.txt}" - corrected_depth: - type: file - description: A text file with corrected depth per bin - pattern: "*.{params.txt}" - - - genome_plot: - type: file - description: A plot with the best-fit genome-wide CNV data - pattern: "*.{genomeWide.pdf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.correctedDepth.txt: + type: file + description: A text file with corrected depth per bin + pattern: "*.{params.txt}" + - ichorcna_params: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.params.txt: + type: file + description: A text file showing the values that ichorCNA has estimated for + tumour fraction, ploidy etc + pattern: "*.{params.txt}" - plots: - type: file - description: Plots with e.g. individual chromosomes and different considered ploidy - pattern: "*.{pdf}" - - - rdata: - type: file - description: RData file containing all the intermediate R objects - pattern: "*.{cng.seg}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/*.pdf: + type: file + description: Plots with e.g. individual chromosomes and different considered + ploidy + pattern: "*.{pdf}" + - genome_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "**/${prefix}_genomeWide.pdf": + type: file + description: A plot with the best-fit genome-wide CNV data + pattern: "*.{genomeWide.pdf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" - "@adamrtalbot" diff --git a/modules/nf-core/icountmini/metagene/meta.yml b/modules/nf-core/icountmini/metagene/meta.yml index 1ed324a8a21..78a833530c1 100644 --- a/modules/nf-core/icountmini/metagene/meta.yml +++ b/modules/nf-core/icountmini/metagene/meta.yml @@ -1,6 +1,6 @@ ---- name: icountmini_metagene -description: Plot a metagene of cross-link events/sites around various transcriptomic landmarks. +description: Plot a metagene of cross-link events/sites around various transcriptomic + landmarks. keywords: - iCLIP - gtf @@ -11,33 +11,36 @@ tools: homepage: https://icount.readthedocs.io/en/latest/ documentation: https://icount.readthedocs.io/en/latest/ licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - - segmentation: - type: file - description: A iCount segmentation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + - - segmentation: + type: file + description: A iCount segmentation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tsv: - type: file - description: Metagene table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - metagene_*/*plot_data.tsv: + type: file + description: Metagene table + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/peaks/meta.yml b/modules/nf-core/icountmini/peaks/meta.yml index 2736ebfda90..fceb24d7040 100644 --- a/modules/nf-core/icountmini/peaks/meta.yml +++ b/modules/nf-core/icountmini/peaks/meta.yml @@ -1,4 +1,3 @@ ---- name: "icountmini_peaks" description: Runs iCount peaks on a BED file of crosslinks keywords: @@ -13,34 +12,37 @@ tools: tool_dev_url: https://github.com/ulelab/iCount-Mini doi: "10.1038/nsmb.1838" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - pattern: "*.{bed}" - - sigxls: - type: file - description: TSV file of sigxls from iCount sigxls - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + pattern: "*.{bed}" + - sigxls: + type: file + description: TSV file of sigxls from iCount sigxls + pattern: "*.{tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - peaks: - type: file - description: Crosslinks deemed significant by iCount - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.peaks.bed.gz": + type: file + description: Crosslinks deemed significant by iCount + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/segment/meta.yml b/modules/nf-core/icountmini/segment/meta.yml index f2b00839d9b..2abf601f438 100644 --- a/modules/nf-core/icountmini/segment/meta.yml +++ b/modules/nf-core/icountmini/segment/meta.yml @@ -1,4 +1,3 @@ ---- name: icountmini_segment description: Formats a GTF file for use with iCount sigxls keywords: @@ -13,29 +12,43 @@ tools: tool_dev_url: https://github.com/ulelab/iCount-Mini doi: "10.1038/nsmb.1838" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gtf: - type: file - description: A GTF file to use for the segmentation - pattern: "*.{gtf}" - - fai: - type: file - description: FAI file corresponding to the reference sequence - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtf: + type: file + description: A GTF file to use for the segmentation + pattern: "*.{gtf}" + - - fai: + type: file + description: FAI file corresponding to the reference sequence + pattern: "*.{fai}" output: - gtf: - type: file - description: Segmented GTF file for use with iCount sigxls - pattern: "*.{gtf}" + - meta: + type: map + description: Groovy Map containing sample information + - "*_seg.gtf": + type: file + description: Segmented GTF file for use with iCount sigxls + pattern: "*.{gtf}" + - regions: + - meta: + type: map + description: Groovy Map containing sample information + - "*_regions.gtf.gz": + type: file + description: Regions file for use with iCount sigxls + pattern: "*.{gtf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/sigxls/meta.yml b/modules/nf-core/icountmini/sigxls/meta.yml index 4a467707ab1..c866404c589 100644 --- a/modules/nf-core/icountmini/sigxls/meta.yml +++ b/modules/nf-core/icountmini/sigxls/meta.yml @@ -1,4 +1,3 @@ ---- name: "icountmini_sigxls" description: Runs iCount sigxls on a BED file of crosslinks keywords: @@ -14,38 +13,47 @@ tools: tool_dev_url: https://github.com/ulelab/iCount-Mini doi: "10.1038/nsmb.1838" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - pattern: "*.{bam,bam.gz}" - - segmentation: - type: file - description: A iCount segmentation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + pattern: "*.{bam,bam.gz}" + - - segmentation: + type: file + description: A iCount segmentation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: Crosslinks deemed significant by iCount - pattern: "*.{bed.gz}" + - sigxls: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sigxls.bed.gz": + type: file + description: sigxls bed file + pattern: "*.{bed.gz}" - scores: - type: file - description: Crosslink scores calculated by iCount - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.scores.tsv": + type: file + description: Crosslink scores calculated by iCount + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/summary/meta.yml b/modules/nf-core/icountmini/summary/meta.yml index 37540429df4..f4f9ef289f7 100644 --- a/modules/nf-core/icountmini/summary/meta.yml +++ b/modules/nf-core/icountmini/summary/meta.yml @@ -1,4 +1,3 @@ ---- name: icountmini_summary description: Report proportion of cross-link events/sites on each region type. keywords: @@ -11,41 +10,56 @@ tools: homepage: https://icount.readthedocs.io/en/latest/ documentation: https://icount.readthedocs.io/en/latest/ licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - - segmentation: - type: file - description: A iCount segmentation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + - - segmentation: + type: file + description: A iCount segmentation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - summary_type: - type: file - description: Summary type output stats file - pattern: "*summary_type.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summary_type.tsv": + type: file + description: Summary type output stats file + pattern: "*summary_type.tsv" - summary_subtype: - type: file - description: Summary subtype output stats file - pattern: "*summary_subtype.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summary_subtype.tsv": + type: file + description: Summary subtype output stats file + pattern: "*summary_subtype.tsv" - summary_gene: - type: file - description: Summary gene output stats file - pattern: "*summary_gene.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summary_gene.tsv": + type: file + description: Summary gene output stats file + pattern: "*summary_gene.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/idemux/meta.yml b/modules/nf-core/idemux/meta.yml index 085e8e9b25c..97bd57bbbba 100644 --- a/modules/nf-core/idemux/meta.yml +++ b/modules/nf-core/idemux/meta.yml @@ -12,38 +12,51 @@ tools: documentation: https://github.com/Lexogen-Tools/idemux tool_dev_url: https://github.com/Lexogen-Tools/idemux licence: ["LEXOGEN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'NVQ', lane:1 ] - - reads: - type: file - description: | - List of input FastQ files - pattern: "Undetermined_S*.fastq.gz" - - samplesheet: - type: file - description: Input samplesheet - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'NVQ', lane:1 ] + - reads: + type: file + description: | + List of input FastQ files + pattern: "Undetermined_S*.fastq.gz" + - samplesheet: + type: file + description: Input samplesheet + pattern: "*.{csv}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Demultiplexed sample FASTQ files + pattern: "*.fastq.gz" + - "[!undetermined]*.fastq.gz": + type: file + description: Demultiplexed sample FASTQ files + pattern: "*.fastq.gz" - undetermined: - type: file - description: Optional undetermined sample FASTQ files - pattern: "Undetermined_R?.fastq.gz" + - meta: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_R?.fastq.gz" + - undetermined_R?.fastq.gz: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_R?.fastq.gz" - stats: - type: file - description: Demultiplexing Stats - pattern: "demultipexing_stats.tsv" + - demultipexing_stats.tsv: + type: file + description: Demultiplexing Stats + pattern: "demultipexing_stats.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jaanckae" maintainers: diff --git a/modules/nf-core/idr/meta.yml b/modules/nf-core/idr/meta.yml index 5f2ab1109e3..ef21bc20843 100644 --- a/modules/nf-core/idr/meta.yml +++ b/modules/nf-core/idr/meta.yml @@ -15,35 +15,40 @@ tools: experiments and provide highly stable thresholds based on reproducibility. tool_dev_url: https://github.com/kundajelab/idr licence: ["GPL v2"] + identifier: biotools:idr input: - - peaks: - type: list - description: BED, narrowPeak or broadPeak files of replicates - pattern: "*" - - peak_type: - type: string - description: Type of peak file - pattern: "{narrowPeak,broadPeak,bed}" - - prefix: - type: string - description: Prefix for output files + - - peaks: + type: list + description: BED, narrowPeak or broadPeak files of replicates + pattern: "*" + - - peak_type: + type: string + description: Type of peak file + pattern: "{narrowPeak,broadPeak,bed}" + - - prefix: + type: string + description: Prefix for output files output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idr: - type: file - description: Text file containing IDR values - pattern: "*.{txt}" + - "*idrValues.txt": + type: file + description: Text file containing IDR values + pattern: "*.{txt}" - log: - type: file - description: Log file - pattern: "*.{txt}" + - "*log.txt": + type: file + description: Log file + pattern: "*.{txt}" - png: - type: file - description: Plot generated by idr - pattern: "*{.png}" + - "*.png": + type: file + description: Plot generated by idr + pattern: "*{.png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/igv/js/meta.yml b/modules/nf-core/igv/js/meta.yml index 48fc3cc57f1..b7f01b44c7f 100644 --- a/modules/nf-core/igv/js/meta.yml +++ b/modules/nf-core/igv/js/meta.yml @@ -18,42 +18,57 @@ tools: tool_dev_url: https://github.com/igvteam/igv.js doi: 10.1093/bioinformatics/btac830 licence: ["MIT"] + identifier: biotools:igv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: Index of sorted BAM/CRAM file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: Index of sorted BAM/CRAM file + pattern: "*.{bai,crai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - browser: - type: file - description: Genome browser HTML file - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genome-browser.html": + type: file + description: Genome browser HTML file + pattern: "*.{html}" - align_files: - type: file - description: Copy of the input sorted BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: Copy of the input sorted BAM/CRAM file + pattern: "*.{bam,cram}" - index_files: - type: file - description: Copy of the input index of sorted BAM/CRAM file - pattern: "*.{bai,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Copy of the input index of sorted BAM/CRAM file + pattern: "*.{bai,crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/igvreports/meta.yml b/modules/nf-core/igvreports/meta.yml index d1170b24710..fc1a9f84eaf 100644 --- a/modules/nf-core/igvreports/meta.yml +++ b/modules/nf-core/igvreports/meta.yml @@ -1,68 +1,73 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "igvreports" -description: A Python application to generate self-contained HTML reports for variant review and other genomic applications +description: A Python application to generate self-contained HTML reports for variant + review and other genomic applications keywords: - vcf - variant - genomics tools: - "igvreports": - description: "Creates self-contained html pages for visual variant review with IGV (igv.js)." + description: "Creates self-contained html pages for visual variant review with + IGV (igv.js)." homepage: "https://github.com/igvteam/igv-reports" documentation: "https://github.com/igvteam/igv-reports" tool_dev_url: "https://github.com/igvteam/igv-reports" doi: "10.1093/bioinformatics/btac830" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sites: - type: file - description: | - VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites - - tracks: - type: file - description: | - List of any set of files of the types that IGV can display, - eg BAM/CRAM, GTF/GFF, VCF, BED, etc - - tracks_indices: - type: file - description: | - Track index files, eg bai/crai files. This may not be required, - but for some file types, eg BAM/CRAM, they are. They are not used in the - igvreports cmds, but may need to exist in the working directory - - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'genome_name' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Reference fasta file index - pattern: "*.{fai}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sites: + type: file + description: | + VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites + - tracks: + type: file + description: | + List of any set of files of the types that IGV can display, + eg BAM/CRAM, GTF/GFF, VCF, BED, etc + - tracks_indicies: + type: file + description: | + List of indices for the tracks + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'genome_name' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fasta,fa}" + - fai: + type: file + description: Reference fasta file index + pattern: "*.{fai}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: | - html report with a table of genomic sites and an embedded - IGV genome browser for viewing data for each site - pattern: "*.{html}" - + - meta: + type: file + description: | + html report with a table of genomic sites and an embedded + IGV genome browser for viewing data for each site + pattern: "*.{html}" + - "*.html": + type: file + description: | + html report with a table of genomic sites and an embedded + IGV genome browser for viewing data for each site + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@souljamie" maintainers: diff --git a/modules/nf-core/ilastik/multicut/meta.yml b/modules/nf-core/ilastik/multicut/meta.yml index 36ac9e90b0e..cab8ffa2acd 100644 --- a/modules/nf-core/ilastik/multicut/meta.yml +++ b/modules/nf-core/ilastik/multicut/meta.yml @@ -1,58 +1,66 @@ name: "ilastik_multicut" -description: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. +description: Ilastik is a tool that utilizes machine learning algorithms to classify + pixels, segment, track and count cells in images. Ilastik contains a graphical user + interface to interactively label pixels. However, this nextflow module will implement + the --headless mode, to apply pixel classification using a pre-trained .ilp file + on an input image. keywords: - multicut - segmentation - pixel classification tools: - "ilastik": - description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis." + description: "Ilastik is a user friendly tool that enables pixel classification, + segmentation and analysis." homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" license: ["GPL3"] + identifier: biotools:ilastik input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - h5: - type: file - description: h5 file containing image stack to classify file - pattern: "*.{h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ilp: - type: file - description: Trained ilastik .ilp project file - pattern: "*.{ilp}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - probs: - type: file - description: Probability map for boundary based segmentation - pattern: "*.{h5,,hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - h5: + type: file + description: h5 file containing image stack to classify file + pattern: "*.{h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ilp: + type: file + description: Trained ilastik .ilp project file + pattern: "*.{ilp}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - probs: + type: file + description: Probability map for boundary based segmentation + pattern: "*.{h5,,hdf5}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out_tiff: - type: file - description: Multicut segmentation mask output. - pattern: "*.{tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tiff": + type: file + description: Multicut segmentation mask output. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/ilastik/pixelclassification/meta.yml b/modules/nf-core/ilastik/pixelclassification/meta.yml index ad100d9b827..5d0403bbb3f 100644 --- a/modules/nf-core/ilastik/pixelclassification/meta.yml +++ b/modules/nf-core/ilastik/pixelclassification/meta.yml @@ -1,47 +1,55 @@ name: "ilastik_pixelclassification" -description: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. +description: Ilastik is a tool that utilizes machine learning algorithms to classify + pixels, segment, track and count cells in images. Ilastik contains a graphical user + interface to interactively label pixels. However, this nextflow module will implement + the --headless mode, to apply pixel classification using a pre-trained .ilp file + on an input image. keywords: - pixel_classification - segmentation - probability_maps tools: - "ilastik": - description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis." + description: "Ilastik is a user friendly tool that enables pixel classification, + segmentation and analysis." homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" licence: ["GPL3"] + identifier: biotools:ilastik input: - - meta: - type: map - description: | - Groovy Map containing sample information for h5 file - e.g. [ id:'test', single_end:false ] - - input_img: - type: file - description: Input img file containing image stack to classify - - meta2: - type: map - description: | - Groovy Map containing sample information for ilp file - e.g. [ id:'test', single_end:false ] - - ilp: - type: file - description: Trained ilastik pixel classification .ilp project file - pattern: "*.{ilp}" + - - meta: + type: map + description: | + Groovy Map containing sample information for h5 file + e.g. [ id:'test', single_end:false ] + - input_img: + type: file + description: Input img file containing image stack to classify + - - meta2: + type: map + description: | + Groovy Map containing sample information for ilp file + e.g. [ id:'test', single_end:false ] + - ilp: + type: file + description: Trained ilastik pixel classification .ilp project file + pattern: "*.{ilp}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Output file from ilastik pixel classification. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: Output file from ilastik pixel classification. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/instrain/compare/meta.yml b/modules/nf-core/instrain/compare/meta.yml index c7b072d5a98..52b5318bc8a 100644 --- a/modules/nf-core/instrain/compare/meta.yml +++ b/modules/nf-core/instrain/compare/meta.yml @@ -14,54 +14,81 @@ tools: tool_dev_url: https://github.com/MrOlm/instrain doi: 10.1038/s41587-020-00797-0 licence: ["MIT"] + identifier: biotools:instrain input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - profiles: - type: directory - description: InStrain profile folders - pattern: "*.IS/" - - bams: - type: file - description: Path to .bam files that were profiled - pattern: "*.{bam,sam}" - - stb_file: - type: file - description: Path to .stb (scaffold to bin) file that was profiled - pattern: "*.stb" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bams: + type: file + description: Path to .bam files that were profiled + pattern: "*.{bam,sam}" + - profiles: + type: directory + description: InStrain profile folders + pattern: "*.IS/" + - - stb_file: + type: file + description: Path to .stb (scaffold to bin) file that was profiled + pattern: "*.stb" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - compare: - type: directory - description: inStrain compare folders - pattern: "*.IS_compare/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare": + type: directory + description: inStrain compare folders + pattern: "*.IS_compare/" - comparisons_table: - type: file - description: Comparisons table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_comparisonsTable.tsv": + type: file + description: Comparisons table + pattern: "*.tsv" - pooled_snv: - type: file - description: Pooled SNV - pattern: "*.tsv" - - snv_info: - type: file - description: SNV information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_pooled_SNV_data.tsv": + type: file + description: Pooled SNV + pattern: "*.tsv" - snv_keys: - type: file - description: SNV keys - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_pooled_SNV_data_keys.tsv": + type: file + description: SNV keys + pattern: "*.tsv" + - snv_info: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_pooled_SNV_info.tsv": + type: file + description: SNV information + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@margotl9" - "@CarsonJM" diff --git a/modules/nf-core/instrain/profile/meta.yml b/modules/nf-core/instrain/profile/meta.yml index 43462ca2f11..04bda267854 100644 --- a/modules/nf-core/instrain/profile/meta.yml +++ b/modules/nf-core/instrain/profile/meta.yml @@ -1,5 +1,8 @@ name: "instrain_profile" -description: inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification +description: inStrain is python program for analysis of co-occurring genome populations + from metagenomes that allows highly accurate genome comparisons, analysis of coverage, + microdiversity, and linkage, and sensitive SNP detection with gene localization + and synonymous non-synonymous identification keywords: - instrain - metagenomics @@ -13,64 +16,104 @@ tools: tool_dev_url: https://github.com/MrOlm/instrain doi: 10.1038/s41587-020-00797-0 licence: ["MIT"] + identifier: biotools:instrain input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test'] - - bam: - type: file - description: Path to .bam file to be profiled - pattern: "*.{bam,sam}" - - genome_fasta: - type: file - description: Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file - pattern: "*.{fasta,fna,fa}" - - genes_fasta: - type: file - description: Path to .fna file of genes to be profiled (OPTIONAL) - pattern: "*.{fasta,fna,fa}" - - stb_file: - type: file - description: Path to .stb (scaffold to bin) file to be profiled (OPTIONAL) - pattern: "*.stb" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test'] + - bam: + type: file + description: Path to .bam file to be profiled + pattern: "*.{bam,sam}" + - - genome_fasta: + type: file + description: Path to .fasta file to be profiled; MUST be the .fasta file that + was mapped to to create the .bam file + pattern: "*.{fasta,fna,fa}" + - - genes_fasta: + type: file + description: Path to .fna file of genes to be profiled (OPTIONAL) + pattern: "*.{fasta,fna,fa}" + - - stb_file: + type: file + description: Path to .stb (scaffold to bin) file to be profiled (OPTIONAL) + pattern: "*.stb" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: directory - description: InStrain profile folder - pattern: "*.IS/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS": + type: directory + description: InStrain profile folder + pattern: "*.IS/" + - snvs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_SNVs.tsv": + type: file + description: SNVs + pattern: "*.tsv" - gene_info: - type: file - description: Gene information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_gene_info.tsv": + type: file + description: Gene information + pattern: "*.tsv" - genome_info: - type: file - description: Genome information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_genome_info.tsv": + type: file + description: Genome information + pattern: "*.tsv" - linkage: - type: file - description: Linkage information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_linkage.tsv": + type: file + description: Linkage information + pattern: "*.tsv" - mapping_info: - type: file - description: Mapping information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_mapping_info.tsv": + type: file + description: Mapping information + pattern: "*.tsv" - scaffold_info: - type: file - description: Scaffold information - pattern: "*.tsv" - - snvs: - type: file - description: SNVs - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_scaffold_info.tsv": + type: file + description: Scaffold information + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mrolm" maintainers: diff --git a/modules/nf-core/interproscan/meta.yml b/modules/nf-core/interproscan/meta.yml index 44cce91b7ab..0bb10f7daf9 100644 --- a/modules/nf-core/interproscan/meta.yml +++ b/modules/nf-core/interproscan/meta.yml @@ -1,5 +1,6 @@ name: "interproscan" -description: Produces protein annotations and predictions from an amino acids FASTA file +description: Produces protein annotations and predictions from an amino acids FASTA + file keywords: - annotation - fasta @@ -8,46 +9,70 @@ keywords: - interproscan tools: - "interproscan": - description: "InterPro integrates together predictive information about proteins function from a number of partner resources" + description: "InterPro integrates together predictive information about proteins + function from a number of partner resources" homepage: "https://www.ebi.ac.uk/interpro/search/sequence/" documentation: "https://interproscan-docs.readthedocs.io" tool_dev_url: "https://github.com/ebi-pf-team/interproscan" doi: "10.1093/bioinformatics/btu031" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing the amino acid or dna query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - interproscan_database: - type: directory - description: Path to the interproscan database (untarred http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing the amino acid or dna query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - interproscan_database: + type: directory + description: Path to the interproscan database (untarred + http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz) output: - tsv: - type: file - description: Tab separated file containing with detailed hits - pattern: "*.{tsv}" + - meta: + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" - xml: - type: file - description: XML file containing with detailed hits - pattern: "*.{xml}" + - meta: + type: file + description: XML file containing with detailed hits + pattern: "*.{xml}" + - "*.xml": + type: file + description: XML file containing with detailed hits + pattern: "*.{xml}" - gff3: - type: file - description: GFF3 file containing with detailed hits - pattern: "*.{gff3}" + - meta: + type: file + description: GFF3 file containing with detailed hits + pattern: "*.{gff3}" + - "*.gff3": + type: file + description: GFF3 file containing with detailed hits + pattern: "*.{gff3}" - json: - type: file - description: JSON file containing with detailed hits - pattern: "*.{json}" + - meta: + type: file + description: JSON file containing with detailed hits + pattern: "*.{json}" + - "*.json": + type: file + description: JSON file containing with detailed hits + pattern: "*.{json}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" - "@mahesh-panchal" diff --git a/modules/nf-core/iphop/download/meta.yml b/modules/nf-core/iphop/download/meta.yml index b3a31992e7b..f4b5939aebb 100644 --- a/modules/nf-core/iphop/download/meta.yml +++ b/modules/nf-core/iphop/download/meta.yml @@ -16,15 +16,18 @@ tools: tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/ doi: "10.1371/journal.pbio.3002083" licence: ["Modified GPL v3"] + identifier: "" output: - iphop_db: - type: directory - description: Directory containing downloaded and md5 checked iPHoP database - pattern: "iphop_db/" + - iphop_db/: + type: directory + description: Directory containing downloaded and md5 checked iPHoP database + pattern: "iphop_db/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/iphop/predict/meta.yml b/modules/nf-core/iphop/predict/meta.yml index ce267dd13be..d115364b822 100644 --- a/modules/nf-core/iphop/predict/meta.yml +++ b/modules/nf-core/iphop/predict/meta.yml @@ -16,41 +16,58 @@ tools: tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/ doi: "10.1371/journal.pbio.3002083" licence: ["Modified GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing phage contigs/scaffolds/chromosomes - pattern: "*.{fasta,fna,fa}" - - iphop_db: - type: directory - description: Directory pointing to iPHoP database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing phage contigs/scaffolds/chromosomes + pattern: "*.{fasta,fna,fa}" + - - iphop_db: + type: directory + description: Directory pointing to iPHoP database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - iphop_genus: - type: file - description: File containing integrated host predictions at genus level, with a minimum score defined by the `--min_score` argument - pattern: "Host_prediction_to_genus_m*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - Host_prediction_to_genus_m*.csv: + type: file + description: File containing integrated host predictions at genus level, with + a minimum score defined by the `--min_score` argument + pattern: "Host_prediction_to_genus_m*.csv" - iphop_genome: - type: file - description: File containing integrated host predictions at host genome level, with a minimum score defined by the `--min_score` argument - pattern: "Host_prediction_to_genome_m*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - Host_prediction_to_genome_m*.csv: + type: file + description: File containing integrated host predictions at host genome level, + with a minimum score defined by the `--min_score` argument + pattern: "Host_prediction_to_genome_m*.csv" - iphop_detailed_output: - type: file - description: File containing each phage's top 5 hits via each method - pattern: "Detailed_output_by_tool.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - Detailed_output_by_tool.csv: + type: file + description: File containing each phage's top 5 hits via each method + pattern: "Detailed_output_by_tool.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/iqtree/meta.yml b/modules/nf-core/iqtree/meta.yml index 40b7601fc15..b20bdd88abf 100644 --- a/modules/nf-core/iqtree/meta.yml +++ b/modules/nf-core/iqtree/meta.yml @@ -1,5 +1,6 @@ name: iqtree -description: Produces a Newick format phylogeny from a multiple sequence alignment using the maxium likelihood algorithm. Capable of bacterial genome size alignments. +description: Produces a Newick format phylogeny from a multiple sequence alignment + using the maxium likelihood algorithm. Capable of bacterial genome size alignments. keywords: - phylogeny - newick @@ -12,205 +13,343 @@ tools: tool_dev_url: https://github.com/iqtree/iqtree2 doi: 10.1093/molbev/msaa015 licence: ["GPL v2-or-later"] + identifier: biotools:iqtree input: - - meta: - type: map - description: | - Groovy map containing sample information for the - alignment/tree file, e.g. [ id: 'test' ] - - alignment: - type: file - description: Input alignment file in PHYLIP, - FASTA, NEXUS, CLUSTAL or MSF format (-s) - pattern: "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}" - - tree: - type: file - description: "File containing one or multiple phylogenetic trees (-t): - - Single tree used e.g. as starting tree for tree search - - Set of trees used e.g. for distance computation, consensus tree construction" - pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" - - tree_te: - type: file - description: "File containing single phylogenetic tree (-te) - Use cases: - - fixed user tree to skip tree search - - ancestral sequence reconstruction" - pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" - - lmclust: - type: file - description: NEXUS file containing taxon clusters - for quartet mapping analysis (-lmclust) - pattern: "*.nex{us}" - - mdef: - type: file - description: NEXUS model file defining new models (-mdef) - pattern: "*.nex{us}" - - partitions_equal: - type: file - description: Partition file for edge-equal partition - model, all partitions share same set of branch lengths (-q) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - partitions_proportional: - type: file - description: Partition file for edge-equal partition - model, all partitions share same set of branch lengths (-spp) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - partitions_unlinked: - type: file - description: Partition file for edge-equal partition - model, all partitions share same set of branch lengths (-sp) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - guide_tree: - type: file - description: File containing guide tree for inference of - site frequency profiles (-ft) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - sitefreq_in: - type: file - description: Site frequency file (-fs) - pattern: "*.sitefreq" - - constraint_tree: - type: file - description: File containing opological constraint tree in - NEWICK format. The constraint tree can be a multifurcating - tree and need not to include all taxa. (-g) - pattern: "*.{nwk,newick}" - - trees_z: - type: file - description: File containing a set of trees for which - log-likelihoods should be computed (-z) - - suptree: - type: file - description: File containing input “target” tree, support - values are extracted from trees passed via -t, and mapped - onto the target tree (-sup) - - trees_rf: - type: file - description: "File containing a second tree set (-rf). Used - for computing the distance to the primary tree set (`tree`)" - pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + - - meta: + type: map + description: | + Groovy map containing sample information for the + alignment/tree file, e.g. [ id: 'test' ] + - alignment: + type: file + description: Input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format + (-s) + pattern: "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}" + - tree: + type: file + description: "File containing one or multiple phylogenetic trees (-t): - Single + tree used e.g. as starting tree for tree search - Set of trees used e.g. for + distance computation, consensus tree construction" + pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + - - tree_te: + type: file + description: "File containing single phylogenetic tree (-te) Use cases: - fixed + user tree to skip tree search - ancestral sequence reconstruction" + pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + - - lmclust: + type: file + description: NEXUS file containing taxon clusters for quartet mapping analysis + (-lmclust) + pattern: "*.nex{us}" + - - mdef: + type: file + description: NEXUS model file defining new models (-mdef) + pattern: "*.nex{us}" + - - partitions_equal: + type: file + description: Partition file for edge-equal partition model, all partitions share + same set of branch lengths (-q) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - partitions_proportional: + type: file + description: Partition file for edge-equal partition model, all partitions share + same set of branch lengths (-spp) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - partitions_unlinked: + type: file + description: Partition file for edge-equal partition model, all partitions share + same set of branch lengths (-sp) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - guide_tree: + type: file + description: File containing guide tree for inference of site frequency profiles + (-ft) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - sitefreq_in: + type: file + description: Site frequency file (-fs) + pattern: "*.sitefreq" + - - constraint_tree: + type: file + description: File containing opological constraint tree in NEWICK format. The + constraint tree can be a multifurcating tree and need not to include all taxa. + (-g) + pattern: "*.{nwk,newick}" + - - trees_z: + type: file + description: File containing a set of trees for which log-likelihoods should + be computed (-z) + - - suptree: + type: file + description: File containing input “target” tree, support values are extracted + from trees passed via -t, and mapped onto the target tree (-sup) + - - trees_rf: + type: file + description: "File containing a second tree set (-rf). Used for computing the + distance to the primary tree set (`tree`)" + pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" output: - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{treefile}" + - meta: + type: file + description: A phylogeny in Newick format + pattern: "*.{treefile}" + - "*.treefile": + type: file + description: A phylogeny in Newick format + pattern: "*.{treefile}" - report: - type: file - description: | - Main report file containing computational - results as well as a textual visualization - of the final tree - pattern: "*.{iqtree}" + - meta: + type: file + description: | + Main report file containing computational + results as well as a textual visualization + of the final tree + pattern: "*.{iqtree}" + - "*.iqtree": + type: file + description: | + Main report file containing computational + results as well as a textual visualization + of the final tree + pattern: "*.{iqtree}" - mldist: - type: file - description: | - File containing the pairwise maximum - likelihood distances as a matrix - pattern: "*.{mldist}" + - meta: + type: file + description: | + File containing the pairwise maximum + likelihood distances as a matrix + pattern: "*.{mldist}" + - "*.mldist": + type: file + description: | + File containing the pairwise maximum + likelihood distances as a matrix + pattern: "*.{mldist}" - lmap_svg: - type: file - description: | - File containing likelihood mapping analysis - results in .svg format (-lmap/-lmclust) - pattern: "*.lmap.svg" + - meta: + type: file + description: | + File containing likelihood mapping analysis + results in .svg format (-lmap/-lmclust) + pattern: "*.lmap.svg" + - "*.lmap.svg": + type: file + description: | + File containing likelihood mapping analysis + results in .svg format (-lmap/-lmclust) + pattern: "*.lmap.svg" - lmap_eps: - type: file - description: | - File containing likelihood mapping analysis - results in .eps format (-lmap/-lmclust) - pattern: "*.lmap.eps" + - meta: + type: file + description: | + File containing likelihood mapping analysis + results in .eps format (-lmap/-lmclust) + pattern: "*.lmap.eps" + - "*.lmap.eps": + type: file + description: | + File containing likelihood mapping analysis + results in .eps format (-lmap/-lmclust) + pattern: "*.lmap.eps" - lmap_quartetlh: - type: file - description: | - File containing quartet log-likelihoods (-wql) - pattern: "*.lmap.quartetlh" + - meta: + type: file + description: | + File containing quartet log-likelihoods (-wql) + pattern: "*.lmap.quartetlh" + - "*.lmap.quartetlh": + type: file + description: | + File containing quartet log-likelihoods (-wql) + pattern: "*.lmap.quartetlh" - sitefreq_out: - type: file - description: | - File containing site frequency profiles (-ft) - pattern: "*.sitefreq" + - meta: + type: file + description: | + File containing site frequency profiles (-ft) + pattern: "*.sitefreq" + - "*.sitefreq": + type: file + description: | + File containing site frequency profiles (-ft) + pattern: "*.sitefreq" - bootstrap: - type: file - description: | - File containing all bootstrap trees (-wbt/-wbtl) - pattern: "*.ufboot" + - meta: + type: file + description: | + File containing all bootstrap trees (-wbt/-wbtl) + pattern: "*.ufboot" + - "*.ufboot": + type: file + description: | + File containing all bootstrap trees (-wbt/-wbtl) + pattern: "*.ufboot" - state: - type: file - description: | - File containing ancestral sequences for all - nodes of the tree by empirical Bayesian method (-asr) - pattern: "*.{state}" + - meta: + type: file + description: | + File containing ancestral sequences for all + nodes of the tree by empirical Bayesian method (-asr) + pattern: "*.{state}" + - "*.state": + type: file + description: | + File containing ancestral sequences for all + nodes of the tree by empirical Bayesian method (-asr) + pattern: "*.{state}" - contree: - type: file - description: | - File containing consensus tree (-con/-bb) - pattern: "*.{contree}" + - meta: + type: file + description: | + File containing consensus tree (-con/-bb) + pattern: "*.{contree}" + - "*.contree": + type: file + description: | + File containing consensus tree (-con/-bb) + pattern: "*.{contree}" - nex: - type: file - description: | - File containing consensus network (-net/-bb) - pattern: "*.{nex}" + - meta: + type: file + description: | + File containing consensus network (-net/-bb) + pattern: "*.{nex}" + - "*.nex": + type: file + description: | + File containing consensus network (-net/-bb) + pattern: "*.{nex}" - splits: - type: file - description: | - File containing consensus network in star-dot format (-wsplits) - pattern: "*.{splits}" + - meta: + type: file + description: | + File containing consensus network in star-dot format (-wsplits) + pattern: "*.{splits}" + - "*.splits": + type: file + description: | + File containing consensus network in star-dot format (-wsplits) + pattern: "*.{splits}" - suptree: - type: file - description: | - File containing tree with assigned support - values based on supplied "target" tree (-sup) - pattern: "*.{suptree}" + - meta: + type: file + description: | + File containing tree with assigned support + values based on supplied "target" tree (-sup) + pattern: "*.{suptree}" + - "*.suptree": + type: file + description: | + File containing tree with assigned support + values based on supplied "target" tree (-sup) + pattern: "*.{suptree}" - alninfo: - type: file - description: | - File containing alignment site statistics (-alninfo) - pattern: "*.{alninfo}" + - meta: + type: file + description: | + File containing alignment site statistics (-alninfo) + pattern: "*.{alninfo}" + - "*.alninfo": + type: file + description: | + File containing alignment site statistics (-alninfo) + pattern: "*.{alninfo}" - partlh: - type: file - description: | - File containing partition log-likelihoods (-wpl) - pattern: "*.{partlh}" + - meta: + type: file + description: | + File containing partition log-likelihoods (-wpl) + pattern: "*.{partlh}" + - "*.partlh": + type: file + description: | + File containing partition log-likelihoods (-wpl) + pattern: "*.{partlh}" - siteprob: - type: file - description: | - File containing site posterior probabilities (-wspr/-wspm/-wspmr) - pattern: "*.{siteprob}" + - meta: + type: file + description: | + File containing site posterior probabilities (-wspr/-wspm/-wspmr) + pattern: "*.{siteprob}" + - "*.siteprob": + type: file + description: | + File containing site posterior probabilities (-wspr/-wspm/-wspmr) + pattern: "*.{siteprob}" - sitelh: - type: file - description: | - File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr) - pattern: "*.{sitelh}" + - meta: + type: file + description: | + File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr) + pattern: "*.{sitelh}" + - "*.sitelh": + type: file + description: | + File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr) + pattern: "*.{sitelh}" - treels: - type: file - description: | - File containing all locally optimal trees (-wt) - pattern: "*.{treels}" + - meta: + type: file + description: | + File containing all locally optimal trees (-wt) + pattern: "*.{treels}" + - "*.treels": + type: file + description: | + File containing all locally optimal trees (-wt) + pattern: "*.{treels}" - rate: - type: file - description: | - File containing inferred site-specific - evolutionary rates (-wsr) - pattern: "*.{rate}" + - meta: + type: file + description: | + File containing inferred site-specific + evolutionary rates (-wsr) + pattern: "*.{rate}" + - "*.rate ": + type: file + description: | + File containing inferred site-specific + evolutionary rates (-wsr) + pattern: "*.{rate}" - mlrate: - type: file - description: | - File containing site-specific subtitution - rates determined by maximum likelihood (--mlrate) - pattern: "*.{mlrate}" + - meta: + type: file + description: | + File containing site-specific subtitution + rates determined by maximum likelihood (--mlrate) + pattern: "*.{mlrate}" + - "*.mlrate": + type: file + description: | + File containing site-specific subtitution + rates determined by maximum likelihood (--mlrate) + pattern: "*.{mlrate}" - exch_matrix: - type: file - description: File containing the exchangeability - matrix obtained from the optimization (--link-exchange-rates) - pattern: "GTRPMIX.nex" + - meta: + type: file + description: File containing the exchangeability matrix obtained from the optimization + (--link-exchange-rates) + pattern: "GTRPMIX.nex" + - GTRPMIX.nex: + type: file + description: File containing the exchangeability matrix obtained from the optimization + (--link-exchange-rates) + pattern: "GTRPMIX.nex" - log: - type: file - description: Log file of entire run - pattern: "*.{log}" + - meta: + type: file + description: Log file of entire run + pattern: "*.{log}" + - "*.log": + type: file + description: Log file of entire run + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" - "@aunderwo" diff --git a/modules/nf-core/islandpath/meta.yml b/modules/nf-core/islandpath/meta.yml index 98d108e3595..b175aa24c71 100644 --- a/modules/nf-core/islandpath/meta.yml +++ b/modules/nf-core/islandpath/meta.yml @@ -6,36 +6,47 @@ keywords: - prediction tools: - "islandpath": - description: "IslandPath-DIMOB is a standalone software to predict genomic islands (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes." + description: "IslandPath-DIMOB is a standalone software to predict genomic islands + (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) + in bacterial and archaeal genomes based on the presence of dinucleotide biases + and mobility genes." homepage: https://github.com/brinkmanlab/islandpath documentation: https://github.com/brinkmanlab/islandpath#readme tool_dev_url: https://github.com/brinkmanlab/islandpath doi: "10.1093/bioinformatics/bty095" licence: ["GPL v3"] + identifier: biotools:islandpath input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genome: - type: file - description: | - Genome file in .gbk or .embl format. - pattern: "*.{gbk, embl, gbff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: | + Genome file in .gbk or .embl format. + pattern: "*.{gbk, embl, gbff}" output: - gff: - type: file - description: GFF file listing the predicted genomic islands and their coordinates - pattern: "*.gff" + - meta: + type: file + description: GFF file listing the predicted genomic islands and their coordinates + pattern: "*.gff" + - "*.gff": + type: file + description: GFF file listing the predicted genomic islands and their coordinates + pattern: "*.gff" - log: - type: file - description: Log file of the islandpath run - pattern: "*.log" + - Dimob.log: + type: file + description: Log file of the islandpath run + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvfe" maintainers: diff --git a/modules/nf-core/ismapper/meta.yml b/modules/nf-core/ismapper/meta.yml index f930901aa2c..bb413e7a9f1 100644 --- a/modules/nf-core/ismapper/meta.yml +++ b/modules/nf-core/ismapper/meta.yml @@ -6,44 +6,48 @@ keywords: - bacteria tools: - ismapper: - description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes. + description: A mapping-based tool for identification of the site and orientation + of IS insertions in bacterial genomes. homepage: https://github.com/jhawkey/IS_mapper documentation: https://github.com/jhawkey/IS_mapper tool_dev_url: https://github.com/jhawkey/IS_mapper doi: "10.1186/s12864-015-1860-2" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A set of paired-end FASTQ files - pattern: "*.{fastq.gz,fq.gz}" - - reference: - type: file - description: Reference genome in GenBank format - pattern: "*.{gbk}" - - query: - type: file - description: Insertion sequences to query in FASTA format - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A set of paired-end FASTQ files + pattern: "*.{fastq.gz,fq.gz}" + - reference: + type: file + description: Reference genome in GenBank format + pattern: "*.{gbk}" + - query: + type: file + description: Insertion sequences to query in FASTA format + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing ISMapper result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing ISMapper result files + pattern: "*/*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/isoseq/cluster/meta.yml b/modules/nf-core/isoseq/cluster/meta.yml index a7879668dde..b3388abf261 100644 --- a/modules/nf-core/isoseq/cluster/meta.yml +++ b/modules/nf-core/isoseq/cluster/meta.yml @@ -12,70 +12,134 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM file generated by isoseq refine - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM file generated by isoseq refine + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - bam: - type: file - description: BAM file of clustered consensus - pattern: "*.transcripts.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.bam": + type: file + description: BAM file of clustered consensus + pattern: "*.transcripts.bam" - pbi: - type: file - description: Pacbio Index of consensus reads generated by clustering - pattern: "*.transcripts.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.bam.pbi": + type: file + description: Pacbio Index of consensus reads generated by clustering + pattern: "*.transcripts.bam.pbi" - cluster: - type: file - description: A two columns (from, to) file describing original read name to new read name - pattern: "*.transcripts.cluster" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.cluster": + type: file + description: A two columns (from, to) file describing original read name to + new read name + pattern: "*.transcripts.cluster" - cluster_report: - type: file - description: A table files clusters (transcripts) members (read) - pattern: "*.transcripts.cluster_report.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.cluster_report.csv": + type: file + description: A table files clusters (transcripts) members (read) + pattern: "*.transcripts.cluster_report.csv" - transcriptset: - type: file - description: A metadata xml file which contains full paths to data files - pattern: "*.transcripts.transcriptset.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.transcriptset.xml": + type: file + description: A metadata xml file which contains full paths to data files + pattern: "*.transcripts.transcriptset.xml" - hq_bam: - type: file - description: High quality reads (when --use-qvs is set) - pattern: "*.transcripts.hq.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.hq.bam": + type: file + description: High quality reads (when --use-qvs is set) + pattern: "*.transcripts.hq.bam" - hq_pbi: - type: file - description: Pacbio index of high quality reads (when --use-qvs is set) - pattern: "*.transcripts.hq.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.hq.bam.pbi": + type: file + description: Pacbio index of high quality reads (when --use-qvs is set) + pattern: "*.transcripts.hq.bam.pbi" - lq_bam: - type: file - description: Low quality reads (when --use-qvs is set) - pattern: "*.transcripts.lq.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.lq.bam": + type: file + description: Low quality reads (when --use-qvs is set) + pattern: "*.transcripts.lq.bam" - lq_pbi: - type: file - description: Pacbio index of low quality reads (when --use-qvs is set) - pattern: "*.transcripts.lq.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.lq.bam.pbi": + type: file + description: Pacbio index of low quality reads (when --use-qvs is set) + pattern: "*.transcripts.lq.bam.pbi" - singletons_bam: - type: file - description: Unclustered reads (when --singletons is set) - pattern: "*.transcripts.singletons.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.singletons.bam": + type: file + description: Unclustered reads (when --singletons is set) + pattern: "*.transcripts.singletons.bam" - singletons_pbi: - type: file - description: Pacbio index of unclustered reads (when --singletons is set) - pattern: "*.transcripts.singletons.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.singletons.bam.pbi": + type: file + description: Pacbio index of unclustered reads (when --singletons is set) + pattern: "*.transcripts.singletons.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/isoseq/refine/meta.yml b/modules/nf-core/isoseq/refine/meta.yml index 40f6c4b0f0a..f15b87d3968 100644 --- a/modules/nf-core/isoseq/refine/meta.yml +++ b/modules/nf-core/isoseq/refine/meta.yml @@ -13,50 +13,80 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test ] - - bam: - type: file - description: BAM file, cleaned ccs generated by lima - pattern: "*.bam" - - primers: - type: file - description: fasta file of primers - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test ] + - bam: + type: file + description: BAM file, cleaned ccs generated by lima + pattern: "*.bam" + - - primers: + type: file + description: fasta file of primers + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - bam: - type: file - description: Set of complete reads (with polyA tail), where the polyA has been trimmed - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: Set of complete reads (with polyA tail), where the polyA has been + trimmed + pattern: "*.bam" - pbi: - type: file - description: Pacbio index file from polyA trimmed reads - pattern: "*.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam.pbi": + type: file + description: Pacbio index file from polyA trimmed reads + pattern: "*.pbi" - consensusreadset: - type: file - description: Metadata about read library - pattern: "*.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.consensusreadset.xml": + type: file + description: Metadata about read library + pattern: "*.xml" - summary: - type: file - description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.filter_summary.report.json": + type: file + description: json file describing number of full length reads, full length non + chimeric reads and full length non chimeric polyA reads + pattern: "*.json" - report: - type: file - description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name) - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.report.csv": + type: file + description: Metadata about primer and polyA detection (primers/polyA/insert + length, strand, primer name) + pattern: "*.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/isoseq3/tag/meta.yml b/modules/nf-core/isoseq3/tag/meta.yml index 55939a04c44..13468839802 100644 --- a/modules/nf-core/isoseq3/tag/meta.yml +++ b/modules/nf-core/isoseq3/tag/meta.yml @@ -1,4 +1,3 @@ ---- name: "isoseq3_tag" description: Extract UMI and cell barcodes keywords: @@ -14,41 +13,50 @@ tools: documentation: "https://isoseq.how/" tool_dev_url: "https://github.com/PacificBiosciences/IsoSeq/tree/master" licence: ["BSD-3-clause-Clear"] + identifier: biotools:isoseq3 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - bam: - type: file - description: BAM file, one full-length CCS file generated by lima - pattern: "*.5p--3p.bam" - - design: - type: string - description: Barcoding design. Specifies which bases to use as cell/molecular barcodes. - pattern: "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\d{1,2}[UBGX])+$" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - bam: + type: file + description: BAM file, one full-length CCS file generated by lima + pattern: "*.5p--3p.bam" + - - design: + type: string + description: Barcoding design. Specifies which bases to use as cell/molecular + barcodes. + pattern: "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\\ + d{1,2}[UBGX])+$" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with full-length tagged reads - pattern: "*.flt.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.flt.bam": + type: file + description: BAM file with full-length tagged reads + pattern: "*.flt.bam" - pbi: - type: file - description: Pacbio index file of full-length tagged reads - pattern: "*.flt.bam.pbi" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.flt.bam.pbi": + type: file + description: Pacbio index file of full-length tagged reads + pattern: "*.flt.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@skraettli" maintainers: diff --git a/modules/nf-core/ivar/consensus/meta.yml b/modules/nf-core/ivar/consensus/meta.yml index 99e11924bf8..afe8a3d6f2d 100644 --- a/modules/nf-core/ivar/consensus/meta.yml +++ b/modules/nf-core/ivar/consensus/meta.yml @@ -11,46 +11,63 @@ tools: homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html licence: ["GPL-3.0-or-later"] + identifier: biotools:andersen-lab_ivar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar consensus - patter: "*.mpileup" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam + file + pattern: "*.bam" + - - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM + file + pattern: "*.fa" + - - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar consensus + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: iVar generated consensus sequence - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: iVar generated consensus sequence + pattern: "*.fa" - qual: - type: file - description: iVar generated quality file - pattern: "*.qual.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.qual.txt": + type: file + description: iVar generated quality file + pattern: "*.qual.txt" - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup": + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/nf-core/ivar/trim/meta.yml b/modules/nf-core/ivar/trim/meta.yml index 3a99f6f3bf4..eaeec80cb4e 100644 --- a/modules/nf-core/ivar/trim/meta.yml +++ b/modules/nf-core/ivar/trim/meta.yml @@ -11,42 +11,51 @@ tools: homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html licence: ["GPL-3.0-or-later"] + identifier: biotools:andersen-lab_ivar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Co-ordinate sorted BAM file - pattern: "*.bam" - - bai: - type: file - description: Index file for co-ordinate sorted BAM file - pattern: "*.bai" - - bed: - type: file - description: BED file with primer labels and positions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Co-ordinate sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index file for co-ordinate sorted BAM file + pattern: "*.bai" + - - bed: + type: file + description: BED file with primer labels and positions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: iVar generated trimmed bam file (unsorted) - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: iVar generated trimmed bam file (unsorted) + pattern: "*.bam" - log: - type: file - description: Log file generated by iVar for use with MultiQC - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file generated by iVar for use with MultiQC + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/nf-core/ivar/variants/meta.yml b/modules/nf-core/ivar/variants/meta.yml index 9dc9b05ca4e..369032bef10 100644 --- a/modules/nf-core/ivar/variants/meta.yml +++ b/modules/nf-core/ivar/variants/meta.yml @@ -11,50 +11,64 @@ tools: homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html licence: ["GPL-3.0-or-later"] + identifier: biotools:andersen-lab_ivar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - fai: - type: file - description: The index for the reference sequence used for mapping and generating the BAM file - pattern: "*.fai" - - gff: - type: file - description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. - patter: "*.gff" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar variants - patter: "*.mpileup" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam + file + pattern: "*.bam" + - - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM + file + pattern: "*.fa" + - - fai: + type: file + description: The index for the reference sequence used for mapping and generating + the BAM file + pattern: "*.fai" + - - gff: + type: file + description: A GFF file in the GFF3 format can be supplied to specify coordinates + of open reading frames (ORFs). In absence of GFF file, amino acid translation + will not be done. + patter: "*.gff" + - - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar variants + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tsv: - type: file - description: iVar generated TSV file with the variants - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: iVar generated TSV file with the variants + pattern: "*.tsv" - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup": + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/nf-core/jasminesv/environment.yml b/modules/nf-core/jasminesv/environment.yml index a0ef927ea41..7a0da03aa06 100644 --- a/modules/nf-core/jasminesv/environment.yml +++ b/modules/nf-core/jasminesv/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::jasminesv=1.1.5 - bioconda::htslib=1.15.1 + - bioconda::jasminesv=1.1.5 diff --git a/modules/nf-core/jasminesv/meta.yml b/modules/nf-core/jasminesv/meta.yml index 5d8b111cb8d..404b3282554 100644 --- a/modules/nf-core/jasminesv/meta.yml +++ b/modules/nf-core/jasminesv/meta.yml @@ -13,61 +13,67 @@ tools: documentation: "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual" tool_dev_url: "https://github.com/mkirsche/Jasmine" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - The VCF files that need to be merged - pattern: "*.{vcf,vcf.gz}" - - bams: - type: list - description: Optional - The BAM files from which the VCFs were created - pattern: "*.bam" - - sample_dists: - type: file - description: Optional - A txt file containing the distance thresholds for each sample - pattern: "*.txt" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Optional - The reference FASTA file used to create the VCFs - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing fasta index information - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: Optional - The index of the reference FASTA file used to create the VCFs - pattern: "*.fai" - - chr_norm: - type: file - description: Optional - A txt file containing the chromosomes and their aliases for normalization - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + The VCF files that need to be merged + pattern: "*.{vcf,vcf.gz}" + - bams: + type: list + description: Optional - The BAM files from which the VCFs were created + pattern: "*.bam" + - sample_dists: + type: file + description: Optional - A txt file containing the distance thresholds for each + sample + pattern: "*.txt" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Optional - The reference FASTA file used to create the VCFs + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing fasta index information + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: Optional - The index of the reference FASTA file used to create + the VCFs + pattern: "*.fai" + - - chr_norm: + type: file + description: Optional - A txt file containing the chromosomes and their aliases + for normalization + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The merged VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The merged VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/jupyternotebook/environment.yml b/modules/nf-core/jupyternotebook/environment.yml index d9ef11a3a9f..a11d11b0c61 100644 --- a/modules/nf-core/jupyternotebook/environment.yml +++ b/modules/nf-core/jupyternotebook/environment.yml @@ -1,9 +1,10 @@ channels: - conda-forge - bioconda + dependencies: - conda-forge::ipykernel=6.0.3 - conda-forge::jupytext=1.11.4 + - conda-forge::matplotlib=3.4.2 - conda-forge::nbconvert=6.1.0 - conda-forge::papermill=2.3.3 - - conda-forge::matplotlib=3.4.2 diff --git a/modules/nf-core/jupyternotebook/meta.yml b/modules/nf-core/jupyternotebook/meta.yml index 162171b62d4..093217416e0 100644 --- a/modules/nf-core/jupyternotebook/meta.yml +++ b/modules/nf-core/jupyternotebook/meta.yml @@ -16,51 +16,66 @@ tools: documentation: https://jupyter.org/documentation tool_dev_url: https://github.com/mwouts/jupytext/ license: ["MIT"] + identifier: "" - papermill: description: Parameterize, execute, and analyze notebooks homepage: https://github.com/nteract/papermill documentation: http://papermill.readthedocs.io/en/latest/ tool_dev_url: https://github.com/nteract/papermill license: ["BSD 3-clause"] + identifier: "" - nbconvert: description: Parameterize, execute, and analyze notebooks homepage: https://nbconvert.readthedocs.io/en/latest/ documentation: https://nbconvert.readthedocs.io/en/latest/ tool_dev_url: https://github.com/jupyter/nbconvert license: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - notebook: - type: file - description: Jupyter notebook or jupytext representation thereof - pattern: "*.{ipynb,py,md,Rmd,myst}" - - parameters: - type: map - description: | - Groovy map with notebook parameters which will be passed - to papermill in order to create parametrized reports. - - input_files: - type: file - description: One or multiple files serving as input data for the notebook. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - notebook: + type: file + description: Jupyter notebook or jupytext representation thereof + pattern: "*.{ipynb,py,md,Rmd,myst}" + - - parameters: + type: map + description: | + Groovy map with notebook parameters which will be passed + to papermill in order to create parametrized reports. + - - input_files: + type: file + description: One or multiple files serving as input data for the notebook. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: HTML report generated from Jupyter notebook - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: HTML report generated from Jupyter notebook + pattern: "*.html" + - artifacts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - artifacts/: + type: directory + description: Directory containing all artifacts generated by the notebook + pattern: "artifacts/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/jvarkit/vcffilterjdk/meta.yml b/modules/nf-core/jvarkit/vcffilterjdk/meta.yml index f4bce92102c..09e2232e9b9 100644 --- a/modules/nf-core/jvarkit/vcffilterjdk/meta.yml +++ b/modules/nf-core/jvarkit/vcffilterjdk/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "jvarkit_vcffilterjdk" description: Filtering VCF with dynamically-compiled java expressions @@ -19,6 +18,7 @@ tools: licence: ["MIT License"] args_id: "$args2" + identifier: "" - "bcftools": description: | View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF @@ -27,91 +27,107 @@ tools: doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] args_id: ["$args1", "$args3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test_reference' ] - - vcf: - type: file - description: Input VCF/BCF file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - tbi: - type: file - description: Optional VCF/BCF index file - pattern: "*.{tbi,csi}" - - regions_file: - type: file - description: Optional. Restrict to regions listed in a file - pattern: "*.{bed,bed.gz,txt,tsv}" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: Fasta reference file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing fasta.fai information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Fasta file index - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing fasta.dict information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing code information - e.g. [ id:'test_reference' ] - - code: - type: file - description: File containing custom user code . May be empty if script if provided via `task.ext.args2`. - pattern: "*.{code,script,txt,tsv,java,js}" - - meta6: - type: map - description: | - Groovy Map containing pedigree information - e.g. [ id:'test_reference' ] - - pedigree: - type: file - description: Optional jvarkit pedigree. - pattern: "*.{tsv,ped,pedigree}" + - - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test_reference' ] + - vcf: + type: file + description: Input VCF/BCF file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - tbi: + type: file + description: Optional VCF/BCF index file + pattern: "*.{tbi,csi}" + - regions_file: + type: file + description: Optional. Restrict to regions listed in a file + pattern: "*.{bed,bed.gz,txt,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: Fasta reference file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fasta.fai information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Fasta file index + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing fasta.dict information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing code information + e.g. [ id:'test_reference' ] + - code: + type: file + description: File containing custom user code . May be empty if script if provided + via `task.ext.args2`. + pattern: "*.{code,script,txt,tsv,java,js}" + - - meta6: + type: map + description: | + Groovy Map containing pedigree information + e.g. [ id:'test_reference' ] + - pedigree: + type: file + description: Optional jvarkit pedigree. + pattern: "*.{tsv,ped,pedigree}" output: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml index c70f23523cb..e71f3d43668 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml @@ -5,4 +5,3 @@ channels: - conda-forge dependencies: - "bioconda::jvarkit=2024.08.25" - - "bioconda:bcftools=1.20" diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml index 0e901704706..68b10488749 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml @@ -1,14 +1,11 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "jvarkit_vcfpolyx" description: annotate VCF files for poly repeats keywords: - vcf - bcf - - variant - annotation - repeats - - polyx tools: - "jvarkit": description: "Java utilities for Bioinformatics." @@ -17,7 +14,7 @@ tools: tool_dev_url: "https://github.com/lindenb/jvarkit" doi: "10.6084/m9.figshare.1425030" licence: ["MIT License"] - args_id: "$args2" + identifier: "" - "bcftools": description: | @@ -26,75 +23,79 @@ tools: documentation: "http://www.htslib.org/doc/bcftools.html" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] - args_id: ["$args1", "$args3"] + identifier: "" + input: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test_reference' ] - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test_reference' ] - - meta3: - type: map - description: | - Groovy Map containing fasta.fai information - e.g. [ id:'test_reference' ] - - meta4: - type: map - description: | - Groovy Map containing fasta.dict information - e.g. [ id:'test_reference' ] - - vcf: - type: file - description: Groovy Map containing reference genome information for vcf - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - tbi: - type: file - description: Optional VCF/BCF index file - pattern: "*.{tbi,csi}" - - regions_file: - type: file - description: Optional. Restrict to regions listed in a file - pattern: "*.{bed,bed.gz,txt,tsv}" - - fasta: - type: file - description: Groovy Map containing reference genome information for fai reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Groovy Map containing reference genome information for fai - pattern: "*.fasta.fai" - - dict: - type: file - description: Groovy Map containing reference genome information for GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing VCF information + - vcf: + type: file + description: Groovy Map containing reference genome information for vcf + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: Groovy Map containing reference genome information for fai reference + fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fasta.fai information + - fai: + type: file + description: Groovy Map containing reference genome information for fai + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing fasta.dict information + - dict: + type: file + description: Groovy Map containing reference genome information for GATK sequence + dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml b/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml index f087b0d89b3..aac166fc7a4 100644 --- a/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml +++ b/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "jvarkit_wgscoverageplotter" description: Plot whole genome coverage from BAM/CRAM file as SVG @@ -18,61 +17,64 @@ tools: tool_dev_url: "https://github.com/lindenb/jvarkit" doi: "10.6084/m9.figshare.1425030" licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference fai information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference dict information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference fai information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference dict information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing Sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Output SVG file - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing Sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: Output SVG file + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/kaiju/kaiju/meta.yml b/modules/nf-core/kaiju/kaiju/meta.yml index 33c85690757..ac9c681ec91 100644 --- a/modules/nf-core/kaiju/kaiju/meta.yml +++ b/modules/nf-core/kaiju/kaiju/meta.yml @@ -1,5 +1,6 @@ name: kaiju_kaiju -description: Taxonomic classification of metagenomic sequence data using a protein reference database +description: Taxonomic classification of metagenomic sequence data using a protein + reference database keywords: - classify - metagenomics @@ -13,37 +14,40 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}" - - db: - type: directory - description: | - List containing the database and nodes files for Kaiju - e.g. [ 'database.fmi', 'nodes.dmp' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}" + - - db: + type: directory + description: | + List containing the database and nodes files for Kaiju + e.g. [ 'database.fmi', 'nodes.dmp' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: Results with taxonomic classification of each read - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Results with taxonomic classification of each read + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@talnor" - "@sofstam" diff --git a/modules/nf-core/kaiju/kaiju2krona/meta.yml b/modules/nf-core/kaiju/kaiju2krona/meta.yml index 355416f84dd..965bf779a0f 100644 --- a/modules/nf-core/kaiju/kaiju2krona/meta.yml +++ b/modules/nf-core/kaiju/kaiju2krona/meta.yml @@ -1,5 +1,6 @@ name: kaiju_kaiju2krona -description: Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona. +description: Convert Kaiju's tab-separated output file into a tab-separated text file + which can be imported into Krona. keywords: - taxonomy - visualisation @@ -13,30 +14,36 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tsv: - type: file - description: Kaiju tab-separated output file - pattern: "*.{tsv,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tsv: + type: file + description: Kaiju tab-separated output file + pattern: "*.{tsv,txt}" + - - db: + type: file + description: Kaiju database file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Krona text-based input file converted from Kaiju report - pattern: "*.{txt,krona}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Krona text-based input file converted from Kaiju report + pattern: "*.{txt,krona}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/kaiju/kaiju2table/meta.yml b/modules/nf-core/kaiju/kaiju2table/meta.yml index 0f62374e8c5..b212cf0e055 100644 --- a/modules/nf-core/kaiju/kaiju2table/meta.yml +++ b/modules/nf-core/kaiju/kaiju2table/meta.yml @@ -12,36 +12,40 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - results: - type: file - description: File containing the kaiju classification results - pattern: "*.{txt}" - - taxon_rank: - type: string - description: | - Taxonomic rank to display in report - pattern: "phylum|class|order|family|genus|species" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Kaiju input file + - - db: + type: file + description: Kaiju database + - - taxon_rank: + type: string + description: | + Taxonomic rank to display in report + pattern: "phylum|class|order|family|genus|species" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - summary: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Kaiju output file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - results: - type: file - description: | - Summary table for a given taxonomic rank - pattern: "*.{tsv}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@talnor" diff --git a/modules/nf-core/kaiju/mergeoutputs/meta.yml b/modules/nf-core/kaiju/mergeoutputs/meta.yml index 4ec5000344c..b3b2deeef86 100644 --- a/modules/nf-core/kaiju/mergeoutputs/meta.yml +++ b/modules/nf-core/kaiju/mergeoutputs/meta.yml @@ -1,5 +1,6 @@ name: kaiju_mergeoutputs -description: Merge two tab-separated output files of Kaiju and Kraken in the column format +description: Merge two tab-separated output files of Kaiju and Kraken in the column + format keywords: - classify - metagenomics @@ -13,40 +14,44 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kaiju: - type: file - description: | - Results with taxonomic classification of each read from Kaiju - - kraken: - type: file - description: | - Results with taxonomic classification of each read from Kraken - pattern: "*.{tsv}" - - db: - type: directory - description: | - List containing the database and nodes files for Kaiju - e.g. [ 'database.fmi', 'nodes.dmp' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kaiju: + type: file + description: | + Results with taxonomic classification of each read from Kaiju + - kraken: + type: file + description: | + Results with taxonomic classification of each read from Kraken + pattern: "*.{tsv}" + - - db: + type: directory + description: | + List containing the database and nodes files for Kaiju + e.g. [ 'database.fmi', 'nodes.dmp' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - merged: - type: file - description: Results with merged taxonomic classification of each read based on the given strategy '1', '2', 'lca' [default] or 'lowest' - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Results with merged taxonomic classification of each read based + on the given strategy '1', '2', 'lca' [default] or 'lowest' + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/kaiju/mkfmi/meta.yml b/modules/nf-core/kaiju/mkfmi/meta.yml index fe06f3588f9..16532703735 100644 --- a/modules/nf-core/kaiju/mkfmi/meta.yml +++ b/modules/nf-core/kaiju/mkfmi/meta.yml @@ -15,30 +15,32 @@ tools: tool_dev_url: "https://github.com/bioinformatics-centre/kaiju" doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Uncompressed Protein FASTA file (mandatory) - pattern: "*.{fa,faa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Uncompressed Protein FASTA file (mandatory) + pattern: "*.{fa,faa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fmi: - type: file - description: Kaiju FM-index file - pattern: "*.{fmi}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fmi": + type: file + description: Kaiju FM-index file + pattern: "*.{fmi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml index 187f6bc3fae..8e9f5f137ee 100644 --- a/modules/nf-core/kalign/align/meta.yml +++ b/modules/nf-core/kalign/align/meta.yml @@ -12,33 +12,39 @@ tools: tool_dev_url: "https://github.com/TimoLassmann/kalign" doi: "10.1093/bioinformatics/btz795" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`. - pattern: "*.{aln}{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file. May be gzipped or uncompressed, depending on if + `compress` is set to `true` or `false`. + pattern: "*.{aln}{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml index d366aeb4553..4541074ed42 100644 --- a/modules/nf-core/kallisto/index/meta.yml +++ b/modules/nf-core/kallisto/index/meta.yml @@ -6,35 +6,40 @@ keywords: - index tools: - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. + description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq + data, or more generally of target sequences using high-throughput sequencing + reads. homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto licence: ["BSD-2-Clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: genome fasta file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: genome fasta file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - index: - type: directory - description: Kallisto genome index - pattern: "*.idx" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - kallisto: + type: directory + description: Kallisto genome index + pattern: "*.idx" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/kallisto/quant/meta.yml b/modules/nf-core/kallisto/quant/meta.yml index d5100290ffb..329268a170d 100644 --- a/modules/nf-core/kallisto/quant/meta.yml +++ b/modules/nf-core/kallisto/quant/meta.yml @@ -6,71 +6,85 @@ keywords: - pseudoalignment tools: - "kallisto": - description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads." + description: "Quantifying abundances of transcripts from RNA-Seq data, or more + generally of target sequences using high-throughput sequencing reads." homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto doi: "10.1038/nbt.3519" licence: ["BSD_2_clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fastq,fastq.gz}" - - index: - type: file - description: Kallisto genome index. - pattern: "*.idx" - - gtf: - type: file - description: Optional gtf file for translation of transcripts into genomic coordinates. - pattern: "*.gtf" - - chromosomes: - type: file - description: Optional tab separated file with chromosome names and lengths. - pattern: "*.tsv" - - fragment_length: - type: integer - description: For single-end mode only, the estimated average fragment length. - - fragment_length_sd: - type: integer - description: For single-end mode only, the estimated standard deviation of the fragment length. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fastq,fastq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Kallisto genome index. + pattern: "*.idx" + - - gtf: + type: file + description: Optional gtf file for translation of transcripts into genomic coordinates. + pattern: "*.gtf" + - - chromosomes: + type: file + description: Optional tab separated file with chromosome names and lengths. + pattern: "*.tsv" + - - fragment_length: + type: integer + description: For single-end mode only, the estimated average fragment length. + - - fragment_length_sd: + type: integer + description: For single-end mode only, the estimated standard deviation of the + fragment length. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Kallisto output file + - json_info: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.run_info.json": + type: file + description: JSON file containing information about the run + pattern: "*.run_info.json" - log: - type: file - description: File containing log information from running kallisto quant - pattern: "*.log.txt" - - abundance: - type: file - description: Plaintext file of the abundance estimates - pattern: "abundance.tsv" - - abundance_hdf5: - type: file - description: | - A HDF5 binary file containing run info, abundance estimates, bootstrap - estimates, and transcript length information - pattern: "abundance.h5" - - run_info: - type: file - description: A json file containing information about the run - pattern: "run_info.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File containing log information from running kallisto quant + pattern: "*.log.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml index 55d5dc6cdc4..c8160d7ad51 100644 --- a/modules/nf-core/kallistobustools/count/meta.yml +++ b/modules/nf-core/kallistobustools/count/meta.yml @@ -8,60 +8,70 @@ keywords: - bustools tools: - kb: - description: kallisto and bustools are wrapped in an easy-to-use program called kb + description: kallisto and bustools are wrapped in an easy-to-use program called + kb homepage: https://www.kallistobus.tools/ documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: kb-ref index file (.idx) - pattern: "*.{idx}" - - t2g: - type: file - description: t2g file from kallisto - pattern: "*t2g.txt" - - t1c: - type: file - description: kb ref's c1 cdna_t2c file - pattern: "*.{cdna_t2c.txt}" - - t2c: - type: file - description: kb ref's c2 intron_t2c file - pattern: "*.{intron_t2c.txt}" - - workflow_mode: - type: string - description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) - pattern: "{standard,lamanno,nac}" - - technology: - type: string - description: String value defining the sequencing technology used. - pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: file + description: kb-ref index file (.idx) + pattern: "*.{idx}" + - - t2g: + type: file + description: t2g file from kallisto + pattern: "*t2g.txt" + - - t1c: + type: file + description: kb ref's c1 cdna_t2c file + pattern: "*.{cdna_t2c.txt}" + - - t2c: + type: file + description: kb ref's c2 intron_t2c file + pattern: "*.{intron_t2c.txt}" + - - technology: + type: string + description: String value defining the sequencing technology used. + pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" + - - workflow_mode: + type: string + description: String value defining workflow to use, can be one of "standard", + "nac", "lamanno" (obsolete) + pattern: "{standard,lamanno,nac}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - count: - type: file - description: kb count output folder - pattern: "*.{count}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.count": + type: file + description: kb count output folder + pattern: "*.{count}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - matrix: + - "*.count/*/*.mtx": + type: file + description: file containing the count matrix + pattern: "*.mtx" authors: - "@flowuenne" maintainers: diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml index 64deab9b53d..6856c7fa532 100644 --- a/modules/nf-core/kallistobustools/ref/meta.yml +++ b/modules/nf-core/kallistobustools/ref/meta.yml @@ -9,54 +9,64 @@ keywords: - index tools: - kb: - description: kallisto|bustools (kb) is a tool developed for fast and efficient processing of single-cell OMICS data. + description: kallisto|bustools (kb) is a tool developed for fast and efficient + processing of single-cell OMICS data. homepage: https://www.kallistobus.tools/ documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python doi: "10.22002/D1.1876" licence: ["MIT"] + identifier: "" input: - - fasta: - type: file - description: Genomic DNA fasta file - pattern: "*.{fasta,fasta.gz}" - - gtf: - type: file - description: Genomic gtf file - pattern: "*.{gtf,gtf.gz}" - - workflow_mode: - type: string - description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) - pattern: "{standard,lamanno,nac}" + - - fasta: + type: file + description: Genomic DNA fasta file + pattern: "*.{fasta,fasta.gz}" + - - gtf: + type: file + description: Genomic gtf file + pattern: "*.{gtf,gtf.gz}" + - - workflow_mode: + type: string + description: String value defining workflow to use, can be one of "standard", + "nac", "lamanno" (obsolete) + pattern: "{standard,lamanno,nac}" output: - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - kb_ref_idx: - type: file - description: Index file from kb ref. - pattern: "*.{idx}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - index: + - kb_ref_out.idx: + type: file + description: kb ref index file + pattern: "*kb_ref_out.idx" - t2g: - type: file - description: Transcript to gene table - pattern: "*t2g.{txt}" + - t2g.txt: + type: file + description: Transcript to gene table + pattern: "*t2g.{txt}" - cdna: - type: file - description: cDNA fasta file - pattern: "*cdna.{fa}" + - cdna.fa: + type: file + description: cDNA fasta file + pattern: "*cdna.{fa}" - intron: - type: file - description: Intron fasta file - pattern: "*intron.{fa}" + - intron.fa: + type: file + description: Intron fasta file + pattern: "*intron.{fa}" - cdna_t2c: - type: file - description: cDNA transcript to capture file - pattern: "*cdna_t2c.{txt}" + - cdna_t2c.txt: + type: file + description: cDNA transcript to capture file + pattern: "*cdna_t2c.{txt}" - intron_t2c: - type: file - description: Intron transcript to capture file - pattern: "*intron_t2c.{txt}" + - intron_t2c.txt: + type: file + description: Intron transcript to capture file + pattern: "*intron_t2c.{txt}" authors: - "@flowuenne" maintainers: diff --git a/modules/nf-core/kat/hist/meta.yml b/modules/nf-core/kat/hist/meta.yml index c933c9582c3..02743621bdd 100644 --- a/modules/nf-core/kat/hist/meta.yml +++ b/modules/nf-core/kat/hist/meta.yml @@ -6,57 +6,91 @@ keywords: - count tools: - "kat": - description: "KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts" + description: "KAT is a suite of tools that analyse jellyfish hashes or sequence + files (fasta or fastq) using kmer counts" homepage: https://www.earlham.ac.uk/kat-tools documentation: https://kat.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/TGAC/KAT doi: 10.1093/bioinformatics/btw663 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: KAT histogram of k-mer counts - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: KAT histogram of k-mer counts + pattern: "*.hist" - json: - type: file - description: KAT histogram summary of distance analysis - pattern: "*.hist.dist_analysis.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.dist_analysis.json": + type: file + description: KAT histogram summary of distance analysis + pattern: "*.hist.dist_analysis.json" - png: - type: file - description: KAT plot of k-mer histogram in PNG format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: KAT plot of k-mer histogram in PNG format + pattern: "*.png" - ps: - type: file - description: KAT plot of k-mer histogram in PS format - pattern: "*.ps" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ps": + type: file + description: KAT plot of k-mer histogram in PS format + pattern: "*.ps" - pdf: - type: file - description: KAT plot of k-mer histogram in PDF format - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: KAT plot of k-mer histogram in PDF format + pattern: "*.pdf" - jellyfish_hash: - type: file - description: Jellyfish hash file - pattern: "*-hist.jf*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-hash.jf*": + type: file + description: Jellyfish hash file + pattern: "*-hist.jf*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/khmer/normalizebymedian/meta.yml b/modules/nf-core/khmer/normalizebymedian/meta.yml index 847d2b84d4d..757c1ae96ec 100644 --- a/modules/nf-core/khmer/normalizebymedian/meta.yml +++ b/modules/nf-core/khmer/normalizebymedian/meta.yml @@ -1,5 +1,7 @@ name: khmer_normalizebymedian -description: Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible. +description: Module that calls normalize-by-median.py from khmer. The module can take + a mix of paired end (interleaved) and single end reads. If both types are provided, + only a single file with single ends is possible. keywords: - digital normalization - khmer @@ -12,27 +14,30 @@ tools: tool_dev_url: https://github.com/dib-lab/khmer doi: "10.12688/f1000research.6924.1" licence: ["BSD License"] + identifier: biotools:khmer input: - - pe_reads: - type: file - description: Paired-end interleaved fastq files - pattern: "*.{fq,fastq}.gz" - - se_reads: - type: file - description: Single-end fastq files - pattern: "*.{fq,fastq}.gz" - - name: - type: string - description: filename for output file(s); ".fastq.gz" will be appended + - - pe_reads: + type: file + description: Paired-end interleaved fastq files + pattern: "*.{fq,fastq}.gz" + - - se_reads: + type: file + description: Single-end fastq files + pattern: "*.{fq,fastq}.gz" + - - name: + type: string + description: filename for output file(s); ".fastq.gz" will be appended output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Interleaved fastq files - pattern: "*.{fq,fastq}.gz" + - ${name}.fastq.gz: + type: file + description: Interleaved fastq files + pattern: "*.{fq,fastq}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/khmer/uniquekmers/meta.yml b/modules/nf-core/khmer/uniquekmers/meta.yml index f875bb7177d..a90294a880e 100644 --- a/modules/nf-core/khmer/uniquekmers/meta.yml +++ b/modules/nf-core/khmer/uniquekmers/meta.yml @@ -1,5 +1,6 @@ name: "khmer_uniquekmers" -description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more +description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal + and more keywords: - khmer - k-mer @@ -12,27 +13,31 @@ tools: tool_dev_url: https://github.com/dib-lab/khmer doi: "10.12688/f1000research.6924.1" licence: ["BSD License"] + identifier: biotools:khmer input: - - fasta: - type: file - description: fasta file - pattern: "*.{fa,fasta}" - - kmer_size: - type: integer - description: k-mer size to use + - - fasta: + type: file + description: fasta file + pattern: "*.{fa,fasta}" + - - kmer_size: + type: integer + description: k-mer size to use output: - report: - type: file - description: Text file containing unique-kmers.py execution report - pattern: "report.txt" + - report.txt: + type: file + description: Text file containing unique-kmers.py execution report + pattern: "report.txt" - kmers: - type: file - description: Text file containing number of kmers - pattern: "kmers.txt" + - kmers.txt: + type: file + description: Text file containing number of kmers + pattern: "kmers.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/kleborate/meta.yml b/modules/nf-core/kleborate/meta.yml index 54337527071..3fe9453a1f3 100644 --- a/modules/nf-core/kleborate/meta.yml +++ b/modules/nf-core/kleborate/meta.yml @@ -1,5 +1,6 @@ name: kleborate -description: Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC). +description: Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae + and the Klebsiella pneumoniae species complex (KpSC). keywords: - screen - assembly @@ -7,36 +8,40 @@ keywords: - pneumoniae tools: - kleborate: - description: Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest + description: Screening Klebsiella genome assemblies for MLST, sub-species, and + other Klebsiella related genes of interest homepage: https://github.com/katholt/Kleborate documentation: https://github.com/katholt/Kleborate/wiki tool_dev_url: https://github.com/katholt/Kleborate doi: 10.1038/s41467-021-24448-3 licence: ["GPL v3 or later (GPL v3+)"] + identifier: biotools:kleborate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastas: - type: list - description: Klebsiella genome assemblies to be screened - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastas: + type: list + description: Klebsiella genome assemblies to be screened + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Result file generated after screening - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Result file generated after screening + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@rpetit3" diff --git a/modules/nf-core/kmcp/compute/meta.yml b/modules/nf-core/kmcp/compute/meta.yml index 20cfe4a2c04..b10494230fc 100644 --- a/modules/nf-core/kmcp/compute/meta.yml +++ b/modules/nf-core/kmcp/compute/meta.yml @@ -9,40 +9,52 @@ keywords: - kmers tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: fasta file, or a directory containing FASTA files - pattern: "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: fasta file, or a directory containing FASTA files + pattern: "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - outdir: - type: directory - description: Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference. - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Output directory containing all .unik files and a summary file + in .txt format. Every .unik file contains the sequence/reference ID,chunk + index, number of chunks, and genome size of reference. + pattern: "*/" - info: - type: file - description: Summary file that is generated for later use - pattern: "*_info.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/_info.txt: + type: file + description: Summary file that is generated for later use + pattern: "*_info.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/index/meta.yml b/modules/nf-core/kmcp/index/meta.yml index 6942dc0fdf2..e3e4a91e352 100644 --- a/modules/nf-core/kmcp/index/meta.yml +++ b/modules/nf-core/kmcp/index/meta.yml @@ -10,40 +10,50 @@ keywords: - index tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - compute_dir: - type: directory - description: Output directory generated by "kmcp compute" - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - compute_dir: + type: directory + description: Output directory generated by "kmcp compute" + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - kmcp: - type: directory - description: Output directory containing the database from k-mer files. - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Output directory containing the database from k-mer files. + pattern: "*/" - log: - type: file - description: A log of kmcp/index output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: A log of kmcp/index output + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/merge/meta.yml b/modules/nf-core/kmcp/merge/meta.yml index 3a367fa42e9..99650fb806b 100644 --- a/modules/nf-core/kmcp/merge/meta.yml +++ b/modules/nf-core/kmcp/merge/meta.yml @@ -9,36 +9,40 @@ keywords: - kmers tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - search_out: - type: file - description: The output file created by kmcp search - pattern: "*.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - search_out: + type: file + description: The output file created by kmcp search + pattern: "*.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - result: - type: file - description: Output file in gzipped format - pattern: "*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Output file in gzipped format + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/profile/meta.yml b/modules/nf-core/kmcp/profile/meta.yml index ba1ca2a27ed..be5fe9cd124 100644 --- a/modules/nf-core/kmcp/profile/meta.yml +++ b/modules/nf-core/kmcp/profile/meta.yml @@ -10,40 +10,43 @@ keywords: - index tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://bioinf.shenwei.me/kmcp/usage/#profile" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - search_results: - type: file - description: Gzipped file output from kmcp search module - pattern: "*.gz" - - db: - type: directory - description: Database directory containing taxdump files and taxid file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - search_results: + type: file + description: Gzipped file output from kmcp search module + pattern: "*.gz" + - - db: + type: directory + description: Database directory containing taxdump files and taxid file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: file - description: Tab-delimited format file with 17 columns. - pattern: "*.profile" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.profile": + type: file + description: Tab-delimited format file with 17 columns. + pattern: "*.profile" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/search/meta.yml b/modules/nf-core/kmcp/search/meta.yml index 6d003b04f69..11baf5bda01 100644 --- a/modules/nf-core/kmcp/search/meta.yml +++ b/modules/nf-core/kmcp/search/meta.yml @@ -9,40 +9,44 @@ keywords: - kmers tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: gzipped fasta or fastq files - pattern: "*.{fq.gz,fastq.gz,fa.gz}" - - db: - type: directory - description: Database directory created by "kmcp index" - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: gzipped fasta or fastq files + pattern: "*.{fq.gz,fastq.gz,fa.gz}" + - - db: + type: directory + description: Database directory created by "kmcp index" + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - result: - type: file - description: Output file in tab-delimited format with 15 columns - pattern: "*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Output file in tab-delimited format with 15 columns + pattern: "*.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kofamscan/meta.yml b/modules/nf-core/kofamscan/meta.yml index 06f2872a4e8..d7cc333db73 100644 --- a/modules/nf-core/kofamscan/meta.yml +++ b/modules/nf-core/kofamscan/meta.yml @@ -1,48 +1,62 @@ name: "kofamscan" -description: Produces annotation using kofamscan against a Profile database and a KO list +description: Produces annotation using kofamscan against a Profile database and a + KO list keywords: - fasta - kegg - kofamscan tools: - "kofamscan": - description: "KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam" + description: "KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH + against KOfam" homepage: "https://www.genome.jp/tools/kofamkoala/" documentation: "https://github.com/takaram/kofam_scan" tool_dev_url: "https://github.com/takaram/kofam_scan" doi: "10.1093/bioinformatics/btz859" licence: ["MIT License"] + identifier: biotools:kofamscan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta}" - - profiles: - type: directory - description: Directory containing the Profiles database - pattern: "*" - - ko_list: - type: file - description: File containing list of KO entries with their data - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta}" + - - profiles: + type: directory + description: Directory containing the Profiles database + pattern: "*" + - - ko_list: + type: file + description: File containing list of KO entries with their data + pattern: "*.{fa,fasta}" output: - txt: - type: file - description: Application-specific text file with hits information - pattern: "*.{txt}" + - meta: + type: file + description: Application-specific text file with hits information + pattern: "*.{txt}" + - "*.txt": + type: file + description: Application-specific text file with hits information + pattern: "*.{txt}" - tsv: - type: file - description: Tab separated file containing with detailed hits - pattern: "*.{tsv}" + - meta: + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/kraken2/add/meta.yml b/modules/nf-core/kraken2/add/meta.yml index e5bc2d79c4f..e1ad7d93aad 100644 --- a/modules/nf-core/kraken2/add/meta.yml +++ b/modules/nf-core/kraken2/add/meta.yml @@ -9,48 +9,52 @@ keywords: - add tools: - kraken2: - description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + description: "Kraken2 is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies." homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fasta: - type: file - description: fasta file that will be added to the database - pattern: "*.{fa,fasta,fna,ffn}" - - taxonomy_names: - type: file - description: used for associating sequences with taxonomy IDs - pattern: "*.dmp" - - taxonomy_nodes: - type: file - description: tree nodes using NCBI taxonomy nomenclature - pattern: "*.dmp" - - accession2taxid: - type: file - description: associates sequence accession IDs to taxonomy IDs - pattern: "*.accession2taxid" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: fasta file that will be added to the database + pattern: "*.{fa,fasta,fna,ffn}" + - - taxonomy_names: + type: file + description: used for associating sequences with taxonomy IDs + pattern: "*.dmp" + - - taxonomy_nodes: + type: file + description: tree nodes using NCBI taxonomy nomenclature + pattern: "*.dmp" + - - accession2taxid: + type: file + description: associates sequence accession IDs to taxonomy IDs + pattern: "*.accession2taxid" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - db: - type: directory - description: contains required files to build the database - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $prefix: + type: directory + description: contains required files to build the database + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/kraken2/build/meta.yml b/modules/nf-core/kraken2/build/meta.yml index 50f6d19379c..6d7da1d14b6 100644 --- a/modules/nf-core/kraken2/build/meta.yml +++ b/modules/nf-core/kraken2/build/meta.yml @@ -8,40 +8,45 @@ keywords: - kraken2 tools: - kraken2: - description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + description: "Kraken2 is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies." homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] args_id: "$args" + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - db: - type: directory - description: contains required files to build the database - pattern: "*/" - - cleaning: - type: boolean - description: activate or deactivate (true or false) cleaning of intermediate files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - db: + type: directory + description: contains required files to build the database + pattern: "*/" + - - cleaning: + type: boolean + description: activate or deactivate (true or false) cleaning of intermediate + files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - db: - type: directory - description: contains the database that can be used to perform taxonomic classification - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $prefix: + type: directory + description: contains the database that can be used to perform taxonomic classification + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/kraken2/buildstandard/meta.yml b/modules/nf-core/kraken2/buildstandard/meta.yml index d09ac3d239f..566b10b5a4e 100644 --- a/modules/nf-core/kraken2/buildstandard/meta.yml +++ b/modules/nf-core/kraken2/buildstandard/meta.yml @@ -10,26 +10,32 @@ keywords: - download tools: - kraken2: - description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + description: "Kraken2 is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies." homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] args_id: "$args" + identifier: biotools:kraken2 input: - - cleaning: - type: boolean - description: activate or deactivate (true or false) cleaning of intermediate files + - - cleaning: + type: boolean + description: activate or deactivate (true or false) cleaning of intermediate + files output: - db: - type: directory - description: Directory containing the Kraken2 'standard' database that can be used to perform taxonomic classification - pattern: "*/" + - $prefix: + type: directory + description: Directory containing the Kraken2 'standard' database that can be + used to perform taxonomic classification + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@egreenberg7" maintainers: diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml index 7909ffe7e17..8693764679c 100644 --- a/modules/nf-core/kraken2/kraken2/meta.yml +++ b/modules/nf-core/kraken2/kraken2/meta.yml @@ -13,63 +13,84 @@ tools: documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - db: - type: directory - description: Kraken2 database - - save_output_fastqs: - type: string - description: | - If true, optional commands are added to save classified and unclassified reads - as fastq files - - save_reads_assignment: - type: string - description: | - If true, an optional command is added to save a file reporting the taxonomic - classification of each input read + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - db: + type: directory + description: Kraken2 database + - - save_output_fastqs: + type: string + description: | + If true, optional commands are added to save classified and unclassified reads + as fastq files + - - save_reads_assignment: + type: string + description: | + If true, an optional command is added to save a file reporting the taxonomic + classification of each input read output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classified_reads_fastq: - type: file - description: | - Reads classified as belonging to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.classified{.,_}*": + type: file + description: | + Reads classified as belonging to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - unclassified_reads_fastq: - type: file - description: | - Reads not classified to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unclassified{.,_}*": + type: file + description: | + Reads not classified to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - classified_reads_assignment: - type: file - description: | - Kraken2 output file indicating the taxonomic assignment of - each input read + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classifiedreads.txt": + type: file + description: | + Kraken2 output file indicating the taxonomic assignment of + each input read - report: - type: file - description: | - Kraken2 report containing stats about classified - and not classifed reads. - pattern: "*.{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: | + Kraken2 report containing stats about classified + and not classifed reads. + pattern: "*.{report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/krakentools/combinekreports/meta.yml b/modules/nf-core/krakentools/combinekreports/meta.yml index b35d12147e6..bb69d34a694 100644 --- a/modules/nf-core/krakentools/combinekreports/meta.yml +++ b/modules/nf-core/krakentools/combinekreports/meta.yml @@ -1,5 +1,6 @@ name: krakentools_combinekreports -description: Takes multiple kraken-style reports and combines them into a single report file +description: Takes multiple kraken-style reports and combines them into a single report + file keywords: - kraken - krakentools @@ -9,33 +10,38 @@ keywords: - merging tools: - krakentools: - description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs. + description: KrakenTools is a suite of scripts to be used for post-analysis of + Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if + using KrakenTools with any of the listed programs. homepage: https://github.com/jenniferlu717/KrakenTools licence: ["GPL v3"] + identifier: biotools:krakentools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kreports: - type: file - description: List of kraken-style report files - pattern: "*.{txt,kreport}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kreports: + type: file + description: List of kraken-style report files + pattern: "*.{txt,kreport}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined kreport file of all input files - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Combined kreport file of all input files + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakentools/extractkrakenreads/meta.yml b/modules/nf-core/krakentools/extractkrakenreads/meta.yml index ee8b125d938..b772ba0f5be 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/meta.yml +++ b/modules/nf-core/krakentools/extractkrakenreads/meta.yml @@ -6,49 +6,64 @@ keywords: - metagenomics tools: - "krakentools": - description: "KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs." + description: "KrakenTools is a suite of scripts to be used for post-analysis of + Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if + using KrakenTools with any of the listed programs." homepage: https://github.com/jenniferlu717/KrakenTools documentation: https://github.com/jenniferlu717/KrakenTools?tab=readme-ov-file#extract_kraken_readspy tool_dev_url: https://github.com/jenniferlu717/KrakenTools doi: 10.1038/s41596-022-00738-y licence: ["GPL v3"] + identifier: biotools:krakentools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - taxid: - type: string - description: A list of taxid separated by spaces - - classified_reads_assignment: - type: file - description: A file contains the taxonomic classification of each input read. - pattern: "*.{classifiedreads.txt}" - - classified_reads_fastq: - type: file - description: Classified reads as belonging to any of the taxa on the kraken2 database. - pattern: "*.{fastq.gz}" - - report: - type: file - description: Optional Kraken2 report containing stats about classified and not classifed reads. - pattern: "*.{report.txt}" - + - - taxid: + type: string + description: A list of taxid separated by spaces + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - classified_reads_assignment: + type: file + description: A file contains the taxonomic classification of each input read. + pattern: "*.{classifiedreads.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - classified_reads_fastq: + type: file + description: Classified reads as belonging to any of the taxa on the kraken2 + database. + pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - report: + type: file + description: Optional Kraken2 report containing stats about classified and not + classifed reads. + pattern: "*.{report.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - extracted_kraken2_reads: - type: file - description: Reads assigned to a taxid list. - pattern: "*.{fastq,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{fastq,fasta}": + type: file + description: Reads assigned to a taxid list. + pattern: "*.{fastq,fasta}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/krakentools/kreport2krona/meta.yml b/modules/nf-core/krakentools/kreport2krona/meta.yml index ae5bf2f15b8..d0f0a57e3b4 100644 --- a/modules/nf-core/krakentools/kreport2krona/meta.yml +++ b/modules/nf-core/krakentools/kreport2krona/meta.yml @@ -7,33 +7,38 @@ keywords: - visualization tools: - krakentools: - description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs. + description: KrakenTools is a suite of scripts to be used for post-analysis of + Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if + using KrakenTools with any of the listed programs. homepage: https://github.com/jenniferlu717/KrakenTools licence: ["GPL v3"] + identifier: biotools:krakentools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kreport: - type: file - description: Kraken report - pattern: "*.{txt,kreport}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kreport: + type: file + description: Kraken report + pattern: "*.{txt,kreport}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Krona text-based input file converted from Kraken report - pattern: "*.{txt,krona}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Krona text-based input file converted from Kraken report + pattern: "*.{txt,krona}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/krakenuniq/build/meta.yml b/modules/nf-core/krakenuniq/build/meta.yml index f63b3250d25..bafc3cfa04e 100644 --- a/modules/nf-core/krakenuniq/build/meta.yml +++ b/modules/nf-core/krakenuniq/build/meta.yml @@ -8,40 +8,48 @@ keywords: - ncbi tools: - "krakenuniq": - description: "Metagenomics classifier with unique k-mer counting for more specific results" + description: "Metagenomics classifier with unique k-mer counting for more specific + results" homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq tool_dev_url: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 licence: ["MIT"] + identifier: biotools:KrakenUniq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - custom_library_dir: - type: directory - description: Optional directory containing custom fasta files for database build - pattern: "*" - - custom_taxonomy_dir: - type: directory - description: Optional directory containing custom taxonomy files for database build - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - custom_library_dir: + type: directory + description: Optional directory containing custom fasta files for database build + pattern: "*" + - custom_taxonomy_dir: + type: directory + description: Optional directory containing custom taxonomy files for database + build + pattern: "*" + - custom_seqid2taxid: + type: file + description: custom seqid2taxid output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: Directory containing KrakenUniq database - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix/: + type: directory + description: Directory containing KrakenUniq database + pattern: "*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakenuniq/download/meta.yml b/modules/nf-core/krakenuniq/download/meta.yml index ace0f6bec46..fdbac474744 100644 --- a/modules/nf-core/krakenuniq/download/meta.yml +++ b/modules/nf-core/krakenuniq/download/meta.yml @@ -8,34 +8,30 @@ keywords: - ncbi tools: - "krakenuniq": - description: "Metagenomics classifier with unique k-mer counting for more specific results" + description: "Metagenomics classifier with unique k-mer counting for more specific + results" homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq tool_dev_url: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 licence: ["MIT"] + identifier: biotools:KrakenUniq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pattern: - type: string - description: Pattern indicating what type of NCBI data to download. See KrakenUniq documnation for possibilities. + - - pattern: + type: string + description: Pattern indicating what type of NCBI data to download. See KrakenUniq + documnation for possibilities. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: directory - description: Directory containing downloaded data with directory naming being the user provided pattern. + - ${pattern}/: + type: directory + description: Directory containing downloaded data with directory naming being + the user provided pattern. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml index bb6409a6289..1af2350d69b 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml @@ -8,77 +8,103 @@ keywords: - db tools: - "krakenuniq": - description: "Metagenomics classifier with unique k-mer counting for more specific results" + description: "Metagenomics classifier with unique k-mer counting for more specific + results" homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 licence: ["MIT"] + identifier: biotools:KrakenUniq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: List of input files containing sequences. All of them must be either in FASTA or FASTQ format. - - sequence_type: - type: string - description: Format of all given sequencing files as literal string, either 'fasta' or 'fastq'. - pattern: "{fasta,fastq}" - - db: - type: directory - description: KrakenUniq database - - ram_chunk_size: - type: string - description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time - pattern: "*GB" - - save_output_reads: - type: boolean - description: | - Optionally, commands are added to save classified and unclassified reads - as FASTQ or FASTA files depending on the input format. When the input - is paired-end, the single output FASTQ contains merged reads. - - report_file: - type: boolean - description: Whether to generate a report of relative abundances. - - save_output: - type: boolean - description: Whether to save a file reporting the taxonomic classification of each input read. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: List of input files containing sequences. All of them must be either + in FASTA or FASTQ format. + - - sequence_type: + type: string + description: Format of all given sequencing files as literal string, either + 'fasta' or 'fastq'. + pattern: "{fasta,fastq}" + - - db: + type: directory + description: KrakenUniq database + - - ram_chunk_size: + type: string + description: Amount of maximum amount of RAM each chunk of database that should + be loaded at any one time + pattern: "*GB" + - - save_output_reads: + type: boolean + description: | + Optionally, commands are added to save classified and unclassified reads + as FASTQ or FASTA files depending on the input format. When the input + is paired-end, the single output FASTQ contains merged reads. + - - report_file: + type: boolean + description: Whether to generate a report of relative abundances. + - - save_output: + type: boolean + description: Whether to save a file reporting the taxonomic classification of + each input read. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classified_reads: - type: file - description: | - Reads classified as belonging to any of the taxa - in the KrakenUniq reference database. - pattern: "*.classified.{fastq,fasta}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.classified.${sequence_type}.gz": + type: file + description: | + Reads classified as belonging to any of the taxa + in the KrakenUniq reference database. + pattern: "*.classified.{fastq,fasta}.gz" - unclassified_reads: - type: file - description: | - Reads not classified to any of the taxa - in the KrakenUniq reference database. - pattern: "*.unclassified.{fastq,fasta}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unclassified.${sequence_type}.gz": + type: file + description: | + Reads not classified to any of the taxa + in the KrakenUniq reference database. + pattern: "*.unclassified.{fastq,fasta}.gz" - classified_assignment: - type: file - description: | - KrakenUniq output file indicating the taxonomic assignment of - each input read ## DOUBLE CHECK!! - pattern: "*.krakenuniq.classified.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.krakenuniq.classified.txt": + type: file + description: | + KrakenUniq output file indicating the taxonomic assignment of + each input read ## DOUBLE CHECK!! + pattern: "*.krakenuniq.classified.txt" - report: - type: file - description: | - KrakenUniq report containing statistics about classified - and unclassified reads. - pattern: "*.krakenuniq.report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.krakenuniq.report.txt": + type: file + description: | + KrakenUniq report containing statistics about classified + and unclassified reads. + pattern: "*.krakenuniq.report.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjamy" - "@Midnighter" diff --git a/modules/nf-core/krona/kronadb/meta.yml b/modules/nf-core/krona/kronadb/meta.yml index 0d42bb10fc2..2eaf3f88097 100644 --- a/modules/nf-core/krona/kronadb/meta.yml +++ b/modules/nf-core/krona/kronadb/meta.yml @@ -6,20 +6,25 @@ keywords: - krona tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: https://github.com/marbl/Krona/wiki/Installing - doi: 10.1186/1471-2105-12-385 -# There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + doi: + 10.1186/1471-2105-12-385 + # There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + identifier: biotools:krona output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: A TAB separated file that contains a taxonomy database. - pattern: "*.{tab}" + - taxonomy/taxonomy.tab: + type: file + description: A TAB separated file that contains a taxonomy database. + pattern: "*.{tab}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjakobs" maintainers: diff --git a/modules/nf-core/krona/ktimporttaxonomy/meta.yml b/modules/nf-core/krona/ktimporttaxonomy/meta.yml index 3504b13e57b..87f84787c1f 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/meta.yml +++ b/modules/nf-core/krona/ktimporttaxonomy/meta.yml @@ -1,5 +1,6 @@ name: krona_ktimporttaxonomy -description: KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot. +description: KronaTools Import Taxonomy imports taxonomy classifications and produces + an interactive Krona plot. keywords: - plot - taxonomy @@ -9,36 +10,47 @@ keywords: - krona chart tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html doi: 10.1186/1471-2105-12-385 + identifier: biotools:krona input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - taxonomy: - type: file - description: | - Path to a Krona taxonomy .tab file normally downloaded and generated by - krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but - must end in `.tab`. - pattern: "*tab" - - report: - type: file - description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored." - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - report: + type: file + description: "A tab-delimited file with taxonomy IDs and (optionally) query + IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy + IDs from column 2, and scores from column 3. Lines beginning with # will + be ignored." + pattern: "*.{tsv}" + - - taxonomy: + type: file + description: | + Path to a Krona taxonomy .tab file normally downloaded and generated by + krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but + must end in `.tab`. + pattern: "*tab" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: A html file containing an interactive krona plot. - pattern: "*.{html}" + - meta: + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + - "*.html": + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjakobs" maintainers: diff --git a/modules/nf-core/krona/ktimporttext/meta.yml b/modules/nf-core/krona/ktimporttext/meta.yml index 5288ea0b47e..56b15096554 100644 --- a/modules/nf-core/krona/ktimporttext/meta.yml +++ b/modules/nf-core/krona/ktimporttext/meta.yml @@ -10,36 +10,45 @@ keywords: - metagenomics tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html tool_dev_url: https://github.com/marbl/Krona doi: 10.1186/1471-2105-12-385 licence: ["https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt"] + identifier: biotools:krona input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - report: - type: file - description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored." - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - report: + type: file + description: "Tab-delimited text file. Each line should be a number followed + by a list of wedges to contribute to (starting from the highest level). If + no wedges are listed (and just a quantity is given), it will contribute to + the top level. If the same lineage is listed more than once, the values will + be added. Quantities can be omitted if -q is specified. Lines beginning with + '#' will be ignored." + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: A html file containing an interactive krona plot. - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.html": + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/krona/ktupdatetaxonomy/meta.yml b/modules/nf-core/krona/ktupdatetaxonomy/meta.yml index 40540cce3ba..d7b5e80d08d 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/meta.yml +++ b/modules/nf-core/krona/ktupdatetaxonomy/meta.yml @@ -7,20 +7,25 @@ keywords: - visualisation tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: https://github.com/marbl/Krona/wiki/Installing - doi: 10.1186/1471-2105-12-385 -# There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + doi: + 10.1186/1471-2105-12-385 + # There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + identifier: biotools:krona output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: A TAB separated file that contains a taxonomy database. - pattern: "*.{tab}" + - taxonomy/taxonomy.tab: + type: file + description: A TAB separated file that contains a taxonomy database. + pattern: "*.{tab}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjakobs" maintainers: diff --git a/modules/nf-core/last/dotplot/meta.yml b/modules/nf-core/last/dotplot/meta.yml index 5243743a5f9..1bb1460cd69 100644 --- a/modules/nf-core/last/dotplot/meta.yml +++ b/modules/nf-core/last/dotplot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_dotplot" description: Makes a dotplot (Oxford Grid) of pair-wise sequence alignments @@ -15,45 +14,61 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" - - format: - type: string - description: Output format (PNG or GIF). - - annot_a: - type: file - description: Annotation file in BED, Repeamasker, genePred or AGP format for the first (horizontal) sequence - pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" - - annot_b: - type: file - description: Annotation file in BED, Repeamasker, genePred or AGP format for the second (vertical) sequence - pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - annot_b: + type: file + description: Annotation file in BED, Repeamasker, genePred or AGP format for + the second (vertical) sequence + pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample2', single_end:false ]` + - annot_a: + type: file + description: Annotation file in BED, Repeamasker, genePred or AGP format for + the first (horizontal) sequence + pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + - - format: + type: string + description: Output format (PNG or GIF). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - png: - type: file - description: Pairwise alignment dot plot image, in PNG format. - pattern: "*.png" - gif: - type: file - description: Pairwise alignment dot plot image, in GIF format. - pattern: "*.gif" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gif": + type: file + description: Pairwise alignment dot plot image, in GIF format. + pattern: "*.gif" + - png: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.png": + type: file + description: Pairwise alignment dot plot image, in PNG format. + pattern: "*.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/lastal/meta.yml b/modules/nf-core/last/lastal/meta.yml index c14fa27989d..ed6610f7ba7 100644 --- a/modules/nf-core/last/lastal/meta.yml +++ b/modules/nf-core/last/lastal/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_lastal" description: Aligns query sequences to target sequences indexed with lastdb @@ -14,42 +13,51 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: FASTA/FASTQ file - pattern: "*.{fasta,fastq}" - - param_file: - type: file - description: Trained parameter file - pattern: "*.train" - - index: - type: directory - description: Directory containing the files of the LAST index - pattern: "lastdb/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: FASTA/FASTQ file + pattern: "*.{fasta,fastq}" + - param_file: + type: file + description: Trained parameter file + pattern: "*.train" + - - index: + type: directory + description: Directory containing the files of the LAST index + pattern: "lastdb/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Gzipped MAF (Multiple Alignment Format) file - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Gzipped MAF (Multiple Alignment Format) file + pattern: "*.{maf.gz}" - multiqc: - type: file - description: Alignment summary for MultiQC - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Alignment summary for MultiQC + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/lastdb/meta.yml b/modules/nf-core/last/lastdb/meta.yml index c3b499e7322..5c7be378602 100644 --- a/modules/nf-core/last/lastdb/meta.yml +++ b/modules/nf-core/last/lastdb/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_lastdb" description: Prepare sequences for subsequent alignment with lastal. @@ -14,31 +13,34 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: > - Sequence file in FASTA or FASTQ format. May be compressed with gzip. - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: > + Sequence file in FASTA or FASTQ format. May be compressed with gzip. + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: directory containing the files of the LAST index - pattern: "lastdb/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - lastdb: + type: directory + description: directory containing the files of the LAST index + pattern: "lastdb/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/mafconvert/meta.yml b/modules/nf-core/last/mafconvert/meta.yml index e9ee29a3a70..0bc690aa766 100644 --- a/modules/nf-core/last/mafconvert/meta.yml +++ b/modules/nf-core/last/mafconvert/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_mafconvert" description: Converts MAF alignments in another format. @@ -14,65 +13,118 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, optionally compressed with gzip - pattern: "*.{maf.gz,maf}" - - format: - type: string - description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, optionally compressed with + gzip + pattern: "*.{maf.gz,maf}" + - - format: + type: string + description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, + sam, or tab) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - axt_gz: - type: file - description: Gzipped pairwise alignment in Axt (Blastz) format (optional) - pattern: "*.axt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.axt.gz": + type: file + description: Gzipped pairwise alignment in Axt (Blastz) format (optional) + pattern: "*.axt.gz" - blast_gz: - type: file - description: Gzipped pairwise alignment in blast format (optional) - pattern: "*.blast.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.blast.gz": + type: file + description: Gzipped pairwise alignment in blast format (optional) + pattern: "*.blast.gz" - blasttab_gz: - type: file - description: Gzipped pairwise alignment in blasttab format (optional) - pattern: "*.blasttab.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.blasttab.gz": + type: file + description: Gzipped pairwise alignment in blasttab format (optional) + pattern: "*.blasttab.gz" - chain_gz: - type: file - description: Gzipped pairwise alignment in UCSC chain format (optional) - pattern: "*.chain.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.chain.gz": + type: file + description: Gzipped pairwise alignment in UCSC chain format (optional) + pattern: "*.chain.gz" - gff_gz: - type: file - description: Gzipped pairwise alignment in GFF format (optional) - pattern: "*.gff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gff.gz": + type: file + description: Gzipped pairwise alignment in GFF format (optional) + pattern: "*.gff.gz" - html_gz: - type: file - description: Gzipped pairwise alignment in HTML format (optional) - pattern: "*.html.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.html.gz": + type: file + description: Gzipped pairwise alignment in HTML format (optional) + pattern: "*.html.gz" - psl_gz: - type: file - description: Gzipped pairwise alignment in PSL (BLAT) format (optional) - pattern: "*.psl.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.psl.gz": + type: file + description: Gzipped pairwise alignment in PSL (BLAT) format (optional) + pattern: "*.psl.gz" - sam_gz: - type: file - description: Gzipped pairwise alignment in SAM format (optional) - pattern: "*.sam.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.sam.gz": + type: file + description: Gzipped pairwise alignment in SAM format (optional) + pattern: "*.sam.gz" - tab_gz: - type: file - description: Gzipped pairwise alignment in TAB format (optional) - pattern: "*.tab.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tab.gz": + type: file + description: Gzipped pairwise alignment in TAB format (optional) + pattern: "*.tab.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aleksandrabliznina" - "@charles-plessy" diff --git a/modules/nf-core/last/mafswap/meta.yml b/modules/nf-core/last/mafswap/meta.yml index aa0fc09d443..4b9642a648a 100644 --- a/modules/nf-core/last/mafswap/meta.yml +++ b/modules/nf-core/last/mafswap/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_mafswap" description: Reorder alignments in a MAF file @@ -14,30 +13,34 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, optionally compressed with gzip - pattern: "*.{maf.gz,maf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, optionally compressed with + gzip + pattern: "*.{maf.gz,maf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/postmask/meta.yml b/modules/nf-core/last/postmask/meta.yml index 7be957ffe65..925e07561d2 100644 --- a/modules/nf-core/last/postmask/meta.yml +++ b/modules/nf-core/last/postmask/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_postmask" description: Post-alignment masking @@ -15,30 +14,34 @@ tools: tool_dev_url: "https://gitlab.com/mcfrith/last" doi: "10.1371/journal.pone.0028819" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, optionally compressed with gzip - pattern: "*.{maf.gz,maf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, optionally compressed with + gzip + pattern: "*.{maf.gz,maf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/split/meta.yml b/modules/nf-core/last/split/meta.yml index 2e23f8b4c6a..7864d0fff32 100644 --- a/modules/nf-core/last/split/meta.yml +++ b/modules/nf-core/last/split/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_split" description: Find split or spliced alignments in a MAF file @@ -15,35 +14,43 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" - multiqc: - type: file - description: Alignment summary for MultiQC - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Alignment summary for MultiQC + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aleksandrabliznina" - "@charles-plessy" diff --git a/modules/nf-core/last/train/meta.yml b/modules/nf-core/last/train/meta.yml index d55e82734b3..d91cecaf796 100644 --- a/modules/nf-core/last/train/meta.yml +++ b/modules/nf-core/last/train/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_train" description: Find suitable score parameters for sequence alignment @@ -14,38 +13,47 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: FASTA/FASTQ file - pattern: "*.{fasta,fastq}" - - index: - type: directory - description: Directory containing the files of the LAST index - pattern: "lastdb/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: FASTA/FASTQ file + pattern: "*.{fasta,fastq}" + - - index: + type: directory + description: Directory containing the files of the LAST index + pattern: "lastdb/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - param_file: - type: file - description: Trained parameter file - pattern: "*.train" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.train": + type: file + description: Trained parameter file + pattern: "*.train" - multiqc: - type: file - description: Alignment parameter summary for MultiQC - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Alignment parameter summary for MultiQC + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aleksandrabliznina" - "@charles-plessy" diff --git a/modules/nf-core/learnmsa/align/meta.yml b/modules/nf-core/learnmsa/align/meta.yml index 66a9f7d12c9..b3e549fea7b 100644 --- a/modules/nf-core/learnmsa/align/meta.yml +++ b/modules/nf-core/learnmsa/align/meta.yml @@ -12,33 +12,38 @@ tools: tool_dev_url: "https://github.com/Gaius-Augustus/learnMSA" doi: "10.1093/gigascience/giac104" licence: ["MIT"] + identifier: biotools:learnMSA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format. May be gz-compressed or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format. May be gz-compressed or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed. - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed. + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/leehom/meta.yml b/modules/nf-core/leehom/meta.yml index 38f5407b334..fb466319fb8 100644 --- a/modules/nf-core/leehom/meta.yml +++ b/modules/nf-core/leehom/meta.yml @@ -17,58 +17,103 @@ tools: tool_dev_url: "https://github.com/grenaud/leeHom" doi: "10.1093/nar/gku699" licence: ["GPL v3"] + identifier: biotools:leehom input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Unaligned BAM or one or two gzipped FASTQ file(s) - pattern: "*.{bam,fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Unaligned BAM or one or two gzipped FASTQ file(s) + pattern: "*.{bam,fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file + pattern: "*.bam" - fq_pass: - type: file - description: Trimmed and merged FASTQ - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fq.gz: + type: file + description: Trimmed and merged FASTQ + pattern: "*.fq.gz" - fq_fail: - type: file - description: Failed trimmed and merged FASTQs - pattern: "*.fail.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fail.fq.gz: + type: file + description: Failed trimmed and merged FASTQs + pattern: "*.fail.fq.gz" - unmerged_r1_fq_pass: - type: file - description: Passed unmerged R1 FASTQs - pattern: "*.r1.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r1.fq.gz: + type: file + description: Passed unmerged R1 FASTQs + pattern: "*.r1.fq.gz" - unmerged_r1_fq_fail: - type: file - description: Failed unmerged R1 FASTQs - pattern: "*.r1.fail.fq.gz" - - unmerged_r2_fq_pass: - type: file - description: Passed unmerged R2 FASTQs - pattern: "*.r2.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r1.fail.fq.gz: + type: file + description: Failed unmerged R1 FASTQs + pattern: "*.r1.fail.fq.gz" - unmerged_r2_fq_pass: - type: file - description: Failed unmerged R2 FASTQs - pattern: "*.r2.fail.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r2.fq.gz: + type: file + description: Passed unmerged R2 FASTQs + pattern: "*.r2.fq.gz" + - unmerged_r2_fq_fail: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r2.fail.fq.gz: + type: file + description: Failed unmerged R2 FASTQs + pattern: "*.r2.fail.fq.gz" - log: - type: file - description: Log file of command - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file of command + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/legsta/meta.yml b/modules/nf-core/legsta/meta.yml index 734498e0612..bccb2e9e8b3 100644 --- a/modules/nf-core/legsta/meta.yml +++ b/modules/nf-core/legsta/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://github.com/tseemann/legsta tool_dev_url: https://github.com/tseemann/legsta licence: ["GPL v3"] + identifier: biotools:legsta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTA, GenBank or EMBL formatted files - pattern: "*.{fasta,gbk,embl}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTA, GenBank or EMBL formatted files + pattern: "*.{fasta,gbk,embl}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited summary of the results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited summary of the results + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/leviosam2/index/meta.yml b/modules/nf-core/leviosam2/index/meta.yml index ab5a3a279b2..780cf230155 100644 --- a/modules/nf-core/leviosam2/index/meta.yml +++ b/modules/nf-core/leviosam2/index/meta.yml @@ -1,4 +1,3 @@ ---- name: "leviosam2_index" description: Index chain files for lift over keywords: @@ -11,34 +10,37 @@ tools: homepage: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" documentation: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - - fai: - type: file - description: FAI (FASTA index) file of the target reference - pattern: "*.{fai}" - - chain: - type: file - description: Chain file to index. - pattern: "*.{chain}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - fai: + type: file + description: FAI (FASTA index) file of the target reference + pattern: "*.{fai}" + - - chain: + type: file + description: Chain file to index. + pattern: "*.{chain}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - clft: - type: file - description: Clft file of indexed chain - pattern: "*.{clft}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - "*.clft": + type: file + description: Clft file of indexed chain + pattern: "*.{clft}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lgrochowalski" maintainers: diff --git a/modules/nf-core/leviosam2/lift/meta.yml b/modules/nf-core/leviosam2/lift/meta.yml index 043e5286b3d..f56b8d33b54 100644 --- a/modules/nf-core/leviosam2/lift/meta.yml +++ b/modules/nf-core/leviosam2/lift/meta.yml @@ -1,6 +1,6 @@ ---- name: "leviosam2_lift" -description: Converting aligned short and long reads records from one reference to another +description: Converting aligned short and long reads records from one reference to + another keywords: - leviosam2 - index @@ -11,39 +11,42 @@ tools: homepage: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" documentation: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - input: - type: file - description: SAM/BAM/CRAM file to be lifted - pattern: "*.{bam}" - - meta_ref: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - clft: - type: file - description: Clft file of indexed ChainMap. - pattern: "*.{clft}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - input: + type: file + description: SAM/BAM/CRAM file to be lifted + pattern: "*.{bam}" + - - meta_ref: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - clft: + type: file + description: Clft file of indexed ChainMap. + pattern: "*.{clft}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - bam: - type: file - description: Lifted bam file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - "*.bam": + type: file + description: Lifted bam file + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lgrochowalski" maintainers: diff --git a/modules/nf-core/liftoff/meta.yml b/modules/nf-core/liftoff/meta.yml index 10e502c150b..a8ed079fbd5 100644 --- a/modules/nf-core/liftoff/meta.yml +++ b/modules/nf-core/liftoff/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "liftoff" description: | @@ -20,51 +19,66 @@ tools: tool_dev_url: "https://github.com/agshumate/Liftoff" doi: "10.1093/bioinformatics/bty191" licence: ["GPL v3 License"] + identifier: biotools:liftoff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - target_fa: - type: file - description: Target assembly in fasta format - pattern: "*.{fsa,fa,fasta}" - - ref_fa: - type: file - description: Reference assembly in fasta format - pattern: "*.{fsa,fa,fasta}" - - ref_annotation: - type: file - description: Reference assembly annotations in gtf or gff3 format - pattern: "*.{gtf,gff3}" - - ref_db: - type: file - description: | - Name of feature database; if not specified, the -g argument must - be provided and a database will be built automatically + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - target_fa: + type: file + description: Target assembly in fasta format + pattern: "*.{fsa,fa,fasta}" + - - ref_fa: + type: file + description: Reference assembly in fasta format + pattern: "*.{fsa,fa,fasta}" + - - ref_annotation: + type: file + description: Reference assembly annotations in gtf or gff3 format + pattern: "*.{gtf,gff3}" + - - ref_db: + type: file + description: | + Name of feature database; if not specified, the -g argument must + be provided and a database will be built automatically output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - gff3: - type: file - description: Lifted annotations for the target assembly in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.gff3: + type: file + description: Lifted annotations for the target assembly in gff3 format + pattern: "*.gff3" - polished_gff3: - type: file - description: Polished lifted annotations for the target assembly in gff3 format - pattern: "*.polished.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.polished.gff3": + type: file + description: Polished lifted annotations for the target assembly in gff3 format + pattern: "*.polished.gff3" - unmapped_txt: - type: file - description: List of unmapped reference annotations - pattern: "*.unmapped.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.unmapped.txt": + type: file + description: List of unmapped reference annotations + pattern: "*.unmapped.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/lima/meta.yml b/modules/nf-core/lima/meta.yml index ad4ebbfa0c5..f22973f0fca 100644 --- a/modules/nf-core/lima/meta.yml +++ b/modules/nf-core/lima/meta.yml @@ -13,82 +13,161 @@ tools: documentation: https://lima.how/ tool_dev_url: https://github.com/pacificbiosciences/barcoding/ licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - ccs: - type: file - description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs - pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" - - primers: - type: file - description: Fasta file, sequences of primers - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ccs: + type: file + description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads + or ccs + pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" + - - primers: + type: file + description: Fasta file, sequences of primers + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: A bam file of ccs purged of primers - pattern: "*.bam" - - pbi: - type: file - description: Pacbio index file of ccs purged of primers - pattern: "*.bam" - - xml: - type: file - description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads. - pattern: "*.xml" - - json: - type: file - description: A metadata json file - pattern: "*.json" - - clips: - type: file - description: A fasta file of clipped primers - pattern: "*.clips" - counts: - type: file - description: A tabulated file of describing pairs of primers - pattern: "*.counts" - - guess: - type: file - description: A second tabulated file of describing pairs of primers (no doc available) - pattern: "*.guess" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.counts": + type: file + description: A tabulated file of describing pairs of primers + pattern: "*.counts" - report: - type: file - description: A tab-separated file about each ZMW, unfiltered - pattern: "*.report" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.report": + type: file + description: A tab-separated file about each ZMW, unfiltered + pattern: "*.report" - summary: - type: file - description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered. - pattern: "*.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.summary": + type: file + description: This file shows how many ZMWs have been filtered, how ZMWs many + are same/different, and how many reads have been filtered. + pattern: "*.summary" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: A bam file of ccs purged of primers + pattern: "*.bam" + - pbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam.pbi": + type: file + description: Pacbio index file of ccs purged of primers + pattern: "*.bam" - fasta: - type: file - description: A fasta file of ccs purged of primers. - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.{fa, fasta}": + type: file + description: A fasta file of ccs purged of primers. + pattern: "*.fa" - fastagz: - type: file - description: A fasta.gz file of ccs purged of primers. - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.{fa.gz, fasta.gz}": + type: file + description: A fasta.gz file of ccs purged of primers. + pattern: "*.fasta.gz" - fastq: - type: file - description: A fastq file of ccs purged of primers. - pattern: "*.fastq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fastq": + type: file + description: A fastq file of ccs purged of primers. + pattern: "*.fastq" - fastqgz: - type: file - description: A fastq.gz file of ccs purged of primers. - pattern: "*.fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fastq.gz": + type: file + description: A fastq.gz file of ccs purged of primers. + pattern: "*.fastq.gz" + - xml: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xml": + type: file + description: An XML file representing a set of a particular sequence data type + such as subreads, references or aligned subreads. + pattern: "*.xml" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: A metadata json file + pattern: "*.json" + - clips: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.clips": + type: file + description: A fasta file of clipped primers + pattern: "*.clips" + - guess: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.guess": + type: file + description: A second tabulated file of describing pairs of primers (no doc + available) + pattern: "*.guess" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/limma/differential/meta.yml b/modules/nf-core/limma/differential/meta.yml index 132573db2cb..f76c57a42b3 100644 --- a/modules/nf-core/limma/differential/meta.yml +++ b/modules/nf-core/limma/differential/meta.yml @@ -13,68 +13,96 @@ tools: tool_dev_url: https://github.com/cran/limma"" doi: "10.18129/B9.bioc.limma" licence: ["LGPL >=3"] + identifier: biotools:limma input: - - meta: - type: map - description: | - Groovy Map containing contrast information. This can be used at the - workflow level to pass optional parameters to the module, e.g. - [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: - '--blocking_variable $meta.blocking'. - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheeet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - intensities: - type: file - description: | - Raw TSV or CSV format expression matrix with probes by row and samples - by column + - - meta: + type: map + description: | + Groovy Map containing contrast information. This can be used at the + workflow level to pass optional parameters to the module, e.g. + [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: + '--blocking_variable $meta.blocking'. + - contrast_variable: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: Sample sheet file + - intensities: + type: file + description: | + Raw TSV or CSV format expression matrix with probes by row and samples + by column output: - results: - type: file - description: TSV-format table of differential expression information as output by Limma - pattern: "*.limma.results.tsv" + - meta: + type: file + description: TSV-format table of differential expression information as output + by Limma + pattern: "*.limma.results.tsv" + - "*.limma.results.tsv": + type: file + description: TSV-format table of differential expression information as output + by Limma + pattern: "*.limma.results.tsv" - md_plot: - type: file - description: Limma mean difference plot - pattern: "*.mean_difference.png" + - meta: + type: file + description: Limma mean difference plot + pattern: "*.mean_difference.png" + - "*.limma.mean_difference.png": + type: file + description: Limma mean difference plot + pattern: "*.mean_difference.png" - rdata: - type: file - description: Serialised MArrayLM object - pattern: "*.MArrayLM.limma.rds" + - meta: + type: file + description: Serialised MArrayLM object + pattern: "*.MArrayLM.limma.rds" + - "*.MArrayLM.limma.rds": + type: file + description: Serialised MArrayLM object + pattern: "*.MArrayLM.limma.rds" - model: - type: file - description: TXT-format limma model - pattern: "*.limma.model.tsv" + - meta: + type: file + description: TXT-format limma model + pattern: "*.limma.model.tsv" + - "*.limma.model.txt": + type: file + description: TXT-format limma model + pattern: "*.limma.model.tsv" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: file + description: dump of R SessionInfo + pattern: "*.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/lissero/meta.yml b/modules/nf-core/lissero/meta.yml index 92a7eee7d65..cf74f9d34b3 100644 --- a/modules/nf-core/lissero/meta.yml +++ b/modules/nf-core/lissero/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/MDU-PHL/LisSero/blob/master/README.md tool_dev_url: https://github.com/MDU-PHL/lissero licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/lofreq/alnqual/meta.yml b/modules/nf-core/lofreq/alnqual/meta.yml index b80a73ce39e..22ddc74db85 100644 --- a/modules/nf-core/lofreq/alnqual/meta.yml +++ b/modules/nf-core/lofreq/alnqual/meta.yml @@ -7,39 +7,43 @@ keywords: - bam tools: - "lofreq": - description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data" + description: "A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data" homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: 10.1093/nar/gks918 licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM/CRAM/SAM file with base and indel alignment qualities - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: BAM/CRAM/SAM file with base and indel alignment qualities + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MarieLataretu" maintainers: diff --git a/modules/nf-core/lofreq/call/meta.yml b/modules/nf-core/lofreq/call/meta.yml index 523790d5932..d2895b8d90a 100644 --- a/modules/nf-core/lofreq/call/meta.yml +++ b/modules/nf-core/lofreq/call/meta.yml @@ -7,42 +7,46 @@ keywords: - lofreq/call tools: - lofreq: - description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data + description: A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: "10.1093/nar/gks918 " licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM input file - pattern: "*.{bam}" - - intervals: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - fasta: - type: file - description: The reference fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM input file + pattern: "*.{bam}" + - intervals: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - - fasta: + type: file + description: The reference fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF output file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF output file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/lofreq/callparallel/meta.yml b/modules/nf-core/lofreq/callparallel/meta.yml index 2884773231e..25a33e85c48 100644 --- a/modules/nf-core/lofreq/callparallel/meta.yml +++ b/modules/nf-core/lofreq/callparallel/meta.yml @@ -7,65 +7,76 @@ keywords: - variants tools: - lofreq: - description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors + description: Lofreq is a fast and sensitive variant-caller for inferring SNVs + and indels from next-generation sequencing data. It's call-parallel programme + predicts variants using multiple processors homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: Tumor sample sorted BAM file - pattern: "*.{bam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bam.bai}" - - intervals: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing sample information about the reference fasta - e.g. [ id:'reference' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing sample information about the reference fasta fai - e.g. [ id:'reference' ] - - fai: - type: file - description: Reference genome FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: Tumor sample sorted BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bam.bai}" + - intervals: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the reference fasta + e.g. [ id:'reference' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information about the reference fasta fai + e.g. [ id:'reference' ] + - fai: + type: file + description: Reference genome FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Predicted variants file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Predicted variants file + pattern: "*.{vcf}" - tbi: - type: file - description: Index of vcf file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of vcf file + pattern: "*.{vcf.gz.tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" - "@bjohnnyd" diff --git a/modules/nf-core/lofreq/filter/meta.yml b/modules/nf-core/lofreq/filter/meta.yml index debc303e7bb..f73d440e387 100644 --- a/modules/nf-core/lofreq/filter/meta.yml +++ b/modules/nf-core/lofreq/filter/meta.yml @@ -1,5 +1,6 @@ name: lofreq_filter -description: Lofreq subcommand to remove variants with low coverage or strand bias potential +description: Lofreq subcommand to remove variants with low coverage or strand bias + potential keywords: - variant calling - low frequency variant calling @@ -8,35 +9,39 @@ keywords: - lofreq/filter tools: - lofreq: - description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data + description: A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: "10.1093/nar/gks918 " licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: VCF filtered output file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/lofreq/indelqual/meta.yml b/modules/nf-core/lofreq/indelqual/meta.yml index ac82792f7e5..00788b114fe 100644 --- a/modules/nf-core/lofreq/indelqual/meta.yml +++ b/modules/nf-core/lofreq/indelqual/meta.yml @@ -8,43 +8,48 @@ keywords: - qualities tools: - lofreq: - description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file + description: Lofreq is a fast and sensitive variant-caller for inferring SNVs + and indels from next-generation sequencing data. It's indelqual programme inserts + indel qualities in a BAM file homepage: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing sample information about the reference fasta - e.g. [ id:'reference' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the reference fasta + e.g. [ id:'reference' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with indel qualities inserted into it - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with indel qualities inserted into it + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" maintainers: diff --git a/modules/nf-core/lofreq/somatic/meta.yml b/modules/nf-core/lofreq/somatic/meta.yml index f29b538481d..face259e530 100644 --- a/modules/nf-core/lofreq/somatic/meta.yml +++ b/modules/nf-core/lofreq/somatic/meta.yml @@ -1,5 +1,6 @@ name: "lofreq_somatic" -description: Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available +description: Lofreq subcommand to call low frequency variants from alignments when + tumor-normal paired samples are available keywords: - variant calling - low frequency variant calling @@ -8,63 +9,68 @@ keywords: - vcf tools: - "lofreq": - description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data" + description: "A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data" homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: 10.1093/nar/gks918 licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: Groovy Map containing reference information - - meta3: - type: map - description: Groovy Map containing reference information - - tumor: - type: file - description: tumor sample input BAM file - pattern: "*.{bam}" - - tumor_index: - type: file - description: tumor sample BAM index file - pattern: "*.{bam.bai}" - - normal: - type: file - description: normal sample input BAM file - pattern: "*.{bam}" - - normal_index: - type: file - description: normal sample BAM index file - pattern: "*.{bam.bai}" - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" - - fai: - type: file - description: Reference genome FASTA index file - pattern: "*.{fai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - tumor: + type: file + description: tumor sample input BAM file + pattern: "*.{bam}" + - tumor_index: + type: file + description: tumor sample BAM index file + pattern: "*.{bam.bai}" + - normal: + type: file + description: normal sample input BAM file + pattern: "*.{bam}" + - normal_index: + type: file + description: normal sample BAM index file + pattern: "*.{bam.bai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - - meta2: + type: map + description: Groovy Map containing reference information + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" + - - meta3: + type: map + description: Groovy Map containing reference information + - fai: + type: file + description: Reference genome FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nevinwu" maintainers: diff --git a/modules/nf-core/lofreq/viterbi/meta.yml b/modules/nf-core/lofreq/viterbi/meta.yml index 197e9158564..f05d2b778d7 100644 --- a/modules/nf-core/lofreq/viterbi/meta.yml +++ b/modules/nf-core/lofreq/viterbi/meta.yml @@ -1,5 +1,6 @@ name: "lofreq_viterbi" -description: Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available +description: Lofreq subcommand to call low frequency variants from alignments when + tumor-normal paired samples are available keywords: - variant calling - low frequency variant calling @@ -8,47 +9,49 @@ keywords: - probabilistic realignment tools: - "lofreq": - description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data" + description: "A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data" homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: 10.1093/nar/gks918 licence: ["MIT"] + identifier: biotools:lofreq input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing sample information about the reference fasta - e.g. [ id:'reference' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the reference fasta + e.g. [ id:'reference' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Realignment and sorted BAM file - pattern: "*.{bam}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Realignment and sorted BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MarieLataretu" maintainers: diff --git a/modules/nf-core/longphase/haplotag/meta.yml b/modules/nf-core/longphase/haplotag/meta.yml index 2fe7c5693b1..d2f2ec8d583 100644 --- a/modules/nf-core/longphase/haplotag/meta.yml +++ b/modules/nf-core/longphase/haplotag/meta.yml @@ -1,88 +1,93 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "longphase_haplotag" -description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. +description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, + small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. keywords: - haplotag - long-read - genomics tools: - "longphase": - description: "LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms." + description: "LongPhase is an ultra-fast program for simultaneously co-phasing + SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio + platforms." homepage: "https://github.com/twolinin/longphase" documentation: "https://github.com/twolinin/longphase" tool_dev_url: "https://github.com/twolinin/longphase" doi: "10.1093/bioinformatics/btac058" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index of sorted BAM/CRAM file - pattern: "*.{bai,crai,csi}" - - snps: - type: file - description: VCF file with SNPs (and INDELs) - pattern: "*.{vcf,vcf.gz}" - - svs: - type: file - description: VCF file with SVs - pattern: "*.{vcf,vcf.gz}" - - mods: - type: file - description: modcall-generated VCF with modifications - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fai: - type: file - description: Reference fai index - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index of sorted BAM/CRAM file + pattern: "*.{bai,crai,csi}" + - snps: + type: file + description: VCF file with SNPs (and INDELs) + pattern: "*.{vcf,vcf.gz}" + - svs: + type: file + description: VCF file with SVs + pattern: "*.{vcf,vcf.gz}" + - mods: + type: file + description: modcall-generated VCF with modifications + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fai: + type: file + description: Reference fai index + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with haplotagged reads - pattern: "*.bam" - - cram: - type: file - description: CRAM file with haplotagged reads - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{bam,cram}": + type: file + description: BAM file with haplotagged reads + pattern: "*.bam" - log: - type: file - description: Log file - pattern: "*.log" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/longphase/phase/environment.yml b/modules/nf-core/longphase/phase/environment.yml index 96e04eb61b9..bb2d0eeebd1 100644 --- a/modules/nf-core/longphase/phase/environment.yml +++ b/modules/nf-core/longphase/phase/environment.yml @@ -1,8 +1,7 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - "bioconda::longphase=1.7.3" - - "bioconda::htslib=1.20" + - bioconda::htslib=1.20 + - bioconda::longphase=1.7.3 diff --git a/modules/nf-core/longphase/phase/meta.yml b/modules/nf-core/longphase/phase/meta.yml index 42899177603..823645d441e 100644 --- a/modules/nf-core/longphase/phase/meta.yml +++ b/modules/nf-core/longphase/phase/meta.yml @@ -1,80 +1,83 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "longphase_phase" -description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. +description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, + small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. keywords: - phase - long-read - genomics tools: - "longphase": - description: "LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms." + description: "LongPhase is an ultra-fast program for simultaneously co-phasing + SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio + platforms." homepage: "https://github.com/twolinin/longphase" documentation: "https://github.com/twolinin/longphase" tool_dev_url: "https://github.com/twolinin/longphase" doi: "10.1093/bioinformatics/btac058" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file(s) - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index of sorted BAM/CRAM file(s) - pattern: "*.{bai,crai,csi}" - - snps: - type: file - description: VCF file with SNPs (and INDELs) - pattern: "*.{vcf,vcf.gz}" - - svs: - type: file - description: VCF file with SVs - pattern: "*.{vcf,vcf.gz}" - - mods: - type: file - description: modcall-generated VCF with modifications - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fai: - type: file - description: Reference fai index - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file(s) + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index of sorted BAM/CRAM file(s) + pattern: "*.{bai,crai,csi}" + - snps: + type: file + description: VCF file with SNPs (and INDELs) + pattern: "*.{vcf,vcf.gz}" + - svs: + type: file + description: VCF file with SVs + pattern: "*.{vcf,vcf.gz}" + - mods: + type: file + description: modcall-generated VCF with modifications + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fai: + type: file + description: Reference fai index + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file with phased variants - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Compressed VCF file with phased variants + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/ltrfinder/meta.yml b/modules/nf-core/ltrfinder/meta.yml index e3c672b9cd3..547fb67d0f8 100644 --- a/modules/nf-core/ltrfinder/meta.yml +++ b/modules/nf-core/ltrfinder/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrfinder" description: | @@ -19,41 +18,52 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_FINDER_parallel" doi: "10.1186/s13100-019-0193-0" licence: ["MIT"] + identifier: "" - "LTR_Finder": - description: An efficient program for finding full-length LTR retrotranspsons in genome sequences + description: An efficient program for finding full-length LTR retrotranspsons + in genome sequences homepage: "https://github.com/xzhub/LTR_Finder" documentation: "https://github.com/xzhub/LTR_Finder" tool_dev_url: "https://github.com/xzhub/LTR_Finder" doi: "10.1093/nar/gkm286" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Genome sequences in fasta format - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome sequences in fasta format + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - scn: - type: file - description: Annotation in LTRharvest or LTR_FINDER format - pattern: "*.scn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Annotation in LTRharvest or LTR_FINDER format + pattern: "*.scn" - gff: - type: file - description: Annotation in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Annotation in gff3 format + pattern: "*.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/ltrharvest/meta.yml b/modules/nf-core/ltrharvest/meta.yml index 256b3ce52f2..18064183d7a 100644 --- a/modules/nf-core/ltrharvest/meta.yml +++ b/modules/nf-core/ltrharvest/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrharvest" description: | @@ -18,6 +17,7 @@ tools: documentation: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" tool_dev_url: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" licence: ["MIT"] + identifier: "" - "gt": description: "The GenomeTools genome analysis system" homepage: "https://genometools.org/index.html" @@ -25,34 +25,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Input genome fasta - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input genome fasta + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff3: - type: file - description: Predicted LTR candidates in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Predicted LTR candidates in gff3 format + pattern: "*.gff3" - scn: - type: file - description: Predicted LTR candidates in scn format - pattern: "*.scn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Predicted LTR candidates in scn format + pattern: "*.scn" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/ltrretriever/lai/meta.yml b/modules/nf-core/ltrretriever/lai/meta.yml index f84cf6ca329..56efcccc05e 100644 --- a/modules/nf-core/ltrretriever/lai/meta.yml +++ b/modules/nf-core/ltrretriever/lai/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrretriever_lai" description: | @@ -20,50 +19,59 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_retriever" doi: "10.1093/nar/gky730" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The genome file that is used to generate everything - pattern: "*.{fsa,fa,fasta}" - - pass_list: - type: file - description: A list of intact LTR-RTs generated by LTR_retriever - pattern: "*.pass.list" - - annotation_out: - type: file - description: RepeatMasker annotation of all LTR sequences in the genome - pattern: "*.out" - - monoploid_seqs: - type: file - description: | - This parameter is mainly for ployploid genomes. User provides a list of - sequence names that represent a monoploid (1x). LAI will be calculated only - on these sequences if provided. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The genome file that is used to generate everything + pattern: "*.{fsa,fa,fasta}" + - - pass_list: + type: file + description: A list of intact LTR-RTs generated by LTR_retriever + pattern: "*.pass.list" + - - annotation_out: + type: file + description: RepeatMasker annotation of all LTR sequences in the genome + pattern: "*.out" + - - monoploid_seqs: + type: file + description: | + This parameter is mainly for ployploid genomes. User provides a list of + sequence names that represent a monoploid (1x). LAI will be calculated only + on these sequences if provided. + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - log: - type: file - description: Log from LAI - pattern: "*.LAI.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.LAI.log": + type: file + description: Log from LAI + pattern: "*.LAI.log" - lai_out: - type: file - description: | - Output file from LAI if LAI is able to estimate the index from the inputs - pattern: "*.LAI.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.LAI.out": + type: file + description: | + Output file from LAI if LAI is able to estimate the index from the inputs + pattern: "*.LAI.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/ltrretriever/ltrretriever/meta.yml b/modules/nf-core/ltrretriever/ltrretriever/meta.yml index a310b04af81..9645de2d957 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/meta.yml +++ b/modules/nf-core/ltrretriever/ltrretriever/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrretriever_ltrretriever" description: Identifies LTR retrotransposons using LTR_retriever @@ -16,67 +15,104 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_retriever" doi: "10.1104/pp.17.01310" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - genome: - type: file - description: Genomic sequences in fasta format - pattern: "*.{fsa,fa,fasta}" - - harvest: - type: file - description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular format - pattern: "*.tabout" - - finder: - type: file - description: LTR-RT candidates from LTR_FINDER - pattern: "*.scn" - - mgescan: - type: file - description: LTR-RT candidates from MGEScan_LTR - pattern: "*.out" - - non_tgca: - type: file - description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format - pattern: "*.tabout" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - genome: + type: file + description: Genomic sequences in fasta format + pattern: "*.{fsa,fa,fasta}" + - - harvest: + type: file + description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular + format + pattern: "*.tabout" + - - finder: + type: file + description: LTR-RT candidates from LTR_FINDER + pattern: "*.scn" + - - mgescan: + type: file + description: LTR-RT candidates from MGEScan_LTR + pattern: "*.out" + - - non_tgca: + type: file + description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in + the old tabular format + pattern: "*.tabout" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - log: - type: file - description: Output log from LTR_retriever - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Output log from LTR_retriever + pattern: "*.log" - pass_list: - type: file - description: Intact LTR-RTs with coordinate and structural information in summary table format - pattern: "*.pass.list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.pass.list: + type: file + description: Intact LTR-RTs with coordinate and structural information in summary + table format + pattern: "*.pass.list" - pass_list_gff: - type: file - description: Intact LTR-RTs with coordinate and structural information in gff3 format - pattern: "*.pass.list.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.pass.list.gff3": + type: file + description: Intact LTR-RTs with coordinate and structural information in gff3 + format + pattern: "*.pass.list.gff3" - ltrlib: - type: file - description: All non-redundant LTR-RTs - pattern: "*.LTRlib.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.LTRlib.fa": + type: file + description: All non-redundant LTR-RTs + pattern: "*.LTRlib.fa" - annotation_out: - type: file - description: Whole-genome LTR-RT annotation by the non-redundant library - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.out: + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library + pattern: "*.out" - annotation_gff: - type: file - description: Whole-genome LTR-RT annotation by the non-redundant library in gff3 format - pattern: "*.out.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.out.gff3": + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library in + gff3 format + pattern: "*.out.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/macrel/contigs/meta.yml b/modules/nf-core/macrel/contigs/meta.yml index ba0b0e6f5d5..c1c03f42526 100644 --- a/modules/nf-core/macrel/contigs/meta.yml +++ b/modules/nf-core/macrel/contigs/meta.yml @@ -1,5 +1,7 @@ name: macrel_contigs -description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found. +description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by + predicting peptides from genomes (provided as contigs) and outputs all the predicted + anti-microbial peptides found. keywords: - AMP - antimicrobial peptides @@ -14,46 +16,76 @@ tools: tool_dev_url: https://github.com/BigDataBiology/macrel doi: "10.7717/peerj.10555" licence: ["MIT"] + identifier: biotools:macrel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A fasta file with nucleotide sequences. - pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A fasta file with nucleotide sequences. + pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - amp_prediction: - type: file - description: A zipped file, with all predicted amps in a table format. - pattern: "*.prediction.gz" - smorfs: - type: file - description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs. - pattern: "*.smorfs.faa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.smorfs.faa.gz": + type: file + description: A zipped fasta file containing aminoacid sequences showing the + general gene prediction information in the contigs. + pattern: "*.smorfs.faa.gz" - all_orfs: - type: file - description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs. - pattern: "*.all_orfs.faa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.all_orfs.faa.gz": + type: file + description: A zipped fasta file containing amino acid sequences showing the + general gene prediction information in the contigs. + pattern: "*.all_orfs.faa.gz" + - amp_prediction: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.prediction.gz": + type: file + description: A zipped file, with all predicted amps in a table format. + pattern: "*.prediction.gz" - readme_file: - type: file - description: A readme file containing tool specific information (e.g. citations, details about the output, etc.). - pattern: "*.md" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.md": + type: file + description: A readme file containing tool specific information (e.g. citations, + details about the output, etc.). + pattern: "*.md" - log_file: - type: file - description: A log file containing the information pertaining to the run. - pattern: "*_log.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*_log.txt": + type: file + description: A log file containing the information pertaining to the run. + pattern: "*_log.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/macs2/callpeak/meta.yml b/modules/nf-core/macs2/callpeak/meta.yml index 68ecd4ef372..149f04df3cd 100644 --- a/modules/nf-core/macs2/callpeak/meta.yml +++ b/modules/nf-core/macs2/callpeak/meta.yml @@ -12,46 +12,75 @@ tools: tool_dev_url: https://github.com/macs3-project/MACS doi: "10.1101/496521" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ipbam: - type: file - description: The ChIP-seq treatment file - - controlbam: - type: file - description: The control file - - macs2_gsize: - type: string - description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ipbam: + type: file + description: The ChIP-seq treatment file + - controlbam: + type: file + description: The control file + - - macs2_gsize: + type: string + description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' + for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and + 'dm' for fruitfly (1.2e8) output: - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - peak: - type: file - description: BED file containing annotated peaks - pattern: "*.gappedPeak,*.narrowPeak}" + - meta: + type: file + description: BED file containing annotated peaks + pattern: "*.gappedPeak,*.narrowPeak}" + - "*.{narrowPeak,broadPeak}": + type: file + description: BED file containing annotated peaks + pattern: "*.gappedPeak,*.narrowPeak}" - xls: - type: file - description: xls file containing annotated peaks - pattern: "*.xls" + - meta: + type: file + description: xls file containing annotated peaks + pattern: "*.xls" + - "*.xls": + type: file + description: xls file containing annotated peaks + pattern: "*.xls" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" - gapped: - type: file - description: Optional BED file containing gapped peak - pattern: "*.gappedPeak" + - meta: + type: file + description: Optional BED file containing gapped peak + pattern: "*.gappedPeak" + - "*.gappedPeak": + type: file + description: Optional BED file containing gapped peak + pattern: "*.gappedPeak" - bed: - type: file - description: Optional BED file containing peak summits locations for every peak - pattern: "*.bed" + - meta: + type: file + description: Optional BED file containing peak summits locations for every peak + pattern: "*.bed" + - "*.bed": + type: file + description: Optional BED file containing peak summits locations for every peak + pattern: "*.bed" - bdg: - type: file - description: Optional bedGraph files for input and treatment input samples - pattern: "*.bdg" + - meta: + type: file + description: Optional bedGraph files for input and treatment input samples + pattern: "*.bdg" + - "*.bdg": + type: file + description: Optional bedGraph files for input and treatment input samples + pattern: "*.bdg" authors: - "@ntoda03" - "@JoseEspinosa" diff --git a/modules/nf-core/macs3/callpeak/meta.yml b/modules/nf-core/macs3/callpeak/meta.yml index 1603b8e2e92..5d97a036ca8 100644 --- a/modules/nf-core/macs3/callpeak/meta.yml +++ b/modules/nf-core/macs3/callpeak/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "macs3_callpeak" description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments @@ -15,58 +14,83 @@ tools: tool_dev_url: "https://github.com/macs3-project/MACS/" doi: "10.1101/496521" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample_1', single_end:false ]` - - ipbam: - type: file - description: The ChIP-seq treatment file - - controlbam: - type: file - description: The control file - - macs3_gsize: - type: string - description: | - Effective genome size. It can be 1.0e+9 or 1000000000, - or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse - (2,652,783,500), 'ce' for C. elegans (100,286,401) - and 'dm' for fruitfly (142,573,017), Default:hs. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample_1', single_end:false ]` + - ipbam: + type: file + description: The ChIP-seq treatment file + - controlbam: + type: file + description: The control file + - - macs3_gsize: + type: string + description: | + Effective genome size. It can be 1.0e+9 or 1000000000, + or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse + (2,652,783,500), 'ce' for C. elegans (100,286,401) + and 'dm' for fruitfly (142,573,017), Default:hs. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - peak: - type: file - description: BED file containing annotated peaks - pattern: "*.gappedPeak,*.narrowPeak}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{narrowPeak,broadPeak}": + type: file + description: BED file containing annotated peaks + pattern: "*.gappedPeak,*.narrowPeak}" - xls: - type: file - description: xls file containing annotated peaks - pattern: "*.xls" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.xls": + type: file + description: xls file containing annotated peaks + pattern: "*.xls" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" - gapped: - type: file - description: Optional BED file containing gapped peak - pattern: "*.gappedPeak" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gappedPeak": + type: file + description: Optional BED file containing gapped peak + pattern: "*.gappedPeak" - bed: - type: file - description: Optional BED file containing peak summits locations for every peak - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bed": + type: file + description: Optional BED file containing peak summits locations for every peak + pattern: "*.bed" - bdg: - type: file - description: Optional bedGraph files for input and treatment input samples - pattern: "*.bdg" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bdg": + type: file + description: Optional bedGraph files for input and treatment input samples + pattern: "*.bdg" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/mafft/meta.yml b/modules/nf-core/mafft/meta.yml index 90b9ed39c32..ed5e1ea31a4 100644 --- a/modules/nf-core/mafft/meta.yml +++ b/modules/nf-core/mafft/meta.yml @@ -6,88 +6,101 @@ keywords: - multiple sequence alignment tools: - "mafft": - description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform + description: Multiple alignment program for amino acid or nucleotide sequences + based on fast Fourier transform homepage: https://mafft.cbrc.jp/alignment/software/ documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html doi: "10.1093/nar/gkf436" licence: ["BSD"] + identifier: biotools:MAFFT - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: biotools:MAFFT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing the sequences to align. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - add: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addfragments: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addfull: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addprofile: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta6: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addlong: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing the sequences to align. May be gzipped or + uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - add: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--add`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addfragments: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addfragments`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addfull: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addfull`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addprofile: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addprofile`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addlong: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addlong`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fas: - type: file - description: Aligned sequences in FASTA format. May be gzipped or uncompressed. - pattern: "*.fas{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fas{.gz,}": + type: file + description: Aligned sequences in FASTA format. May be gzipped or uncompressed. + pattern: "*.fas{.gz,}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/mageck/count/meta.yml b/modules/nf-core/mageck/count/meta.yml index 6450de0a6b2..4b5e425a03e 100644 --- a/modules/nf-core/mageck/count/meta.yml +++ b/modules/nf-core/mageck/count/meta.yml @@ -1,5 +1,6 @@ name: "mageck_count" -description: mageck count for functional genomics, reads are usually mapped to a specific sgRNA +description: mageck count for functional genomics, reads are usually mapped to a specific + sgRNA keywords: - sort - functional genomics @@ -7,43 +8,54 @@ keywords: - CRISPR-Cas9 tools: - mageck: - description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data." + description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), + an algorithm to process, QC, analyze and visualize CRISPR screening data." homepage: "https://sourceforge.net/p/mageck/wiki/Home/" documentation: "https://sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command" doi: "10.1186/s13059-014-0554-4" licence: ["BSD License"] + identifier: biotools:mageck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - library: - type: file - description: library file containing the sgRNA and gene name - pattern: "*.{csv,txt,tsv}" - - inputfile: - type: file - description: library fastq file containing the sgRNA and gene name or count table containing the sgRNA and number of reads to per sample - pattern: "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputfile: + type: file + description: library fastq file containing the sgRNA and gene name or count + table containing the sgRNA and number of reads to per sample + pattern: "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" + - - library: + type: file + description: library file containing the sgRNA and gene name + pattern: "*.{csv,txt,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - norm: - type: file - description: File containing normalized read counts - pattern: "*.count_normalized.txt" - count: - type: file - description: File containing read counts - pattern: "*.countsummary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*count.txt": + type: file + description: File containing read counts + pattern: "*.countsummary.txt" + - norm: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.count_normalized.txt": + type: file + description: File containing normalized read counts + pattern: "*.count_normalized.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/mle/meta.yml b/modules/nf-core/mageck/mle/meta.yml index 0b944aafa86..8c577fbd51b 100644 --- a/modules/nf-core/mageck/mle/meta.yml +++ b/modules/nf-core/mageck/mle/meta.yml @@ -6,52 +6,62 @@ keywords: - CRISPR tools: - "mageck": - description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data." + description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), + an algorithm to process, QC, analyze and visualize CRISPR screening data." homepage: "https://sourceforge.net/p/mageck/wiki/Home/#mle" documentation: "https://sourceforge.net/p/mageck/wiki/Home/" tool_dev_url: "https://bitbucket.org/liulab/mageck/src" doi: "10.1186/s13059-015-0843-6" licence: ["BSD"] + identifier: biotools:mageck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - count_table: - type: file - description: | - Count table file. - Each line in the table should include - sgRNA name (1st column), target gene (2nd column) - and read counts in each sample. - pattern: "*.{txt,tsv}" - - design_matrix: - type: file - description: Design matrix describing the samples and conditions - pattern: "*.{txt,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - count_table: + type: file + description: | + Count table file. + Each line in the table should include + sgRNA name (1st column), target gene (2nd column) + and read counts in each sample. + pattern: "*.{txt,tsv}" + - - design_matrix: + type: file + description: Design matrix describing the samples and conditions + pattern: "*.{txt,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gene_summary: - type: file - description: | - Gene summary file describing the fitness score - and associated p-values. - pattern: "*.{gene_summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gene_summary.txt": + type: file + description: | + Gene summary file describing the fitness score + and associated p-values. + pattern: "*.{gene_summary}" - sgrna_summary: - type: file - description: | - sgRNA summary file describing the sgRNA and - associated gene - pattern: "*.{gene_summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sgrna_summary.txt": + type: file + description: | + sgRNA summary file describing the sgRNA and + associated gene + pattern: "*.{gene_summary}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/test/meta.yml b/modules/nf-core/mageck/test/meta.yml index d0d93f33f9d..790367774aa 100644 --- a/modules/nf-core/mageck/test/meta.yml +++ b/modules/nf-core/mageck/test/meta.yml @@ -1,59 +1,76 @@ name: "mageck_test" -description: Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens. +description: Mageck test performs a robust ranking aggregation (RRA) to identify positively + or negatively selected genes in functional genomics screens. keywords: - sort - rra - CRISPR tools: - mageck: - description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data." + description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), + an algorithm to process, QC, analyze and visualize CRISPR screening data." homepage: "https://sourceforge.net/p/mageck/wiki/Home/#mle" documentation: "https://sourceforge.net/p/mageck/wiki/Home/" tool_dev_url: "https://bitbucket.org/liulab/mageck/src" doi: "10.1186/s13059-015-0843-6" licence: ["BSD License"] + identifier: biotools:mageck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - count_table: - type: file - description: | - Count table file. - Each line in the table should include - sgRNA name (1st column), target gene (2nd column) - and read counts in each sample. - pattern: "*.{txt,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - count_table: + type: file + description: | + Count table file. + Each line in the table should include + sgRNA name (1st column), target gene (2nd column) + and read counts in each sample. + pattern: "*.{txt,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gene_summary: - type: file - description: | - Gene summary file describing the fitness score - and associated p-values. - pattern: "*.{gene_summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gene_summary.txt": + type: file + description: | + Gene summary file describing the fitness score + and associated p-values. + pattern: "*.{gene_summary.txt}" - sgrna_summary: - type: file - description: | - sgRNA summary file describing the sgRNA and - associated gene - pattern: "*.{sgrna_summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sgrna_summary.txt": + type: file + description: | + sgRNA summary file describing the sgRNA and + associated gene + pattern: "*.{sgrna_summary.txt}" - r_script: - type: file - description: | - R script allowing to output plots - from main hit genes - pattern: "*.R" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.R": + type: file + description: | + R script allowing to output plots + from main hit genes + pattern: "*.R" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/magus/align/meta.yml b/modules/nf-core/magus/align/meta.yml index f9ada96a23d..e5d7cdb0c46 100644 --- a/modules/nf-core/magus/align/meta.yml +++ b/modules/nf-core/magus/align/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "magus_align" description: Multiple Sequence Alignment using Graph Clustering @@ -15,53 +14,53 @@ tools: tool_dev_url: "https://github.com/vlasmirnov/MAGUS" doi: "10.1093/bioinformatics/btaa992" licence: ["MIT"] + identifier: biotools:magus input: - - meta: - type: map - description: | - Groovy Map containing the fasta meta information - e.g. `[ id:'test', single_end:false ]` - - - meta2: - type: map - description: | - Groovy Map containing sample information for the specified guide tree (if supplied) - e.g. `[ id:'test', single_end:false ]` - - - fasta: - type: file - description: Input sequences in FASTA format. - pattern: "*.{fa,fna,fasta}" - - - tree: - type: file - description: Optional path to a file containing a guide tree in newick format to use as input. - If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, MAGUS will construct its own guide tree. If empty, `fasttree` is used as a default. - pattern: "*.{dnd,tree}" - - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. - + - - meta: + type: map + description: | + Groovy Map containing the fasta meta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Input sequences in FASTA format. + pattern: "*.{fa,fna,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information for the specified guide tree (if supplied) + e.g. `[ id:'test', single_end:false ]` + - tree: + type: file + description: Optional path to a file containing a guide tree in newick format + to use as input. If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, + MAGUS will construct its own guide tree. If empty, `fasttree` is used as a + default. + pattern: "*.{dnd,tree}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample meta information. - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - alignment: - type: file - description: File containing the output alignment, in FASTA format containing gaps. - The sequences may be in a different order than in the input FASTA. - The output file may or may not be gzipped, depending on the value supplied to `compress`. - pattern: "*.aln{.gz,}" - + - meta: + type: map + description: | + Groovy Map containing sample meta information. + e.g. `[ id:'test', single_end:false ]` + - "*.aln{.gz,}": + type: file + description: File containing the output alignment, in FASTA format containing + gaps. The sequences may be in a different order than in the input FASTA. The + output file may or may not be gzipped, depending on the value supplied to + `compress`. + pattern: "*.aln{.gz,}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" diff --git a/modules/nf-core/magus/guidetree/meta.yml b/modules/nf-core/magus/guidetree/meta.yml index 7d21391ad85..2cc3020d959 100644 --- a/modules/nf-core/magus/guidetree/meta.yml +++ b/modules/nf-core/magus/guidetree/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "magus_guidetree" description: Multiple Sequence Alignment using Graph Clustering @@ -15,35 +14,33 @@ tools: tool_dev_url: "https://github.com/vlasmirnov/MAGUS" doi: "10.1093/bioinformatics/btaa992" licence: ["MIT"] + identifier: biotools:magus input: - - meta: - type: map - description: | - Groovy Map containing fasta meta information - e.g. `[ id:'test', single_end:false ]` - - - fasta: - type: file - description: Input sequences in FASTA format. - pattern: "*.{fa,fna,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing fasta meta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Input sequences in FASTA format. + pattern: "*.{fa,fna,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tree: - type: file - description: File containing the output guidetree, in newick format. - pattern: "*.tree" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tree": + type: file + description: File containing the output guidetree, in newick format. + pattern: "*.tree" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" diff --git a/modules/nf-core/malt/build/meta.yml b/modules/nf-core/malt/build/meta.yml index b95fc527007..da1fc6c260d 100644 --- a/modules/nf-core/malt/build/meta.yml +++ b/modules/nf-core/malt/build/meta.yml @@ -1,5 +1,7 @@ name: malt_build -description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. +description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and + analysis tool designed for processing high-throughput sequencing data, especially + in the context of metagenomics. keywords: - malt - alignment @@ -17,32 +19,36 @@ tools: documentation: https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf doi: "10.1038/s41559-017-0446-6" licence: ["GPL v3"] + identifier: "" input: - - fastas: - type: file - description: Directory of, or list of FASTA reference files for indexing - pattern: "*/|*.fasta" - - gff: - type: file - description: Directory of, or GFF3 files of input FASTA files - pattern: "*/|*.gff|*.gff3" - - mapping_db: - type: file - description: MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html - pattern: "*.db" + - - fastas: + type: file + description: Directory of, or list of FASTA reference files for indexing + pattern: "*/|*.fasta" + - - gff: + type: file + description: Directory of, or GFF3 files of input FASTA files + pattern: "*/|*.gff|*.gff3" + - - mapping_db: + type: file + description: MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html + pattern: "*.db" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Directory containing MALT database index directory - pattern: "malt_index/" + - malt_index/: + type: directory + description: Directory containing MALT database index directory + pattern: "malt_index/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log: - type: file - description: Log file from STD out of malt-build - pattern: "malt-build.log" + - malt-build.log: + type: file + description: Log file from STD out of malt-build + pattern: "malt-build.log" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/malt/run/meta.yml b/modules/nf-core/malt/run/meta.yml index 5bb7d9b3f32..ed92805a1d0 100644 --- a/modules/nf-core/malt/run/meta.yml +++ b/modules/nf-core/malt/run/meta.yml @@ -1,5 +1,7 @@ name: malt_run -description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. +description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and + analysis tool designed for processing high-throughput sequencing data, especially + in the context of metagenomics. keywords: - malt - alignment @@ -16,37 +18,54 @@ tools: documentation: https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf doi: "10.1038/s41559-017-0446-6" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastqs: - type: file - description: Input FASTQ files - pattern: "*.{fastq.gz,fq.gz}" - - index: - type: directory - description: Index/database directory from malt-build - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastqs: + type: file + description: Input FASTQ files + pattern: "*.{fastq.gz,fq.gz}" + - - index: + type: directory + description: Index/database directory from malt-build + pattern: "*/" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rma6: - type: file - description: MEGAN6 RMA6 file - pattern: "*.rma6" + - meta: + type: file + description: MEGAN6 RMA6 file + pattern: "*.rma6" + - "*.rma6": + type: file + description: MEGAN6 RMA6 file + pattern: "*.rma6" - alignments: - type: file - description: Alignment files in Tab, Text or MEGAN-compatible SAM format - pattern: "*.{tab,txt,sam}" + - meta: + type: file + description: Alignment files in Tab, Text or MEGAN-compatible SAM format + pattern: "*.{tab,txt,sam}" + - "*.{tab,text,sam,tab.gz,text.gz,sam.gz}": + type: file + description: Alignment files in Tab, Text or MEGAN-compatible SAM format + pattern: "*.{tab,txt,sam}" - log: - type: file - description: Log of verbose MALT stdout - pattern: "*-malt-run.log" + - meta: + type: file + description: Log of verbose MALT stdout + pattern: "*-malt-run.log" + - "*.log": + type: file + description: Log of verbose MALT stdout + pattern: "*-malt-run.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/maltextract/meta.yml b/modules/nf-core/maltextract/meta.yml index f7648d807c1..129315a61c9 100644 --- a/modules/nf-core/maltextract/meta.yml +++ b/modules/nf-core/maltextract/meta.yml @@ -1,5 +1,6 @@ name: maltextract -description: Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening +description: Tool for evaluation of MALT results for true positives of ancient metagenomic + taxonomic screening keywords: - malt - MaltExtract @@ -22,33 +23,40 @@ tools: tool_dev_url: https://github.com/rhuebler/hops doi: "10.1186/s13059-019-1903-0" licence: ["GPL 3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rma6: - type: file - description: RMA6 files from MALT - pattern: "*.rma6" - - taxon_list: - type: file - description: List of target taxa to evaluate - pattern: "*.txt" - - ncbi_dir: - type: directory - description: Directory containing NCBI taxonomy map and tre files - pattern: "${ncbi_dir}/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rma6: + type: file + description: RMA6 files from MALT + pattern: "*.rma6" + - - taxon_list: + type: file + description: List of target taxa to evaluate + pattern: "*.txt" + - - ncbi_dir: + type: directory + description: Directory containing NCBI taxonomy map and tre files + pattern: "${ncbi_dir}/" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing MaltExtract text results files - pattern: "results/" + - meta: + type: directory + description: Directory containing MaltExtract text results files + pattern: "results/" + - results: + type: directory + description: Directory containing MaltExtract text results files + pattern: "results/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/manta/convertinversion/meta.yml b/modules/nf-core/manta/convertinversion/meta.yml index 865ef87c513..3a70814d7f7 100644 --- a/modules/nf-core/manta/convertinversion/meta.yml +++ b/modules/nf-core/manta/convertinversion/meta.yml @@ -1,5 +1,7 @@ name: "manta_convertinversion" -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. This script reformats inversions into single inverted sequence + junctions which was the format used in Manta versions <= 1.4.0. keywords: - structural variants - conversion @@ -12,43 +14,52 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file produces by Manta - pattern: "*.vcf.gz" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file produces by Manta + pattern: "*.vcf.gz" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with reformatted inversions - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file with reformatted inversions + pattern: "*.vcf.gz" - tbi: - type: file - description: TBI file produces by Manta - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: TBI file produces by Manta + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/manta/germline/meta.yml b/modules/nf-core/manta/germline/meta.yml index 72ed15f8bc2..4072ab8e564 100644 --- a/modules/nf-core/manta/germline/meta.yml +++ b/modules/nf-core/manta/germline/meta.yml @@ -1,5 +1,7 @@ name: manta_germline -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. It is optimized for analysis of germline variation in small sets + of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs @@ -16,84 +18,117 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file. For joint calling use a list of files. - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM/CRAM/SAM index file. For joint calling use a list of files. - pattern: "*.{bai,crai,sai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_tbi: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file. For joint calling use a list of files. + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM/CRAM/SAM index file. For joint calling use a list of files. + pattern: "*.{bai,crai,sai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_tbi: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + - - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - diploid_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*diploid_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - diploid_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*diploid_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/manta/somatic/meta.yml b/modules/nf-core/manta/somatic/meta.yml index e658edaaa4c..11f1fc1ca0a 100644 --- a/modules/nf-core/manta/somatic/meta.yml +++ b/modules/nf-core/manta/somatic/meta.yml @@ -1,5 +1,7 @@ name: manta_somatic -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. It is optimized for analysis of germline variation in small sets + of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs @@ -16,100 +18,145 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_normal: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_normal: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - input_tumor: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_tumor: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_tbi: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_normal: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - input_tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_tumor: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_tbi: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + - - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_small_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_small_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - diploid_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diploid_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - diploid_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diploid_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - somatic_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - somatic_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@nvnieuwk" diff --git a/modules/nf-core/manta/tumoronly/meta.yml b/modules/nf-core/manta/tumoronly/meta.yml index 63556c59b4e..6f629b24dc4 100644 --- a/modules/nf-core/manta/tumoronly/meta.yml +++ b/modules/nf-core/manta/tumoronly/meta.yml @@ -1,5 +1,7 @@ name: manta_tumoronly -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. It is optimized for analysis of germline variation in small sets + of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs @@ -16,84 +18,117 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_tbi: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_tbi: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + - - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - tumor_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*tumor_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - tumor_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*tumor_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@nvnieuwk" diff --git a/modules/nf-core/mapad/index/meta.yml b/modules/nf-core/mapad/index/meta.yml index 2c94d9fc6a9..3b7d0addc8b 100644 --- a/modules/nf-core/mapad/index/meta.yml +++ b/modules/nf-core/mapad/index/meta.yml @@ -12,30 +12,33 @@ tools: documentation: "https://github.com/mpieva/mapAD" tool_dev_url: "https://github.com/mpieva/mapAD" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: mapAD genome index files - pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mapad/: + type: directory + description: mapAD genome index files + pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jch-13" maintainers: diff --git a/modules/nf-core/mapad/map/meta.yml b/modules/nf-core/mapad/map/meta.yml index 1ca5e9d2cd2..c83c28202f7 100644 --- a/modules/nf-core/mapad/map/meta.yml +++ b/modules/nf-core/mapad/map/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mapad_map" description: Map short-reads to an indexed reference genome @@ -33,62 +32,66 @@ tools: documentation: "https://github.com/mpieva/mapAD" tool_dev_url: "https://github.com/mpieva/mapAD" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory) - pattern: "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: mapAD genome index files (mandatory) - pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" - - mismatch_parameter: - type: float - description: | - Minimum probability of the number of mismatches under `-D` base error rate - - double_stranded_library: - type: boolean - description: Library preparation method - specify if double stranded else it's assumed single stranded - - five_prime_overhang: - type: float - description: 5'-overhang length parameter - - three_prime_overhang: - type: float - description: 3'-overhang length parameter - - deam_rate_double_stranded: - type: float - description: Deamination rate in double-stranded stem of a read - - deam_rate_single_stranded: - type: float - description: Deamination rate in single-stranded ends of a read - - indel_rate: - type: float - description: Expected rate of indels between reads and reference + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory) + pattern: "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: mapAD genome index files (mandatory) + pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + - - mismatch_parameter: + type: float + description: | + Minimum probability of the number of mismatches under `-D` base error rate + - - double_stranded_library: + type: boolean + description: Library preparation method - specify if double stranded else it's + assumed single stranded + - - five_prime_overhang: + type: float + description: 5'-overhang length parameter + - - three_prime_overhang: + type: float + description: 3'-overhang length parameter + - - deam_rate_double_stranded: + type: float + description: Deamination rate in double-stranded stem of a read + - - deam_rate_single_stranded: + type: float + description: Deamination rate in single-stranded ends of a read + - - indel_rate: + type: float + description: Expected rate of indels between reads and reference output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Output BAM/SAM file containing read alignments - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM/SAM file containing read alignments + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jch-13" maintainers: diff --git a/modules/nf-core/mapdamage2/meta.yml b/modules/nf-core/mapdamage2/meta.yml index 884e520aff8..f27fc17f131 100644 --- a/modules/nf-core/mapdamage2/meta.yml +++ b/modules/nf-core/mapdamage2/meta.yml @@ -1,5 +1,6 @@ name: mapdamage2 -description: Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. +description: Computational framework for tracking and quantifying DNA damage patterns + among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. keywords: - ancient DNA - DNA damage @@ -14,98 +15,202 @@ tools: tool_dev_url: https://github.com/ginolhac/mapDamage doi: "10.1093/bioinformatics/btt193" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Fasta file, the reference the input BAM was mapped against - pattern: "*.{fasta}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - fasta: + type: file + description: Fasta file, the reference the input BAM was mapped against + pattern: "*.{fasta}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - runtime_log: - type: file - description: Log file with a summary of command lines used and timestamps. - pattern: "Runtime_log.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Runtime_log.txt: + type: file + description: Log file with a summary of command lines used and timestamps. + pattern: "Runtime_log.txt" - fragmisincorporation_plot: - type: file - description: A pdf file that displays both fragmentation and misincorporation patterns. - pattern: "Fragmisincorporation_plot.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Fragmisincorporation_plot.pdf: + type: file + description: A pdf file that displays both fragmentation and misincorporation + patterns. + pattern: "Fragmisincorporation_plot.pdf" - length_plot: - type: file - description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. - pattern: "Length_plot.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Length_plot.pdf: + type: file + description: A pdf file that displays length distribution of singleton reads + per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end + are also displayed per strand. + pattern: "Length_plot.pdf" - misincorporation: - type: file - description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. - pattern: "misincorporation.txt" - - pctot_freq: - type: file - description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. - pattern: "5pCtoT_freq.txt" - - pgtoa_freq: - type: file - description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. - pattern: "3pGtoA_freq.txt" - - dnacomp: - type: file - description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. - pattern: "dnacomp.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/misincorporation.txt: + type: file + description: Contains a table with occurrences for each type of mutations and + relative positions from the reads ends. + pattern: "misincorporation.txt" - lgdistribution: - type: file - description: Contains a table with read length distributions per strand. - pattern: "lgdistribution.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/lgdistribution.txt: + type: file + description: Contains a table with read length distributions per strand. + pattern: "lgdistribution.txt" + - dnacomp: + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/dnacomp.txt: + type: file + description: Contains a table of the reference genome base composition per position, + inside reads and adjacent regions. + pattern: "dnacomp.txt" - stats_out_mcmc_hist: - type: file - description: A MCMC histogram for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_hist.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_hist.pdf: + type: file + description: A MCMC histogram for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_hist.pdf" - stats_out_mcmc_iter: - type: file - description: Values for the damage parameters and log likelihood in each MCMC iteration. - pattern: "Stats_out_MCMC_iter.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_iter.csv: + type: file + description: Values for the damage parameters and log likelihood in each MCMC + iteration. + pattern: "Stats_out_MCMC_iter.csv" - stats_out_mcmc_trace: - type: file - description: A MCMC trace plot for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_trace.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_trace.pdf: + type: file + description: A MCMC trace plot for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_trace.pdf" - stats_out_mcmc_iter_summ_stat: - type: file - description: Summary statistics for the damage parameters estimated posterior distributions. - pattern: "Stats_out_MCMC_iter_summ_stat.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_iter_summ_stat.csv: + type: file + description: Summary statistics for the damage parameters estimated posterior + distributions. + pattern: "Stats_out_MCMC_iter_summ_stat.csv" - stats_out_mcmc_post_pred: - type: file - description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. - pattern: "Stats_out_MCMC_post_pred.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_post_pred.pdf: + type: file + description: Empirical misincorporation frequency and posterior predictive intervals + from the fitted model. + pattern: "Stats_out_MCMC_post_pred.pdf" - stats_out_mcmc_correct_prob: - type: file - description: Position specific probability of a C->T and G->A misincorporation is due to damage. - pattern: "Stats_out_MCMC_correct_prob.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_correct_prob.csv: + type: file + description: Position specific probability of a C->T and G->A misincorporation + is due to damage. + pattern: "Stats_out_MCMC_correct_prob.csv" - dnacomp_genome: - type: file - description: Contains the global reference genome base composition (computed by seqtk). - pattern: "dnacomp_genome.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/dnacomp_genome.csv: + type: file + description: Contains the global reference genome base composition (computed + by seqtk). + pattern: "dnacomp_genome.csv" - rescaled: - type: file - description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. - pattern: "*.{bam}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/*rescaled.bam: + type: file + description: Rescaled BAM file, where likely post-mortem damaged bases have + downscaled quality scores. + pattern: "*.{bam}" + - pctot_freq: + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/5pCtoT_freq.txt: + type: file + description: Contains frequencies of Cytosine to Thymine mutations per position + from the 5'-ends. + pattern: "5pCtoT_freq.txt" + - pgtoa_freq: + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/3pGtoA_freq.txt: + type: file + description: Contains frequencies of Guanine to Adenine mutations per position + from the 3'-ends. + pattern: "3pGtoA_freq.txt" - fasta: - type: file - description: Allignments in a FASTA file, only if flagged by -d. - pattern: "*.{fasta}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/*.fasta: + type: file + description: Allignments in a FASTA file, only if flagged by -d. + pattern: "*.{fasta}" - folder: - type: directory - description: Folder created when --plot-only, --rescale and --stats-only flags are passed. - pattern: "*/" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*/": + type: directory + description: Folder created when --plot-only, --rescale and --stats-only flags + are passed. + pattern: "*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/mash/dist/meta.yml b/modules/nf-core/mash/dist/meta.yml index e0827c1be6d..3b7ce0ad6c7 100644 --- a/modules/nf-core/mash/dist/meta.yml +++ b/modules/nf-core/mash/dist/meta.yml @@ -13,34 +13,37 @@ tools: tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] + identifier: biotools:mash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reference: - type: file - description: FASTA, FASTQ or Mash sketch - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" - - query: - type: file - description: FASTA, FASTQ or Mash sketch - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: FASTA, FASTQ or Mash sketch + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" + - - reference: + type: file + description: FASTA, FASTQ or Mash sketch + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - dist: - type: file - description: The results from mash dist - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: The results from mash dist + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/mash/screen/meta.yml b/modules/nf-core/mash/screen/meta.yml index 9b482bef158..751cfd06cd8 100644 --- a/modules/nf-core/mash/screen/meta.yml +++ b/modules/nf-core/mash/screen/meta.yml @@ -13,34 +13,41 @@ tools: tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] + identifier: biotools:mash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query: - type: file - description: Query sequences - pattern: "*.fastq.gz" - - sequence_sketch: - type: file - description: Sequence files to match against - pattern: "*.msh" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: Query sequences + pattern: "*.fastq.gz" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences_sketch: + type: file + description: sketch file of sequences output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - screen: - type: file - description: List of sequences from fastx_db similar to query sequences - pattern: "*.screen" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.screen": + type: file + description: List of sequences from fastx_db similar to query sequences + pattern: "*.screen" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/mash/sketch/meta.yml b/modules/nf-core/mash/sketch/meta.yml index ac23657258c..f253717dc13 100644 --- a/modules/nf-core/mash/sketch/meta.yml +++ b/modules/nf-core/mash/sketch/meta.yml @@ -16,33 +16,42 @@ tools: tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] + identifier: biotools:mash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input paired-end FastQ files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input paired-end FastQ files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mash: - type: file - description: Sketch output - pattern: "*.{mash}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.msh": + type: file + description: Sketch output + pattern: "*.{mash}" - stats: - type: file - description: Sketch statistics - pattern: "*.{mash_stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mash_stats": + type: file + description: Sketch statistics + pattern: "*.{mash_stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@thanhleviet" maintainers: diff --git a/modules/nf-core/mashmap/meta.yml b/modules/nf-core/mashmap/meta.yml index f9a608c8aff..f53cd79130a 100644 --- a/modules/nf-core/mashmap/meta.yml +++ b/modules/nf-core/mashmap/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mashmap" -description: Mashmap is an approximate long read or contig mapper based on Jaccard similarity +description: Mashmap is an approximate long read or contig mapper based on Jaccard + similarity keywords: - mapper - aligner @@ -15,41 +15,43 @@ tools: tool_dev_url: "https://github.com/marbl/MashMap" doi: "10.1007/978-3-319-56970-3_5" licence: ["Public Domain"] + identifier: biotools:mashmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - - reference: - type: file - description: Input fasta file containing reference sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reference: + type: file + description: Input fasta file containing reference sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mberacochea" diff --git a/modules/nf-core/mashtree/meta.yml b/modules/nf-core/mashtree/meta.yml index e110fc45d1e..56d1e422587 100644 --- a/modules/nf-core/mashtree/meta.yml +++ b/modules/nf-core/mashtree/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: https://github.com/lskatz/mashtree doi: "10.21105/joss.01762" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTA, FASTQ, GenBank, or Mash sketch files - pattern: "*.{fna,fna.gz,fasta,fasta.gz,fa,fa.gz,gbk,gbk.gz,fastq.gz,msh}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTA, FASTQ, GenBank, or Mash sketch files + pattern: "*.{fna,fna.gz,fasta,fasta.gz,fa,fa.gz,gbk,gbk.gz,fastq.gz,msh}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tree: - type: file - description: A Newick formatted tree file - pattern: "*.{dnd}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dnd": + type: file + description: A Newick formatted tree file + pattern: "*.{dnd}" - matrix: - type: file - description: A TSV matrix of pair-wise Mash distances - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV matrix of pair-wise Mash distances + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/maxbin2/meta.yml b/modules/nf-core/maxbin2/meta.yml index 65535c38765..6b5a98c766d 100644 --- a/modules/nf-core/maxbin2/meta.yml +++ b/modules/nf-core/maxbin2/meta.yml @@ -11,67 +11,118 @@ keywords: - contigs tools: - maxbin2: - description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. + description: MaxBin is software for binning assembled metagenomic sequences based + on an Expectation-Maximization algorithm. homepage: https://sourceforge.net/projects/maxbin/ documentation: https://sourceforge.net/projects/maxbin/ tool_dev_url: https://sourceforge.net/projects/maxbin/ doi: "10.1093/bioinformatics/btv638" licence: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - contigs: - type: file - description: Multi FASTA file containing assembled contigs of a given sample - pattern: "*.fasta" - - reads: - type: file - description: Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files. - pattern: "*.fasta" - - abund: - type: file - description: Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs: + type: file + description: Multi FASTA file containing assembled contigs of a given sample + pattern: "*.fasta" + - reads: + type: file + description: Reads used to assemble contigs in FASTA or FASTQ format. Do not + supply at the same time as abundance files. + pattern: "*.fasta" + - abund: + type: file + description: Contig abundance files, i.e. reads against each contig. See MaxBin2 + README for details. Do not supply at the same time as read files. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - binned_fastas: - type: file - description: Binned contigs, one per bin designated with numeric IDs - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta.gz": + type: file + description: Binned contigs, one per bin designated with numeric IDs + pattern: "*.fasta.gz" - summary: - type: file - description: Summary file describing which contigs are being classified into which bin - pattern: "*.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary": + type: file + description: Summary file describing which contigs are being classified into + which bin + pattern: "*.summary" - log: - type: file - description: Log file recording the core steps of MaxBin algorithm - pattern: "*.log.gz" - - marker: - type: file - description: Marker gene presence numbers for each bin - pattern: "*.marker.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log.gz": + type: file + description: Log file recording the core steps of MaxBin algorithm + pattern: "*.log.gz" + - marker_counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.marker.gz": + type: file + description: Marker counts + pattern: "*.marker.gz" - unbinned_fasta: - type: file - description: All sequences that pass the minimum length threshold but are not classified successfully. - pattern: "*.noclass.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.noclass.gz": + type: file + description: All sequences that pass the minimum length threshold but are not + classified successfully. + pattern: "*.noclass.gz" - tooshort_fasta: - type: file - description: All sequences that do not meet the minimum length threshold. - pattern: "*.tooshort.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tooshort.gz": + type: file + description: All sequences that do not meet the minimum length threshold. + pattern: "*.tooshort.gz" + - marker_bins: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bin.tar.gz": - marker_genes: - type: file - description: All sequences that do not meet the minimum length threshold. - pattern: "*.marker_of_each_gene.tar.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_gene.tar.gz": + type: file + description: Marker genes + pattern: "*_gene.tar.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/maxquant/lfq/meta.yml b/modules/nf-core/maxquant/lfq/meta.yml index 634f70eafd6..ad60199f120 100644 --- a/modules/nf-core/maxquant/lfq/meta.yml +++ b/modules/nf-core/maxquant/lfq/meta.yml @@ -1,47 +1,51 @@ name: maxquant_lfq -description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER" +description: Run standard proteomics data analysis with MaxQuant, mostly dedicated + to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER" keywords: - sort - proteomics - mass-spectroscopy tools: - maxquant: - description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted. + description: MaxQuant is a quantitative proteomics software package designed for + analyzing large mass-spectrometric data sets. License restricted. homepage: https://www.maxquant.org/ documentation: http://coxdocs.org/doku.php?id=maxquant:start licence: ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"] + identifier: biotools:maxquant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - raw: - type: file - description: raw files with mass spectra - pattern: "*.{raw,RAW,Raw}" - - fasta: - type: file - description: fasta file with protein sequences - pattern: "*.{fasta}" - - parfile: - type: file - description: MaxQuant parameter file (XML) - pattern: "*.{xml}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file with protein sequences + pattern: "*.{fasta}" + - paramfile: + type: file + description: MaxQuant parameter file + - - raw: + type: file + description: raw files with mass spectra + pattern: "*.{raw,RAW,Raw}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - maxquant_txt: - type: file - description: tables with peptides and protein information - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: tables with peptides and protein information + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@veitveit" maintainers: diff --git a/modules/nf-core/mcquant/meta.yml b/modules/nf-core/mcquant/meta.yml index 1423074bddb..76ef8ac3396 100644 --- a/modules/nf-core/mcquant/meta.yml +++ b/modules/nf-core/mcquant/meta.yml @@ -1,5 +1,6 @@ name: "mcquant" -description: Mcquant extracts single-cell data given a multi-channel image and a segmentation mask. +description: Mcquant extracts single-cell data given a multi-channel image and a segmentation + mask. keywords: - quantification - image_analysis @@ -7,54 +8,58 @@ keywords: - highly_multiplexed_imaging tools: - "mcquant": - description: "Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output." + description: "Module for single-cell data extraction given a segmentation mask + and multi-channel image. The CSV structure is aligned with histoCAT output." homepage: "https://github.com/labsyspharm/quantification" documentation: "https://github.com/labsyspharm/quantification/blob/master/README.md" tool_dev_url: "https://github.com/labsyspharm/quantification" doi: 10.1038/s41592-021-01308-y licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - image: - type: file - description: Multi-channel image file - pattern: "*.{tiff,tif,h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mask: - type: file - description: Labeled segmentation mask for image - pattern: "*.{tiff,tif,h5,hdf5}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - markerfile: - type: file - description: Marker file with channel names for image to quantify - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - image: + type: file + description: Multi-channel image file + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mask: + type: file + description: Labeled segmentation mask for image + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - markerfile: + type: file + description: Marker file with channel names for image to quantify + pattern: "*.{csv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Quantified regionprops_table - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Quantified regionprops_table + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/mcroni/meta.yml b/modules/nf-core/mcroni/meta.yml index 570a9cca160..0a1f3fc4d04 100644 --- a/modules/nf-core/mcroni/meta.yml +++ b/modules/nf-core/mcroni/meta.yml @@ -6,39 +6,49 @@ keywords: - mcr-1 tools: - "mcroni": - description: "Scripts for finding and processing promoter variants upstream of mcr-1" + description: "Scripts for finding and processing promoter variants upstream of + mcr-1" homepage: "https://github.com/liampshaw/mcroni" documentation: "https://github.com/liampshaw/mcroni" tool_dev_url: "https://github.com/liampshaw/mcroni" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A fasta file. - pattern: "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A fasta file. + pattern: "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: mcroni results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: mcroni results in TSV format + pattern: "*.tsv" - fa: - type: file - description: mcr-1 matching sequences - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: mcr-1 matching sequences + pattern: "*.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/mcstaging/imc2mc/meta.yml b/modules/nf-core/mcstaging/imc2mc/meta.yml index 6dbbc29f73f..ee596f61f5e 100644 --- a/modules/nf-core/mcstaging/imc2mc/meta.yml +++ b/modules/nf-core/mcstaging/imc2mc/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mcstaging_imc2mc" -description: Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal. +description: Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files + to .tif files with OME-XML metadata. Includes optional hot pixel removal. keywords: - imaging - ome-tif @@ -14,38 +14,36 @@ tools: documentation: "https://github.com/SchapiroLabor/imc2mc/README.md" tool_dev_url: "https://github.com/SchapiroLabor/imc2mc" licence: ["GPL-3.0 license"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - txtfile: - type: file - description: Acquisition .txt file - pattern: "*.{txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - txtfile: + type: file + description: Acquisition .txt file + pattern: "*.{txt}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tif: - type: file - description: One output .tif file containing acquisition and metadata - pattern: "*.{tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tif": + type: file + description: One output .tif file containing acquisition and metadata + pattern: "*.{tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MargotCh" maintainers: diff --git a/modules/nf-core/mcstaging/phenoimager2mc/meta.yml b/modules/nf-core/mcstaging/phenoimager2mc/meta.yml index 2e387a89621..8c3fab20a96 100644 --- a/modules/nf-core/mcstaging/phenoimager2mc/meta.yml +++ b/modules/nf-core/mcstaging/phenoimager2mc/meta.yml @@ -1,6 +1,7 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mcstaging_phenoimager2mc" -description: Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input. +description: Staging module for MCMICRO transforming PhenoImager .tif files into stacked + and normalized ome-tif files per cycle, compatible as ASHLAR input. keywords: - imaging - registration @@ -14,36 +15,34 @@ tools: documentation: "https://github.com/SchapiroLabor/phenoimager2mc/README.md" tool_dev_url: "https://github.com/SchapiroLabor/phenoimager2mc" licence: ["GPL-2.0 license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - tiles: - type: list - description: Folder or list with .tif files of one cycle from PhenoImager - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tiles: + type: list + description: Folder or list with .tif files of one cycle from PhenoImager output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tif: - type: file - description: One output .tif file containing concatenated tiles of the cycle. - pattern: "*.{tif,tiff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tif": + type: file + description: One output .tif file containing concatenated tiles of the cycle. + pattern: "*.{tif,tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@chiarasch" maintainers: diff --git a/modules/nf-core/md5sum/meta.yml b/modules/nf-core/md5sum/meta.yml index 1659ae7007a..363d763faf2 100644 --- a/modules/nf-core/md5sum/meta.yml +++ b/modules/nf-core/md5sum/meta.yml @@ -10,30 +10,38 @@ tools: homepage: "https://www.gnu.org" documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files: - type: file - description: Any number of files. One md5sum file will be generated for each. - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files: + type: file + description: Any number of files. One md5sum file will be generated for each. + pattern: "*.*" + - - as_separate_files: + type: boolean + description: | + If true, each file will have its own md5sum file. If false, all files will be + checksummed into a single md5sum file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checksum: - type: file - description: File containing checksum - pattern: "*.md5" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.md5": + type: file + description: File containing checksum + pattern: "*.md5" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/medaka/meta.yml b/modules/nf-core/medaka/meta.yml index 9ed3589dd5e..d267488c9b1 100644 --- a/modules/nf-core/medaka/meta.yml +++ b/modules/nf-core/medaka/meta.yml @@ -1,5 +1,6 @@ name: medaka -description: A tool to create consensus sequences and variant calls from nanopore sequencing data +description: A tool to create consensus sequences and variant calls from nanopore + sequencing data keywords: - assembly - polishing @@ -11,34 +12,37 @@ tools: documentation: https://nanoporetech.github.io/medaka/index.html tool_dev_url: https://github.com/nanoporetech/medaka licence: ["Mozilla Public License 2.0"] + identifier: biotools:medaka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input nanopore fasta/FastQ files - pattern: "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" - - assembly: - type: file - description: Genome assembly - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input nanopore fasta/FastQ files + pattern: "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" + - assembly: + type: file + description: Genome assembly + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly: - type: file - description: Polished genome assembly - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa.gz": + type: file + description: Polished genome assembly + pattern: "*.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/megahit/meta.yml b/modules/nf-core/megahit/meta.yml index 656f4f8ac17..04dab4c22f6 100644 --- a/modules/nf-core/megahit/meta.yml +++ b/modules/nf-core/megahit/meta.yml @@ -8,69 +8,106 @@ keywords: - metagenomics tools: - megahit: - description: "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph" + description: "An ultra-fast single-node solution for large and complex metagenomics + assembly via succinct de Bruijn graph" homepage: https://github.com/voutcn/megahit documentation: https://github.com/voutcn/megahit tool_dev_url: https://github.com/voutcn/megahit doi: "10.1093/bioinformatics/btv033" licence: ["GPL v3"] args_id: "$args" + identifier: biotools:megahit - pigz: description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" args_id: "$args2" + identifier: biotools:megahit input: - - meta: - type: map - description: | - Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) - e.g. [ id:'test', single_end:false ] - - reads1: - type: file - description: | - A single or list of input FastQ files for single-end or R1 of paired-end library(s), - respectively in gzipped or uncompressed FASTQ or FASTA format. - - reads2: - type: file - description: | - A single or list of input FastQ files for R2 of paired-end library(s), - respectively in gzipped or uncompressed FASTQ or FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) + e.g. [ id:'test', single_end:false ] + - reads1: + type: file + description: | + A single or list of input FastQ files for single-end or R1 of paired-end library(s), + respectively in gzipped or uncompressed FASTQ or FASTA format. + - reads2: + type: file + description: | + A single or list of input FastQ files for R2 of paired-end library(s), + respectively in gzipped or uncompressed FASTQ or FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - contigs: - type: file - description: Final final contigs result of the assembly in FASTA format. - pattern: "*.contigs.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.fa.gz": + type: file + description: Final final contigs result of the assembly in FASTA format. + pattern: "*.contigs.fa.gz" - k_contigs: - type: file - description: Contigs assembled from the de Bruijn graph of order-K - pattern: "k*.contigs.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.contigs.fa.gz: + type: file + description: Contigs assembled from the de Bruijn graph of order-K + pattern: "k*.contigs.fa.gz" - addi_contigs: - type: file - description: Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K - pattern: "k*.addi.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.addi.fa.gz: + type: file + description: Contigs assembled after iteratively removing local low coverage + unitigs in the de Bruijn graph of order-K + pattern: "k*.addi.fa.gz" - local_contigs: - type: file - description: Contigs of the locally assembled contigs for k=K - pattern: "k*.local.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.local.fa.gz: + type: file + description: Contigs of the locally assembled contigs for k=K + pattern: "k*.local.fa.gz" - kfinal_contigs: - type: file - description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty - pattern: "k*.final.contigs.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.final.contigs.fa.gz: + type: file + description: Stand-alone contigs for k=K; if local assembly is turned on, the + file will be empty + pattern: "k*.final.contigs.fa.gz" - log: - type: file - description: Log file containing statistics of the assembly output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing statistics of the assembly output + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/megan/daa2info/meta.yml b/modules/nf-core/megan/daa2info/meta.yml index 5b1c7e36638..a38bb0986b4 100644 --- a/modules/nf-core/megan/daa2info/meta.yml +++ b/modules/nf-core/megan/daa2info/meta.yml @@ -14,37 +14,46 @@ tools: tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" licence: ["GPL >=3"] + identifier: biotools:megan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - daa: - type: file - description: DAA file from DIAMOND - pattern: "*.daa" - - megan_summary: - type: boolean - description: Specify whether to generate a MEGAN summary file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - daa: + type: file + description: DAA file from DIAMOND + pattern: "*.daa" + - - megan_summary: + type: boolean + description: Specify whether to generate a MEGAN summary file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt_gz: - type: file - description: Compressed text file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Compressed text file + pattern: "*.txt.gz" - megan: - type: file - description: Optionally generated MEGAN summary file - pattern: "*.megan" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.megan": + type: file + description: Optionally generated MEGAN summary file + pattern: "*.megan" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml index 158c86742fa..3cd0facc3fe 100644 --- a/modules/nf-core/megan/rma2info/meta.yml +++ b/modules/nf-core/megan/rma2info/meta.yml @@ -13,37 +13,46 @@ tools: tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" licence: ["GPL >=3"] + identifier: biotools:megan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rma6: - type: file - description: RMA6 file from MEGAN or MALT - pattern: "*.rma6" - - megan_summary: - type: boolean - description: Specify whether to generate an MEGAN summary file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rma6: + type: file + description: RMA6 file from MEGAN or MALT + pattern: "*.rma6" + - - megan_summary: + type: boolean + description: Specify whether to generate an MEGAN summary file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Compressed text file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Compressed text file + pattern: "*.txt.gz" - megan_summary: - type: file - description: Optionally generated MEGAN summary file - pattern: "*.megan" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.megan": + type: file + description: Optionally generated MEGAN summary file + pattern: "*.megan" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/meningotype/meta.yml b/modules/nf-core/meningotype/meta.yml index 9bb624a9ea9..7fe755ab690 100644 --- a/modules/nf-core/meningotype/meta.yml +++ b/modules/nf-core/meningotype/meta.yml @@ -6,35 +6,39 @@ keywords: - serotype tools: - meningotype: - description: In silico serotyping and finetyping (porA and fetA) of Neisseria meningitidis + description: In silico serotyping and finetyping (porA and fetA) of Neisseria + meningitidis homepage: https://github.com/MDU-PHL/meningotype documentation: https://github.com/MDU-PHL/meningotype tool_dev_url: https://github.com/MDU-PHL/meningotype licence: ["GPL v3"] + identifier: biotools:meningotype input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/merfin/hist/meta.yml b/modules/nf-core/merfin/hist/meta.yml index a2c80d06a9c..f9064cc106d 100644 --- a/modules/nf-core/merfin/hist/meta.yml +++ b/modules/nf-core/merfin/hist/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "merfin_hist" -description: Compare k-mer frequency in reads and assembly to devise the metrics K* and QV* +description: Compare k-mer frequency in reads and assembly to devise the metrics K* + and QV* keywords: - assembly - evaluation @@ -9,71 +9,76 @@ keywords: - completeness tools: - "merfin": - description: "Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of [Merqury](https://github.com/marbl/merqury)) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads." + description: "Merfin (k-mer based finishing tool) is a suite of subtools to variant + filtering, assembly evaluation and polishing via k-mer validation. The subtool + -hist estimates the QV (quality value of [Merqury](https://github.com/marbl/merqury)) + for each scaffold/contig and genome-wide averages. In addition, Merfin produces + a QV* estimate, which accounts also for kmers that are seen in excess with respect + to their expected multiplicity predicted from the reads." homepage: "https://github.com/arangrhie/merfin" documentation: "https://github.com/arangrhie/merfin/wiki/Best-practices-for-Merfin" doi: "10.1038/s41592-022-01445-y" licence: ["Apache-2.0"] + identifier: biotools:merfin input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fasta_assembly: - type: file - description: Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED] - pattern: "*.{fasta, fasta.gz}" - - - meta1: - type: map - description: | - Groovy Map containing sample read information - e.g. `[ id:'sample1', single_end:false ]` - - - meryl_db_reads: - type: file - description: K-mer database produced from raw reads using Meryl [REQUIRED] - pattern: "*.{meryl_db}" - - - lookup_table: - type: file - description: Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL] - pattern: "lookup_table.txt" - - - seqmers: - type: file - description: Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL] - pattern: "*.{meryl_db}" - - - peak: - type: float - description: Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED] - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta_assembly: + type: file + description: Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED] + pattern: "*.{fasta, fasta.gz}" + - - meta1: + type: map + description: | + Groovy Map containing sample read information + e.g. `[ id:'sample1', single_end:false ]` + - meryl_db_reads: + type: file + description: K-mer database produced from raw reads using Meryl [REQUIRED] + pattern: "*.{meryl_db}" + - - lookup_table: + type: file + description: Input vector of k-mer probabilities (obtained by genomescope2 with + parameter --fitted_hist) [OPTIONAL] + pattern: "lookup_table.txt" + - - seqmers: + type: file + description: Input for pre-built sequence meryl db. By default, the sequence + meryl db will be generated from the input genome assembly [OPTIONAL] + pattern: "*.{meryl_db}" + - - peak: + type: float + description: Input to hard set copy 1 and infer multiplicity to copy number. + Can be calculated using genomescope2 [REQUIRED] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - hist: - type: file - description: The generated 0-centered k* histogram for sequences in . Positive k* values are expected collapsed copies. Negative k* values are expected expanded copies. Closer to 0 means the expected and found k-mers are well balenced, 1:1. - pattern: "*.{hist}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.hist": + type: file + description: The generated 0-centered k* histogram for sequences in . + Positive k* values are expected collapsed copies. Negative k* values are expected + expanded copies. Closer to 0 means the expected and found k-mers are well + balenced, 1:1. + pattern: "*.{hist}" - log_stderr: - type: file - description: Log (stderr) of hist tool execution. The QV and QV* metrics are reported at the end. - pattern: "*.{hist.stderr.log}" - + - "*.hist.stderr.log": + type: file + description: Log (stderr) of hist tool execution. The QV and QV* metrics are + reported at the end. + pattern: "*.{hist.stderr.log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rodtheo" maintainers: diff --git a/modules/nf-core/merqury/hapmers/meta.yml b/modules/nf-core/merqury/hapmers/meta.yml index 6693f540e7f..2c37d3acf76 100644 --- a/modules/nf-core/merqury/hapmers/meta.yml +++ b/modules/nf-core/merqury/hapmers/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "merqury_hapmers" description: A script to generate hap-mer dbs for trios @@ -13,57 +12,85 @@ tools: tool_dev_url: "https://github.com/marbl/merqury" doi: "10.1186/s13059-020-02134-9" licence: ["United States Government Work"] + identifier: biotools:merqury input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - child_meryl: - type: directory - description: Childs' k-mers (all, from WGS reads) - pattern: "*.meryl" - - maternal_meryl: - type: directory - description: Haplotype1 k-mers (all, ex. maternal) - pattern: "*.meryl" - - paternal_meryl: - type: directory - description: Haplotype2 k-mers (all, ex. paternal) - pattern: "*.meryl" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - child_meryl: + type: directory + description: Childs' k-mers (all, from WGS reads) + pattern: "*.meryl" + - - maternal_meryl: + type: directory + description: Haplotype1 k-mers (all, ex. maternal) + pattern: "*.meryl" + - - paternal_meryl: + type: directory + description: Haplotype2 k-mers (all, ex. paternal) + pattern: "*.meryl" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mat_hapmer_meryl: - type: directory - description: Inherited maternal hap-mer dbs - pattern: "*_mat.hapmer.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_mat.hapmer.meryl": + type: directory + description: Inherited maternal hap-mer dbs + pattern: "*_mat.hapmer.meryl" - pat_hapmer_meryl: - type: directory - description: Inherited paternal hap-mer dbs - pattern: "*_pat.hapmer.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_pat.hapmer.meryl": + type: directory + description: Inherited paternal hap-mer dbs + pattern: "*_pat.hapmer.meryl" - inherited_hapmers_fl_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.fl.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.fl.png" - inherited_hapmers_ln_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.ln.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.ln.png" - inherited_hapmers_st_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.st.png" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.st.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.st.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/merqury/merqury/meta.yml b/modules/nf-core/merqury/merqury/meta.yml index 19cb11b38f4..7e8d875a66d 100644 --- a/modules/nf-core/merqury/merqury/meta.yml +++ b/modules/nf-core/merqury/merqury/meta.yml @@ -10,92 +10,187 @@ tools: tool_dev_url: "https://github.com/marbl/merqury" doi: "10.1186/s13059-020-02134-9" licence: ["PUBLIC DOMAIN"] + identifier: biotools:merqury input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_db: - type: file - description: "Meryl read database" - - assembly: - type: file - description: FASTA assembly file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_db: + type: file + description: "Meryl read database" + - assembly: + type: file + description: FASTA assembly file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly_only_kmers_bed: - type: file - description: "The positions of the k-mers found only in an assembly for further investigation in .bed" - pattern: "*_only.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_only.bed": + type: file + description: "The positions of the k-mers found only in an assembly for further + investigation in .bed" + pattern: "*_only.bed" - assembly_only_kmers_wig: - type: file - description: "The positions of the k-mers found only in an assembly for further investigation in .wig" - pattern: "*_only.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_only.wig": + type: file + description: "The positions of the k-mers found only in an assembly for further + investigation in .wig" + pattern: "*_only.wig" - stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.completeness.stats": + type: file + description: Assembly statistics file + pattern: "*.completeness.stats" - dist_hist: - type: file - description: Histogram - pattern: "*.dist_only.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dist_only.hist": + type: file + description: Histogram + pattern: "*.dist_only.hist" - spectra_cn_fl_png: - type: file - description: "Unstacked copy number spectra filled plot in PNG format" - pattern: "*.spectra-cn.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.fl.png": + type: file + description: "Unstacked copy number spectra filled plot in PNG format" + pattern: "*.spectra-cn.fl.png" + - spectra_cn_hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.hist": + type: file + description: "Copy number spectra histogram" + pattern: "*.spectra-cn.hist" - spectra_cn_ln_png: - type: file - description: "Unstacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.ln.png": + type: file + description: "Unstacked copy number spectra line plot in PNG format" + pattern: "*.spectra-cn.ln.png" - spectra_cn_st_png: - type: file - description: "Stacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.st.png" - - spectra_cn_hist: - type: file - description: "Copy number spectra histogram" - pattern: "*.spectra-cn.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.st.png": + type: file + description: "Stacked copy number spectra line plot in PNG format" + pattern: "*.spectra-cn.st.png" - spectra_asm_fl_png: - type: file - description: "Unstacked assembly spectra filled plot in PNG format" - pattern: "*.spectra-asm.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.fl.png": + type: file + description: "Unstacked assembly spectra filled plot in PNG format" + pattern: "*.spectra-asm.fl.png" + - spectra_asm_hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.hist": + type: file + description: "Assembly spectra histogram" + pattern: "*.spectra-asm.hist" - spectra_asm_ln_png: - type: file - description: "Unstacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.ln.png": + type: file + description: "Unstacked assembly spectra line plot in PNG format" + pattern: "*.spectra-asm.ln.png" - spectra_asm_st_png: - type: file - description: "Stacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.st.png" - - spectra_asm_hist: - type: file - description: "Assembly spectra histogram" - pattern: "*.spectra-asm.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.st.png": + type: file + description: "Stacked assembly spectra line plot in PNG format" + pattern: "*.spectra-asm.st.png" - assembly_qv: - type: file - description: "Assembly consensus quality estimation" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.qv: + type: file + description: "Assembly consensus quality estimation" + pattern: "*.qv" - scaffold_qv: - type: file - description: "Scaffold consensus quality estimation" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.qv: + type: file + description: "Scaffold consensus quality estimation" + pattern: "*.qv" - read_ploidy: - type: file - description: "Ploidy estimate from read k-mer database" - pattern: "*.hist.ploidy" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.ploidy": + type: file + description: "Ploidy estimate from read k-mer database" + pattern: "*.hist.ploidy" - hapmers_blob_png: - type: file - description: "Hap-mer blob plot" - pattern: "*.hapmers.blob.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hapmers.blob.png": + type: file + description: "Hap-mer blob plot" + pattern: "*.hapmers.blob.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/merquryfk/katcomp/meta.yml b/modules/nf-core/merquryfk/katcomp/meta.yml index 15de4294974..f629c2a0f68 100644 --- a/modules/nf-core/merquryfk/katcomp/meta.yml +++ b/modules/nf-core/merquryfk/katcomp/meta.yml @@ -10,62 +10,95 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" license: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk1_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk1_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - fastk2_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk2_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk1_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk1_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" + - fastk2_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk2_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filled_png: - type: file - description: Comparison of Kmers between sample 1 and 2 in filled PNG format. - pattern: "*.fi.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.png": + type: file + description: Comparison of Kmers between sample 1 and 2 in filled PNG format. + pattern: "*.fi.png" - line_png: - type: file - description: Comparison of Kmers between sample 1 and 2 in line PNG format. - pattern: "*.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.png": + type: file + description: Comparison of Kmers between sample 1 and 2 in line PNG format. + pattern: "*.ln.png" - stacked_png: - type: file - description: Comparison of Kmers between sample 1 and 2 in stacked PNG format. - pattern: "*.st.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.png": + type: file + description: Comparison of Kmers between sample 1 and 2 in stacked PNG format. + pattern: "*.st.png" - filled_pdf: - type: file - description: Comparison of Kmers between sample 1 and 2 in filled PDF format. - pattern: "*.fi.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.pdf": + type: file + description: Comparison of Kmers between sample 1 and 2 in filled PDF format. + pattern: "*.fi.pdf" - line_pdf: - type: file - description: Comparison of Kmers between sample 1 and 2 in line PDF format. - pattern: "*.ln.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.pdf": + type: file + description: Comparison of Kmers between sample 1 and 2 in line PDF format. + pattern: "*.ln.pdf" - stacked_pdf: - type: file - description: Comparison of Kmers between sample 1 and 2 in stacked PDF format. - pattern: "*.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.pdf": + type: file + description: Comparison of Kmers between sample 1 and 2 in stacked PDF format. + pattern: "*.st.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/merquryfk/katgc/meta.yml b/modules/nf-core/merquryfk/katgc/meta.yml index f3689b0370c..0d553d5c2c0 100644 --- a/modules/nf-core/merquryfk/katgc/meta.yml +++ b/modules/nf-core/merquryfk/katgc/meta.yml @@ -11,54 +11,87 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" license: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: ktab files from the program FastK - pattern: "*.ktab*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: ktab files from the program FastK + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filled_gc_plot_png: - type: file - description: A filled GC content plot in PNG format - pattern: "*.fi.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.png": + type: file + description: A filled GC content plot in PNG format + pattern: "*.fi.png" - filled_gc_plot_pdf: - type: file - description: A filled GC content plot in PDF format - pattern: "*.fi.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.pdf": + type: file + description: A filled GC content plot in PDF format + pattern: "*.fi.pdf" - line_gc_plot_png: - type: file - description: A line GC content plot in PNG format - pattern: "*.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.png": + type: file + description: A line GC content plot in PNG format + pattern: "*.ln.png" - line_gc_plot_pdf: - type: file - description: A line GC content plot in PDF format - pattern: "*.ln.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.pdf": + type: file + description: A line GC content plot in PDF format + pattern: "*.ln.pdf" - stacked_gc_plot_png: - type: file - description: A stacked GC content plot in PNG format - pattern: "*.st.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.png": + type: file + description: A stacked GC content plot in PNG format + pattern: "*.st.png" - stacked_gc_plot_pdf: - type: file - description: A stacked GC content plot in PDF format - pattern: "*.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.pdf": + type: file + description: A stacked GC content plot in PDF format + pattern: "*.st.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml index bba26d12411..82bfbec4653 100644 --- a/modules/nf-core/merquryfk/merquryfk/meta.yml +++ b/modules/nf-core/merquryfk/merquryfk/meta.yml @@ -10,110 +10,205 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - matktab: - type: file - description: trio maternal histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - patktab: - type: file - description: trio paternal histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - assembly: - type: file - description: Genome (primary) assembly files (fasta format) - pattern: ".fasta" - - haplotigs: - type: file - description: Assembly haplotigs (fasta format) - pattern: ".fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" + - assembly: + type: file + description: Genome (primary) assembly files (fasta format) + pattern: ".fasta" + - haplotigs: + type: file + description: Assembly haplotigs (fasta format) + pattern: ".fasta" + - - matktab: + type: file + description: trio maternal histogram ktab files from the program FastK (option + -t) + pattern: "*.ktab*" + - - patktab: + type: file + description: trio paternal histogram ktab files from the program FastK (option + -t) + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.completeness.stats: + type: file + description: Assembly statistics file + pattern: "*.completeness.stats" - bed: - type: file - description: Assembly only kmer positions not supported by reads in bed format - pattern: "*_only.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*_only.bed: + type: file + description: Assembly only kmer positions not supported by reads in bed format + pattern: "*_only.bed" + - assembly_qv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.qv: + type: file + description: "error and qv table for each scaffold of the assembly" + pattern: "*.qv" - spectra_cn_fl: - type: file - description: "Unstacked copy number spectra filled plot in PNG or PDF format" - pattern: "*.spectra-cn.fl.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.fl.{png,pdf}: + type: file + description: "Unstacked copy number spectra filled plot in PNG or PDF format" + pattern: "*.spectra-cn.fl.{png,pdf}" - spectra_cn_ln: - type: file - description: "Unstacked copy number spectra line plot in PNG or PDF format" - pattern: "*.spectra-cn.ln.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.ln.{png,pdf}: + type: file + description: "Unstacked copy number spectra line plot in PNG or PDF format" + pattern: "*.spectra-cn.ln.{png,pdf}" - spectra_cn_st: - type: file - description: "Stacked copy number spectra line plot in PNG or PDF format" - pattern: "*.spectra-cn.st.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.st.{png,pdf}: + type: file + description: "Stacked copy number spectra line plot in PNG or PDF format" + pattern: "*.spectra-cn.st.{png,pdf}" + - qv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.qv: + type: file + description: "error and qv of each assembly as a whole" + pattern: "*.qv" - spectra_asm_fl: - type: file - description: "Unstacked assembly spectra filled plot in PNG or PDF format" - pattern: "*.spectra-asm.fl.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.fl.{png,pdf}: + type: file + description: "Unstacked assembly spectra filled plot in PNG or PDF format" + pattern: "*.spectra-asm.fl.{png,pdf}" - spectra_asm_ln: - type: file - description: "Unstacked assembly spectra line plot in PNG or PDF format" - pattern: "*.spectra-asm.ln.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.ln.{png,pdf}: + type: file + description: "Unstacked assembly spectra line plot in PNG or PDF format" + pattern: "*.spectra-asm.ln.{png,pdf}" - spectra_asm_st: - type: file - description: "Stacked assembly spectra line plot in PNG or PDF format" - pattern: "*.spectra-asm.st.{png,pdf}" - - assembly_qv: - type: file - description: "error and qv table for each scaffold of the assembly" - pattern: "*.qv" - - qv: - type: file - description: "error and qv of each assembly as a whole" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.st.{png,pdf}: + type: file + description: "Stacked assembly spectra line plot in PNG or PDF format" + pattern: "*.spectra-asm.st.{png,pdf}" - phased_block_bed: - type: file - description: Assembly kmer positions seperated by block in bed format - pattern: "*.phased.block.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.phased_block.bed: + type: file + description: Assembly kmer positions seperated by block in bed format + pattern: "*.phased.block.bed" - phased_block_stats: - type: file - description: phased assembly statistics file - pattern: "*.phased.block.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.phased_block.stats: + type: file + description: phased assembly statistics file + pattern: "*.phased.block.stats" - continuity_N: - type: file - description: "Stacked assembly N continuity plot in PNG or PDF format" - pattern: "*.continuity.N.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.continuity.N.{pdf,png}: + type: file + description: "Stacked assembly N continuity plot in PNG or PDF format" + pattern: "*.continuity.N.{png,pdf}" - block_N: - type: file - description: "Stacked assembly N continuity by block plot in PNG or PDF format" - pattern: "*.block.N.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.block.N.{pdf,png}: + type: file + description: "Stacked assembly N continuity by block plot in PNG or PDF format" + pattern: "*.block.N.{png,pdf}" - block_blob: - type: file - description: "Stacked assembly block plot in PNG or PDF format" - pattern: "*.block.blob.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.block.blob.{pdf,png}: + type: file + description: "Stacked assembly block plot in PNG or PDF format" + pattern: "*.block.blob.{png,pdf}" - hapmers_blob: - type: file - description: "Stacked assembly hapmers block plot in PNG or PDF format" - pattern: "*.hapmers.blob.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hapmers.blob.{pdf,png}: + type: file + description: "Stacked assembly hapmers block plot in PNG or PDF format" + pattern: "*.hapmers.blob.{png,pdf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" - "@yumisims" diff --git a/modules/nf-core/merquryfk/ploidyplot/meta.yml b/modules/nf-core/merquryfk/ploidyplot/meta.yml index 62fa9857b18..ab3756efad5 100644 --- a/modules/nf-core/merquryfk/ploidyplot/meta.yml +++ b/modules/nf-core/merquryfk/ploidyplot/meta.yml @@ -10,54 +10,87 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: ktab files from the program FastK - pattern: "*.ktab*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: ktab files from the program FastK + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filled_ploidy_plot_png: - type: file - description: A filled ploidy plot in PNG format - pattern: "*.fi.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.png": + type: file + description: A filled ploidy plot in PNG format + pattern: "*.fi.png" - filled_ploidy_plot_pdf: - type: file - description: A filled ploidy plot in PDF format - pattern: "*.fi.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.pdf": + type: file + description: A filled ploidy plot in PDF format + pattern: "*.fi.pdf" - line_ploidy_plot_png: - type: file - description: A line ploidy plot in PNG format - pattern: "*.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.png": + type: file + description: A line ploidy plot in PNG format + pattern: "*.ln.png" - line_ploidy_plot_pdf: - type: file - description: A lin4 ploidy plot in PDF format - pattern: "*.ln.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.pdf": + type: file + description: A lin4 ploidy plot in PDF format + pattern: "*.ln.pdf" - stacked_ploidy_plot_png: - type: file - description: A stacked ploidy plot in PNG format - pattern: "*.st.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.png": + type: file + description: A stacked ploidy plot in PNG format + pattern: "*.st.png" - stacked_ploidy_plot_pdf: - type: file - description: A stacked ploidy plot in PDF format - pattern: "*.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.pdf": + type: file + description: A stacked ploidy plot in PDF format + pattern: "*.st.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/count/meta.yml b/modules/nf-core/meryl/count/meta.yml index 809a32fec41..a110a610160 100644 --- a/modules/nf-core/meryl/count/meta.yml +++ b/modules/nf-core/meryl/count/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - meryl_db: - type: directory - description: A Meryl k-mer database - pattern: "*.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.meryl": + type: directory + description: A Meryl k-mer database + pattern: "*.meryl" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/histogram/meta.yml b/modules/nf-core/meryl/histogram/meta.yml index c974558c8a7..dce558ed26a 100644 --- a/modules/nf-core/meryl/histogram/meta.yml +++ b/modules/nf-core/meryl/histogram/meta.yml @@ -11,32 +11,35 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_db: - type: directory - description: Meryl k-mer database - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_db: + type: directory + description: Meryl k-mer database + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: Histogram of k-mers - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram of k-mers + pattern: "*.hist" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/unionsum/meta.yml b/modules/nf-core/meryl/unionsum/meta.yml index 77d0784c530..e9e1305126c 100644 --- a/modules/nf-core/meryl/unionsum/meta.yml +++ b/modules/nf-core/meryl/unionsum/meta.yml @@ -11,32 +11,35 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_dbs: - type: directory - description: Meryl k-mer databases - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_dbs: + type: directory + description: Meryl k-mer databases + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - meryl_db: - type: directory - description: A Meryl k-mer database that is the union sum of the input databases - pattern: "*.unionsum.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unionsum.meryl": + type: directory + description: A Meryl k-mer database that is the union sum of the input databases + pattern: "*.unionsum.meryl" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml index 97aa50356bb..0f851e554f6 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml @@ -15,34 +15,37 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/ doi: "10.7717/peerj.7359" licence: ["BSD-3-clause-LBNL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file of reads aligned on the assembled contigs - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bam.bai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file of reads aligned on the assembled contigs + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bam.bai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - depth: - type: file - description: Text file listing the coverage per contig - pattern: ".txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Text file listing the coverage per contig + pattern: ".txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/metabat2/metabat2/meta.yml b/modules/nf-core/metabat2/metabat2/meta.yml index 09306c8e701..5d720867b49 100644 --- a/modules/nf-core/metabat2/metabat2/meta.yml +++ b/modules/nf-core/metabat2/metabat2/meta.yml @@ -15,52 +15,79 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/ doi: "10.7717/peerj.7359" licence: ["BSD-3-clause-LBNL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the assembled contigs - pattern: "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}" - - depth: - type: file - description: | - Optional text file listing the coverage per contig pre-generated - by metabat2_jgisummarizebamcontigdepths - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the assembled contigs + pattern: "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}" + - depth: + type: file + description: | + Optional text file listing the coverage per contig pre-generated + by metabat2_jgisummarizebamcontigdepths + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: Bins created from assembled contigs in fasta file - pattern: "*.fa.gz" - tooshort: - type: file - description: Contigs that did not pass length filtering - pattern: "*.tooShort.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tooShort.fa.gz": + type: file + description: Contigs that did not pass length filtering + pattern: "*.tooShort.fa.gz" - lowdepth: - type: file - description: Contigs that did not have sufficient depth for binning - pattern: "*.lowDepth.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lowDepth.fa.gz": + type: file + description: Contigs that did not have sufficient depth for binning + pattern: "*.lowDepth.fa.gz" - unbinned: - type: file - description: Contigs that pass length and depth filtering but could not be binned - pattern: "*.unbinned.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unbinned.fa.gz": + type: file + description: Contigs that pass length and depth filtering but could not be binned + pattern: "*.unbinned.fa.gz" - membership: - type: file - description: cluster memberships as a matrix format. - pattern: "*.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv.gz": + type: file + description: cluster memberships as a matrix format. + pattern: "*.tsv.gz" + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*[!lowDepth|tooShort|unbinned].fa.gz": + type: file + description: Bins created from assembled contigs in fasta file + pattern: "*.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/metaeuk/easypredict/meta.yml b/modules/nf-core/metaeuk/easypredict/meta.yml index 3943926ca3d..5f5012cd516 100644 --- a/modules/nf-core/metaeuk/easypredict/meta.yml +++ b/modules/nf-core/metaeuk/easypredict/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "metaeuk_easypredict" description: Annotation of eukaryotic metagenomes using MetaEuk @@ -8,51 +7,75 @@ keywords: - fasta tools: - "metaeuk": - description: "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics" + description: "MetaEuk - sensitive, high-throughput gene discovery and annotation + for large-scale eukaryotic metagenomics" homepage: https://github.com/soedinglab/metaeuk documentation: https://github.com/soedinglab/metaeuk tool_dev_url: https://github.com/soedinglab/metaeuk doi: "10.1186/s40168-020-00808-x" licence: ["GPL v3"] + identifier: biotools:MetaEuk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide FASTA file for annotation - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - database: - type: file - description: Either a fasta file containing protein sequences, or a directory containing an mmseqs2-formatted protein database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide FASTA file for annotation + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - database: + type: file + description: Either a fasta file containing protein sequences, or a directory + containing an mmseqs2-formatted protein database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - faa: - type: file - description: Protein FASTA file containing the exons from the input FASTA file - pattern: "*.{fas}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fas: + type: file + description: Protein FASTA file containing the exons from the input FASTA file + pattern: "*.{fas}" - codon: - type: file - description: Nucleotide FASTA file of protein-coding sequences - pattern: "*.{codon.fas}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.codon.fas: + type: file + description: Nucleotide FASTA file of protein-coding sequences + pattern: "*.{codon.fas}" - tsv: - type: file - description: TSV file containing locations of each protein coding sequence in the input fasta - pattern: "*.headersMap.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file containing locations of each protein coding sequence in + the input fasta + pattern: "*.headersMap.{tsv}" - gff: - type: file - description: Annotation file in GFF format - pattern: "*.{gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff": + type: file + description: Annotation file in GFF format + pattern: "*.{gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/metamaps/classify/meta.yml b/modules/nf-core/metamaps/classify/meta.yml index 32c3dd49a75..844adc8adef 100644 --- a/modules/nf-core/metamaps/classify/meta.yml +++ b/modules/nf-core/metamaps/classify/meta.yml @@ -13,73 +13,110 @@ tools: tool_dev_url: https://github.com/DiltheyLab/MetaMaps doi: "10.1038/s41467-019-10934-2" licence: ["Public Domain"] + identifier: biotools:metamaps input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - classification_res: - type: file - description: Coordinates where reads map - pattern: "*.{classification_res}" - - meta_file: - type: file - description: Statistics for mapping result - pattern: "*.{classification_res.meta}" - - meta_unmappedreadsLengths: - type: file - description: Statistics for length of unmapped reads - pattern: "*.{classification_res.meta.unmappedReadsLengths}" - - para_file: - type: file - description: Log with parameters - pattern: "*.{classification_res.parameters}" - - database_folder: - type: directory - description: Path to MetaMaps database - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - classification_res: + type: file + description: Coordinates where reads map + pattern: "*.{classification_res}" + - meta_file: + type: file + description: Statistics for mapping result + pattern: "*.{classification_res.meta}" + - meta_unmappedreadsLengths: + type: file + description: Statistics for length of unmapped reads + pattern: "*.{classification_res.meta.unmappedReadsLengths}" + - para_file: + type: file + description: Log with parameters + pattern: "*.{classification_res.parameters}" + - - database_folder: + type: directory + description: Path to MetaMaps database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wimp: - type: file - description: Sample composition at different taxonomic levels - pattern: "*.{classification_res.EM.WIMP}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.WIMP": + type: file + description: Sample composition at different taxonomic levels + pattern: "*.{classification_res.EM.WIMP}" - evidence_unknown_species: - type: file - description: Statistics on read identities and zero-coverage regions - pattern: "*.{classification_res.EM.evidenceUnknownSpecies}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.evidenceUnknownSpecies": + type: file + description: Statistics on read identities and zero-coverage regions + pattern: "*.{classification_res.EM.evidenceUnknownSpecies}" - reads2taxon: - type: file - description: Taxon ID assignement of reads - pattern: "*.{classification_res.EM.reads2Taxon}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.reads2Taxon": + type: file + description: Taxon ID assignement of reads + pattern: "*.{classification_res.EM.reads2Taxon}" - em: - type: file - description: The final and complete set of approximate read mappings - pattern: "*.{classification_res.EM}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM": + type: file + description: The final and complete set of approximate read mappings + pattern: "*.{classification_res.EM}" - contig_coverage: - type: file - description: Read coverage for contigs - pattern: "*.{classification_res.EM.contigCoverage}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.contigCoverage": + type: file + description: Read coverage for contigs + pattern: "*.{classification_res.EM.contigCoverage}" - length_and_id: - type: file - description: Read length and estimated identity for all reads - pattern: "*.{classification_res.EM.lengthAndIdentitiesPerMappingUnit}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.lengthAndIdentitiesPerMappingUnit": + type: file + description: Read length and estimated identity for all reads + pattern: "*.{classification_res.EM.lengthAndIdentitiesPerMappingUnit}" - krona: - type: file - description: Taxon ID assignement of reads in Krona format - pattern: "*.{classification_res.EM.reads2Taxon.krona}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.reads2Taxon.krona": + type: file + description: Taxon ID assignement of reads in Krona format + pattern: "*.{classification_res.EM.reads2Taxon.krona}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@henningonsbring" - "@sofstam" diff --git a/modules/nf-core/metamaps/mapdirectly/meta.yml b/modules/nf-core/metamaps/mapdirectly/meta.yml index 4ac8e940373..d3d49b1d4f3 100644 --- a/modules/nf-core/metamaps/mapdirectly/meta.yml +++ b/modules/nf-core/metamaps/mapdirectly/meta.yml @@ -13,49 +13,68 @@ tools: tool_dev_url: https://github.com/DiltheyLab/MetaMaps doi: "10.1038/s41467-019-10934-2" licence: ["Public Domain"] + identifier: biotools:metamaps input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input fastq file containing query sequences - pattern: "*.{fq,fastq,fastq.gz,fq.gz}" - - database: - type: file - description: Database file in fasta format - pattern: "*.{fa,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input fastq file containing query sequences + pattern: "*.{fq,fastq,fastq.gz,fq.gz}" + - - database: + type: file + description: Database file in fasta format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - classification_res: - type: file - description: Coordinates where reads map - pattern: "*.{classification_res}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res": + type: file + description: Coordinates where reads map + pattern: "*.{classification_res}" - meta_file: - type: file - description: Statistics for mapping result - pattern: "*.{classification_res.meta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.meta": + type: file + description: Statistics for mapping result + pattern: "*.{classification_res.meta}" - meta_unmappedreadsLengths: - type: file - description: Statistics for length of unmapped reads - pattern: "*.{classification_res.meta.unmappedReadsLengths}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.meta.unmappedReadsLengths": + type: file + description: Statistics for length of unmapped reads + pattern: "*.{classification_res.meta.unmappedReadsLengths}" - para_file: - type: file - description: Log with parameters - pattern: "*.{classification_res.parameters}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.parameters": + type: file + description: Log with parameters + pattern: "*.{classification_res.parameters}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@henningonsbring" - "@sofstam" diff --git a/modules/nf-core/metaphlan/makedb/meta.yml b/modules/nf-core/metaphlan/makedb/meta.yml index d19ba30758d..d371ca64a0a 100644 --- a/modules/nf-core/metaphlan/makedb/meta.yml +++ b/modules/nf-core/metaphlan/makedb/meta.yml @@ -7,20 +7,24 @@ keywords: - metagenomics tools: - metaphlan: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] + identifier: biotools:metaphlan output: - db: - type: directory - description: Output directory containing the indexed METAPHLAN database - pattern: "*/" + - metaphlan_db_latest: + type: directory + description: Output directory containing the indexed METAPHLAN database + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml b/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml index 03aaae06f7a..7272add26e4 100644 --- a/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml +++ b/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml @@ -8,35 +8,39 @@ keywords: - profiles tools: - metaphlan4: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.1038/s41587-023-01688-w" licence: ["MIT License"] + identifier: biotools:metaphlan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profiles: - type: file - description: List of per-sample MetaPhlAn4 taxonomic abundance tables - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profiles: + type: file + description: List of per-sample MetaPhlAn4 taxonomic abundance tables + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined MetaPhlAn4 table - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: Combined MetaPhlAn4 table + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@LilyAnderssonLee" diff --git a/modules/nf-core/metaphlan/metaphlan/meta.yml b/modules/nf-core/metaphlan/metaphlan/meta.yml index d9be48e406e..e1dab779117 100644 --- a/modules/nf-core/metaphlan/metaphlan/meta.yml +++ b/modules/nf-core/metaphlan/metaphlan/meta.yml @@ -1,5 +1,6 @@ name: metaphlan_metaphlan -description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. +description: MetaPhlAn is a tool for profiling the composition of microbial communities + from metagenomic shotgun sequencing data. keywords: - metagenomics - classification @@ -8,49 +9,71 @@ keywords: - sam tools: - metaphlan: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.1038/s41587-023-01688-w" licence: ["MIT License"] + identifier: biotools:metaphlan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out) - pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" - - metaphlan_db_latest: - type: file - description: | - Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/. - Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN! - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Metaphlan can classify the metagenome from a variety of input data + types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced + SAM files (produced from alignments to the MetaPHlAn marker database) and + intermediate bowtie2 alignment files (bowtie2out) + pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" + - - metaphlan_db_latest: + type: file + description: | + Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/. + Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN! + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: file - description: Tab-separated output file of the predicted taxon relative abundances - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_profile.txt": + type: file + description: Tab-separated output file of the predicted taxon relative abundances + pattern: "*.{txt}" - biom: - type: file - description: General-use format for representing biological sample by observation contingency tables - pattern: "*.{biom}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.biom": + type: file + description: General-use format for representing biological sample by observation + contingency tables + pattern: "*.{biom}" - bt2out: - type: file - description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 ) - pattern: "*.{bowtie2out.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bowtie2out.txt": + type: file + description: Intermediate Bowtie2 output produced from mapping the metagenome + against the MetaPHlAn marker database ( not compatible with `bowtie2out` files + generated with MetaPhlAn versions below 3 ) + pattern: "*.{bowtie2out.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon09" - "@LilyAnderssonLee" diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml b/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml index ff87b4e696b..95ae8c083a4 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml @@ -8,35 +8,39 @@ keywords: - profiles tools: - metaphlan3: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profiles: - type: file - description: List of per-sample MetaPhlAn3 taxonomic abundance tables - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profiles: + type: file + description: List of per-sample MetaPhlAn3 taxonomic abundance tables + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined MetaPhlAn3 table - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: Combined MetaPhlAn3 table + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/metaphlan3/metaphlan3/meta.yml b/modules/nf-core/metaphlan3/metaphlan3/meta.yml index 1e64797f612..cc521e9c42c 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/meta.yml +++ b/modules/nf-core/metaphlan3/metaphlan3/meta.yml @@ -1,5 +1,6 @@ name: metaphlan3_metaphlan3 -description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. +description: MetaPhlAn is a tool for profiling the composition of microbial communities + from metagenomic shotgun sequencing data. keywords: - metagenomics - classification @@ -8,49 +9,69 @@ keywords: - fasta tools: - metaphlan3: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out) - pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" - - metaphlan_db: - type: file - description: | - Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/. - Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3! - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Metaphlan 3.0 can classify the metagenome from a variety of input + data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced + SAM files (produced from alignments to the MetaPHlAn marker database) and + intermediate bowtie2 alignment files (bowtie2out) + pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" + - - metaphlan_db: + type: file + description: | + Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/. + Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3! + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: file - description: Tab-separated output file of the predicted taxon relative abundances - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_profile.txt": + type: file + description: Tab-separated output file of the predicted taxon relative abundances + pattern: "*.{txt}" - biom: - type: file - description: General-use format for representing biological sample by observation contingency tables - pattern: "*.{biom}" - - bowtie2out: - type: file - description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 ) - pattern: "*.{bowtie2out.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.biom": + type: file + description: General-use format for representing biological sample by observation + contingency tables + pattern: "*.{biom}" + - bt2out: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bowtie2out.txt": + type: file + description: Bowtie2 output file + pattern: "*.{bowtie2out.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon09" maintainers: diff --git a/modules/nf-core/methyldackel/extract/meta.yml b/modules/nf-core/methyldackel/extract/meta.yml index 7ce950c7fc0..2f17738f831 100644 --- a/modules/nf-core/methyldackel/extract/meta.yml +++ b/modules/nf-core/methyldackel/extract/meta.yml @@ -18,46 +18,55 @@ tools: homepage: https://github.com/dpryan79/MethylDackel documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md licence: ["MIT"] + identifier: biotools:methyldackel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.fai" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: FASTA index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedgraph: - type: file - description: bedGraph file, containing per-base methylation metrics - pattern: "*.bedGraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file, containing per-base methylation metrics + pattern: "*.bedGraph" - methylkit: - type: file - description: methylKit file, containing per-base methylation metrics - pattern: "*.methylKit" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.methylKit": + type: file + description: methylKit file, containing per-base methylation metrics + pattern: "*.methylKit" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/methyldackel/mbias/meta.yml b/modules/nf-core/methyldackel/mbias/meta.yml index e3b55f97271..10b3dcad903 100644 --- a/modules/nf-core/methyldackel/mbias/meta.yml +++ b/modules/nf-core/methyldackel/mbias/meta.yml @@ -19,42 +19,45 @@ tools: homepage: https://github.com/dpryan79/MethylDackel documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md licence: ["MIT"] + identifier: biotools:methyldackel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Text file containing methylation bias - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mbias.txt": + type: file + description: Text file containing methylation bias + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/midas/run/meta.yml b/modules/nf-core/midas/run/meta.yml index e41505ebd1c..6a7a5866015 100644 --- a/modules/nf-core/midas/run/meta.yml +++ b/modules/nf-core/midas/run/meta.yml @@ -6,44 +6,48 @@ keywords: - abundance tools: - "midas": - description: "An integrated pipeline for estimating strain-level genomic variation from metagenomic data" + description: "An integrated pipeline for estimating strain-level genomic variation + from metagenomic data" homepage: "https://github.com/snayfach/MIDAS" documentation: "https://github.com/snayfach/MIDAS" tool_dev_url: "https://github.com/snayfach/MIDAS" doi: "10.1101/gr.201863.115" licence: ["GPL v3"] + identifier: biotools:midashla input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Reads in FASTQ format - pattern: "*.{fastq.gz}" - - db: - type: file - description: A database formatted for MIDAS - pattern: "*.{db}" - - mode: - type: string - description: The mode to run MIDAS is - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Reads in FASTQ format + pattern: "*.{fastq.gz}" + - - db: + type: file + description: A database formatted for MIDAS + pattern: "*.{db}" + - - mode: + type: string + description: The mode to run MIDAS is + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: A directory of results from MIDAS run - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: file + description: A directory of results from MIDAS run + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/mindagap/duplicatefinder/meta.yml b/modules/nf-core/mindagap/duplicatefinder/meta.yml index b92d419c7bd..437bdcba424 100644 --- a/modules/nf-core/mindagap/duplicatefinder/meta.yml +++ b/modules/nf-core/mindagap/duplicatefinder/meta.yml @@ -6,38 +6,42 @@ keywords: - spatial_transcriptomics tools: - "mindagap": - description: "Takes a single panorama image and fills the empty grid lines with neighbour-weighted values." + description: "Takes a single panorama image and fills the empty grid lines with + neighbour-weighted values." homepage: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" documentation: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" tool_dev_url: "https://github.com/ViriatoII/MindaGap" licence: ["BSD 3-clause License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - spot_table: - type: file - description: tsv file containing one spot per row with order x,y,z,gene without column header. - pattern: "*.{tsv,txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - spot_table: + type: file + description: tsv file containing one spot per row with order x,y,z,gene without + column header. + pattern: "*.{tsv,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - marked_dups_spots: - type: file - description: tsv file containing one spot per row, with duplicated spots labeled with "Duplicated" in their gene column. - pattern: "*.{markedDups.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*markedDups.txt": + type: file + description: tsv file containing one spot per row, with duplicated spots labeled + with "Duplicated" in their gene column. + pattern: "*.{markedDups.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/mindagap/mindagap/meta.yml b/modules/nf-core/mindagap/mindagap/meta.yml index efd00004739..ef617400b8b 100644 --- a/modules/nf-core/mindagap/mindagap/meta.yml +++ b/modules/nf-core/mindagap/mindagap/meta.yml @@ -1,40 +1,47 @@ name: "mindagap_mindagap" -description: Takes a single panorama image and fills the empty grid lines with neighbour-weighted values. +description: Takes a single panorama image and fills the empty grid lines with neighbour-weighted + values. keywords: - imaging - resolve_bioscience - spatial_transcriptomics tools: - "mindagap": - description: "Mindagap is a collection of tools to process multiplexed FISH data, such as produced by Resolve Biosciences Molecular Cartography." + description: "Mindagap is a collection of tools to process multiplexed FISH data, + such as produced by Resolve Biosciences Molecular Cartography." homepage: "https://github.com/ViriatoII/MindaGap" documentation: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" tool_dev_url: "https://github.com/ViriatoII/MindaGap" licence: ["BSD-3-Clause license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - panorama: - type: file - description: A tiff file containing gridlines as produced by Molecular Cartography imaging. - pattern: "*.{tif,tiff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - panorama: + type: file + description: A tiff file containing gridlines as produced by Molecular Cartography + imaging. + pattern: "*.{tif,tiff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tiff: - type: file - description: A tiff file with gridlines filled based on consecutive gaussian blurring. - pattern: "*.{tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tif,tiff}": + type: file + description: A tiff file with gridlines filled based on consecutive gaussian + blurring. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ViriatoII" - "@flowuenne" diff --git a/modules/nf-core/minia/meta.yml b/modules/nf-core/minia/meta.yml index 04fd8f88c85..b1751e07168 100644 --- a/modules/nf-core/minia/meta.yml +++ b/modules/nf-core/minia/meta.yml @@ -12,38 +12,53 @@ tools: homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia licence: ["AGPL-3.0-or-later"] + identifier: biotools:minia input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input reads in FastQ format - pattern: "*.{fastq.gz, fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input reads in FastQ format + pattern: "*.{fastq.gz, fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - contigs: - type: file - description: The assembled contigs - pattern: "*.contigs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.fa": + type: file + description: The assembled contigs + pattern: "*.contigs.fa" - unitigs: - type: file - description: The assembled unitigs - pattern: "*.unitigs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unitigs.fa": + type: file + description: The assembled unitigs + pattern: "*.unitigs.fa" - h5: - type: file - description: Minia output h5 file - pattern: "*{.h5}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.h5": + type: file + description: Minia output h5 file + pattern: "*{.h5}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index 9387eea6b56..84fd414ab06 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -6,44 +6,54 @@ keywords: - nanopore tools: - miniasm: - description: Ultrafast de novo assembly for long noisy reads (though having no consensus step) + description: Ultrafast de novo assembly for long noisy reads (though having no + consensus step) homepage: https://github.com/lh3/miniasm documentation: https://github.com/lh3/miniasm tool_dev_url: https://github.com/lh3/miniasm doi: "10.1093/bioinformatics/btw152" licence: ["MIT"] + identifier: biotools:miniasm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input PacBio/ONT FastQ files. - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" - - paf: - type: file - description: Alignment in PAF format - pattern: "*{.paf,.paf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input PacBio/ONT FastQ files. + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - paf: + type: file + description: Alignment in PAF format + pattern: "*{.paf,.paf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gfa: - type: file - description: Assembly graph - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa.gz": + type: file + description: Assembly graph + pattern: "*.gfa.gz" - assembly: - type: file - description: Genome assembly - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta.gz": + type: file + description: Genome assembly + pattern: "*.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml index 8996f881a21..a4cfc891a53 100644 --- a/modules/nf-core/minimap2/align/meta.yml +++ b/modules/nf-core/minimap2/align/meta.yml @@ -14,62 +14,77 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FASTA or FASTQ files of size 1 and 2 for single-end - and paired-end data, respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_ref'] - - reference: - type: file - description: | - Reference database in FASTA format. - - bam_format: - type: boolean - description: Specify that output should be in BAM format - - bam_index_extension: - type: string - description: BAM alignment index extension (e.g. "bai") - - cigar_paf_format: - type: boolean - description: Specify that output CIGAR should be in PAF format - - cigar_bam: - type: boolean - description: | - Write CIGAR with >65535 ops at the CG tag. This is recommended when - doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FASTA or FASTQ files of size 1 and 2 for single-end + and paired-end data, respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_ref'] + - reference: + type: file + description: | + Reference database in FASTA format. + - - bam_format: + type: boolean + description: Specify that output should be in BAM format + - - bam_index_extension: + type: string + description: BAM alignment index extension (e.g. "bai") + - - cigar_paf_format: + type: boolean + description: Specify that output CIGAR should be in PAF format + - - cigar_bam: + type: boolean + description: | + Write CIGAR with >65535 ops at the CG tag. This is recommended when + doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - bam: - type: file - description: Alignment in BAM format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Alignment in BAM format + pattern: "*.bam" - index: - type: file - description: BAM alignment index - pattern: "*.bam.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.${bam_index_extension}": + type: file + description: BAM alignment index + pattern: "*.bam.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" - "@sofstam" diff --git a/modules/nf-core/minimap2/index/meta.yml b/modules/nf-core/minimap2/index/meta.yml index 1d29e3f2d68..57c80e29fca 100644 --- a/modules/nf-core/minimap2/index/meta.yml +++ b/modules/nf-core/minimap2/index/meta.yml @@ -11,30 +11,33 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - Reference database in FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Minimap2 fasta index. - pattern: "*.mmi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mmi": + type: file + description: Minimap2 fasta index. + pattern: "*.mmi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/miniprot/align/meta.yml b/modules/nf-core/miniprot/align/meta.yml index 8b4ffe9edaa..aadd6fdfdd1 100644 --- a/modules/nf-core/miniprot/align/meta.yml +++ b/modules/nf-core/miniprot/align/meta.yml @@ -14,40 +14,49 @@ tools: homepage: https://github.com/lh3/miniprot documentation: https://github.com/lh3/miniprot licence: ["MIT"] + identifier: biotools:miniprot input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pep: - type: file - description: a fasta file contains one or multiple protein sequences - - meta2: - type: map - description: | - Groovy Map containing reference information - - ref: - type: file - description: Reference database in FASTA format or miniprot index format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pep: + type: file + description: a fasta file contains one or multiple protein sequences + - - meta2: + type: map + description: | + Groovy Map containing reference information + - ref: + type: file + description: Reference database in FASTA format or miniprot index format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - gff: - type: file - description: Alignment in gff format - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff": + type: file + description: Alignment in gff format + pattern: "*.gff" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" - "@muffato" diff --git a/modules/nf-core/miniprot/index/meta.yml b/modules/nf-core/miniprot/index/meta.yml index 779a636dded..bd076ada1cb 100644 --- a/modules/nf-core/miniprot/index/meta.yml +++ b/modules/nf-core/miniprot/index/meta.yml @@ -12,30 +12,33 @@ tools: homepage: https://github.com/lh3/miniprot documentation: https://github.com/lh3/miniprot licence: ["MIT"] + identifier: biotools:miniprot input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - Reference database in FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: miniprot fasta index. - pattern: "*.mpi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpi": + type: file + description: miniprot fasta index. + pattern: "*.mpi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" - "@muffato" diff --git a/modules/nf-core/miranda/meta.yml b/modules/nf-core/miranda/meta.yml index 2f551da0def..ecfd2e59bc1 100644 --- a/modules/nf-core/miranda/meta.yml +++ b/modules/nf-core/miranda/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://cbio.mskcc.org/miRNA2003/miranda.html" doi: "10.1186/gb-2003-5-1-r1" licence: ["GNU Public License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - query: - type: file - description: FASTA file containing the microRNA query sequences - pattern: "*.{fa,fasta}" - - mirbase: - type: file - description: FASTA file containing the sequence(s) to be scanned - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - query: + type: file + description: FASTA file containing the microRNA query sequences + pattern: "*.{fa,fasta}" + - - mirbase: + type: file + description: FASTA file containing the sequence(s) to be scanned + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - txt: - type: file - description: Reformatted TXT file containing microRNA targets - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.txt": + type: file + description: Reformatted TXT file containing microRNA targets + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/mirtop/counts/meta.yml b/modules/nf-core/mirtop/counts/meta.yml index 904dbd3102f..679df7b0abf 100644 --- a/modules/nf-core/mirtop/counts/meta.yml +++ b/modules/nf-core/mirtop/counts/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_counts" -description: mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples. +description: mirtop counts generates a file with the minimal information about each + sequence and the count data in columns for each samples. keywords: - mirna - isomir @@ -13,44 +13,55 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - counts/*.tsv: + type: file + description: TSV file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/export/meta.yml b/modules/nf-core/mirtop/export/meta.yml index d797f78373d..25f66c3b6e4 100644 --- a/modules/nf-core/mirtop/export/meta.yml +++ b/modules/nf-core/mirtop/export/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_export" -description: mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package +description: mirtop export generates files such as fasta, vcf or compatible with isomiRs + bioconductor package keywords: - mirna - isomir @@ -13,52 +13,75 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*_rawData.tsv: + type: file + description: TSV file + pattern: "*.{tsv}" - fasta: - type: file - description: FASTA file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*.fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa}" - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*.vcf*: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/gff/meta.yml b/modules/nf-core/mirtop/gff/meta.yml index 454d5edfe1d..8e23f054e26 100644 --- a/modules/nf-core/mirtop/gff/meta.yml +++ b/modules/nf-core/mirtop/gff/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_gff" description: mirtop gff generates the GFF3 adapter format to capture miRNA variations @@ -13,44 +12,55 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: GFF file - pattern: "*.{gff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop/*mirtop.gff: + type: file + description: GFF file + pattern: "*.{gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/stats/meta.yml b/modules/nf-core/mirtop/stats/meta.yml index 1bcd224832d..ebce7d99fe2 100644 --- a/modules/nf-core/mirtop/stats/meta.yml +++ b/modules/nf-core/mirtop/stats/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_stats" -description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category. +description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF + file by isomiR category. keywords: - mirna - isomir @@ -13,37 +13,44 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: Mirtop GFF file obtained with mirtop_gff - pattern: "*.{gff}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: Mirtop GFF file obtained with mirtop_gff + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: TXT file with stats - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - stats/*.txt: + type: file + description: TXT file with stats + pattern: "*.{txt}" - log: - type: file - description: log file with stats - pattern: "*.{log}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - stats/*_stats.log: + type: file + description: log file with stats + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtrace/qc/meta.yml b/modules/nf-core/mirtrace/qc/meta.yml index 9870437d98d..e83ab389781 100644 --- a/modules/nf-core/mirtrace/qc/meta.yml +++ b/modules/nf-core/mirtrace/qc/meta.yml @@ -1,68 +1,108 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtrace_qc" -description: "A tool for quality control and tracing taxonomic origins of microRNA sequencing data" +description: "A tool for quality control and tracing taxonomic origins of microRNA + sequencing data" keywords: - microRNA - smrnaseq - QC tools: - "mirtrace": - description: "miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum." + description: "miRTrace is a new quality control and taxonomic tracing tool developed + specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized + by profiling sequencing quality, read length, sequencing depth and miRNA complexity + and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, + rRNAs and sequencing artifacts). In addition to these routine quality control + (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins + of small RNA-Seq data based on the composition of clade-specific miRNAs. This + feature can be used to detect cross-clade contaminations in typical lab settings. + It can also be applied for more specific applications in forensics, food quality + control and clinical diagnosis, for instance tracing the origins of meat products + or detecting parasitic microRNAs in host serum." homepage: "https://github.com/friedlanderlab/mirtrace/tree/master" documentation: "https://github.com/friedlanderlab/mirtrace/blob/master/release-bundle-includes/doc/manual/mirtrace_manual.pdf" tool_dev_url: "https://github.com/friedlanderlab/mirtrace/tree/master" doi: "10.1186/s13059-018-1588-9" licence: ["GPL v2"] + identifier: biotools:miRTrace input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - reads: - type: file - description: microRNA sequencing data - pattern: "*.{fastq,fastq.gz}" - - mirtrace_config: - type: file - description: (Optional) CSV with list of FASTQ files to process with one entry per row. No headers. Each row consists of the following columns "FASTQ file path, id, adapter, PHRED-ASCII-offset". - - mirtrace_species: - type: string - description: Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens) - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: microRNA sequencing data + pattern: "*.{fastq,fastq.gz}" + - mirtrace_config: + type: file + description: (Optional) CSV with list of FASTQ files to process with one entry + per row. No headers. Each row consists of the following columns "FASTQ file + path, id, adapter, PHRED-ASCII-offset". + - - mirtrace_species: + type: string + description: Target species in microRNA sequencing data (miRbase encoding, e.g. + “hsa” for Homo sapiens) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: HTML file - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.html": + type: file + description: HTML file + pattern: "*.{html}" - json: - type: file - description: JSON file - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: JSON file + pattern: "*.{json}" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: TSV file + pattern: "*.{tsv}" - all_fa: - type: file - description: QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance. - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - qc_passed_reads.all.collapsed/*.{fa,fasta}: + type: file + description: QC-passed reads in FASTA file. Identical reads are collapsed. Entries + are sorted by abundance. + pattern: "*.{fa,fasta}" - rnatype_unknown_fa: - type: file - description: Unknown RNA type QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance. - pattern: "*.{fa,fasta}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}: + type: file + description: Unknown RNA type QC-passed reads in FASTA file. Identical reads + are collapsed. Entries are sorted by abundance. + pattern: "*.{fa,fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mitohifi/findmitoreference/meta.yml b/modules/nf-core/mitohifi/findmitoreference/meta.yml index 462da521c66..bb3d9e09f5f 100644 --- a/modules/nf-core/mitohifi/findmitoreference/meta.yml +++ b/modules/nf-core/mitohifi/findmitoreference/meta.yml @@ -12,24 +12,42 @@ tools: tool_dev_url: https://github.com/marcelauliano/MitoHiFi doi: "10.1101/2022.12.23.521667" licence: ["MIT"] + identifier: biotools:mitohifi input: - - species: - type: string - description: Latin name of the species for which a mitochondrial genome should be fetched - pattern: "[A-Z]?[a-z]* [a-z]*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - species: + type: string + description: Latin name of the species for which a mitochondrial genome should + be fetched + pattern: "[A-Z]?[a-z]* [a-z]*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Downloaded mitochondrial genome in Fasta format - pattern: "*.{fasta,fa}" + - meta: + type: file + description: Downloaded mitochondrial genome in Fasta format + pattern: "*.{fasta,fa}" + - "*.fasta": + type: file + description: Downloaded mitochondrial genome in Fasta format + pattern: "*.{fasta,fa}" - gb: - type: file - description: Downloaded mitochondrial genome in Genbank format - pattern: "*.gb" + - meta: + type: file + description: Downloaded mitochondrial genome in Genbank format + pattern: "*.gb" + - "*.gb": + type: file + description: Downloaded mitochondrial genome in Genbank format + pattern: "*.gb" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@verku" maintainers: diff --git a/modules/nf-core/mitohifi/mitohifi/meta.yml b/modules/nf-core/mitohifi/mitohifi/meta.yml index bd80dc27234..2924dbe8f34 100644 --- a/modules/nf-core/mitohifi/mitohifi/meta.yml +++ b/modules/nf-core/mitohifi/mitohifi/meta.yml @@ -12,96 +12,188 @@ tools: tool_dev_url: https://github.com/marcelauliano/MitoHiFi doi: "10.1101/2022.12.23.521667" licence: ["MIT"] + identifier: biotools:mitohifi input: - - input: - type: file - description: Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified in ext.args2 - pattern: "*.{fa,fa.gz,fasta,fasta.gz}" - - ref_fa: - type: file - description: Reference sequence - pattern: "*.{fa,fasta}" - - ref_gb: - type: file - description: Reference annotation - pattern: "*.{gb}" - - input_mode: - type: string - description: Specifies type of input - reads or contigs - pattern: "{r,c}" - - code: - type: integer - description: Mitochndrial code for annotation - pattern: "[0-9]*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified + in ext.args2 + pattern: "*.{fa,fa.gz,fasta,fasta.gz}" + - - ref_fa: + type: file + description: Reference sequence + pattern: "*.{fa,fasta}" + - - ref_gb: + type: file + description: Reference annotation + pattern: "*.{gb}" + - - input_mode: + type: string + description: Specifies type of input - reads or contigs + pattern: "{r,c}" + - - mito_code: + type: string + description: Mitochondrial genetic code output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Mitochondrial sequence - pattern: "*.{fasta,fa}" + - meta: + type: file + description: Mitochondrial sequence + pattern: "*.{fasta,fa}" + - "*fasta": + type: file + description: Mitochondrial sequence + pattern: "*.{fasta,fa}" + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*contigs_stats.tsv": + type: file + description: Contigs statistics + pattern: "*contigs_stats.tsv" - gb: - type: file - description: Genome annotation in case mitofinder was used - pattern: "*.gb" + - meta: + type: file + description: Genome annotation in case mitofinder was used + pattern: "*.gb" + - "*gb": + type: file + description: Genome annotation in case mitofinder was used + pattern: "*.gb" - gff: - type: file - description: Genome annotation in case mitos was used - pattern: "*.gff" + - meta: + type: file + description: Genome annotation in case mitos was used + pattern: "*.gff" + - "*gff": + type: file + description: Genome annotation in case mitos was used + pattern: "*.gff" - all_potential_contigs: - type: file - description: Contains sequences of all potential contigs - pattern: "*all_potential_contigs.fa" + - meta: + type: file + description: Contains sequences of all potential contigs + pattern: "*all_potential_contigs.fa" + - "*all_potential_contigs.fa": + type: file + description: Contains sequences of all potential contigs + pattern: "*all_potential_contigs.fa" - contigs_annotations: - type: file - description: Graphical representation of annotated genes and tRNAs - pattern: "*contigs_annotations.png" + - meta: + type: file + description: Graphical representation of annotated genes and tRNAs + pattern: "*contigs_annotations.png" + - "*contigs_annotations.png": + type: file + description: Graphical representation of annotated genes and tRNAs + pattern: "*contigs_annotations.png" - contigs_circularization: - type: directory - description: Contains circularization reports - pattern: "*contigs_circularization" + - meta: + type: directory + description: Contains circularization reports + pattern: "*contigs_circularization" + - "*contigs_circularization": + type: directory + description: Contains circularization reports + pattern: "*contigs_circularization" - contigs_filtering: - type: directory - description: Contains files with initial blast matches - pattern: "*contigs_filtering" + - meta: + type: directory + description: Contains files with initial blast matches + pattern: "*contigs_filtering" + - "*contigs_filtering": + type: directory + description: Contains files with initial blast matches + pattern: "*contigs_filtering" - coverage_mapping: - type: directory - description: Contains statistics on coverage mapping - pattern: "*coverage_mapping" + - meta: + type: directory + description: Contains statistics on coverage mapping + pattern: "*coverage_mapping" + - "*coverage_mapping": + type: directory + description: Contains statistics on coverage mapping + pattern: "*coverage_mapping" - coverage_plot: - type: file - description: Read coverage plot for mitochondrial contigs - pattern: "*coverage_plot.png" + - meta: + type: file + description: Read coverage plot for mitochondrial contigs + pattern: "*coverage_plot.png" + - "*coverage_plot.png": + type: file + description: Read coverage plot for mitochondrial contigs + pattern: "*coverage_plot.png" - final_mitogenome_annotation: - type: file - description: Graphical representation of annotated genes for the final mito contig - pattern: "*final_mitogenome.annotation.png" + - meta: + type: file + description: Graphical representation of annotated genes for the final mito + contig + pattern: "*final_mitogenome.annotation.png" + - "*final_mitogenome.annotation.png": + type: file + description: Graphical representation of annotated genes for the final mito + contig + pattern: "*final_mitogenome.annotation.png" - final_mitogenome_choice: - type: directory - description: Files with potential contigs clusterings and alignments - pattern: "*final_mitogenome_choice" + - meta: + type: directory + description: Files with potential contigs clusterings and alignments + pattern: "*final_mitogenome_choice" + - "*final_mitogenome_choice": + type: directory + description: Files with potential contigs clusterings and alignments + pattern: "*final_mitogenome_choice" - final_mitogenome_coverage: - type: file - description: Graphical representation of reads coverage plot for the final mito contig - pattern: "*final_mitogenome.coverage.png" + - meta: + type: file + description: Graphical representation of reads coverage plot for the final mito + contig + pattern: "*final_mitogenome.coverage.png" + - "*final_mitogenome.coverage.png": + type: file + description: Graphical representation of reads coverage plot for the final mito + contig + pattern: "*final_mitogenome.coverage.png" - potential_contigs: - type: directory - description: Files with sequences and annotations of the potential contigs - pattern: "*potential_contigs" + - meta: + type: directory + description: Files with sequences and annotations of the potential contigs + pattern: "*potential_contigs" + - "*potential_contigs": + type: directory + description: Files with sequences and annotations of the potential contigs + pattern: "*potential_contigs" - reads_mapping_and_assembly: - type: directory - description: Read mapping files for run from the raw reads - pattern: "*reads_mapping_and_assembly" + - meta: + type: directory + description: Read mapping files for run from the raw reads + pattern: "*reads_mapping_and_assembly" + - "*reads_mapping_and_assembly": + type: directory + description: Read mapping files for run from the raw reads + pattern: "*reads_mapping_and_assembly" - shared_genes: - type: directory - description: Report on genes shared with the reference genome - pattern: "*shared_genes.tsv" + - meta: + type: directory + description: Report on genes shared with the reference genome + pattern: "*shared_genes.tsv" + - "*shared_genes.tsv": + type: directory + description: Report on genes shared with the reference genome + pattern: "*shared_genes.tsv" - versions: - type: file - description: Software versions used in the run - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ksenia-krasheninnikova" maintainers: diff --git a/modules/nf-core/mlst/meta.yml b/modules/nf-core/mlst/meta.yml index 5a4ec8871a4..90663c0ac26 100644 --- a/modules/nf-core/mlst/meta.yml +++ b/modules/nf-core/mlst/meta.yml @@ -10,30 +10,33 @@ tools: description: Scan contig files against PubMLST typing schemes homepage: https://github.com/tseemann/mlst licence: ["GPL v2"] + identifier: biotools:mlst input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly fasta file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly fasta file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: MLST calls in tsv format - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: MLST calls in tsv format + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lskatz" - "@tseemann" diff --git a/modules/nf-core/mmseqs/cluster/meta.yml b/modules/nf-core/mmseqs/cluster/meta.yml index 0c1cfb3c362..ec974854282 100644 --- a/modules/nf-core/mmseqs/cluster/meta.yml +++ b/modules/nf-core/mmseqs/cluster/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_cluster" description: Cluster sequences using MMSeqs2 cluster. @@ -11,34 +10,38 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input_db: - type: directory - description: a MMseqs2 database used for clustering + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_input: + type: file + description: Input database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db_cluster: - type: file - description: a clustered MMseqs2 database used for clustering + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}/: + type: file + description: a clustered MMseqs2 database used for clustering - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/createdb/meta.yml b/modules/nf-core/mmseqs/createdb/meta.yml index a011020b9b6..c392a360f80 100644 --- a/modules/nf-core/mmseqs/createdb/meta.yml +++ b/modules/nf-core/mmseqs/createdb/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_createdb" description: Create an MMseqs database from an existing FASTA/Q file @@ -11,35 +10,40 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - sequence: - type: file - description: Input sequences in FASTA/Q (zipped or unzipped) format to parse into an mmseqs database - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - sequence: + type: file + description: Input sequences in FASTA/Q (zipped or unzipped) format to parse + into an mmseqs database + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db: - type: directory - description: The created MMseqs2 database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}/: + type: directory + description: The created MMseqs2 database - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/createindex/meta.yml b/modules/nf-core/mmseqs/createindex/meta.yml index 0e34e5bb510..c118ea3fdbc 100644 --- a/modules/nf-core/mmseqs/createindex/meta.yml +++ b/modules/nf-core/mmseqs/createindex/meta.yml @@ -8,34 +8,43 @@ keywords: - indexing tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db: - type: directory - description: | - Directory containing the DB to be indexed - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db: + type: directory + description: | + Directory containing the DB to be indexed + pattern: "*" output: - - versions: - type: file - description: | - File containing software versions - pattern: "versions.yml" - db_indexed: - type: directory - description: | - Directory containing the DB and the generated indexes - pattern: "*" + - meta: + type: directory + description: | + Directory containing the DB and the generated indexes + pattern: "*" + - db: + type: directory + description: | + Directory containing the DB and the generated indexes + pattern: "*" + - versions: + - versions.yml: + type: file + description: | + File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/mmseqs/createtsv/meta.yml b/modules/nf-core/mmseqs/createtsv/meta.yml index e85b066f890..5a50ff349c0 100644 --- a/modules/nf-core/mmseqs/createtsv/meta.yml +++ b/modules/nf-core/mmseqs/createtsv/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_createtsv" -description: Create a tsv file from a query and a target database as well as the result database +description: Create a tsv file from a query and a target database as well as the result + database keywords: - protein sequence - databases @@ -12,53 +12,58 @@ keywords: - tsv tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_result: - type: directory - description: an MMseqs2 database with result data - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_query: - type: directory - description: an MMseqs2 database with query data - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_target: - type: directory - description: an MMseqs2 database with target data + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_result: + type: directory + description: an MMseqs2 database with result data + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_query: + type: directory + description: an MMseqs2 database with query data + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_target: + type: directory + description: an MMseqs2 database with target data output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - tsv: - type: file - description: The resulting tsv file created using the query, target and result MMseqs databases - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tsv": + type: file + description: The resulting tsv file created using the query, target and result + MMseqs databases + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/databases/meta.yml b/modules/nf-core/mmseqs/databases/meta.yml index 803a87f6243..be9380fb197 100644 --- a/modules/nf-core/mmseqs/databases/meta.yml +++ b/modules/nf-core/mmseqs/databases/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_databases" description: Download an mmseqs-formatted database @@ -9,24 +8,29 @@ keywords: - searching tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - database: - type: string - description: Database available through the mmseqs2 databases interface - see https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details + - - database: + type: string + description: Database available through the mmseqs2 databases interface - see + https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - database: - type: directory - description: Directory containing processed mmseqs database + - ${prefix}/: + type: directory + description: Directory containing processed mmseqs database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/mmseqs/easysearch/meta.yml b/modules/nf-core/mmseqs/easysearch/meta.yml index 5c7b0971d39..acf1b20d4dc 100644 --- a/modules/nf-core/mmseqs/easysearch/meta.yml +++ b/modules/nf-core/mmseqs/easysearch/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_easysearch" description: Searches for the sequences of a fasta file in a databse using MMseqs2 @@ -9,44 +8,48 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing input fasta file information - e.g. `[ id:'test' ]` - - fasta: - type: file - description: Fasta file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test' ]` - - db_target: - type: directory - description: an MMseqs2 database with target data, e.g. uniref90 + - - meta: + type: map + description: | + Groovy Map containing input fasta file information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Fasta file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test' ]` + - db_target: + type: directory + description: an MMseqs2 database with target data, e.g. uniref90 output: - - meta: - type: map - description: | - Groovy Map containing input fasta file information - e.g. `[ id:'test']` - tsv: - type: file - description: tsv file with the results of the search - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing input fasta file information + e.g. `[ id:'test']` + - ${prefix}.tsv: + type: file + description: tsv file with the results of the search + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/mmseqs/linclust/meta.yml b/modules/nf-core/mmseqs/linclust/meta.yml index 8513b3ebdd0..986e2d83d0a 100644 --- a/modules/nf-core/mmseqs/linclust/meta.yml +++ b/modules/nf-core/mmseqs/linclust/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_linclust" description: Cluster sequences in linear time using MMSeqs2 linclust. @@ -11,34 +10,38 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input_db: - type: directory - description: a MMseqs2 database used for clustering + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_input: + type: file + description: Input database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db_cluster: - type: directory - description: a clustered MMseqs2 database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}/: + type: directory + description: a clustered MMseqs2 database - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/mmseqs/search/meta.yml b/modules/nf-core/mmseqs/search/meta.yml index 5376bdbd0eb..e722862ad75 100644 --- a/modules/nf-core/mmseqs/search/meta.yml +++ b/modules/nf-core/mmseqs/search/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_search" -description: Search and calculate a score for similar sequences in a query and a target database. +description: Search and calculate a score for similar sequences in a query and a target + database. keywords: - protein sequence - databases @@ -11,42 +11,46 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - query_db: - type: directory - description: an MMseqs2 database with query data - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - target_db: - type: directory - description: an MMseqs2 database with target data, e.g. uniref90 + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_query: + type: file + description: Query database + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_target: + type: file + description: Target database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db_search: - type: directory - description: an MMseqs2 database with search results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}: + type: directory + description: an MMseqs2 database with search results + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/taxonomy/meta.yml b/modules/nf-core/mmseqs/taxonomy/meta.yml index d836029cf9a..15756feb8c5 100644 --- a/modules/nf-core/mmseqs/taxonomy/meta.yml +++ b/modules/nf-core/mmseqs/taxonomy/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mmseqs_taxonomy" -description: Computes the lowest common ancestor by identifying the query sequence homologs against the target database. +description: Computes the lowest common ancestor by identifying the query sequence + homologs against the target database. keywords: - protein sequence - nucleotide sequence @@ -11,37 +11,41 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_query: - type: directory - description: An MMseqs2 database with query data - - db_target: - type: directory - description: an MMseqs2 database with target data including the taxonomy classification + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_query: + type: directory + description: An MMseqs2 database with query data + - - db_target: + type: directory + description: an MMseqs2 database with target data including the taxonomy classification output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db_taxonomy: - type: directory - description: An MMseqs2 database with target data including the taxonomy classification + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}_taxonomy: + type: directory + description: An MMseqs2 database with target data including the taxonomy classification - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml b/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml index 37c7554fca6..4e8890addfa 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml @@ -1,5 +1,6 @@ name: "mmseqs_tsv2exprofiledb" -description: Conversion of expandable profile to databases to the MMseqs2 databases format +description: Conversion of expandable profile to databases to the MMseqs2 databases + format keywords: - protein sequence - databases @@ -8,29 +9,33 @@ keywords: - indexing tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - db: - type: directory - description: | - Directory containing the DB to be indexed - pattern: "*" + - - db: + type: directory + description: | + Directory containing the DB to be indexed + pattern: "*" output: - - versions: - type: file - description: | - File containing software versions - pattern: "versions.yml" - db_exprofile: - type: directory - description: | - Directory containing the expandable profile DB - pattern: "*" + - db: + type: directory + description: | + Directory containing the expandable profile DB + pattern: "*" + - versions: + - versions.yml: + type: file + description: | + File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/mobsuite/recon/meta.yml b/modules/nf-core/mobsuite/recon/meta.yml index 65d67ff0912..f60522c3f2c 100644 --- a/modules/nf-core/mobsuite/recon/meta.yml +++ b/modules/nf-core/mobsuite/recon/meta.yml @@ -6,48 +6,71 @@ keywords: - cluster tools: - mobsuite: - description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. + description: Software tools for clustering, reconstruction and typing of plasmids + from draft assemblies. homepage: https://github.com/phac-nml/mob-suite documentation: https://github.com/phac-nml/mob-suite tool_dev_url: https://github.com/phac-nml/mob-suite doi: "10.1099/mgen.0.000435" licence: ["Apache License, Version 2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A bacterial genome assembly in FASTA format - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A bacterial genome assembly in FASTA format + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - chromosome: - type: file - description: FASTA file of all contigs found to belong to the chromosome - pattern: "chromosome.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/chromosome.fasta: + type: file + description: FASTA file of all contigs found to belong to the chromosome + pattern: "chromosome.fasta" - contig_report: - type: file - description: Assignment of the contig to chromosome or a particular plasmid grouping - pattern: "contig_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/contig_report.txt: + type: file + description: Assignment of the contig to chromosome or a particular plasmid + grouping + pattern: "contig_report.txt" - plasmids: - type: file - description: Each plasmid group is written to an individual FASTA - pattern: "plasmid_*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/plasmid_*.fasta: + type: file + description: Each plasmid group is written to an individual FASTA + pattern: "plasmid_*.fasta" - mobtyper_results: - type: file - description: Aggregate MOB-typer report files for all identified plasmid - pattern: "mobtyper_results.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/mobtyper_results.txt: + type: file + description: Aggregate MOB-typer report files for all identified plasmid + pattern: "mobtyper_results.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml index eb2875f439b..2f274d0c8cd 100644 --- a/modules/nf-core/modkit/pileup/meta.yml +++ b/modules/nf-core/modkit/pileup/meta.yml @@ -6,67 +6,83 @@ keywords: - long-read tools: - "modkit": - description: A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data + description: A bioinformatics tool for working with modified bases in Oxford Nanopore + sequencing data homepage: https://github.com/nanoporetech/modkit documentation: https://github.com/nanoporetech/modkit tool_dev_url: https://github.com/nanoporetech/modkit licence: ["Oxford Nanopore Technologies PLC. Public License Version 1.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Associated index file for BAM - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing BED file information - e.g. `[ id:'regions' ]` - - bed: - type: file - description: - BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the - file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Associated index file for BAM + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference sequence in FASTA format. Required for motif (e.g. CpG) + filtering + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing BED file information + e.g. `[ id:'regions' ]` + - bed: + type: file + description: BED file that will restrict threshold estimation and pileup results + to positions overlapping intervals in the file + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: bedMethyl output file(s) - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: bedMethyl output file(s) + pattern: "*.bed" - bedgraph: - type: file - description: bedgraph output files - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bedgraph": + type: file + description: bedgraph output files + pattern: "*.bedgraph" - log: - type: file - description: File for debug logs to be written to - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.log": + type: file + description: File for debug logs to be written to + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Michal-Babins" - "@fellen31" diff --git a/modules/nf-core/molkartgarage/clahe/meta.yml b/modules/nf-core/molkartgarage/clahe/meta.yml index 9ca71304aa3..6952813af3e 100644 --- a/modules/nf-core/molkartgarage/clahe/meta.yml +++ b/modules/nf-core/molkartgarage/clahe/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "molkartgarage_clahe" -description: Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images. +description: Contrast-limited adjusted histogram equalization (CLAHE) on single-channel + tif images. keywords: - clahe - image_processing @@ -9,43 +9,42 @@ keywords: - correction tools: - "molkartgarage": - description: "One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines." + description: "One-stop-shop for scripts and tools for processing data for molkart + and spatial omics pipelines." homepage: https://github.com/SchapiroLabor/molkart-local/tree/main documentation: https://github.com/SchapiroLabor/molkart-local/tree/main tool_dev_url: https://github.com/SchapiroLabor/molkart-local/blob/main/scripts/molkart_clahe.py licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - image: - type: file - description: Single-channel tiff file to be corrected. - pattern: "*.{tif,tiff}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - image: + type: file + description: Single-channel tiff file to be corrected. + pattern: "*.{tif,tiff}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - img_clahe: - type: file - description: CLAHE corrected tiff file. - pattern: "*.{tiff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.tiff": + type: file + description: CLAHE corrected tiff file. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kbestak" maintainers: diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index 9caaf2cdbc7..dc783c9006a 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -12,91 +12,161 @@ tools: documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 licence: ["MIT"] + identifier: biotools:mosdepth input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index for BAM/CRAM file - pattern: "*.{bai,crai}" - - bed: - type: file - description: BED file with intersected intervals - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index for BAM/CRAM file + pattern: "*.{bai,crai}" + - bed: + type: file + description: BED file with intersected intervals + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - global_txt: - type: file - description: Text file with global cumulative coverage distribution - pattern: "*.{global.dist.txt}" - - regions_txt: - type: file - description: Text file with region cumulative coverage distribution - pattern: "*.{region.dist.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.global.dist.txt": + type: file + description: Text file with global cumulative coverage distribution + pattern: "*.{global.dist.txt}" - summary_txt: - type: file - description: Text file with summary mean depths per chromosome and regions - pattern: "*.{summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.txt": + type: file + description: Text file with summary mean depths per chromosome and regions + pattern: "*.{summary.txt}" + - regions_txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.region.dist.txt": + type: file + description: Text file with region cumulative coverage distribution + pattern: "*.{region.dist.txt}" + - per_base_d4: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.d4": + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" - per_base_bed: - type: file - description: BED file with per-base coverage - pattern: "*.{per-base.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz": + type: file + description: BED file with per-base coverage + pattern: "*.{per-base.bed.gz}" - per_base_csi: - type: file - description: Index file for BED file with per-base coverage - pattern: "*.{per-base.bed.gz.csi}" - - per_base_d4: - type: file - description: D4 file with per-base coverage - pattern: "*.{per-base.d4}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz.csi": + type: file + description: Index file for BED file with per-base coverage + pattern: "*.{per-base.bed.gz.csi}" - regions_bed: - type: file - description: BED file with per-region coverage - pattern: "*.{regions.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz": + type: file + description: BED file with per-region coverage + pattern: "*.{regions.bed.gz}" - regions_csi: - type: file - description: Index file for BED file with per-region coverage - pattern: "*.{regions.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz.csi": + type: file + description: Index file for BED file with per-region coverage + pattern: "*.{regions.bed.gz.csi}" - quantized_bed: - type: file - description: BED file with binned coverage - pattern: "*.{quantized.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz": + type: file + description: BED file with binned coverage + pattern: "*.{quantized.bed.gz}" - quantized_csi: - type: file - description: Index file for BED file with binned coverage - pattern: "*.{quantized.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz.csi": + type: file + description: Index file for BED file with binned coverage + pattern: "*.{quantized.bed.gz.csi}" - thresholds_bed: - type: file - description: BED file with the number of bases in each region that are covered at or above each threshold - pattern: "*.{thresholds.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz": + type: file + description: BED file with the number of bases in each region that are covered + at or above each threshold + pattern: "*.{thresholds.bed.gz}" - thresholds_csi: - type: file - description: Index file for BED file with threshold coverage - pattern: "*.{thresholds.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz.csi": + type: file + description: Index file for BED file with threshold coverage + pattern: "*.{thresholds.bed.gz.csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/motus/downloaddb/meta.yml b/modules/nf-core/motus/downloaddb/meta.yml index 6cf509e97ee..38f9afbe005 100644 --- a/modules/nf-core/motus/downloaddb/meta.yml +++ b/modules/nf-core/motus/downloaddb/meta.yml @@ -9,28 +9,29 @@ keywords: - download tools: - "motus": - description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data." + description: "The mOTU profiler is a computational tool that estimates relative + taxonomic abundance of known and currently unknown microbial community members + using metagenomic shotgun sequencing data." documentation: "https://github.com/motu-tool/mOTUs/wiki" tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" licence: ["GPL v3"] + identifier: "" input: - - motus_downloaddb: - type: directory - description: | - The mOTUs downloadDB script source file. - It is the source file installed or - remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py - pattern: "downloadDB.py" + - - motus_downloaddb_script: + type: file + description: The script to download the mOTUs database output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: The mOTUs database directory - pattern: "db_mOTU" + - db_mOTU/: + type: directory + description: The mOTUs database directory + pattern: "db_mOTU" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/motus/merge/meta.yml b/modules/nf-core/motus/merge/meta.yml index 0d7af231a9b..57c95a547ff 100644 --- a/modules/nf-core/motus/merge/meta.yml +++ b/modules/nf-core/motus/merge/meta.yml @@ -16,37 +16,54 @@ tools: tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" licence: ["GPL v3"] + identifier: "" input: - - input: - type: file - description: | - List of output files (more than one) from motus profile, - or a single directory containing motus output files. - - db: - type: directory - description: | - mOTUs database downloaded by `motus downloadDB` - pattern: "db_mOTU/" - - profile_version_yml: - type: file - description: | - A single versions.yml file output from motus/profile. motus/merge cannot reconstruct - this itself without having the motus database present and configured with the tool - so here we take it from what is already reported by the upstream module. - pattern: "versions.yml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: | + List of output files (more than one) from motus profile, + or a single directory containing motus output files. + - - db: + type: directory + description: | + mOTUs database downloaded by `motus downloadDB` + pattern: "db_mOTU/" + - - profile_version_yml: + type: file + description: | + A single versions.yml file output from motus/profile. motus/merge cannot reconstruct + this itself without having the motus database present and configured with the tool + so here we take it from what is already reported by the upstream module. + pattern: "versions.yml" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: OTU table in txt format, if BIOM format not requested - pattern: "*.txt" + - meta: + type: file + description: OTU table in txt format, if BIOM format not requested + pattern: "*.txt" + - "*.txt": + type: file + description: OTU table in txt format, if BIOM format not requested + pattern: "*.txt" - biom: - type: file - description: OTU table in biom format, if BIOM format requested - pattern: "*.biom" + - meta: + type: file + description: OTU table in biom format, if BIOM format requested + pattern: "*.biom" + - "*.biom": + type: file + description: OTU table in biom format, if BIOM format requested + pattern: "*.biom" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/motus/profile/meta.yml b/modules/nf-core/motus/profile/meta.yml index d6fffebcc5b..8ce98f569c3 100644 --- a/modules/nf-core/motus/profile/meta.yml +++ b/modules/nf-core/motus/profile/meta.yml @@ -13,51 +13,72 @@ tools: tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, - respectively. - Or the intermediate bam file mapped by bwa to the mOTUs database or - the output bam file from motus profile. - Or the intermediate mgc read counts table. - pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}" - - db: - type: directory - description: | - mOTUs database downloaded by `motus downloadDB` + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, + respectively. + Or the intermediate bam file mapped by bwa to the mOTUs database or + the output bam file from motus profile. + Or the intermediate mgc read counts table. + pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}" + - - db: + type: directory + description: | + mOTUs database downloaded by `motus downloadDB` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out: - type: file - description: Results with taxonomic classification of each read - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out": + type: file + description: Results with taxonomic classification of each read + pattern: "*.out" - bam: - type: file - description: Optional intermediate sorted BAM file from BWA - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Optional intermediate sorted BAM file from BWA + pattern: "*.{bam}" - mgc: - type: file - description: Optional intermediate mgc read count table file saved with `-M`. - pattern: "*.{mgc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mgc": + type: file + description: Optional intermediate mgc read count table file saved with `-M`. + pattern: "*.{mgc}" - log: - type: file - description: Standard error logging file containing summary statistics - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Standard error logging file containing summary statistics + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/msisensor/msi/meta.yml b/modules/nf-core/msisensor/msi/meta.yml index 3d4620b4c2f..29d0ed33a8e 100644 --- a/modules/nf-core/msisensor/msi/meta.yml +++ b/modules/nf-core/msisensor/msi/meta.yml @@ -1,5 +1,6 @@ name: msisensor_msi -description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data +description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing + data keywords: - homoploymer - microsatellite @@ -7,62 +8,83 @@ keywords: - instability tools: - msisensor: - description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. + description: MSIsensor is a C++ program to detect replication slippage variants + at microsatellite regions, and differentiate them as somatic or germline. homepage: https://github.com/ding-lab/msisensor doi: "10.1093/bioinformatics/btt755" licence: ["MIT"] + identifier: biotools:msisensor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal_bam: - type: file - description: Coordinate sorted BAM/CRAM/SAM file from normal tissue - pattern: "*.{bam,cram,sam}" - - normal_bai: - type: file - description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue - pattern: "*.{bam,cram,sam}" - - tumor_bam: - type: file - description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue - pattern: "*.{bam,cram,sam}" - - tumor_bai: - type: file - description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue - pattern: "*.{bam,cram,sam}" - - homopolymers: - type: file - description: Output file from MSIsensor scan module - pattern: "*.msisensor_scan.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal_bam: + type: file + description: Coordinate sorted BAM/CRAM/SAM file from normal tissue + pattern: "*.{bam,cram,sam}" + - normal_bai: + type: file + description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue + pattern: "*.{bam,cram,sam}" + - tumor_bam: + type: file + description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue + pattern: "*.{bam,cram,sam}" + - tumor_bai: + type: file + description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue + pattern: "*.{bam,cram,sam}" + - metascan: + type: file + description: metascan file + - homopolymers: + type: file + description: Output file from MSIsensor scan module + pattern: "*.msisensor_scan.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Output file from MSIsensor msi module + - output_dis: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_dis: + type: file + description: Output file from MSIsensor module + - output_germline: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_germline: + type: file + description: Output file from MSIsensor module + - output_somatic: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_somatic: + type: file + description: Output file from MSIsensor module - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: MSIsensor MSI final report file - pattern: "*.output" - - txt: - type: file - description: MSIsensor MSI DIS report file - pattern: "*.output_dis" - - txt: - type: file - description: MSIsensor MSI germline report file - pattern: "*.output_germline" - - txt: - type: file - description: MSIsensor MSI somatic report file - pattern: "*.output_somatic" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevbrick" maintainers: diff --git a/modules/nf-core/msisensor/scan/meta.yml b/modules/nf-core/msisensor/scan/meta.yml index 2b786cecd85..ae2cc7b9f70 100644 --- a/modules/nf-core/msisensor/scan/meta.yml +++ b/modules/nf-core/msisensor/scan/meta.yml @@ -6,34 +6,38 @@ keywords: - MSI tools: - msisensor: - description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. + description: MSIsensor is a C++ program to detect replication slippage variants + at microsatellite regions, and differentiate them as somatic or germline. homepage: https://github.com/ding-lab/msisensor doi: "10.1093/bioinformatics/btt755" licence: ["MIT"] + identifier: biotools:msisensor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: MSIsensor scan output file of homopolymers & minisatellites - pattern: "*.msisensor_scan.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: MSIsensor scan output file of homopolymers & minisatellites + pattern: "*.msisensor_scan.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevbrick" maintainers: diff --git a/modules/nf-core/msisensor2/msi/meta.yml b/modules/nf-core/msisensor2/msi/meta.yml index 49722516889..123dcd8e7ae 100644 --- a/modules/nf-core/msisensor2/msi/meta.yml +++ b/modules/nf-core/msisensor2/msi/meta.yml @@ -8,52 +8,83 @@ keywords: - cfDNA tools: - "msisensor2": - description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data." + description: "MSIsensor2 is a novel algorithm based machine learning, featuring + a large upgrade in the microsatellite instability (MSI) detection for tumor + only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) + and other sample types. The original MSIsensor is specially designed for tumor/normal + paired sequencing data." homepage: "https://github.com/niu-lab/msisensor2" documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md" tool_dev_url: "https://github.com/niu-lab/msisensor2" license: ["GPL-3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tumor_bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - normal_bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - intervals: - type: file - description: BED - pattern: "*.bed" - - models: - type: file - description: Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan) - pattern: "*/*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tumor_bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - tumor_bam_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - normal_bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - normal_bam_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - intervals: + type: file + description: BED + pattern: "*.bed" + - - scan: + type: file + description: Input scan file from MSIsensor2 scan module + - - models: + type: file + description: Folder of MSISensor2 models (available from Github or as a product + of msisensor2/scan) + pattern: "*/*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - msi: - type: file - description: MSI classifications as a text file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: MSI classifications as a text file - distribution: - type: file - description: Read count distributions of MSI regions + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_dis: + type: file + description: Read count distributions of MSI regions - somatic: - type: file - description: Somatic MSI regions detected. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_somatic: + type: file + description: Somatic MSI regions detected. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/msisensor2/scan/meta.yml b/modules/nf-core/msisensor2/scan/meta.yml index 6baeb6b3ed1..3d993f1b2fd 100644 --- a/modules/nf-core/msisensor2/scan/meta.yml +++ b/modules/nf-core/msisensor2/scan/meta.yml @@ -7,28 +7,34 @@ keywords: - tumor tools: - "msisensor2": - description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data." + description: "MSIsensor2 is a novel algorithm based machine learning, featuring + a large upgrade in the microsatellite instability (MSI) detection for tumor + only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) + and other sample types. The original MSIsensor is specially designed for tumor/normal + paired sequencing data." homepage: "https://github.com/niu-lab/msisensor2" documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md" tool_dev_url: "https://github.com/niu-lab/msisensor2" licence: ["GPL-3.0"] + identifier: "" input: - - fasta: - type: file - description: Path to reference genome. - pattern: "*.fasta" - - output: - type: string - description: Name of output MSI scan to write. + - - fasta: + type: file + description: Path to reference genome. + pattern: "*.fasta" + - - output: + type: string + description: Name of output MSI scan to write. output: + - scan: + - output_path: + type: file + description: Path to output MSI scan file. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Output scan of MSI regions in FASTA file. - pattern: "*" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/msisensorpro/msisomatic/meta.yml b/modules/nf-core/msisensorpro/msisomatic/meta.yml index 7f7f4281e3d..48daa6cc645 100644 --- a/modules/nf-core/msisensorpro/msisomatic/meta.yml +++ b/modules/nf-core/msisensorpro/msisomatic/meta.yml @@ -1,5 +1,7 @@ name: msisensorpro_msisomatic -description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input +description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients + with next generation sequencing data. It accepts the whole genome sequencing, whole + exome sequencing and target region (panel) sequencing data as input keywords: - micro-satellite-scan - msisensor-pro @@ -7,68 +9,91 @@ keywords: - somatic tools: - msisensorpro: - description: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + description: Microsatellite Instability (MSI) detection using high-throughput + sequencing data. homepage: https://github.com/xjtu-omics/msisensor-pro documentation: https://github.com/xjtu-omics/msisensor-pro/wiki tool_dev_url: https://github.com/xjtu-omics/msisensor-pro doi: "10.1016/j.gpb.2020.02.001" licence: ["Custom Licence"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - normal_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - tumor: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - tumor_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - intervals: - type: file - description: bed file containing interval information, optional - pattern: "*.{bed}" - - fasta: - type: file - description: Reference genome - pattern: "*.{fasta}" - - msisensor_scan: - type: file - description: Output from msisensor-pro/scan, containing list of msi regions - pattern: "*.list" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - normal_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - tumor_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - intervals: + type: file + description: bed file containing interval information, optional + pattern: "*.{bed}" + - - fasta: + type: file + description: Reference genome + pattern: "*.{fasta}" + - - msisensor_scan: + type: file + description: Output from msisensor-pro/scan, containing list of msi regions + pattern: "*.list" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output_report: - type: file - description: File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: File containing final report with all detected microsatellites, + unstable somatic microsatellites, msi score - output_dis: - type: file - description: File containing distribution results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_dis: + type: file + description: File containing distribution results - output_germline: - type: file - description: File containing germline results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_germline: + type: file + description: File containing germline results - output_somatic: - type: file - description: File containing somatic results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_somatic: + type: file + description: File containing somatic results - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/msisensorpro/scan/meta.yml b/modules/nf-core/msisensorpro/scan/meta.yml index aec743ede56..ac9674b8385 100644 --- a/modules/nf-core/msisensorpro/scan/meta.yml +++ b/modules/nf-core/msisensorpro/scan/meta.yml @@ -1,41 +1,47 @@ name: msisensorpro_scan -description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input +description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients + with next generation sequencing data. It accepts the whole genome sequencing, whole + exome sequencing and target region (panel) sequencing data as input keywords: - micro-satellite-scan - msisensor-pro - scan tools: - msisensorpro: - description: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + description: Microsatellite Instability (MSI) detection using high-throughput + sequencing data. homepage: https://github.com/xjtu-omics/msisensor-pro documentation: https://github.com/xjtu-omics/msisensor-pro/wiki tool_dev_url: https://github.com/xjtu-omics/msisensor-pro doi: "10.1016/j.gpb.2020.02.001" licence: ["Custom Licence"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference genome - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - list: - type: file - description: File containing microsatellite list - pattern: "*.{list}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list": + type: file + description: File containing microsatellite list + pattern: "*.{list}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/mtmalign/align/meta.yml b/modules/nf-core/mtmalign/align/meta.yml index 1e444e1c6ba..281434da0ad 100644 --- a/modules/nf-core/mtmalign/align/meta.yml +++ b/modules/nf-core/mtmalign/align/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mtmalign_align" description: Aligns protein structures using mTM-align @@ -15,42 +14,54 @@ tools: tool_dev_url: "http://yanglab.nankai.edu.cn/mTM-align/" doi: "10.1093/bioinformatics/btx828" licence: ["None"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - pdbs: - type: file - description: Input protein structures in PDB format. Files may be gzipped or uncompressed. - They should contain exactly one chain! - pattern: "*.{pdb}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - pdbs: + type: file + description: Input protein structures in PDB format. Files may be gzipped or + uncompressed. They should contain exactly one chain! + pattern: "*.{pdb}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment in FASTA format. May be gzipped or uncompressed. - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "${prefix}.aln${compress ? '.gz' : ''}": + type: file + description: Alignment in FASTA format. May be gzipped or uncompressed. + pattern: "*.aln{.gz,}" - structure: - type: file - description: Overlaid structures in PDB format. May be gzipped or uncompressed. - pattern: "${prefix}.pdb{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "${prefix}.pdb${compress ? '.gz' : ''}": + type: file + description: Overlaid structures in PDB format. May be gzipped or uncompressed. + pattern: "${prefix}.pdb{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" maintainers: diff --git a/modules/nf-core/mtnucratio/meta.yml b/modules/nf-core/mtnucratio/meta.yml index 6c289720dd4..fc4075022ab 100644 --- a/modules/nf-core/mtnucratio/meta.yml +++ b/modules/nf-core/mtnucratio/meta.yml @@ -1,5 +1,6 @@ name: mtnucratio -description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file. +description: A small Java tool to calculate ratios between MT and nuclear sequencing + reads in a given BAM file. keywords: - mtnucratio - ratio @@ -16,37 +17,50 @@ tools: tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: (coordinate) sorted BAM/SAM file - pattern: "*.{bam,sam}" - - mt_id: - type: string - description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: (coordinate) sorted BAM/SAM file + pattern: "*.{bam,sam}" + - - mt_id: + type: string + description: Identifier of the contig/chromosome of interest (e.g. chromosome, + contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for + mitochondria output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mtnucratio: - type: file - description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio) - pattern: "*.mtnucratio" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mtnucratio": + type: file + description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, + mt_nuc_ratio) + pattern: "*.mtnucratio" - json: - type: file - description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file, containing metadata map with sample name, tool name + and version, and metrics as in txt file + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/mudskipper/bulk/meta.yml b/modules/nf-core/mudskipper/bulk/meta.yml index 1edfb4df7ae..93a4758ad9f 100644 --- a/modules/nf-core/mudskipper/bulk/meta.yml +++ b/modules/nf-core/mudskipper/bulk/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mudskipper_bulk" description: Convert genomic BAM/SAM files to transcriptomic BAM/RAD files. @@ -11,50 +10,59 @@ keywords: - rad tools: - "mudskipper": - description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files." + description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic + BAM/RAD files." homepage: "https://github.com/OceanGenomics/mudskipper" documentation: "https://github.com/OceanGenomics/mudskipper" tool_dev_url: "https://github.com/OceanGenomics/mudskipper" licence: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Name-Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - gtf: - type: file - description: Annotation file - pattern: "*.{gtf,gff,gff3}" - - index: - type: directory - description: Annotation index created by mudskipper/index - - rad: - type: string - description: File type - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Name-Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - index: + type: directory + description: Annotation index created by mudskipper/index + - - gtf: + type: file + description: Annotation file + pattern: "*.{gtf,gff,gff3}" + - - rad: + type: string + description: File type output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.bam: + type: file + description: Sorted BAM file + pattern: "*.bam" - rad: - type: file - description: RAD file - pattern: "*.rad" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.rad: + type: file + description: RAD file + pattern: "*.rad" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" diff --git a/modules/nf-core/mudskipper/index/meta.yml b/modules/nf-core/mudskipper/index/meta.yml index 3421f672729..1df41388f29 100644 --- a/modules/nf-core/mudskipper/index/meta.yml +++ b/modules/nf-core/mudskipper/index/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mudskipper_index" -description: Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files. +description: Build and store a gtf index, which is useful for converting genomic BAM/SAM + files to transcriptomic BAM/SAM files. keywords: - bam - transcriptome @@ -11,27 +11,29 @@ keywords: - sam tools: - "mudskipper": - description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files." + description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic + BAM/RAD files." homepage: "https://github.com/OceanGenomics/mudskipper" documentation: "https://github.com/OceanGenomics/mudskipper" tool_dev_url: "https://github.com/OceanGenomics/mudskipper" licence: ["BSD 3-clause"] + identifier: "" input: - - gtf: - type: file - description: Transcript annotation file. - pattern: "*.{gtf,gff,gff3}" - + - - gtf: + type: file + description: Transcript annotation file. + pattern: "*.{gtf,gff,gff3}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Mudskipper index for running mudskipper conversion tools - pattern: "*/" - + - index/: + type: directory + description: Mudskipper index for running mudskipper conversion tools + pattern: "*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 0fe1264441d..f1cd99b0792 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 382c08cbc25..b16c1879238 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,53 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multivcfanalyzer/meta.yml b/modules/nf-core/multivcfanalyzer/meta.yml index 01663745253..6c1a8b6f0d5 100644 --- a/modules/nf-core/multivcfanalyzer/meta.yml +++ b/modules/nf-core/multivcfanalyzer/meta.yml @@ -1,5 +1,6 @@ name: "multivcfanalyzer" -description: SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA +description: SNP table generator from GATK UnifiedGenotyper with functionality geared + for aDNA keywords: - vcf - ancient DNA @@ -9,111 +10,194 @@ keywords: - SNP table tools: - "multivcfanalyzer": - description: "MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA. License on Github repository." + description: "MultiVCFAnalyzer is a VCF file post-processing tool tailored for + aDNA. License on Github repository." homepage: "https://github.com/alexherbig/MultiVCFAnalyzer" documentation: "https://github.com/alexherbig/MultiVCFAnalyzer" tool_dev_url: "https://github.com/alexherbig/MultiVCFAnalyzer" doi: "10.1038/nature13591" licence: ["GPL >=3"] + identifier: "" input: - - vcfs: - type: file - description: One or a list of uncompressed VCF file - pattern: "*.vcf" - - fasta: - type: file - description: Reference genome VCF was generated against - pattern: "*.{fasta,fna,fa}" - - snpeff_results: - type: file - description: Results from snpEff in txt format (Optional) - pattern: "*.txt" - - gff: - type: file - description: GFF file corresponding to reference genome fasta (Optional) - pattern: "*.gff" - - allele_freqs: - type: boolean - description: | - Whether to include the percentage of reads a given allele is - present in in the SNP table. - - genotype_quality: - type: integer - description: | - Minimum GATK genotyping threshold threshold of which a SNP call - falling under is 'discarded' - - coverage: - type: integer - description: | - Minimum number of a reads that a position must be covered by to be - reported - - homozygous_freq: - type: integer - description: Fraction of reads a base must have to be called 'homozygous' - - heterozygous_freq: - type: integer - description: | - Fraction of which whereby if a call falls above this value, and lower - than the homozygous threshold, a base will be called 'heterozygous'. - - gff_exclude: - type: file - description: | - file listing positions that will be 'filtered' (i.e. ignored) - (Optional) - pattern: "*.vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcfs: + type: file + description: One or a list of uncompressed VCF file + pattern: "*.vcf" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference genome VCF was generated against + pattern: "*.{fasta,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - snpeff_results: + type: file + description: Results from snpEff in txt format (Optional) + pattern: "*.txt" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gff: + type: file + description: GFF file corresponding to reference genome fasta (Optional) + pattern: "*.gff" + - - allele_freqs: + type: boolean + description: | + Whether to include the percentage of reads a given allele is + present in in the SNP table. + - - genotype_quality: + type: integer + description: | + Minimum GATK genotyping threshold threshold of which a SNP call + falling under is 'discarded' + - - coverage: + type: integer + description: | + Minimum number of a reads that a position must be covered by to be + reported + - - homozygous_freq: + type: integer + description: Fraction of reads a base must have to be called 'homozygous' + - - heterozygous_freq: + type: integer + description: | + Fraction of which whereby if a call falls above this value, and lower + than the homozygous threshold, a base will be called 'heterozygous'. + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gff_exclude: + type: file + description: | + file listing positions that will be 'filtered' (i.e. ignored) + (Optional) + pattern: "*.vcf" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - full_alignment: - type: file - description: Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls - pattern: ".fasta.gz" + - meta: + type: file + description: Fasta a fasta file of all positions contained in the VCF files + i.e. including ref calls + pattern: ".fasta.gz" + - fullAlignment.fasta.gz: + type: file + description: Fasta a fasta file of all positions contained in the VCF files + i.e. including ref calls + pattern: ".fasta.gz" - info_txt: - type: file - description: Information about the run - pattern: ".txt" + - meta: + type: file + description: Information about the run + pattern: ".txt" + - info.txt: + type: file + description: Information about the run + pattern: ".txt" - snp_alignment: - type: file - description: A fasta file of just SNP positions with samples only - pattern: ".fasta.gz" + - meta: + type: file + description: A fasta file of just SNP positions with samples only + pattern: ".fasta.gz" + - snpAlignment.fasta.gz: + type: file + description: A fasta file of just SNP positions with samples only + pattern: ".fasta.gz" - snp_genome_alignment: - type: file - description: A fasta file of just SNP positions with reference genome - pattern: ".fasta.gz" + - meta: + type: file + description: A fasta file of just SNP positions with reference genome + pattern: ".fasta.gz" + - snpAlignmentIncludingRefGenome.fasta.gz: + type: file + description: A fasta file of just SNP positions with reference genome + pattern: ".fasta.gz" - snpstatistics: - type: file - description: Some basic statistics about the SNP calls of each sample - pattern: ".tsv" + - meta: + type: file + description: Some basic statistics about the SNP calls of each sample + pattern: ".tsv" + - snpStatistics.tsv: + type: file + description: Some basic statistics about the SNP calls of each sample + pattern: ".tsv" - snptable: - type: file - description: Basic SNP table of combined positions taken from each VCF file - pattern: ".tsv" + - meta: + type: file + description: Basic SNP table of combined positions taken from each VCF file + pattern: ".tsv" + - snpTable.tsv: + type: file + description: Basic SNP table of combined positions taken from each VCF file + pattern: ".tsv" - snptable_snpeff: - type: file - description: Input file for SnpEff - pattern: ".tsv" + - meta: + type: file + description: Input file for SnpEff + pattern: ".tsv" + - snpTableForSnpEff.tsv: + type: file + description: Input file for SnpEff + pattern: ".tsv" - snptable_uncertainty: - type: file - description: Same as above, but with lower case characters indicating uncertain calls - pattern: ".tsv" + - meta: + type: file + description: Same as above, but with lower case characters indicating uncertain + calls + pattern: ".tsv" + - snpTableWithUncertaintyCalls.tsv: + type: file + description: Same as above, but with lower case characters indicating uncertain + calls + pattern: ".tsv" - structure_genotypes: - type: file - description: Input file for STRUCTURE - pattern: ".tsv" + - meta: + type: file + description: Input file for STRUCTURE + pattern: ".tsv" + - structureGenotypes.tsv: + type: file + description: Input file for STRUCTURE + pattern: ".tsv" - structure_genotypes_nomissing: - type: file - description: Alternate input file for STRUCTURE - pattern: ".tsv" + - meta: + type: file + description: Alternate input file for STRUCTURE + pattern: ".tsv" + - structureGenotypes_noMissingData-Columns.tsv: + type: file + description: Alternate input file for STRUCTURE + pattern: ".tsv" - json: - type: file - description: Summary statistics in MultiQC JSON format - pattern: ".json" + - meta: + type: file + description: Summary statistics in MultiQC JSON format + pattern: ".json" + - MultiVCFAnalyzer.json: + type: file + description: Summary statistics in MultiQC JSON format + pattern: ".json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/mummer/meta.yml b/modules/nf-core/mummer/meta.yml index 9e100f44bd4..3a4be42f0d6 100644 --- a/modules/nf-core/mummer/meta.yml +++ b/modules/nf-core/mummer/meta.yml @@ -12,34 +12,38 @@ tools: tool_dev_url: http://mummer.sourceforge.net/ doi: 10.1186/gb-2004-5-2-r12 licence: ["The Artistic License"] + identifier: biotools:mummer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: FASTA file of the reference sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - query: - type: file - description: FASTA file of the query sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: FASTA file of the reference sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - query: + type: file + description: FASTA file of the query sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - coords: - type: file - description: File containing coordinates of matches between reference and query sequence - pattern: "*.coords" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coords": + type: file + description: File containing coordinates of matches between reference and query + sequence + pattern: "*.coords" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" - "@sateeshperi" diff --git a/modules/nf-core/muscle/meta.yml b/modules/nf-core/muscle/meta.yml index c03941bd050..be60ba21bdc 100644 --- a/modules/nf-core/muscle/meta.yml +++ b/modules/nf-core/muscle/meta.yml @@ -1,58 +1,108 @@ name: muscle -description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two +description: MUSCLE is a program for creating multiple alignments of amino acid or + nucleotide sequences. A range of options are provided that give you the choice of + optimizing accuracy, speed, or some compromise between the two keywords: - msa - multiple sequence alignment - phylogeny tools: - muscle: - description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput + description: MUSCLE is a multiple sequence alignment tool with high accuracy and + throughput homepage: https://www.drive5.com/muscle documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840 doi: "10.1093/nar/gkh340" licence: ["http://www.drive5.com/muscle/manual/license.html"] + identifier: biotools:muscle input: - - fasta: - type: file - description: Input sequences for alignment must be in FASTA format - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input sequences for alignment must be in FASTA format + pattern: "*.{fasta,fa,fna}" output: - aligned_fasta: - type: file - description: Multiple sequence alignment produced in FASTA format - pattern: "*.{afa}" - - msf: - type: file - description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW) - pattern: "*.{msf}" - - clustalw: - type: file - description: Multiple sequence alignment produced in ClustalW format without base/residue numbering - pattern: "*.{clw}" + - meta: + type: file + description: Multiple sequence alignment produced in FASTA format + pattern: "*.{afa}" + - "*.afa": + type: file + description: Multiple sequence alignment produced in FASTA format + pattern: "*.{afa}" - phyi: - type: file - description: Multiple sequence alignment produced in PHYLIP interleaved format - pattern: "*.{phyi}" + - meta: + type: file + description: Multiple sequence alignment produced in PHYLIP interleaved format + pattern: "*.{phyi}" + - "*.phyi": + type: file + description: Multiple sequence alignment produced in PHYLIP interleaved format + pattern: "*.{phyi}" - phys: - type: file - description: Multiple sequence alignment produced in PHYLIP sequential format - pattern: "*.{phys}" + - meta: + type: file + description: Multiple sequence alignment produced in PHYLIP sequential format + pattern: "*.{phys}" + - "*.phys": + type: file + description: Multiple sequence alignment produced in PHYLIP sequential format + pattern: "*.{phys}" + - clustalw: + - meta: + type: file + description: Multiple sequence alignment produced in ClustalW format without + base/residue numbering + pattern: "*.{clw}" + - "*.clw": + type: file + description: Multiple sequence alignment produced in ClustalW format without + base/residue numbering + pattern: "*.{clw}" - html: - type: file - description: Multiple sequence alignment produced in HTML format - pattern: "*.{html}" + - meta: + type: file + description: Multiple sequence alignment produced in HTML format + pattern: "*.{html}" + - "*.html": + type: file + description: Multiple sequence alignment produced in HTML format + pattern: "*.{html}" + - msf: + - meta: + type: file + description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW) + pattern: "*.{msf}" + - "*.msf": + type: file + description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW) + pattern: "*.{msf}" - tree: - type: file - description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment - pattern: "*.{tree}" + - meta: + type: file + description: NJ or UPGMA tree in Newick format produced from a multiple sequence + alignment + pattern: "*.{tree}" + - "*.tree": + type: file + description: NJ or UPGMA tree in Newick format produced from a multiple sequence + alignment + pattern: "*.{tree}" - log: - type: file - description: Log file of MUSCLE run - pattern: "*{.log}" + - "*.log": + type: file + description: Log file of MUSCLE run + pattern: "*{.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon" maintainers: diff --git a/modules/nf-core/muscle5/super5/meta.yml b/modules/nf-core/muscle5/super5/meta.yml index 057128dc855..0959c565fe5 100644 --- a/modules/nf-core/muscle5/super5/meta.yml +++ b/modules/nf-core/muscle5/super5/meta.yml @@ -1,5 +1,7 @@ name: "muscle5_super5" -description: Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags. +description: Muscle is a program for creating multiple alignments of amino acid or + nucleotide sequences. This particular module uses the super5 algorithm for very + big alignments. It can permutate the guide tree according to a set of flags. keywords: - align - msa @@ -11,37 +13,44 @@ tools: documentation: "https://drive5.com/muscle5/manual/" doi: "10.1101/2021.06.20.449169" licence: ["Public Domain"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input sequences for alignment must be in FASTA format - pattern: "*.{fasta,fa,fna}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input sequences for alignment must be in FASTA format + pattern: "*.{fasta,fa,fna}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - alignment: - type: file - description: Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input! - pattern: "*.{aln.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.aln{.gz,}": + type: file + description: Multiple sequence alignment produced in gzipped FASTA format. If + '-perm all' is passed in ext.args, this will be multiple files per input! + pattern: "*.{aln.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alessiovignoli" - "@JoseEspinosa" diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml index f7aaa455613..c83f22f79b7 100644 --- a/modules/nf-core/mygene/meta.yml +++ b/modules/nf-core/mygene/meta.yml @@ -12,42 +12,49 @@ tools: tool_dev_url: "https://github.com/biothings/mygene.py" doi: "10.1093/nar/gks1114" licence: ["Apache-2.0"] + identifier: biotools:mygene input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gene_list: - type: file - description: A tsv/csv file that contains a list of gene ids in one of the columns. - By default, the column name should be "gene_id", but this can be changed - by using "--columname gene_id" in ext.args. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gene_list: + type: file + description: A tsv/csv file that contains a list of gene ids in one of the columns. + By default, the column name should be "gene_id", but this can be changed by + using "--columname gene_id" in ext.args. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - gmt: - type: file - description: | - Each row contains the GO id, a description, and a list of gene ids. - pattern: "*.gmt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gmt": + type: file + description: | + Each row contains the GO id, a description, and a list of gene ids. + pattern: "*.gmt" - tsv: - type: file - description: | - (optional) A tsv file with the following columns: - query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: | + (optional) A tsv file with the following columns: + query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" maintainers: diff --git a/modules/nf-core/mykrobe/predict/meta.yml b/modules/nf-core/mykrobe/predict/meta.yml index ad5652ada18..57a3a440838 100644 --- a/modules/nf-core/mykrobe/predict/meta.yml +++ b/modules/nf-core/mykrobe/predict/meta.yml @@ -12,38 +12,47 @@ tools: tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe" doi: "10.1038/ncomms10063" licence: ["MIT"] + identifier: biotools:Mykrobe input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: BAM or FASTQ file - pattern: "*.{bam,fastq.gz,fq.gz}" - - species: - type: string - description: Species to make AMR prediction against - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: BAM or FASTQ file + pattern: "*.{bam,fastq.gz,fq.gz}" + - - species: + type: string + description: Species to make AMR prediction against + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: AMR predictions in CSV format - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.csv: + type: file + description: AMR predictions in CSV format + pattern: "*.csv" - json: - type: file - description: AMR predictions in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.json: + type: file + description: AMR predictions in JSON format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/nanocomp/meta.yml b/modules/nf-core/nanocomp/meta.yml index 85ddf0cd28f..3b482d3c9c2 100644 --- a/modules/nf-core/nanocomp/meta.yml +++ b/modules/nf-core/nanocomp/meta.yml @@ -12,94 +12,190 @@ tools: homepage: "https://github.com/wdecoster/nanocomp" documentation: "https://github.com/wdecoster/nanocomp" licence: ["MIT License"] + identifier: biotools:nanocomp input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - filelist: - type: file - description: List of all the files you want to compare, they have to be all the same filetype (either fastq, fasta, bam or Nanopore sequencing summary) - pattern: "*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - filelist: + type: file + description: List of all the files you want to compare, they have to be all + the same filetype (either fastq, fasta, bam or Nanopore sequencing summary) + pattern: "*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - report_html: - type: file - description: Summary of all collected statistics - pattern: "*NanoComp-report.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp-report.html": + type: file + description: Summary of all collected statistics + pattern: "*NanoComp-report.html" - lengths_violin_html: - type: file - description: Violin plot of the sequence lengths - pattern: "*NanoComp_lengths_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_lengths_violin.html": + type: file + description: Violin plot of the sequence lengths + pattern: "*NanoComp_lengths_violin.html" - log_length_violin_html: - type: file - description: Violin plot of the sequence lengths, log function applied - pattern: "*NanoComp_log_length_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_log_length_violin.html": + type: file + description: Violin plot of the sequence lengths, log function applied + pattern: "*NanoComp_log_length_violin.html" - n50_html: - type: file - description: Bar plot of N50 sequence length per sample - pattern: "*NanoComp_N50.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_N50.html": + type: file + description: Bar plot of N50 sequence length per sample + pattern: "*NanoComp_N50.html" - number_of_reads_html: - type: file - description: Bar plot of number of reads per sample - pattern: "*NanoComp_number_of_reads.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_number_of_reads.html": + type: file + description: Bar plot of number of reads per sample + pattern: "*NanoComp_number_of_reads.html" - overlay_histogram_html: - type: file - description: Histogram of all read lengths per sample - pattern: "*NanoComp_OverlayHistogram.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram.html": + type: file + description: Histogram of all read lengths per sample + pattern: "*NanoComp_OverlayHistogram.html" - overlay_histogram_normalized_html: - type: file - description: Normalized histogram of all read lengths per sample - pattern: "*NanoComp_OverlayHistogram_Normalized.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram_Normalized.html": + type: file + description: Normalized histogram of all read lengths per sample + pattern: "*NanoComp_OverlayHistogram_Normalized.html" - overlay_log_histogram_html: - type: file - description: Histogram of all read lengths per sample, log function applied - pattern: "*NanoComp_OverlayLogHistogram.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayLogHistogram.html": + type: file + description: Histogram of all read lengths per sample, log function applied + pattern: "*NanoComp_OverlayLogHistogram.html" - overlay_log_histogram_normalized_html: - type: file - description: Normalized histogram of all read lengths per sample, log function applied - pattern: "*NanoComp_OverlayLogHistogram_Normalized.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayLogHistogram_Normalized.html": + type: file + description: Normalized histogram of all read lengths per sample, log function + applied + pattern: "*NanoComp_OverlayLogHistogram_Normalized.html" - total_throughput_html: - type: file - description: Barplot comparing throughput in bases - pattern: "*NanoComp_total_throughput.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_total_throughput.html": + type: file + description: Barplot comparing throughput in bases + pattern: "*NanoComp_total_throughput.html" - quals_violin_html: - type: file - description: Violin plot of base qualities, only for bam, fastq and sequencing summary input - pattern: "*NanoComp_quals_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_quals_violin.html": + type: file + description: Violin plot of base qualities, only for bam, fastq and sequencing + summary input + pattern: "*NanoComp_quals_violin.html" - overlay_histogram_identity_html: - type: file - description: Histogram of perfect reference identity, only for bam input - pattern: "*NanoComp_OverlayHistogram_Identity.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram_Identity.html": + type: file + description: Histogram of perfect reference identity, only for bam input + pattern: "*NanoComp_OverlayHistogram_Identity.html" - overlay_histogram_phredscore_html: - type: file - description: Histogram of phred scores, only for bam input - pattern: "*NanoComp_OverlayHistogram_PhredScore.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram_PhredScore.html": + type: file + description: Histogram of phred scores, only for bam input + pattern: "*NanoComp_OverlayHistogram_PhredScore.html" - percent_identity_violin_html: - type: file - description: Violin plot comparing perfect reference identity, only for bam input - pattern: "*NanoComp_percentIdentity_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_percentIdentity_violin.html": + type: file + description: Violin plot comparing perfect reference identity, only for bam + input + pattern: "*NanoComp_percentIdentity_violin.html" - active_pores_over_time_html: - type: file - description: Scatter plot of active pores over time, only for sequencing summary input - pattern: "*NanoComp_ActivePoresOverTime.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_ActivePoresOverTime.html": + type: file + description: Scatter plot of active pores over time, only for sequencing summary + input + pattern: "*NanoComp_ActivePoresOverTime.html" - cumulative_yield_plot_gigabases_html: - type: file - description: Scatter plot of cumulative yield, only for sequencing summary input - pattern: "*NanoComp_CumulativeYieldPlot_Gigabases.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_CumulativeYieldPlot_Gigabases.html": + type: file + description: Scatter plot of cumulative yield, only for sequencing summary input + pattern: "*NanoComp_CumulativeYieldPlot_Gigabases.html" - sequencing_speed_over_time_html: - type: file - description: Scatter plot of sequencing speed over time, only for sequencing summary input - pattern: "*NanoComp_sequencing_speed_over_time.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_sequencing_speed_over_time.html": + type: file + description: Scatter plot of sequencing speed over time, only for sequencing + summary input + pattern: "*NanoComp_sequencing_speed_over_time.html" - stats_txt: - type: file - description: txt file with basic statistics - pattern: "*NanoStats.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoStats.txt": + type: file + description: txt file with basic statistics + pattern: "*NanoStats.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@paulwolk" maintainers: diff --git a/modules/nf-core/nanofilt/meta.yml b/modules/nf-core/nanofilt/meta.yml index af15136ce1a..ed495e3a2b7 100644 --- a/modules/nf-core/nanofilt/meta.yml +++ b/modules/nf-core/nanofilt/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "nanofilt" description: Filtering and trimming of Oxford Nanopore Sequencing data @@ -14,45 +13,43 @@ tools: tool_dev_url: "https://github.com/wdecoster/nanofilt" doi: "10.1093/bioinformatics/bty149" licence: ["GLP-3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: Gunziped fastq files from Oxford Nanopore sequencing. - pattern: "*.fastq.gz" - - - summary_file: - type: file - description: Optional - Albacore or guppy summary file for quality scores - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Gunziped fastq files from Oxford Nanopore sequencing. + pattern: "*.fastq.gz" + - - summary_file: + type: file + description: Optional - Albacore or guppy summary file for quality scores output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - filtreads: - type: file - description: Gunziped fastq files after filtering. - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq.gz": + type: file + description: Gunziped fastq files after filtering. + pattern: "*.fastq.gz" - log_file: - type: file - description: Log file generated by --logfile option in NanoFilt, the file must end with .log extension. - pattern: "*.log" - + - "*.log": + type: file + description: Log file generated by --logfile option in NanoFilt, the file must + end with .log extension. + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lfreitasl" maintainers: diff --git a/modules/nf-core/nanolyse/meta.yml b/modules/nf-core/nanolyse/meta.yml index 20a1b289cc1..b0db2b7f8fd 100644 --- a/modules/nf-core/nanolyse/meta.yml +++ b/modules/nf-core/nanolyse/meta.yml @@ -11,40 +11,44 @@ tools: homepage: https://github.com/wdecoster/nanolyse documentation: https://github.com/wdecoster/nanolyse#nanolyse licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - Basecalled reads in FASTQ.GZ format - pattern: "*.fastq.gz" - - fasta: - type: file - description: | - A reference fasta file against which to filter. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + Basecalled reads in FASTQ.GZ format + pattern: "*.fastq.gz" + - - fasta: + type: file + description: | + A reference fasta file against which to filter. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Reads with contaminants removed in FASTQ format - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Reads with contaminants removed in FASTQ format + pattern: "*.fastq.gz" - log: - type: file - description: Log of the Nanolyse run. - pattern: "*.log" + - "*.log": + type: file + description: Log of the Nanolyse run. + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" maintainers: diff --git a/modules/nf-core/nanomonsv/parse/meta.yml b/modules/nf-core/nanomonsv/parse/meta.yml index db42b42adbd..5b92be94ba9 100644 --- a/modules/nf-core/nanomonsv/parse/meta.yml +++ b/modules/nf-core/nanomonsv/parse/meta.yml @@ -21,62 +21,107 @@ tools: tool_dev_url: https://github.com/friend1ws/nanomonsv doi: "10.1101/2020.07.22.214262 " licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Aligned BAM file - pattern: "*.{bam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Aligned BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - insertions: - type: file - description: Gzipped BED file containing reads supporting insertions - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.insertion.sorted.bed.gz: + type: file + description: Gzipped BED file containing reads supporting insertions + pattern: "*.{bed.gz}" - insertions_index: - type: file - description: Index for gzipped BED file containing reads supporting insertions - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.insertion.sorted.bed.gz.tbi: + type: file + description: Index for gzipped BED file containing reads supporting insertions + pattern: "*.{bed.gz.tbi}" - deletions: - type: file - description: Gzipped BED file containing reads supporting deletions - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.deletion.sorted.bed.gz: + type: file + description: Gzipped BED file containing reads supporting deletions + pattern: "*.{bed.gz}" - deletions_index: - type: file - description: Index for gzipped BED file containing reads supporting deletions - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.deletion.sorted.bed.gz.tbi: + type: file + description: Index for gzipped BED file containing reads supporting deletions + pattern: "*.{bed.gz.tbi}" - rearrangements: - type: file - description: Gzipped BED file containing reads supporting rearrangements - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.rearrangement.sorted.bedpe.gz: + type: file + description: Gzipped BED file containing reads supporting rearrangements + pattern: "*.{bed.gz}" - rearrangements_index: - type: file - description: Index for gzipped BED file containing reads supporting rearrangements - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.rearrangement.sorted.bedpe.gz.tbi: + type: file + description: Index for gzipped BED file containing reads supporting rearrangements + pattern: "*.{bed.gz.tbi}" - bp_info: - type: file - description: Gzipped BED file containing breakpoint info - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bp_info.sorted.bed.gz: + type: file + description: Gzipped BED file containing breakpoint info + pattern: "*.{bed.gz}" - bp_info_index: - type: file - description: Index for gzipped BED file containing breakpoint info - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bp_info.sorted.bed.gz.tbi: + type: file + description: Index for gzipped BED file containing breakpoint info + pattern: "*.{bed.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@awgymer" maintainers: diff --git a/modules/nf-core/nanoplot/meta.yml b/modules/nf-core/nanoplot/meta.yml index 46fbd562bc7..8af83355ecd 100644 --- a/modules/nf-core/nanoplot/meta.yml +++ b/modules/nf-core/nanoplot/meta.yml @@ -14,46 +14,62 @@ tools: homepage: http://nanoplot.bioinf.be documentation: https://github.com/wdecoster/NanoPlot licence: ["GPL-3.0-or-later"] + identifier: biotools:nanoplot input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input basecalled-FastQ files. - - summary_txt: - type: file - description: | - List of sequencing_summary.txt files from running basecalling. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ontfile: + type: file + description: ONT file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: NanoPlot report - pattern: "*{.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: NanoPlot report + pattern: "*{.html}" - png: - type: file - description: Plots generated by NanoPlot - pattern: "*{.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: Plots generated by NanoPlot + pattern: "*{.png}" - txt: - type: file - description: Stats from NanoPlot - pattern: "*{.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Stats from NanoPlot + pattern: "*{.txt}" - log: - type: file - description: log file of NanoPlot run - pattern: "*{.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: log file of NanoPlot run + pattern: "*{.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa" diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml index 85c0c9789a1..0ff2b9b4efe 100644 --- a/modules/nf-core/nanoq/meta.yml +++ b/modules/nf-core/nanoq/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "nanoq" -description: Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads. +description: Nanoq implements ultra-fast read filters and summary reports for high-throughput + nanopore reads. keywords: - nanoq - Read filters @@ -15,45 +15,48 @@ tools: tool_dev_url: "https://github.com/esteinig/nanoq" doi: "10.21105/joss.02991" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - ontreads: - type: file - description: Compressed or uncompressed nanopore reads in fasta or fastq formats. - pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}" - - - output_format: - type: string - description: "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ontreads: + type: file + description: Compressed or uncompressed nanopore reads in fasta or fastq formats. + pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}" + - - output_format: + type: string + description: "Specifies the output format. One of these formats: fasta, fastq; + fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - stats: - type: file - description: Summary report of reads statistics. - pattern: "*.{stats,json}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{stats,json}": + type: file + description: Summary report of reads statistics. + pattern: "*.{stats,json}" - reads: - type: file - description: Filtered reads. - pattern: "*.{fasta,fastq}{,.gz,.bz2,.lzma}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_filtered.${output_format}": + type: file + description: Filtered reads. + pattern: "*.{fasta,fastq}{,.gz,.bz2,.lzma}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/narfmap/align/environment.yml b/modules/nf-core/narfmap/align/environment.yml index 57ce13586f1..9a0831a3d28 100644 --- a/modules/nf-core/narfmap/align/environment.yml +++ b/modules/nf-core/narfmap/align/environment.yml @@ -1,9 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - # renovate: datasource=conda depName=bioconda/narfmap - narfmap=1.4.2 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.18 - pigz=2.8 + - samtools=1.18 diff --git a/modules/nf-core/narfmap/align/meta.yml b/modules/nf-core/narfmap/align/meta.yml index 0924a0b0805..557507c9abd 100644 --- a/modules/nf-core/narfmap/align/meta.yml +++ b/modules/nf-core/narfmap/align/meta.yml @@ -13,35 +13,64 @@ tools: documentation: https://github.com/edmundmiller/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage tool_dev_url: https://github.com/edmundmiller/narfmap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - hashmap: - type: file - description: NARFMAP hash table - pattern: "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - hashmap: + type: file + description: NARFMAP hash table + pattern: "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fa,fna}" + - - sort_bam: + type: boolean + description: Sort the BAM file after alignment output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: Log file of NARFMAP run + pattern: "*{.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/narfmap/hashtable/meta.yml b/modules/nf-core/narfmap/hashtable/meta.yml index 9b6715af8bf..7fc344ce836 100644 --- a/modules/nf-core/narfmap/hashtable/meta.yml +++ b/modules/nf-core/narfmap/hashtable/meta.yml @@ -12,29 +12,32 @@ tools: documentation: https://github.com/edmundmiller/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage tool_dev_url: https://github.com/edmundmiller/narfmap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - hashmap: - type: file - description: NARFMAP hash table - pattern: "*.{cmp,.bin,.txt}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - narfmap: + type: file + description: NARFMAP hash table + pattern: "*.{cmp,.bin,.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/ncbigenomedownload/meta.yml b/modules/nf-core/ncbigenomedownload/meta.yml index e7d37201073..794d931038a 100644 --- a/modules/nf-core/ncbigenomedownload/meta.yml +++ b/modules/nf-core/ncbigenomedownload/meta.yml @@ -11,85 +11,169 @@ tools: documentation: https://github.com/kblin/ncbi-genome-download tool_dev_url: https://github.com/kblin/ncbi-genome-download licence: ["Apache Software License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - accessions: - type: file - description: List of accessions (one per line) to download - pattern: "*.txt" - - taxids: - type: file - description: List of taxids (one per line) to download - pattern: "*.txt" - - groups: - type: string - description: NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral'] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - - accessions: + type: file + description: List of accessions (one per line) to download + pattern: "*.txt" + - - taxids: + type: file + description: List of taxids (one per line) to download + pattern: "*.txt" + - - groups: + type: string + description: NCBI taxonomic groups to download. Can be a comma-separated list. + Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', + 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral'] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gbk: - type: file - description: GenBank format of the genomic sequence(s) in the assembly - pattern: "*_genomic.gbff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genomic.gbff.gz": + type: file + description: GenBank format of the genomic sequence(s) in the assembly + pattern: "*_genomic.gbff.gz" - fna: - type: file - description: FASTA format of the genomic sequence(s) in the assembly. - pattern: "*_genomic.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genomic.fna.gz": + type: file + description: FASTA format of the genomic sequence(s) in the assembly. + pattern: "*_genomic.fna.gz" - rm: - type: file - description: RepeatMasker output for eukaryotes. - pattern: "*_rm.out.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rm.out.gz": + type: file + description: RepeatMasker output for eukaryotes. + pattern: "*_rm.out.gz" - features: - type: file - description: Tab-delimited text file reporting locations and attributes for a subset of annotated features - pattern: "*_feature_table.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_feature_table.txt.gz": + type: file + description: Tab-delimited text file reporting locations and attributes for + a subset of annotated features + pattern: "*_feature_table.txt.gz" - gff: - type: file - description: Annotation of the genomic sequence(s) in GFF3 format - pattern: "*_genomic.gff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genomic.gff.gz": + type: file + description: Annotation of the genomic sequence(s) in GFF3 format + pattern: "*_genomic.gff.gz" - faa: - type: file - description: FASTA format of the accessioned protein products annotated on the genome assembly. - pattern: "*_protein.faa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_protein.faa.gz": + type: file + description: FASTA format of the accessioned protein products annotated on the + genome assembly. + pattern: "*_protein.faa.gz" - gpff: - type: file - description: GenPept format of the accessioned protein products annotated on the genome assembly. - pattern: "*_protein.gpff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_protein.gpff.gz": + type: file + description: GenPept format of the accessioned protein products annotated on + the genome assembly. + pattern: "*_protein.gpff.gz" - wgs_gbk: - type: file - description: GenBank flat file format of the WGS master for the assembly - pattern: "*_wgsmaster.gbff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_wgsmaster.gbff.gz": + type: file + description: GenBank flat file format of the WGS master for the assembly + pattern: "*_wgsmaster.gbff.gz" - cds: - type: file - description: FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly - pattern: "*_cds_from_genomic.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_cds_from_genomic.fna.gz": + type: file + description: FASTA format of the nucleotide sequences corresponding to all CDS + features annotated on the assembly + pattern: "*_cds_from_genomic.fna.gz" - rna: - type: file - description: FASTA format of accessioned RNA products annotated on the genome assembly - pattern: "*_rna.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rna.fna.gz": + type: file + description: FASTA format of accessioned RNA products annotated on the genome + assembly + pattern: "*_rna.fna.gz" - rna_fna: - type: file - description: FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly - pattern: "*_rna_from_genomic.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rna_from_genomic.fna.gz": + type: file + description: FASTA format of the nucleotide sequences corresponding to all RNA + features annotated on the assembly + pattern: "*_rna_from_genomic.fna.gz" - report: - type: file - description: Tab-delimited text file reporting the name, role and sequence accession.version for objects in the assembly - pattern: "*_assembly_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_assembly_report.txt": + type: file + description: Tab-delimited text file reporting the name, role and sequence accession.version + for objects in the assembly + pattern: "*_assembly_report.txt" - stats: - type: file - description: Tab-delimited text file reporting statistics for the assembly - pattern: "*_assembly_stats.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_assembly_stats.txt": + type: file + description: Tab-delimited text file reporting statistics for the assembly + pattern: "*_assembly_stats.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/ncbitools/vecscreen/meta.yml b/modules/nf-core/ncbitools/vecscreen/meta.yml index 45f0f7e2780..54f28f6c3b6 100644 --- a/modules/nf-core/ncbitools/vecscreen/meta.yml +++ b/modules/nf-core/ncbitools/vecscreen/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "NCBITOOLS_VECSCREEN" -description: NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose +description: NCBI tool for detecting vector contamination in nucleic acid sequences. + This tool is older than NCBI's FCS-adaptor, which is for the same purpose keywords: - assembly - genomics @@ -17,34 +17,43 @@ tools: documentation: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/interpretation/" tool_dev_url: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/" licence: ["The Open Database License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'6973' ] - - fasta_file: - type: file - description: FASTA file that will be screened for contaminants - - adapters_database_file: - type: file - description: Path to a nucleotide BLAST database file with vector sequences - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'6973' ] + - fasta_file: + type: file + description: FASTA file that will be screened for contaminants + - - adapters_database_meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - adapters_database_directory: + type: directory + description: Directory containing the adapters database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'9606' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vecscreen_output: - type: file - description: VecScreen report file. This can be in different formats depending on the value of the optional -f parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0 - pattern: "*.vecscreen.out" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'9606' ] + - ${meta.id}.vecscreen.out: + type: file + description: VecScreen report file. This can be in different formats depending + on the value of the optional -f parameter. 0 = HTML format, with alignments. + 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, + no alignments. default = 0 + pattern: "*.vecscreen.out" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@eeaunin" diff --git a/modules/nf-core/nextclade/datasetget/meta.yml b/modules/nf-core/nextclade/datasetget/meta.yml index 290ed0cd926..c60721da694 100644 --- a/modules/nf-core/nextclade/datasetget/meta.yml +++ b/modules/nf-core/nextclade/datasetget/meta.yml @@ -1,34 +1,40 @@ name: nextclade_datasetget -description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) +description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, + and sequence quality checks (C++ implementation) keywords: - nextclade - variant - consensus tools: - nextclade: - description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks + description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence + quality checks homepage: https://github.com/nextstrain/nextclade documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade licence: ["MIT"] + identifier: biotools:nextclade input: - - dataset: - type: string - description: Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command. - pattern: ".+" - - tag: - type: string - description: Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command. - pattern: ".+" + - - dataset: + type: string + description: Name of dataset to retrieve. A list of available datasets can be + obtained using the nextclade dataset list command. + pattern: ".+" + - - tag: + type: string + description: Version tag of the dataset to download. A list of available datasets + can be obtained using the nextclade dataset list command. + pattern: ".+" output: + - dataset: + - $prefix: + type: directory + description: Directory containing the dataset - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - prefix: - type: directory - description: A directory containing the dataset files needed for nextclade run - pattern: "prefix" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@antunderwood" - "@drpatelh" diff --git a/modules/nf-core/nextclade/run/meta.yml b/modules/nf-core/nextclade/run/meta.yml index bb7bf6c2d0e..4062b3f4d57 100644 --- a/modules/nf-core/nextclade/run/meta.yml +++ b/modules/nf-core/nextclade/run/meta.yml @@ -1,81 +1,140 @@ name: nextclade_run -description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) +description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality + checks (C++ implementation) keywords: - nextclade - variant - consensus tools: - nextclade: - description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks + description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence + quality checks homepage: https://github.com/nextstrain/nextclade documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade licence: ["MIT"] + identifier: biotools:nextclade input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - dataset: - type: directory - description: Path containing the dataset files obtained by running nextclade dataset get - pattern: "*" - - fasta: - type: file - description: FASTA file containing one or more consensus sequences - pattern: "*.{fasta,fa}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing one or more consensus sequences + pattern: "*.{fasta,fa}" + - - dataset: + type: directory + description: Path containing the dataset files obtained by running nextclade + dataset get + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: CSV file containing nextclade results - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.csv: + type: file + description: CSV file containing nextclade results + pattern: "*.{csv}" - csv_errors: - type: file - description: CSV file containing errors from nextclade results - pattern: "*.{errors.csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.errors.csv: + type: file + description: CSV file containing errors from nextclade results + pattern: "*.{errors.csv}" - csv_insertions: - type: file - description: CSV file containing insertions from nextclade results - pattern: "*.{insertions.csv}" - - fasta_aligned: - type: file - description: FASTA file containing aligned sequences from nextclade results - pattern: "*.{aligned.fasta}" - - fasta_translation: - type: file - description: FASTA file containing aligned peptides from nextclade results - pattern: "*.{_translation.}*.{fasta}" - - ndjson: - type: file - description: newline-delimited JSON file containing nextclade results - pattern: "*.{ndjson}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.insertions.csv: + type: file + description: CSV file containing insertions from nextclade results + pattern: "*.{insertions.csv}" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: TSV file containing nextclade results + pattern: "*.{tsv}" - json: - type: file - description: JSON file containing nextclade results - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.json: + type: file + description: JSON file containing nextclade results + pattern: "*.{json}" - json_auspice: - type: file - description: Auspice JSON V2 containing nextclade results - pattern: "*.{tree.json}" - - tsv: - type: file - description: TSV file containing nextclade results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.auspice.json: + type: file + description: Auspice JSON V2 containing nextclade results + pattern: "*.{tree.json}" + - ndjson: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ndjson: + type: file + description: newline-delimited JSON file containing nextclade results + pattern: "*.{ndjson}" + - fasta_aligned: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.aligned.fasta: + type: file + description: FASTA file containing aligned sequences from nextclade results + pattern: "*.{aligned.fasta}" + - fasta_translation: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_translation.*.fasta": + type: file + description: FASTA file containing aligned peptides from nextclade results + pattern: "*.{_translation.}*.{fasta}" - nwk: - type: file - description: NWK file containing nextclade results - pattern: "*.{nwk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.nwk: + type: file + description: NWK file containing nextclade results + pattern: "*.{nwk}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@antunderwood" - "@drpatelh" diff --git a/modules/nf-core/nextgenmap/meta.yml b/modules/nf-core/nextgenmap/meta.yml index 3b05d8eb893..dd8cb2a6c08 100644 --- a/modules/nf-core/nextgenmap/meta.yml +++ b/modules/nf-core/nextgenmap/meta.yml @@ -18,39 +18,42 @@ tools: documentation: https://github.com/Cibiv/NextGenMap/wiki doi: 10.1093/bioinformatics/btt468 licence: ["MIT"] + identifier: biotools:nextgenmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1, if meta.single_end is true, and 2 - if meta.single_end is false. - - fasta: - type: file - description: | - Genomic reference fasta file - pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1, if meta.single_end is true, and 2 + if meta.single_end is false. + - - fasta: + type: file + description: | + Genomic reference fasta file + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information. First item of tuple with - bam, below. - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: | - Output BAM file containing read alignments. Second item of tuple with - meta, above - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information. First item of tuple with + bam, below. + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: | + Output BAM file containing read alignments. Second item of tuple with + meta, above + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@cmatkhan" maintainers: diff --git a/modules/nf-core/ngmaster/meta.yml b/modules/nf-core/ngmaster/meta.yml index b4a3677ef31..7f6eaefd600 100644 --- a/modules/nf-core/ngmaster/meta.yml +++ b/modules/nf-core/ngmaster/meta.yml @@ -6,36 +6,40 @@ keywords: - serotype tools: - ngmaster: - description: In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) + description: In silico multi-antigen sequence typing for Neisseria gonorrhoeae + (NG-MAST) homepage: https://github.com/MDU-PHL/ngmaster/blob/master/README.md documentation: https://github.com/MDU-PHL/ngmaster/blob/master/README.md tool_dev_url: https://github.com/MDU-PHL/ngmaster doi: "10.1099/mgen.0.000076" licence: ["GPL v3 only"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/ngmerge/meta.yml b/modules/nf-core/ngmerge/meta.yml index 7e83a14a0af..0d2305728cd 100644 --- a/modules/nf-core/ngmerge/meta.yml +++ b/modules/nf-core/ngmerge/meta.yml @@ -1,4 +1,3 @@ ---- name: "ngmerge" description: Merging paired-end reads and removing sequencing adapters. keywords: @@ -13,39 +12,54 @@ tools: tool_dev_url: "https://github.com/jsh58/NGmerge" doi: "10.1186/s12859-018-2579-2" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: | - List of input FastQ files of size 2; i.e., paired-end data. - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: | + List of input FastQ files of size 2; i.e., paired-end data. + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_reads: - type: file - description: fastq file merged reads - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.merged.fq.gz": + type: file + description: fastq file merged reads + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - unstitched_read1: - type: file - description: fastq file unstitched read 1 - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_1.fastq.gz": + type: file + description: fastq file unstitched read 1 + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - unstitched_read2: - type: file - description: fastq file unstitched read 2 - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_2.fastq.gz": + type: file + description: fastq file unstitched read 2 + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charlotteanne" - "@jsh58" diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml index 961462b3f7d..54a611812df 100644 --- a/modules/nf-core/ngsbits/samplegender/meta.yml +++ b/modules/nf-core/ngsbits/samplegender/meta.yml @@ -1,4 +1,3 @@ ---- name: "ngsbits_samplegender" description: Determines the gender of a sample from the BAM/CRAM file. keywords: @@ -13,56 +12,60 @@ tools: documentation: "https://github.com/imgag/ngs-bits" tool_dev_url: "https://github.com/imgag/ngs-bits" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: One or more BAM/CRAM files to determine the gender of - pattern: "*.{bam,cram}" - - bai: - type: file - description: The index file(s) from the input BAM/CRAM file(s) - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference fasta information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA to use (mandatory when CRAM files are used) - pattern: "*.{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference fasta index information - e.g. [ id:'test' ] - - fasta: - type: file - description: The index of the reference FASTA to use (mandatory when CRAM files are used) - pattern: "*.fai" - - method: - type: string - description: The method to use to define the gender (posibilities are 'xy', 'hetx' and 'sry') - pattern: "(xy|hetx|sry)" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: One or more BAM/CRAM files to determine the gender of + pattern: "*.{bam,cram}" + - bai: + type: file + description: The index file(s) from the input BAM/CRAM file(s) + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference fasta information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA to use (mandatory when CRAM files are used) + pattern: "*.{fasta,fa,fna}" + - - meta2: + type: map + description: | + Groovy Map containing reference fasta information + e.g. [ id:'test' ] + - fai: + type: file + description: The index file from the reference FASTA + pattern: "*.fai" + - - method: + type: string + description: The method to use to define the gender (posibilities are 'xy', + 'hetx' and 'sry') + pattern: "(xy|hetx|sry)" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: An output TSV file containing the results of the gender prediction - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: An output TSV file containing the results of the gender prediction + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ngscheckmate/fastq/meta.yml b/modules/nf-core/ngscheckmate/fastq/meta.yml index 3553deaca6d..47a6aaf7541 100644 --- a/modules/nf-core/ngscheckmate/fastq/meta.yml +++ b/modules/nf-core/ngscheckmate/fastq/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ngscheckmate_fastq" -description: Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. This module generates vaf files for individual fastq file(s), + ready for the vafncm module. keywords: - ngscheckmate - matching @@ -9,45 +10,52 @@ keywords: - qc tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information about the fastq files - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: Raw fastq files for one sample, single or paired end. - pattern: "*.{fastq.gz}" - - meta2: - type: file - description: | - Groovy Map containing sample information about the NGSCheckMate SNP pt file - e.g. `[ id:'test', single_end:false ]` - - snp_pt: - type: file - description: PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository. - pattern: "*.{pt}" + - - meta: + type: map + description: | + Groovy Map containing sample information about the fastq files + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: Raw fastq files for one sample, single or paired end. + pattern: "*.{fastq.gz}" + - - meta2: + type: file + description: | + Groovy Map containing sample information about the NGSCheckMate SNP pt file + e.g. `[ id:'test', single_end:false ]` + - snp_pt: + type: file + description: PT file containing SNP data, generated by ngscheckmate/patterngenerator. + For human data, use the files from NGSCheckMate's github repository. + pattern: "*.{pt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - vaf: - type: file - description: Text file containing reference/alt allele depth for each SNP position contained in the PT file. - pattern: "*.{vaf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vaf": + type: file + description: Text file containing reference/alt allele depth for each SNP position + contained in the PT file. + pattern: "*.{vaf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ngscheckmate/ncm/meta.yml b/modules/nf-core/ngscheckmate/ncm/meta.yml index 0defad00644..06c131d6b07 100644 --- a/modules/nf-core/ngscheckmate/ncm/meta.yml +++ b/modules/nf-core/ngscheckmate/ncm/meta.yml @@ -1,70 +1,105 @@ name: ngscheckmate_ncm -description: Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. Designed for humans on vcf or bam files. keywords: - ngscheckmate - matching - snp tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - files: - type: file - description: VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too. - pattern: "*.{vcf,vcf.gz,bam,bai}" - - meta2: - type: map - description: | - Groovy Map containing SNP information - e.g. [ id:'test' ] - - snp_bed: - type: file - description: BED file containing the SNPs to analyse - pattern: "*.{bed}" - - meta3: - type: map - description: | - Groovy Map containing reference fasta index information - e.g. [ id:'test' ] - - fasta: - type: file - description: fasta file for the genome, only used in the bam mode - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - files: + type: file + description: VCF or BAM files for each sample, in a merged channel (possibly + gzipped). BAM files require an index too. + pattern: "*.{vcf,vcf.gz,bam,bai}" + - - meta2: + type: map + description: | + Groovy Map containing SNP information + e.g. [ id:'test' ] + - snp_bed: + type: file + description: BED file containing the SNPs to analyse + pattern: "*.{bed}" + - - meta3: + type: map + description: | + Groovy Map containing reference fasta index information + e.g. [ id:'test' ] + - fasta: + type: file + description: fasta file for the genome, only used in the bam mode + pattern: "*.{bed}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pdf: - type: file - description: A pdf containing a dendrogram showing how the samples match up - pattern: "*.{pdf}" - corr_matrix: - type: file - description: A text file containing the correlation matrix between each sample - pattern: "*corr_matrix.txt" + - meta: + type: file + description: A text file containing the correlation matrix between each sample + pattern: "*corr_matrix.txt" + - "*_corr_matrix.txt": + type: file + description: A text file containing the correlation matrix between each sample + pattern: "*corr_matrix.txt" - matched: - type: file - description: A txt file containing only the samples that match with each other - pattern: "*matched.txt" + - meta: + type: file + description: A txt file containing only the samples that match with each other + pattern: "*matched.txt" + - "*_matched.txt": + type: file + description: A txt file containing only the samples that match with each other + pattern: "*matched.txt" - all: - type: file - description: A txt file containing all the sample comparisons, whether they match or not - pattern: "*all.txt" + - meta: + type: file + description: A txt file containing all the sample comparisons, whether they + match or not + pattern: "*all.txt" + - "*_all.txt": + type: file + description: A txt file containing all the sample comparisons, whether they + match or not + pattern: "*all.txt" + - pdf: + - meta: + type: file + description: A pdf containing a dendrogram showing how the samples match up + pattern: "*.{pdf}" + - "*.pdf": + type: file + description: A pdf containing a dendrogram showing how the samples match up + pattern: "*.{pdf}" - vcf: - type: file - description: If ran in bam mode, vcf files for each sample giving the SNP calls used - pattern: "*.vcf" + - meta: + type: file + description: If ran in bam mode, vcf files for each sample giving the SNP calls + used + pattern: "*.vcf" + - "*.vcf": + type: file + description: If ran in bam mode, vcf files for each sample giving the SNP calls + used + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ngscheckmate/patterngenerator/meta.yml b/modules/nf-core/ngscheckmate/patterngenerator/meta.yml index 92c9ec1da41..370060bcf1b 100644 --- a/modules/nf-core/ngscheckmate/patterngenerator/meta.yml +++ b/modules/nf-core/ngscheckmate/patterngenerator/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ngscheckmate_patterngenerator" -description: Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. This module generates PT files from a bed file containing individual + positions. keywords: - ngscheckmate - matching @@ -9,48 +10,59 @@ keywords: - qc tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information about the bed file - e.g. `[ id:'test', single_end:false ]` - - bed: - type: file - description: BED file containing population-level SNPs to use - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing sample information about the fasta genome - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Genome fasta file - pattern: "*.fasta" - - bowtie_index: - type: directory - description: Folder of Bowtie genome index files + - - meta: + type: map + description: | + Groovy Map containing sample information about the bed file + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: BED file containing population-level SNPs to use + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the fasta genome + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bowtie_index: + type: directory + description: Folder of Bowtie genome index files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pt: - type: file - description: Generated binary pattern file, containing FASTQ strings to match from within raw data - pattern: "*.pt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.pt": + type: file + description: Generated binary pattern file, containing FASTQ strings to match + from within raw data + pattern: "*.pt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ngscheckmate/vafncm/meta.yml b/modules/nf-core/ngscheckmate/vafncm/meta.yml index 3877a88bff5..e96f65a371b 100644 --- a/modules/nf-core/ngscheckmate/vafncm/meta.yml +++ b/modules/nf-core/ngscheckmate/vafncm/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ngscheckmate_vafncm" -description: Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. This module generates PT files from a bed file containing individual + positions. keywords: - ngscheckmate - matching @@ -9,48 +10,75 @@ keywords: - qc tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information about the combined set of files - e.g. `[ id:'combined' ]` - - vafs: - type: file - description: Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq - pattern: "*.{vaf}" + - - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - vafs: + type: file + description: Text files containing information about reference/alternate allele + depths for the SNP positions, generated by ngscheckmate/fastq + pattern: "*.{vaf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information about the combined set of files - e.g. `[ id:'combined' ]` - pdf: - type: file - description: A pdf containing a dendrogram showing how the samples match up. | Note due to a bug in the R script used by the tool this is not produced when only two samples are given. - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*.pdf": + type: file + description: A pdf containing a dendrogram showing how the samples match up. + | Note due to a bug in the R script used by the tool this is not produced + when only two samples are given. + pattern: "*.{pdf}" - corr_matrix: - type: file - description: A text file containing the correlation matrix between each sample - pattern: "*corr_matrix.txt" - - matched: - type: file - description: A txt file containing only the samples that match with each other - pattern: "*matched.txt" + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*_corr_matrix.txt": + type: file + description: A text file containing the correlation matrix between each sample + pattern: "*corr_matrix.txt" - all: - type: file - description: A txt file containing all the sample comparisons, whether they match or not - pattern: "*all.txt" + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*_all.txt": + type: file + description: A txt file containing all the sample comparisons, whether they + match or not + pattern: "*all.txt" + - matched: + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*_matched.txt": + type: file + description: A txt file containing only the samples that match with each other + pattern: "*matched.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/nonpareil/curve/meta.yml b/modules/nf-core/nonpareil/curve/meta.yml index 87aaa363e82..cd80f16fe96 100644 --- a/modules/nf-core/nonpareil/curve/meta.yml +++ b/modules/nf-core/nonpareil/curve/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "nonpareil_curve" -description: Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file +description: Visualise metagenome redundancy curve in PNG format from a single Nonpareil + npo file keywords: - metagenomics - statistics @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - npo: - type: file - description: Single npo redundancy summary file from nonpareil itself - pattern: "*.npo" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - npo: + type: file + description: Single npo redundancy summary file from nonpareil itself + pattern: "*.npo" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: PNG file of the Nonpareil curve - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.png": + type: file + description: PNG file of the Nonpareil curve + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nonpareil/nonpareil/meta.yml b/modules/nf-core/nonpareil/nonpareil/meta.yml index 59f8bc05610..9890166dd13 100644 --- a/modules/nf-core/nonpareil/nonpareil/meta.yml +++ b/modules/nf-core/nonpareil/nonpareil/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "nonpareil_nonpareil" description: Calculate metagenome redundancy curve from FASTQ files @@ -17,50 +16,71 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: FASTQ or FASTA file (ideally uncompressed, but not required) - pattern: "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}" - - format: - type: string - description: File format of input file - pattern: "fasta|fastq" - - mode: - type: string - description: Mode of redundancy estimation - pattern: "kmer|alignment" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: FASTQ or FASTA file (ideally uncompressed, but not required) + pattern: "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}" + - - format: + type: string + description: File format of input file + pattern: "fasta|fastq" + - - mode: + type: string + description: Mode of redundancy estimation + pattern: "kmer|alignment" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - npa: - type: file - description: Raw redundancy values - pattern: "*.npa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npa": + type: file + description: Raw redundancy values + pattern: "*.npa" - npc: - type: file - description: Mates distribution file - pattern: "*.npc" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npc": + type: file + description: Mates distribution file + pattern: "*.npc" - npl: - type: file - description: Log file - pattern: "*.npl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npl": + type: file + description: Log file + pattern: "*.npl" - npo: - type: file - description: Redundancy summary file - pattern: "*.npo" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npo": + type: file + description: Redundancy summary file + pattern: "*.npo" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml b/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml index a4aeeb63d34..1649b990a42 100644 --- a/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml +++ b/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "nonpareil_nonpareilcurvesr" -description: Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files +description: Generate summary reports with raw data for Nonpareil NPO curves, including + MultiQC compatible JSON/TSV files keywords: - metagenomics - statistics @@ -18,45 +18,67 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - npos: - type: file - description: One or a list of Nonpareil NPO files (From nonpareil/nonpareil) - pattern: "*.{npo}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - npos: + type: file + description: One or a list of Nonpareil NPO files (From nonpareil/nonpareil) + pattern: "*.{npo}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: Raw nonpareil data used for generating and plotting curves in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: Raw nonpareil data used for generating and plotting curves in JSON + format + pattern: "*.json" - tsv: - type: file - description: Raw nonpareil data used for generating and plotting curves in JSON format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '*.tsv" ': + type: file + description: Raw nonpareil data used for generating and plotting curves in JSON + format + pattern: "*.tsv" - csv: - type: file - description: Raw nonpareil data used for generating and plotting curves in JSON format - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '*.csv" ': + type: file + description: Raw nonpareil data used for generating and plotting curves in JSON + format + pattern: "*.csv" - pdf: - type: file - description: Plotted nonpareil curves in PDF format - pattern: "*.pdf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '*.pdf" ': + type: file + description: Plotted nonpareil curves in PDF format + pattern: "*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nonpareil/set/meta.yml b/modules/nf-core/nonpareil/set/meta.yml index 74a26122eab..511eeb4fd6a 100644 --- a/modules/nf-core/nonpareil/set/meta.yml +++ b/modules/nf-core/nonpareil/set/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "nonpareil_set" -description: Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image +description: Visualise metagenome redundancy curves in PNG format from multiple Nonpareil + npo files in a single image keywords: - metagenomics - statistics @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - npos: - type: file - description: A list of npo redundancy summary files from nonpareil itself - pattern: "*.npo" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - npos: + type: file + description: A list of npo redundancy summary files from nonpareil itself + pattern: "*.npo" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: PNG file of all the Nonpareil curves of the input npo files - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.png": + type: file + description: PNG file of all the Nonpareil curves of the input npo files + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nucmer/meta.yml b/modules/nf-core/nucmer/meta.yml index 8cc8f1639f0..1c93f6b43cf 100644 --- a/modules/nf-core/nucmer/meta.yml +++ b/modules/nf-core/nucmer/meta.yml @@ -1,48 +1,59 @@ name: nucmer -description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. +description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide + sequences. keywords: - align - nucleotide - sequence tools: - nucmer: - description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. + description: NUCmer is a pipeline for the alignment of multiple closely related + nucleotide sequences. homepage: http://mummer.sourceforge.net/ documentation: http://mummer.sourceforge.net/ tool_dev_url: http://mummer.sourceforge.net/ doi: "10.1186/gb-2004-5-2-r12" licence: ["The Artistic License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: FASTA file of the reference sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - query: - type: file - description: FASTA file of the query sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: FASTA file of the reference sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - query: + type: file + description: FASTA file of the query sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - delta: - type: file - description: File containing coordinates of matches between reference and query + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.delta": + type: file + description: File containing coordinates of matches between reference and query - coords: - type: file - description: NUCmer1.1 coords output file - pattern: "*.{coords}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coords": + type: file + description: NUCmer1.1 coords output file + pattern: "*.{coords}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/oatk/meta.yml b/modules/nf-core/oatk/meta.yml index 022482078cc..95196adc3e2 100644 --- a/modules/nf-core/oatk/meta.yml +++ b/modules/nf-core/oatk/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "oatk" description: An nf-core module for the OATK @@ -17,147 +16,195 @@ tools: tool_dev_url: "https://github.com/c-zhou/oatk" doi: "10.5281/zenodo.10400173" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'Cladonia_norvegica' ] - - - reads: - type: file - description: HiFi reads in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz}" - - - mito_hmm: - type: file - description: mitochondria gene annotation HMM profile database - pattern: "*.{fa,fam}" - - - mito_hmm_h3f: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3f}" - - - mito_hmm_h3i: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3i}" - - - mito_hmm_h3m: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3m}" - - - mito_hmm_h3p: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3p}" - - - pltd_hmm: - type: file - description: plastid gene annotation HMM profile database - pattern: "*.{fa,fam}" - - - pltd_hmm_h3f: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3f}" - - - pltd_hmm_h3i: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3i}" - - - pltd_hmm_h3m: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3m}" - - - pltd_hmm_h3p: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3p}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'Cladonia_norvegica' ] + - reads: + type: file + description: HiFi reads in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz}" + - - mito_hmm: + type: file + description: mitochondria gene annotation HMM profile database + pattern: "*.{fa,fam}" + - mito_hmm_h3f: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3f}" + - mito_hmm_h3i: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3i}" + - mito_hmm_h3m: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3m}" + - mito_hmm_h3p: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3p}" + - - pltd_hmm: + type: file + description: plastid gene annotation HMM profile database + pattern: "*.{fa,fam}" + - pltd_hmm_h3f: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3f}" + - pltd_hmm_h3i: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3i}" + - pltd_hmm_h3m: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3m}" + - pltd_hmm_h3p: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3p}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - mito_fasta: - type: file - description: the structure-solved MT contigs - pattern: "*mito.ctg.fasta" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*mito.ctg.fasta": + type: file + description: the structure-solved MT contigs + pattern: "*mito.ctg.fasta" - pltd_fasta: - type: file - description: the structure-solved PT contigs - pattern: "*pltd.ctg.fasta" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pltd.ctg.fasta": + type: file + description: the structure-solved PT contigs + pattern: "*pltd.ctg.fasta" - mito_bed: - type: file - description: the gene annotation for the MT sequences - pattern: "*mito.ctg.bed" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*mito.ctg.bed": + type: file + description: the gene annotation for the MT sequences + pattern: "*mito.ctg.bed" - pltd_bed: - type: file - description: the gene annotation for the PT sequences - pattern: "*pltd.ctg.bed" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pltd.ctg.bed": + type: file + description: the gene annotation for the PT sequences + pattern: "*pltd.ctg.bed" - mito_gfa: - type: file - description: the subgraph for the MT genome - pattern: "*mito.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*mito.gfa": + type: file + description: the subgraph for the MT genome + pattern: "*mito.gfa" - pltd_gfa: - type: file - description: the subgraph for the PT genome - pattern: "*pltd.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pltd.gfa": + type: file + description: the subgraph for the PT genome + pattern: "*pltd.gfa" - annot_mito_txt: - type: file - description: the MT gene annotation file over all assembled sequences - pattern: "*annot_mito.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annot_mito.txt": + type: file + description: the MT gene annotation file over all assembled sequences + pattern: "*annot_mito.txt" - annot_pltd_txt: - type: file - description: the PT gene annotation file over all assembled sequences - pattern: "*annot_pltd.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annot_pltd.txt": + type: file + description: the PT gene annotation file over all assembled sequences + pattern: "*annot_pltd.txt" - clean_gfa: - type: file - description: the GFA file for the clean genome assembly - pattern: "*utg.clean.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.clean.gfa": + type: file + description: the GFA file for the clean genome assembly + pattern: "*utg.clean.gfa" - final_gfa: - type: file - description: the GFA file for the final genome assembly - pattern: "*utg.final.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.final.gfa": + type: file + description: the GFA file for the final genome assembly + pattern: "*utg.final.gfa" - initial_gfa: - type: file - description: the GFA file for the initial genome assembly - pattern: "*utg.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.gfa": + type: file + description: the GFA file for the initial genome assembly + pattern: "*utg.gfa" - multiplex_gfa: - type: file - description: the mutliplexed GFA file - pattern: "*utg.multiplex.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.multiplex.gfa": + type: file + description: the mutliplexed GFA file + pattern: "*utg.multiplex.gfa" - unzip_gfa: - type: file - description: the unzipped GFA file - pattern: "*utg.unzip.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.unzip.gfa": + type: file + description: the unzipped GFA file + pattern: "*utg.unzip.gfa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ksenia-krasheninnikova" diff --git a/modules/nf-core/odgi/build/meta.yml b/modules/nf-core/odgi/build/meta.yml index 8ec55074659..f9028ae3925 100644 --- a/modules/nf-core/odgi/build/meta.yml +++ b/modules/nf-core/odgi/build/meta.yml @@ -13,30 +13,34 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format - pattern: "*.{gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format + pattern: "*.{gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - og: - type: file - description: File containing a pangenome graph in ODGI binary format. Usually ends with '.og' - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: File containing a pangenome graph in ODGI binary format. Usually + ends with '.og' + pattern: "*.{og}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/draw/meta.yml b/modules/nf-core/odgi/draw/meta.yml index 807463ac29c..063071c6a0d 100644 --- a/modules/nf-core/odgi/draw/meta.yml +++ b/modules/nf-core/odgi/draw/meta.yml @@ -13,34 +13,37 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or ODGI binary format - pattern: "*.{gfa,og}" - - lay: - type: file - description: 2D layout from 'odgi layout' in LAY binary format - pattern: "*.{lay}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or ODGI binary format + pattern: "*.{gfa,og}" + - lay: + type: file + description: 2D layout from 'odgi layout' in LAY binary format + pattern: "*.{lay}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: File in PNG format containing a 2D drawing of a pangenome graph - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: File in PNG format containing a 2D drawing of a pangenome graph + pattern: "*.{png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/layout/meta.yml b/modules/nf-core/odgi/layout/meta.yml index 5d7694a3c8e..83c1483f12c 100644 --- a/modules/nf-core/odgi/layout/meta.yml +++ b/modules/nf-core/odgi/layout/meta.yml @@ -1,5 +1,6 @@ name: "odgi_layout" -description: Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted. +description: Establish 2D layouts of the graph using path-guided stochastic gradient + descent. The graph must be sorted and id-compacted. keywords: - variation graph - pangenome graph @@ -13,34 +14,47 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lay: - type: file - description: File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified. - pattern: "*.{lay}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lay": + type: file + description: File containing a 2D layout of a pangenome graph in a binary format. + Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. + Either this or the TSV layout output must be specified. + pattern: "*.{lay}" - tsv: - type: file - description: File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: File containing a 2D layout of a pangenome graph in TSV format. + Optional output specified by the `--tsv FILE` argument. Either this or the + binary layout output must be specified. + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/sort/meta.yml b/modules/nf-core/odgi/sort/meta.yml index 792dc381c59..6ce0493162b 100644 --- a/modules/nf-core/odgi/sort/meta.yml +++ b/modules/nf-core/odgi/sort/meta.yml @@ -1,5 +1,6 @@ name: "odgi_sort" -description: Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm. +description: Apply different kind of sorting algorithms to a graph. The most prominent + one is the PG-SGD sorting algorithm. keywords: - variation graph - pangenome graph @@ -13,30 +14,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sorted_graph: - type: file - description: 1D sorted pangenome graph in ODGI binary format - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: 1D sorted pangenome graph in ODGI binary format + pattern: "*.{og}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/squeeze/meta.yml b/modules/nf-core/odgi/squeeze/meta.yml index 5ffaa618d10..3e016908049 100644 --- a/modules/nf-core/odgi/squeeze/meta.yml +++ b/modules/nf-core/odgi/squeeze/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graphs: - type: file - description: Pangenome graph files in ODGI format. - pattern: "*.{og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graphs: + type: file + description: Pangenome graph files in ODGI format. + pattern: "*.{og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - graph: - type: file - description: Squeezed pangenome graph in ODGI format. - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: Squeezed pangenome graph in ODGI format. + pattern: "*.{og}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/stats/meta.yml b/modules/nf-core/odgi/stats/meta.yml index e8e26e02839..c679e1362d4 100644 --- a/modules/nf-core/odgi/stats/meta.yml +++ b/modules/nf-core/odgi/stats/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in binary ODGI or in GFA v1.0 format - pattern: "*.{og,gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in binary ODGI or in GFA v1.0 format + pattern: "*.{og,gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Optional output file that contains graph statistics in TSV format. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og.stats.tsv": + type: file + description: Optional output file that contains graph statistics in TSV format. + pattern: "*.{tsv}" - yaml: - type: file - description: Optional output file that contains graph statistics in YAML format. - pattern: "*.{yaml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og.stats.yaml": + type: file + description: Optional output file that contains graph statistics in YAML format. + pattern: "*.{yaml}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/unchop/meta.yml b/modules/nf-core/odgi/unchop/meta.yml index 5dc31f0697e..e7a510f8830 100644 --- a/modules/nf-core/odgi/unchop/meta.yml +++ b/modules/nf-core/odgi/unchop/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - unchopped_graph: - type: file - description: Unchopped pangenome graph in ODGI binary format - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: Unchopped pangenome graph in ODGI binary format + pattern: "*.{og}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/view/meta.yml b/modules/nf-core/odgi/view/meta.yml index 2b8b0d4d529..e67a4bd7f9c 100644 --- a/modules/nf-core/odgi/view/meta.yml +++ b/modules/nf-core/odgi/view/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gfa: - type: file - description: File containing a pangenome graph in GFA v1.0 format. - pattern: "*.{gfa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa": + type: file + description: File containing a pangenome graph in GFA v1.0 format. + pattern: "*.{gfa}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/viz/meta.yml b/modules/nf-core/odgi/viz/meta.yml index 8f8a0370653..9c021edc5e6 100644 --- a/modules/nf-core/odgi/viz/meta.yml +++ b/modules/nf-core/odgi/viz/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in binary ODGI or in GFA v1.0 format - pattern: "*.{og,gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in binary ODGI or in GFA v1.0 format + pattern: "*.{og,gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: A 1D visualization of a pangenome graph. - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: A 1D visualization of a pangenome graph. + pattern: "*.{png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/oncocnv/meta.yml b/modules/nf-core/oncocnv/meta.yml index 4f1bde83f6f..049029a0ad5 100644 --- a/modules/nf-core/oncocnv/meta.yml +++ b/modules/nf-core/oncocnv/meta.yml @@ -12,53 +12,70 @@ tools: tool_dev_url: "https://github.com/BoevaLab/ONCOCNV/" doi: "10.1093/bioinformatics/btu436" license: ["GPL-3.0-or-later"] + identifier: biotools:oncocnv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal: - type: file - description: BAM files - pattern: "*.bam" - - normal_index: - type: file - description: BAM file indices - pattern: "*.bam.bai" - - tumor: - type: file - description: BAM files - pattern: "*.bam" - - tumor_index: - type: file - description: BAM file indices - pattern: "*.bam.bai" - - bed: - type: file - description: annotated BED file containing target regions - pattern: "*.bed" - - fasta: - type: file - description: genome FASTA file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal: + type: file + description: BAM files + pattern: "*.bam" + - normal_index: + type: file + description: BAM file indices + pattern: "*.bam.bai" + - tumor: + type: file + description: BAM files + pattern: "*.bam" + - tumor_index: + type: file + description: BAM file indices + pattern: "*.bam.bai" + - - bed: + type: file + description: annotated BED file containing target regions + pattern: "*.bed" + - - fasta: + type: file + description: genome FASTA file + pattern: "*.fasta" output: - png: - type: file - description: PNG file containing profile plot - pattern: "*.profile.png" + - meta: + type: file + description: PNG file containing profile plot + pattern: "*.profile.png" + - "*.profile.png": + type: file + description: PNG file containing profile plot + pattern: "*.profile.png" - profile: - type: file - description: TXT file containing profile data - pattern: "*.profile.txt" + - meta: + type: file + description: TXT file containing profile data + pattern: "*.profile.txt" + - "*.profile.txt": + type: file + description: TXT file containing profile data + pattern: "*.profile.txt" - summary: - type: file - description: TXT file containing summarized data - pattern: "*.summary.txt" + - meta: + type: file + description: TXT file containing summarized data + pattern: "*.summary.txt" + - "*.summary.txt": + type: file + description: TXT file containing summarized data + pattern: "*.summary.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" maintainers: diff --git a/modules/nf-core/openms/decoydatabase/meta.yml b/modules/nf-core/openms/decoydatabase/meta.yml index 4979b8475ac..ce9399d27c4 100644 --- a/modules/nf-core/openms/decoydatabase/meta.yml +++ b/modules/nf-core/openms/decoydatabase/meta.yml @@ -8,36 +8,40 @@ keywords: - fasta tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Fasta file containing protein sequences - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Fasta file containing protein sequences + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - decoy_fasta: - type: file - description: Fasta file containing proteins and decoy proteins - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta": + type: file + description: Fasta file containing proteins and decoy proteins + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/idfilter/meta.yml b/modules/nf-core/openms/idfilter/meta.yml index 02667aa066b..d333e4b3b11 100644 --- a/modules/nf-core/openms/idfilter/meta.yml +++ b/modules/nf-core/openms/idfilter/meta.yml @@ -7,43 +7,45 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - id_file: - type: file - description: Peptide-spectrum matches. - pattern: "*.{idXML,consensusXML}" - - filter_file: - type: file - description: Optional idXML file to filter on/out peptides or proteins - patter: "*.{idXML,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - id_file: + type: file + description: Peptide-spectrum matches. + pattern: "*.{idXML,consensusXML}" + - filter_file: + type: file + description: Optional idXML file to filter on/out peptides or proteins + patter: "*.{idXML,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filtered: - type: file - description: Filtered peptide-spectrum matches. - pattern: "*.{idXML,consensusXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{idXML,consensusXML}": + type: file + description: Filtered peptide-spectrum matches. + pattern: "*.{idXML,consensusXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/idmassaccuracy/meta.yml b/modules/nf-core/openms/idmassaccuracy/meta.yml index e14a2eb09bb..5e8b1f2fdbd 100644 --- a/modules/nf-core/openms/idmassaccuracy/meta.yml +++ b/modules/nf-core/openms/idmassaccuracy/meta.yml @@ -1,55 +1,64 @@ name: "openms_idmassaccuracy" -description: Calculates a distribution of the mass error from given mass spectra and IDs. +description: Calculates a distribution of the mass error from given mass spectra and + IDs. keywords: - mass_error - openms - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - mzmls: - type: file - description: | - List containing one or more mzML files - e.g. `[ 'file1.mzML', 'file2.mzML' ]` - pattern: "*.{mzML}" - - idxmls: - type: file - description: | - List containing one or more idXML files - e.g. `[ 'file1.idXML', 'file2.idXML' ]` - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - mzmls: + type: file + description: | + List containing one or more mzML files + e.g. `[ 'file1.mzML', 'file2.mzML' ]` + pattern: "*.{mzML}" + - idxmls: + type: file + description: | + List containing one or more idXML files + e.g. `[ 'file1.idXML', 'file2.idXML' ]` + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - frag_err: - type: file - description: TSV file containing the fragment mass errors - pattern: "*frag_mass_err.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*frag_mass_err.tsv": + type: file + description: TSV file containing the fragment mass errors + pattern: "*frag_mass_err.{tsv}" - prec_err: - type: file - description: Optional TSV file containing the precursor mass errors - pattern: "*prec_mass_err.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*prec_mass_err.tsv": + type: file + description: Optional TSV file containing the precursor mass errors + pattern: "*prec_mass_err.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" diff --git a/modules/nf-core/openms/idmerger/meta.yml b/modules/nf-core/openms/idmerger/meta.yml index 19df33fb0f5..bf87a645e0b 100644 --- a/modules/nf-core/openms/idmerger/meta.yml +++ b/modules/nf-core/openms/idmerger/meta.yml @@ -7,40 +7,42 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - idxmls: - type: file - description: | - List containing 2 or more idXML files - e.g. `[ 'file1.idXML', 'file2.idXML' ]` - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - idxmls: + type: file + description: | + List containing 2 or more idXML files + e.g. `[ 'file1.idXML', 'file2.idXML' ]` + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxml: - type: file - description: Merged idXML output file - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.idXML": + type: file + description: Merged idXML output file + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" diff --git a/modules/nf-core/openms/idripper/meta.yml b/modules/nf-core/openms/idripper/meta.yml index 8170e796535..ac35b7bc732 100644 --- a/modules/nf-core/openms/idripper/meta.yml +++ b/modules/nf-core/openms/idripper/meta.yml @@ -1,5 +1,6 @@ name: openms_idripper -description: Split a merged identification file into their originating identification files +description: Split a merged identification file into their originating identification + files keywords: - split - idXML @@ -7,39 +8,41 @@ keywords: - proteomics tools: - openms: - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - merged_idxml: - type: file - description: Merged idXML file - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - merged_idxml: + type: file + description: Merged idXML file + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxmls: - type: file - description: Multiple idXML files - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: Multiple idXML files + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/idscoreswitcher/meta.yml b/modules/nf-core/openms/idscoreswitcher/meta.yml index d37fcd8b9fe..ac4c5070313 100644 --- a/modules/nf-core/openms/idscoreswitcher/meta.yml +++ b/modules/nf-core/openms/idscoreswitcher/meta.yml @@ -1,5 +1,6 @@ name: "openms_idscoreswitcher" -description: Switches between different scores of peptide or protein hits in identification data +description: Switches between different scores of peptide or protein hits in identification + data keywords: - switch - score @@ -8,41 +9,43 @@ keywords: - proteomics tools: - openms: - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - idxml: - type: file - description: Identification file containing a primary PSM score - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - idxml: + type: file + description: Identification file containing a primary PSM score + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxml: - type: file - description: | - Identification file containing a new primary PSM score - obtained from a specified meta value - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: | + Identification file containing a new primary PSM score + obtained from a specified meta value + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/peakpickerhires/meta.yml b/modules/nf-core/openms/peakpickerhires/meta.yml index 479d8192281..b10460b9422 100644 --- a/modules/nf-core/openms/peakpickerhires/meta.yml +++ b/modules/nf-core/openms/peakpickerhires/meta.yml @@ -1,5 +1,6 @@ name: "openms_peakpickerhires" -description: A tool for peak detection in high-resolution profile data (Orbitrap or FTICR) +description: A tool for peak detection in high-resolution profile data (Orbitrap or + FTICR) keywords: - peak picking - mzml @@ -7,39 +8,41 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - mzml: - type: file - description: Mass spectrometer output file in mzML format - pattern: "*.{mzML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - mzml: + type: file + description: Mass spectrometer output file in mzML format + pattern: "*.{mzML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mzml: - type: file - description: Peak-picked mass spectrometer output file in mzML format - pattern: "*.{mzML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.mzML": + type: file + description: Peak-picked mass spectrometer output file in mzML format + pattern: "*.{mzML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/peptideindexer/meta.yml b/modules/nf-core/openms/peptideindexer/meta.yml index 94759d352c5..10f808d2385 100644 --- a/modules/nf-core/openms/peptideindexer/meta.yml +++ b/modules/nf-core/openms/peptideindexer/meta.yml @@ -1,4 +1,3 @@ ---- name: "openms_peptideindexer" description: Refreshes the protein references for all peptide hits. keywords: @@ -8,42 +7,49 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - id_file: - type: file - description: idXML identification file - pattern: "*.{idXML}" - - id_fasta: - type: file - description: Input sequence database in FASTA format - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - id_file: + type: file + description: idXML identification file + pattern: "*.{idXML}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - id_fasta: + type: file + description: Input sequence database in FASTA format + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - id_file_pi: - type: file - description: Refreshed idXML identification file - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: Refreshed idXML identification file + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml index e37f6af8264..fc7e688102d 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml +++ b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml @@ -8,47 +8,55 @@ keywords: - proteomics tools: - openms: - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/nmeth.3959" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mzml: - type: file - description: File containing mass spectra in mzML format - pattern: "*.{mzML}" - - fasta: - type: file - description: Protein sequence database containing targets and decoys - pattern: "*.{fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mzml: + type: file + description: File containing mass spectra in mzML format + pattern: "*.{mzML}" + - fasta: + type: file + description: Protein sequence database containing targets and decoys + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxml: - type: file - description: File containing target and decoy hits in idXML format - pattern: "*.{idXML}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: File containing target and decoy hits in idXML format + pattern: "*.{idXML}" - pin: - type: file - description: TSV file tailored as Percolator input (pin) file - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: TSV file tailored as Percolator input (pin) file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/optitype/meta.yml b/modules/nf-core/optitype/meta.yml index 980596ab77e..eb5bfef8682 100644 --- a/modules/nf-core/optitype/meta.yml +++ b/modules/nf-core/optitype/meta.yml @@ -11,38 +11,47 @@ tools: documentation: https://github.com/FRED-2/OptiType doi: "10.1093/bioinformatics/btu548" licence: ["BSD-3-Clause"] + identifier: biotools:optitype input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', seq_type:'DNA' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hla_type: - type: file - description: HLA type - pattern: "${prefix}/*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', seq_type:'DNA' ] + - ${prefix}/*.tsv: + type: file + description: HLA type + pattern: "${prefix}/*.tsv" - coverage_plot: - type: file - description: OptiType coverage plot - pattern: "${prefix}/*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', seq_type:'DNA' ] + - ${prefix}/*.pdf: + type: file + description: OptiType coverage plot + pattern: "${prefix}/*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" maintainers: diff --git a/modules/nf-core/orthofinder/meta.yml b/modules/nf-core/orthofinder/meta.yml index 8c7689b3e86..4aeb46b3b4d 100644 --- a/modules/nf-core/orthofinder/meta.yml +++ b/modules/nf-core/orthofinder/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "orthofinder" -description: OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. +description: OrthoFinder is a fast, accurate and comprehensive platform for comparative + genomics. keywords: - genomics - orthogroup @@ -12,50 +12,59 @@ keywords: - phylogeny tools: - "orthofinder": - description: "Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!" + description: "Accurate inference of orthogroups, orthologues, gene trees and rooted + species tree made easy!" homepage: "https://github.com/davidemms/OrthoFinder" documentation: "https://github.com/davidemms/OrthoFinder" tool_dev_url: "https://github.com/davidemms/OrthoFinder" doi: "10.1186/s13059-019-1832-y" licence: ["GPL v3"] + identifier: biotools:OrthoFinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastas: - type: list - description: Input fasta files - pattern: "*.{fa,faa,fasta,fas,pep}" - - meta2: - type: map - description: | - Groovy Map containing a name - e.g. `[ id:'folder1' ]` - - prior_run: - type: directory - description: | - A folder container containing a previous WorkingDirectory from Orthofinder. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastas: + type: list + description: Input fasta files + pattern: "*.{fa,faa,fasta,fas,pep}" + - - meta2: + type: map + description: | + Groovy Map containing a name + e.g. `[ id:'folder1' ]` + - prior_run: + type: directory + description: | + A folder container containing a previous WorkingDirectory from Orthofinder. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - orthofinder: - type: directory - description: Orthofinder output directory + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $prefix: + type: directory + description: Orthofinder output directory - working: - type: directory - description: Orthofinder output WorkingDirectory (used for the orthofinder resume function) - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $prefix/WorkingDirectory: + type: directory + description: Orthofinder output WorkingDirectory (used for the orthofinder resume + function) + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/paftools/sam2paf/meta.yml b/modules/nf-core/paftools/sam2paf/meta.yml index 438ab2dd4bb..e58297401ef 100644 --- a/modules/nf-core/paftools/sam2paf/meta.yml +++ b/modules/nf-core/paftools/sam2paf/meta.yml @@ -11,30 +11,28 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: An input bam file to be converted into paf. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: An input bam file to be converted into paf. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: | - An output paf containing detailed data about the sample - pattern: "${prefix}.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/pairix/meta.yml b/modules/nf-core/pairix/meta.yml index f5277182514..e94f2d32844 100644 --- a/modules/nf-core/pairix/meta.yml +++ b/modules/nf-core/pairix/meta.yml @@ -13,29 +13,36 @@ tools: documentation: "https://github.com/4dn-dcic/pairix" tool_dev_url: "https://github.com/4dn-dcic/pairix" licence: ["MIT"] + identifier: biotools:pairix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pair: - type: file - description: pair file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pair: + type: file + description: pair file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: file - description: pair index file - pattern: "*.px2" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pair: + type: file + description: pair index file + pattern: "*.px2" + - "*.px2": + type: file + description: pair index file + pattern: "*.px2" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/dedup/meta.yml b/modules/nf-core/pairtools/dedup/meta.yml index 3c67e3fbe26..0f2860e005d 100644 --- a/modules/nf-core/pairtools/dedup/meta.yml +++ b/modules/nf-core/pairtools/dedup/meta.yml @@ -12,33 +12,42 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: pair file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: pair file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairs: - type: file - description: Duplicates removed pairs - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: Duplicates removed pairs + pattern: "*.{pairs.gz}" - stat: - type: file - description: stats of the pairs - pattern: "*.{pairs.stat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.stat": + type: file + description: stats of the pairs + pattern: "*.{pairs.stat}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/flip/meta.yml b/modules/nf-core/pairtools/flip/meta.yml index 58739acb3ca..c2122019d93 100644 --- a/modules/nf-core/pairtools/flip/meta.yml +++ b/modules/nf-core/pairtools/flip/meta.yml @@ -11,32 +11,35 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sam: - type: file - description: pair file - - chromsizes: - type: file - description: chromosome size file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sam: + type: file + description: pair file + - - chromsizes: + type: file + description: chromosome size file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - flip: - type: file - description: output file of flip - pattern: "*.{flip.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flip.gz": + type: file + description: output file of flip + pattern: "*.{flip.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/merge/meta.yml b/modules/nf-core/pairtools/merge/meta.yml index b7bccc3c1ee..790c5bbcd7d 100644 --- a/modules/nf-core/pairtools/merge/meta.yml +++ b/modules/nf-core/pairtools/merge/meta.yml @@ -11,29 +11,32 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - allpairs: - type: file - description: All pair files to merge + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - allpairs: + type: file + description: All pair files to merge output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairs: - type: file - description: Merged pairs file - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pairs.gz": + type: file + description: Merged pairs file + pattern: "*.{pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" maintainers: diff --git a/modules/nf-core/pairtools/parse/meta.yml b/modules/nf-core/pairtools/parse/meta.yml index e7e448efd74..27411d02164 100644 --- a/modules/nf-core/pairtools/parse/meta.yml +++ b/modules/nf-core/pairtools/parse/meta.yml @@ -11,37 +11,46 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - chromsizes: - type: file - description: chromosome size file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - chromsizes: + type: file + description: chromosome size file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairsam: - type: file - description: parsed pair file - pattern: "*.{pairsam.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairsam.gz": + type: file + description: parsed pair file + pattern: "*.{pairsam.gz}" - stat: - type: file - description: stats of the pairs - pattern: "*.{pairsam.stat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairsam.stat": + type: file + description: stats of the pairs + pattern: "*.{pairsam.stat}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/restrict/meta.yml b/modules/nf-core/pairtools/restrict/meta.yml index 12f6b9863c5..c43a35bb183 100644 --- a/modules/nf-core/pairtools/restrict/meta.yml +++ b/modules/nf-core/pairtools/restrict/meta.yml @@ -11,35 +11,38 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: pairs file - - frag: - type: file - description: | - a tab-separated BED file with the positions of restriction fragments - (chrom, start, end). - Can be generated using cooler digest. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: pairs file + - - frag: + type: file + description: | + a tab-separated BED file with the positions of restriction fragments + (chrom, start, end). + Can be generated using cooler digest. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - restrict: - type: file - description: Filtered pairs file - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: Filtered pairs file + pattern: "*.{pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/select/meta.yml b/modules/nf-core/pairtools/select/meta.yml index e9aef9a22d7..47ef25e1442 100644 --- a/modules/nf-core/pairtools/select/meta.yml +++ b/modules/nf-core/pairtools/select/meta.yml @@ -11,33 +11,42 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: pairs file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: pairs file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - selected: - type: file - description: Selected pairs file - pattern: "*.{selected.pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selected.pairs.gz": + type: file + description: Selected pairs file + pattern: "*.{selected.pairs.gz}" - unselected: - type: file - description: Rest pairs file. - pattern: "*.{unselected.pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unselected.pairs.gz": + type: file + description: Rest pairs file. + pattern: "*.{unselected.pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/sort/meta.yml b/modules/nf-core/pairtools/sort/meta.yml index 987aebb0f51..b1650e8ff7a 100644 --- a/modules/nf-core/pairtools/sort/meta.yml +++ b/modules/nf-core/pairtools/sort/meta.yml @@ -11,29 +11,32 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: A pairs file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: A pairs file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sorted: - type: file - description: Sorted pairs file - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: Sorted pairs file + pattern: "*.{pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@nservant" diff --git a/modules/nf-core/pairtools/split/meta.yml b/modules/nf-core/pairtools/split/meta.yml index e659f93a8ae..7ff8fe132ca 100644 --- a/modules/nf-core/pairtools/split/meta.yml +++ b/modules/nf-core/pairtools/split/meta.yml @@ -11,35 +11,42 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: pairsam file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: pairsam file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairs: - type: file - description: Duplicates removed pairs - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.split.pairs.gz": + type: file + description: Duplicates removed pairs + pattern: "*.{pairs.gz}" - bam: - type: file - description: Output BAM file - pattern: "*.bam" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" diff --git a/modules/nf-core/pairtools/stats/meta.yml b/modules/nf-core/pairtools/stats/meta.yml index da2a1fa3f1c..f3ab7a3d9f8 100644 --- a/modules/nf-core/pairtools/stats/meta.yml +++ b/modules/nf-core/pairtools/stats/meta.yml @@ -11,29 +11,32 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: pairs file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: pairs file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.stat": + type: file + description: Pairs statistics + pattern: "*{.pairs.stat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - stat: - type: file - description: stats of the pairs - pattern: "*.{pairs.stat}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" maintainers: diff --git a/modules/nf-core/panacus/histgrowth/meta.yml b/modules/nf-core/panacus/histgrowth/meta.yml index 800170c182b..a9b94020a2b 100644 --- a/modules/nf-core/panacus/histgrowth/meta.yml +++ b/modules/nf-core/panacus/histgrowth/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "panacus_histgrowth" -description: Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file +description: Calculates a coverage histogram from a GFA file and constructs a growth + table from this as either a TSV or HTML file keywords: - statistics - pangenome @@ -14,49 +14,50 @@ tools: homepage: "https://github.com/marschall-lab/panacus" documentation: "https://github.com/marschall-lab/panacus" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - gfa: - type: file - description: GFA file containing a graph without overlapping nodes - pattern: "*.gfa" - - bed_subset: - type: file - description: Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for getting counts by subsetting the graph - pattern: "*.{txt, bed}" - - bed_exclude: - type: file - description: Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for excluding bp/nodes/edges that intersect these paths - pattern: "*.{txt, bed}" - - tsv_groupby: - type: file - description: Optional 2-column TSV file containing path to group mapping according to which counts from different paths get merged - pattern: "*.{txt, bed}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - gfa: + type: file + description: GFA file containing a graph without overlapping nodes + pattern: "*.gfa" + - - bed_subset: + type: file + description: Optional 1-column TXT-list of paths or 3-/12-column BED file of + path coordinates for getting counts by subsetting the graph + pattern: "*.{txt, bed}" + - - bed_exclude: + type: file + description: Optional 1-column TXT-list of paths or 3-/12-column BED file of + path coordinates for excluding bp/nodes/edges that intersect these paths + pattern: "*.{txt, bed}" + - - tsv_groupby: + type: file + description: Optional 2-column TSV file containing path to group mapping according + to which counts from different paths get merged + pattern: "*.{txt, bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file containing the statistics. Alternatively, the HTML file can be the output - pattern: "*.tsv" - - html: - type: file - description: HTML file containing a report with the statistics. Alternatively, the TSV file can be the output - pattern: "*.html" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{tsv, html}": + type: file + description: TSV file containing the statistics. Alternatively, the HTML file + can be the output + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heringerp" maintainers: diff --git a/modules/nf-core/panacus/visualize/meta.yml b/modules/nf-core/panacus/visualize/meta.yml index 3b2fd6df8b3..59aaa8a4e34 100644 --- a/modules/nf-core/panacus/visualize/meta.yml +++ b/modules/nf-core/panacus/visualize/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "panacus_visualize" description: Create visualizations from a tsv coverage histogram created with panacus. @@ -15,33 +14,34 @@ tools: homepage: "https://github.com/marschall-lab/panacus" documentation: "https://github.com/marschall-lab/panacus" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - tsv: - type: file - description: TSV coverage histogram created with panacus histgrowth - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - tsv: + type: file + description: TSV coverage histogram created with panacus histgrowth + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - image: - type: file - description: Visualizations created from the coverage histogram - pattern: "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}": + type: file + description: Visualizations created from the coverage histogram + pattern: "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heringerp" maintainers: diff --git a/modules/nf-core/panaroo/run/meta.yml b/modules/nf-core/panaroo/run/meta.yml index 47655d218a9..d69339e72e4 100644 --- a/modules/nf-core/panaroo/run/meta.yml +++ b/modules/nf-core/panaroo/run/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: "https://github.com/gtonkinhill/panaroo" doi: "10.1186/s13059-020-02090-4" licence: ["MIT"] + identifier: biotools:panaroo input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: A set of GFF3 formatted files - pattern: "*.{gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: A set of GFF3 formatted files + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing Panaroo result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing Panaroo result files + pattern: "*/*" - aln: - type: file - description: Core-genome alignment produced by Panaroo (Optional) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/core_gene_alignment.aln: + type: file + description: Core-genome alignment produced by Panaroo (Optional) + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/pangolin/meta.yml b/modules/nf-core/pangolin/meta.yml index 6493f2c8290..9220aefc145 100644 --- a/modules/nf-core/pangolin/meta.yml +++ b/modules/nf-core/pangolin/meta.yml @@ -11,24 +11,31 @@ tools: homepage: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description licence: ["GPL-3.0-or-later"] + identifier: biotools:pangolin_cov-lineages input: - - meta: - type: map - description: | - Groovy Map containing sample information - - fasta: - type: file - description: | - The genome assembly to be evaluated + - - meta: + type: map + description: | + Groovy Map containing sample information + - fasta: + type: file + description: | + The genome assembly to be evaluated output: - report: - type: file - description: Pangolin lineage report - pattern: "*.{csv}" + - meta: + type: file + description: Pangolin lineage report + pattern: "*.{csv}" + - "*.csv": + type: file + description: Pangolin lineage report + pattern: "*.{csv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml index d76ee61a066..09fdbacab1b 100644 --- a/modules/nf-core/parabricks/applybqsr/meta.yml +++ b/modules/nf-core/parabricks/applybqsr/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_applybqsr" -description: NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR). +description: NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration + (BQSR). keywords: - bqsr - bam @@ -11,50 +12,63 @@ tools: homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/" licence: ["https://docs.nvidia.com/clara/parabricks/3.8.0/gettingstarted.html#licensing"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - - input: - type: file - description: bam file for sample to be variant called. - pattern: "*.bam" - - input_index: - type: file - description: bai index corresponding to input bam file. Only necessary if intervals are provided. - pattern: "*.bai" - - bqsr_table: - type: file - description: Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator. - pattern: "*.table" - - interval_file: - type: file - description: File or files containing genomic intervals for use in base quality score recalibration. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - fasta: - type: file - description: Reference fasta - must be unzipped. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bam_index: + type: file + description: BAM index file + pattern: "*.bai" + - bqsr_table: + type: file + description: Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator. + pattern: "*.table" + - intervals: + type: file + description: intervals + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - bam: - type: file - description: BAM file after applying BQSR. - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.bam": + type: file + description: BAM file after applying BQSR. + pattern: "*.bam" - bai: - type: file - description: bai index corresponding to output bam file. - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.bai": + type: file + description: bai index corresponding to output bam file. + pattern: "*.bai" + - versions: + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" maintainers: diff --git a/modules/nf-core/parabricks/dbsnp/meta.yml b/modules/nf-core/parabricks/dbsnp/meta.yml index 0ee3fbc38b3..095110cf45e 100644 --- a/modules/nf-core/parabricks/dbsnp/meta.yml +++ b/modules/nf-core/parabricks/dbsnp/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_dbsnp" -description: NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database +description: NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based + on dbSNP database keywords: - annotation - dbsnp @@ -11,40 +12,41 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.2.0/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - vcf_file: - type: file - description: VCF file undergoing annotation. - pattern: "*.vcf" - - dbsnp_file: - type: file - description: dbSNP file required for annotation. - pattern: "*.vcf.gz" - - tabix_file: - type: file - description: dbSNP file index. - pattern: "*.vcf.gz.tbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - vcf_file: + type: file + description: VCF file undergoing annotation. + pattern: "*.vcf" + - dbsnp_file: + type: file + description: dbSNP file required for annotation. + pattern: "*.vcf.gz" + - tabix_file: + type: file + description: dbSNP file index. + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf": + type: file + description: VCF file. + pattern: "*{.vcf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - ann_vcf: - type: file - description: Annotated VCF file - pattern: "*.vcf" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Furentsu" diff --git a/modules/nf-core/parabricks/deepvariant/meta.yml b/modules/nf-core/parabricks/deepvariant/meta.yml index b68e96e5c29..55998ea65e9 100644 --- a/modules/nf-core/parabricks/deepvariant/meta.yml +++ b/modules/nf-core/parabricks/deepvariant/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_deepvariant" -description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant. +description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating + deepvariant. keywords: - variant - deep variant @@ -12,49 +13,52 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.0.1/documentation/ licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing tumor sample information - id must match read groups for this sample. - [ id:'test'] - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - [ id:'test'] - - input: - type: file - description: bam file for sample to be variant called. - pattern: "*.bam" - - input_index: - type: file - description: bai index corresponding to input bam file. Only necessary if intervals are provided. - pattern: "*.bai" - - interval_file: - type: file - description: file or files containing genomic intervals for use in base quality score recalibration. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing tumor sample information - id must match read groups for this sample. + [ id:'test'] + - input: + type: file + description: bam file for sample to be variant called. + pattern: "*.bam" + - input_index: + type: file + description: bai index corresponding to input bam file. Only necessary if intervals + are provided. + pattern: "*.bai" + - interval_file: + type: file + description: file or files containing genomic intervals for use in base quality + score recalibration. + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + [ id:'test'] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - vcf: - type: file - description: Variant file. - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: Variant file. + pattern: "*.vcf" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" diff --git a/modules/nf-core/parabricks/fq2bam/meta.yml b/modules/nf-core/parabricks/fq2bam/meta.yml index d8f60f3b4ba..c86ff19aade 100644 --- a/modules/nf-core/parabricks/fq2bam/meta.yml +++ b/modules/nf-core/parabricks/fq2bam/meta.yml @@ -1,5 +1,7 @@ name: "parabricks_fq2bam" -description: NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked. +description: NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, + and duplicate marking. Note this nf-core module requires files to be copied into + the working directory and not symlinked. keywords: - align - sort @@ -11,70 +13,86 @@ tools: homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/4.0.1/Documentation/" licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: fastq.gz files - pattern: "*.fastq.gz" - - interval_file: - type: file - description: (optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR) - pattern: "*.{bed,interval_list,picard,list,intervals}" - - meta2: - type: map - description: | - Groovy Map containing fasta information - - fasta: - type: file - description: reference fasta file - must be unzipped - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing index information - - index: - type: file - description: reference BWA index - pattern: "*.{amb,ann,bwt,pac,sa}" - - known_sites: - type: file - description: (optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR. - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq.gz files + pattern: "*.fastq.gz" + - interval_file: + type: file + description: (optional) file(s) containing genomic intervals for use in base + quality score recalibration (BQSR) + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: reference fasta file - must be unzipped + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing index information + - index: + type: file + description: reference BWA index + pattern: "*.{amb,ann,bwt,pac,sa}" + - - known_sites: + type: file + description: (optional) known sites file(s) for calculating BQSR. markdups must + be true to perform BQSR. + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.bam" - bai: - type: file - description: index corresponding to sorted BAM file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: index corresponding to sorted BAM file + pattern: "*.bai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - qc_metrics: - type: directory - description: (optional) optional directory of qc metrics - pattern: "qc_metrics" + - qc_metrics: + type: directory + description: (optional) optional directory of qc metrics + pattern: "qc_metrics" - bqsr_table: - type: file - description: (optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr - pattern: "*.table" + - "*.table": + type: file + description: (optional) table from base quality score recalibration calculation, + to be used with parabricks/applybqsr + pattern: "*.table" - duplicate_metrics: - type: file - description: (optional) metrics calculated from marking duplcates in the bam file - pattern: "*-duplicate-metrics.txt" + - duplicate-metrics.txt: + type: file + description: (optional) metrics calculated from marking duplcates in the bam + file + pattern: "*-duplicate-metrics.txt" authors: - "@bsiranosian" - "@adamrtalbot" diff --git a/modules/nf-core/parabricks/genotypegvcf/meta.yml b/modules/nf-core/parabricks/genotypegvcf/meta.yml index 21ccf18860b..a876011edd0 100644 --- a/modules/nf-core/parabricks/genotypegvcf/meta.yml +++ b/modules/nf-core/parabricks/genotypegvcf/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_genotypegvcf" -description: NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs +description: NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating + GATK GenotypeGVCFs keywords: - joint-genotyping - gvcf @@ -12,42 +13,43 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.2.0/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - [ id:'test'] - - input: - type: file - description: gvcf file for samples to be jointly genotyped. - pattern: "*.{g.vcf,g.vcf.gz}" - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - input: + type: file + description: gvcf file for samples to be jointly genotyped. + pattern: "*.{g.vcf,g.vcf.gz}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + [ id:'test'] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: vcf file after gvcf conversion. - pattern: "*.vcf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.vcf": + type: file + description: vcf file after gvcf conversion. + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Furentsu" - "@bsiranosian" diff --git a/modules/nf-core/parabricks/haplotypecaller/meta.yml b/modules/nf-core/parabricks/haplotypecaller/meta.yml index 1b8ca3dd48c..be0c8328390 100644 --- a/modules/nf-core/parabricks/haplotypecaller/meta.yml +++ b/modules/nf-core/parabricks/haplotypecaller/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_haplotypecaller" -description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller. +description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating + GATK haplotypecaller. keywords: - variant - vcf @@ -11,49 +12,51 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.2.0/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - [ id:'test'] - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - [ id:'test'] - - input: - type: file - description: bam file for sample to be variant called. - pattern: "*.bam" - - input_index: - type: file - description: (Optional) bai index corresponding to input bam file. Only necessary when using intervals. - pattern: "*.bai" - - interval_file: - type: file - description: file or files containing genomic intervals. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information. + [ id:'test'] + - input: + type: file + description: bam file for sample to be variant called. + pattern: "*.bam" + - input_index: + type: file + description: (Optional) bai index corresponding to input bam file. Only necessary + when using intervals. + pattern: "*.bai" + - interval_file: + type: file + description: file or files containing genomic intervals. + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + [ id:'test'] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - vcf: - type: file - description: variant file. - pattern: "*.vcf" - + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: variant file. + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" diff --git a/modules/nf-core/parabricks/indexgvcf/meta.yml b/modules/nf-core/parabricks/indexgvcf/meta.yml index 50097d90a2f..be57547075a 100644 --- a/modules/nf-core/parabricks/indexgvcf/meta.yml +++ b/modules/nf-core/parabricks/indexgvcf/meta.yml @@ -13,31 +13,32 @@ tools: homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/" licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing gvcf information - - gvcf: - type: file - description: gvcf file to be indexed - pattern: "*.{vcf,vcf.gz}" - + - - meta: + type: map + description: | + Groovy Map containing gvcf information + - gvcf: + type: file + description: gvcf file to be indexed + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing output information - gvcf_index: - type: file - description: Indexed gvcf file - pattern: "*.g.vcf" + - meta: + type: map + description: | + Groovy Map containing output information + - "*.g.vcf*": + type: file + description: Indexed gvcf file + pattern: "*.g.vcf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Furentsu" - "@bsiranosian" diff --git a/modules/nf-core/parabricks/mutectcaller/meta.yml b/modules/nf-core/parabricks/mutectcaller/meta.yml index ce50cd3d14c..e3c2a37e0ff 100644 --- a/modules/nf-core/parabricks/mutectcaller/meta.yml +++ b/modules/nf-core/parabricks/mutectcaller/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_mutectcaller" -description: NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. +description: NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating + GATK Mutect2. keywords: - variant - vcf @@ -12,69 +13,80 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.0.1/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples. - [ id:'test', tumor_id:'tumor', normal_id:'normal' ] - - tumor_bam: - type: file - description: bam file for tumor sample. - pattern: "*.bam" - - tumor_bam_index: - type: file - description: (Optional) bai index corresponding to tumor bam file. Only required if intervals are provided. - pattern: "*.bam" - - normal_bam: - type: file - description: (Optional) bam file for normal sample in tumor-vs-normal calling. - pattern: "*.bam" - - normal_bam_index: - type: file - description: (Optional) bai index corresponding to normal bam file. Only required if intervals are provided. - pattern: "*.bam" - - interval_file: - type: file - description: (Optional) file or files containing genomic intervals for use in base quality score recalibration. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - ref_meta: - type: map - description: | - Groovy Map containing reference information - [ id:'homo_sapiens' ] - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - - panel_of_normals: - type: file - description: (Optional) pannel of normals file. - pattern: "*.vcf.gz" - - panel_of_normals_index: - type: file - description: (Optional) tbi index corresponding to pannel of normals file. - pattern: "*.tbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples. + [ id:'test', tumor_id:'tumor', normal_id:'normal' ] + - tumor_bam: + type: file + description: bam file for tumor sample. + pattern: "*.bam" + - tumor_bam_index: + type: file + description: (Optional) bai index corresponding to tumor bam file. Only required + if intervals are provided. + pattern: "*.bam" + - normal_bam: + type: file + description: (Optional) bam file for normal sample in tumor-vs-normal calling. + pattern: "*.bam" + - normal_bam_index: + type: file + description: (Optional) bai index corresponding to normal bam file. Only required + if intervals are provided. + pattern: "*.bam" + - interval_file: + type: file + description: (Optional) file or files containing genomic intervals for use in + base quality score recalibration. + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information + [ id:'homo_sapiens' ] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" + - - panel_of_normals: + type: file + description: (Optional) pannel of normals file. + pattern: "*.vcf.gz" + - - panel_of_normals_index: + type: file + description: (Optional) tbi index corresponding to pannel of normals file. + pattern: "*.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Compressed variants file. Will include an annoted vcf file if pannel of normals is used. - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Compressed variants file. Will include an annoted vcf file if pannel + of normals is used. + pattern: "*.vcf.gz" - stats: - type: file - description: Variant statistics. - pattern: "*.vcf.gz.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz.stats": + type: file + description: Variant statistics. + pattern: "*.vcf.gz.stats" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" diff --git a/modules/nf-core/paraclu/meta.yml b/modules/nf-core/paraclu/meta.yml index fc61d788dbb..96d1bb9dea1 100644 --- a/modules/nf-core/paraclu/meta.yml +++ b/modules/nf-core/paraclu/meta.yml @@ -11,34 +11,37 @@ tools: documentation: https://gitlab.com/mcfrith/paraclu tool_dev_url: https://gitlab.com/mcfrith/paraclu licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file - pattern: "*.bed" - - min_cluster: - type: integer - description: Minimum size of cluster - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file + pattern: "*.bed" + - - min_cluster: + type: integer + description: Minimum size of cluster + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: clustered BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: clustered BED file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mashehu" maintainers: diff --git a/modules/nf-core/paragraph/idxdepth/meta.yml b/modules/nf-core/paragraph/idxdepth/meta.yml index 19e90df24b8..9af96b918b5 100644 --- a/modules/nf-core/paragraph/idxdepth/meta.yml +++ b/modules/nf-core/paragraph/idxdepth/meta.yml @@ -13,56 +13,67 @@ tools: tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" licence: ["Apache License 2.0"] + identifier: biotools:Paragraph input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing information for the fasta - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing information for the fasta_fai - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Reference genome FASTA - pattern: "*.{fasta,fna,fa}" - - fasta_fai: - type: file - description: Index of the reference genome FASTA - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing information for the fasta + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome FASTA + pattern: "*.{fasta,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing information for the fasta_fai + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: Index of the reference genome FASTA + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - depth: - type: file - description: A JSON file containing depth, depth variance, read length and other parameters - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: A JSON file containing depth, depth variance, read length and other + parameters + pattern: "*.json" - binned_depth: - type: file - description: A TSV file containing the binned normalized depth. Can only be calculated for CRAM files - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV file containing the binned normalized depth. Can only be + calculated for CRAM files + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/paragraph/multigrmpy/meta.yml b/modules/nf-core/paragraph/multigrmpy/meta.yml index 56075bbf1da..34138d5e597 100644 --- a/modules/nf-core/paragraph/multigrmpy/meta.yml +++ b/modules/nf-core/paragraph/multigrmpy/meta.yml @@ -14,70 +14,81 @@ tools: tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" licence: ["Apache License 2.0"] + identifier: biotools:Paragraph input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variants: - type: file - description: A VCF or JSON file containing called structural variants - pattern: "*.{vcf,json}" - - variants_index: - type: file - description: The index for the VCF file - pattern: "*.tbi" - - reads: - type: file - description: BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest` - pattern: "*.{bam,cram}" - - reads_index: - type: file - description: The index/indices for the BAM/CRAM file(s) - pattern: "*.{bai,crai}" - - manifest: - type: file - description: | - A tab separated file containing information on the BAM/CRAM files. - This information can be generated using paragraph/idxdepth. - More information can be found here: https://github.com/Illumina/paragraph#sample-manifest - - meta2: - type: map - description: | - Groovy Map containing sample information for the FASTA file - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference FASTA file used to generate the VCF and BAM/CRAM files - pattern: "*.{fa,fasta,fna}" - - meta3: - type: map - description: | - Groovy Map containing sample information for the FASTA index file - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variants: + type: file + description: A VCF or JSON file containing called structural variants + pattern: "*.{vcf,json}" + - variants_index: + type: file + description: The index for the VCF file + pattern: "*.tbi" + - reads: + type: file + description: BAM or CRAM file(s) to genotype against. These should be specified + inside the `manifest` + pattern: "*.{bam,cram}" + - reads_index: + type: file + description: The index/indices for the BAM/CRAM file(s) + pattern: "*.{bai,crai}" + - manifest: + type: file + description: | + A tab separated file containing information on the BAM/CRAM files. + This information can be generated using paragraph/idxdepth. + More information can be found here: https://github.com/Illumina/paragraph#sample-manifest + - - meta2: + type: map + description: | + Groovy Map containing sample information for the FASTA file + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference FASTA file used to generate the VCF and BAM/CRAM + files + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing sample information for the FASTA index file + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The genotyped VCF file in BGZIP format - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The genotyped VCF file in BGZIP format + pattern: "*.vcf.gz" - json: - type: file - description: The genotyped JSON file in GZIP format - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json.gz": + type: file + description: The genotyped JSON file in GZIP format + pattern: "*.json.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/paragraph/vcf2paragraph/meta.yml b/modules/nf-core/paragraph/vcf2paragraph/meta.yml index c60991218c9..6ae3b93b759 100644 --- a/modules/nf-core/paragraph/vcf2paragraph/meta.yml +++ b/modules/nf-core/paragraph/vcf2paragraph/meta.yml @@ -12,30 +12,42 @@ tools: tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" licence: ["Apache License 2.0"] + identifier: biotools:Paragraph input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF/BCF file - pattern: "*.{vcf,bcf}(.gz)?" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file + pattern: "*.{vcf,bcf}(.gz)?" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference genome VCF was generated against + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - graph: - type: file - description: The created graph in BGZIP format - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json.gz": + type: file + description: The created graph in BGZIP format + pattern: "*.json.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml index e6cc6d63578..50c3c9e04aa 100644 --- a/modules/nf-core/paraphase/meta.yml +++ b/modules/nf-core/paraphase/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "paraphase" description: "HiFi-based caller for highly homologous genes" @@ -14,73 +13,96 @@ tools: tool_dev_url: "https://github.com/PacificBiosciences/paraphase" doi: "10.1016/j.ajhg.2023.01.001" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - - bai: - type: file - description: Index of BAM file - pattern: "*.bai" - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing config information - e.g. [ id:'config' ] - - config: - type: file - description: Config file - pattern: "*.yaml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index of BAM file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing config information + e.g. [ id:'config' ] + - config: + type: file + description: Config file + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.json": + type: file + description: Summary of haplotype and variant calls + pattern: "*.paraphase.json" - bam: - type: file - description: (re)aligned BAM file - pattern: "*.paraphase.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.bam": + type: file + description: (re)aligned BAM file + pattern: "*.paraphase.bam" - bai: - type: file - description: Index of (re)aligned BAM file - pattern: "*.paraphase.bam.bai" - - json: - type: file - description: Summary of haplotype and variant calls - pattern: "*.paraphase.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.bam.bai": + type: file + description: Index of (re)aligned BAM file + pattern: "*.paraphase.bam.bai" - vcf: - type: file - description: compressed VCF file(s) per gene - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - ${prefix}_paraphase_vcfs/*.vcf.gz: + type: file + description: compressed VCF file(s) per gene + pattern: "*.vcf.gz" - vcf_index: - type: file - description: compressed VCF file index - pattern: "*.vcf.gz.{tbi,csi}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - ${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}: + type: file + description: compressed VCF file index + pattern: "*.vcf.gz.{tbi,csi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/pasty/meta.yml b/modules/nf-core/pasty/meta.yml index 8f7de15f429..6705a4a636e 100644 --- a/modules/nf-core/pasty/meta.yml +++ b/modules/nf-core/pasty/meta.yml @@ -12,38 +12,53 @@ tools: documentation: "https://github.com/rpetit3/pasty" tool_dev_url: "https://github.com/rpetit3/pasty" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: An assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: An assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file with the predicted serogroup - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: A tab-delimited file with the predicted serogroup + pattern: "*.tsv" - blast: - type: file - description: A tab-delimited file of all blast hits - pattern: "*.blastn.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.blastn.tsv: + type: file + description: A tab-delimited file of all blast hits + pattern: "*.blastn.tsv" - details: - type: file - description: A tab-delimited file with details for each serogroup - pattern: "*.details.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.details.tsv: + type: file + description: A tab-delimited file with details for each serogroup + pattern: "*.details.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/pbbam/pbmerge/meta.yml b/modules/nf-core/pbbam/pbmerge/meta.yml index 83c664d6d15..5debcce908b 100644 --- a/modules/nf-core/pbbam/pbmerge/meta.yml +++ b/modules/nf-core/pbbam/pbmerge/meta.yml @@ -1,5 +1,7 @@ name: pbbam_pbmerge -description: The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities. +description: The pbbam software package provides components to create, query, & edit + PacBio BAM files and associated indices. These components include a core C++ library, + bindings for additional languages, and command-line utilities. keywords: - pbbam - pbmerge @@ -11,34 +13,43 @@ tools: documentation: https://pbbam.readthedocs.io/en/latest/tools/pbmerge.html tool_dev_url: https://github.com/pacificbiosciences/pbbam/ licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM files to merge - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM files to merge + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: The merged bam file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: The merged bam file + pattern: "*.bam" - pbi: - type: file - description: BAM Pacbio index file - pattern: "*.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pbi": + type: file + description: BAM Pacbio index file + pattern: "*.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/pbccs/meta.yml b/modules/nf-core/pbccs/meta.yml index ded53e06ac2..28c53ac0a1d 100644 --- a/modules/nf-core/pbccs/meta.yml +++ b/modules/nf-core/pbccs/meta.yml @@ -7,61 +7,89 @@ keywords: - subreads tools: - pbccs: - description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads) + description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads + (HiFi Reads) homepage: https://github.com/PacificBiosciences/pbbioconda documentation: https://ccs.how/ tool_dev_url: https://github.com/PacificBiosciences/ccs licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: id of the split file - - bam: - type: file - description: Raw subreads bam - pattern: "*.subreads.bam" - - pbi: - type: file - description: Pacbio BAM Index - pattern: "*.pbi" - - chunk_num: - type: integer - description: BAM part to process - - chunk_on: - type: integer - description: Total number of bam parts to process + - - meta: + type: map + description: | + Groovy Map containing sample information + id: id of the split file + - bam: + type: file + description: Raw subreads bam + pattern: "*.subreads.bam" + - pbi: + type: file + description: Pacbio BAM Index + pattern: "*.pbi" + - - chunk_num: + type: integer + description: BAM part to process + - - chunk_on: + type: integer + description: Total number of bam parts to process output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: CCS sequences in bam format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chunk*.bam": + type: file + description: CCS sequences in bam format + pattern: "*.bam" - pbi: - type: file - description: PacBio Index of CCS sequences - pattern: "*.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chunk*.bam.pbi": + type: file + description: PacBio Index of CCS sequences + pattern: "*.pbi" - report_txt: - type: file - description: Summary of CCS in txt format - pattern: ".txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.report.txt" ': + type: file + description: Summary of CCS in txt format + pattern: ".txt" - report_json: - type: file - description: Summary of CCS in txt json - pattern: ".json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.report.json" ': + type: file + description: Summary of CCS in txt json + pattern: ".json" - metrics: - type: file - description: Metrics about zmws - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json.gz": + type: file + description: Metrics about zmws + pattern: "*.json.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/pbptyper/meta.yml b/modules/nf-core/pbptyper/meta.yml index c12086adbd2..97cec8479cf 100644 --- a/modules/nf-core/pbptyper/meta.yml +++ b/modules/nf-core/pbptyper/meta.yml @@ -7,43 +7,53 @@ keywords: - assembly tools: - "pbptyper": - description: "In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies" + description: "In silico Penicillin Binding Protein (PBP) typer for Streptococcus + pneumoniae assemblies" homepage: "https://github.com/rpetit3/pbptyper" documentation: "https://github.com/rpetit3/pbptyper" tool_dev_url: "https://github.com/rpetit3/pbptyper" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: An assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" - - db: - type: file - description: A reference PBP database (optional) - pattern: "*.{fasta,fna,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: An assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" + - - db: + type: file + description: A reference PBP database (optional) + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file with the predicted PBP type - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: A tab-delimited file with the predicted PBP type + pattern: "*.tsv" - blast: - type: file - description: A tab-delimited file of all blast hits - pattern: "*.tblastn.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tblastn.tsv": + type: file + description: A tab-delimited file of all blast hits + pattern: "*.tblastn.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/pbtk/bam2fastq/meta.yml b/modules/nf-core/pbtk/bam2fastq/meta.yml index 1ba2d7511f4..fbc16a3bf1e 100644 --- a/modules/nf-core/pbtk/bam2fastq/meta.yml +++ b/modules/nf-core/pbtk/bam2fastq/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "pbtk_bam2fastq" description: converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq @@ -15,41 +14,38 @@ tools: tool_dev_url: "https://github.com/PacificBiosciences/pbtk" doi: "no DOI available" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - - bam: - type: file - description: PacBio BAM file - pattern: "*.bam" - - - pbi: - type: file - description: PacBio BAM file index (.pbi) - pattern: "*.pbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - bam: + type: file + description: PacBio BAM file + pattern: "*.bam" + - pbi: + type: file + description: PacBio BAM file index (.pbi) + pattern: "*.pbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: Gzipped FASTQ file - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.$extension": + type: file + description: Gzipped FASTQ file + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mbeavitt" - "@gallvp" diff --git a/modules/nf-core/pbtk/pbindex/meta.yml b/modules/nf-core/pbtk/pbindex/meta.yml index 1bf31965389..012ca995365 100644 --- a/modules/nf-core/pbtk/pbindex/meta.yml +++ b/modules/nf-core/pbtk/pbindex/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pbtk_pbindex" -description: Minimalistic tool which creates an index file that enables random access into PacBio BAM files +description: Minimalistic tool which creates an index file that enables random access + into PacBio BAM files keywords: - genomics - bam @@ -14,34 +14,34 @@ tools: documentation: "https://github.com/PacificBiosciences/pbtk" tool_dev_url: "https://github.com/PacificBiosciences/pbtk" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - bam: - type: file - description: Input BAM file - pattern: "*.bam" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Input BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pbi: - type: file - description: Index file - pattern: "*.bam.pbi" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.pbi": + type: file + description: Index file + pattern: "*.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/pear/meta.yml b/modules/nf-core/pear/meta.yml index 8f100600364..a09b2901dcd 100644 --- a/modules/nf-core/pear/meta.yml +++ b/modules/nf-core/pear/meta.yml @@ -1,5 +1,6 @@ name: "pear" -description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. +description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read + merger. keywords: - pair-end - read @@ -10,38 +11,57 @@ tools: homepage: "https://cme.h-its.org/exelixis/web/software/pear/" documentation: "https://cme.h-its.org/exelixis/web/software/pear/doc.html" licence: ["Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported"] + identifier: biotools:pear input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - reads: - type: file - description: | - List of input FastQ files with paired-end reads forward and reverse. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - reads: + type: file + description: | + List of input FastQ files with paired-end reads forward and reverse. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembled: - type: file - description: FastQ file containing Assembled reads. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.assembled.fastq.gz": + type: file + description: FastQ file containing Assembled reads. + pattern: "*.{fastq.gz}" - unassembled: - type: file - description: FastQ files containing Unassembled forward and reverse reads. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.unassembled.forward.fastq.gz": + type: file + description: FastQ files containing Unassembled forward and reverse reads. + pattern: "*.{fastq.gz}" + - "*.unassembled.reverse.fastq.gz": + type: file + description: FastQ files containing Unassembled forward and reverse reads. + pattern: "*.{fastq.gz}" - discarded: - type: file - description: FastQ file containing discarded reads. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.discarded.fastq.gz": + type: file + description: FastQ file containing discarded reads. + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/peddy/meta.yml b/modules/nf-core/peddy/meta.yml index 24a82e190fe..6b6b7347d03 100644 --- a/modules/nf-core/peddy/meta.yml +++ b/modules/nf-core/peddy/meta.yml @@ -6,56 +6,78 @@ keywords: - family tools: - peddy: - description: genotype, ped correspondence check, ancestry check, sex check. directly, quickly on VCF + description: genotype, ped correspondence check, ancestry check, sex check. directly, + quickly on VCF homepage: https://github.com/brentp/peddy documentation: https://peddy.readthedocs.io/en/latest/ tool_dev_url: https://github.com/brentp/peddy doi: "10.1016/j.ajhg.2017.01.017" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" - - ped: - type: file - description: PED/FAM file - pattern: "*.{ped,fam}" - - vcf_tbi: - type: file - description: TBI file - pattern: "*.{vcf.gz.tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" + - vcf_tbi: + type: file + description: TBI file + pattern: "*.{vcf.gz.tbi}" + - - ped: + type: file + description: PED/FAM file + pattern: "*.{ped,fam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ped: - type: file - description: PED/FAM file - pattern: "*.peddy.{ped}" - html: - type: file - description: HTML file - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: HTML file + pattern: "*.{html}" - csv: - type: file - description: CSV file - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: CSV file + pattern: "*.{csv}" + - ped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.peddy.ped": + type: file + description: PED/FAM file + pattern: "*.peddy.{ped}" - png: - type: file - description: PNG file - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: PNG file + pattern: "*.{png}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/peka/meta.yml b/modules/nf-core/peka/meta.yml index 6c1adf1db1f..8ec588131fa 100644 --- a/modules/nf-core/peka/meta.yml +++ b/modules/nf-core/peka/meta.yml @@ -1,4 +1,3 @@ ---- name: "peka" description: Runs PEKA CLIP peak k-mer analysis keywords: @@ -9,55 +8,124 @@ keywords: - k-mer tools: - "peka": - description: "Positionally-enriched k-mer analysis (PEKA) is a software package for identifying enriched protein-RNA binding motifs from CLIP datasets" + description: "Positionally-enriched k-mer analysis (PEKA) is a software package + for identifying enriched protein-RNA binding motifs from CLIP datasets" homepage: "https://github.com/ulelab/peka" documentation: "https://github.com/ulelab/peka" tool_dev_url: "https://github.com/ulelab/peka" doi: "10.1186/s13059-022-02755-2" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: BED file of peak regions - pattern: "*.{bed,bed.gz}" - - crosslinks: - type: file - description: BED file of crosslinks - pattern: "*.{bed,bed.gz}" - - fasta: - type: file - description: Genome reference sequence used - pattern: "*.{fa,fasta}" - - fai: - type: file - description: FAI file corresponding to the reference sequence - pattern: "*.{fai}" - - gtf: - type: file - description: A segmented GTF used to annotate peaks - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peaks: + type: file + description: BED file of peak regions + pattern: "*.{bed,bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - crosslinks: + type: file + description: BED file of crosslinks + pattern: "*.{bed,bed.gz}" + - - fasta: + type: file + description: Genome reference sequence used + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: FAI file corresponding to the reference sequence + pattern: "*.{fai}" + - - gtf: + type: file + description: A segmented GTF used to annotate peaks + pattern: "*.{gtf}" output: - cluster: - type: file - description: TSV file of summed occurrence distributions of k-mers within defined clusters - pattern: "*.tsv" + - meta: + type: file + description: TSV file of summed occurrence distributions of k-mers within defined + clusters + pattern: "*.tsv" + - "*mer_cluster_distribution*": + type: file + description: TSV file of summed occurrence distributions of k-mers within defined + clusters + pattern: "*.tsv" - distribution: - type: file - description: TSV file with calculated PEKA score and occurrence distribution for all possible k-mers - pattern: "*.tsv" + - meta: + type: file + description: TSV file with calculated PEKA score and occurrence distribution + for all possible k-mers + pattern: "*.tsv" + - "*mer_distribution*": + type: file + description: TSV file with calculated PEKA score and occurrence distribution + for all possible k-mers + pattern: "*.tsv" + - rtxn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*rtxn*": + type: file + description: rtxn file + pattern: "*rtxn*" - pdf: - type: file - description: PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites - pattern: "*.pdf" + - meta: + type: file + description: PDF file with graphs showing k-mer occurrence distributions around + thresholded crosslink sites + pattern: "*.pdf" + - "*.pdf": + type: file + description: PDF file with graphs showing k-mer occurrence distributions around + thresholded crosslink sites + pattern: "*.pdf" + - tsites: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*thresholded_sites*.bed.gz": + type: file + description: BED file of thresholded sites + pattern: "*thresholded_sites*.bed.gz" + - oxn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*oxn*.bed.gz": + type: file + description: BED file of oxn sites + pattern: "*oxn*.bed.gz" + - clust: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_clusters.csv": + type: file + description: CSV file of clusters + pattern: "*_clusters.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kkuret" - "@codeprimate123" diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml index 276f6fddf6f..d9c7cdac832 100644 --- a/modules/nf-core/phantompeakqualtools/meta.yml +++ b/modules/nf-core/phantompeakqualtools/meta.yml @@ -19,40 +19,55 @@ tools: tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools" doi: "10.1101/gr.136184.111" licence: ["BSD-3-clause"] + identifier: biotools:phantompeakqualtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spp: - type: file - description: | - A ChIP-Seq Processing Pipeline file containing - peakshift/phantomPeak results - pattern: "*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out": + type: file + description: | + A ChIP-Seq Processing Pipeline file containing + peakshift/phantomPeak results + pattern: "*.{out}" - pdf: - type: file - description: A pdf containing save cross-correlation plots - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: A pdf containing save cross-correlation plots + pattern: "*.{pdf}" - rdata: - type: file - description: Rdata file containing the R session - pattern: "*.{Rdata}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Rdata": + type: file + description: Rdata file containing the R session + pattern: "*.{Rdata}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/pharokka/installdatabases/meta.yml b/modules/nf-core/pharokka/installdatabases/meta.yml index a4d0f63d6d5..e70d8f7edba 100644 --- a/modules/nf-core/pharokka/installdatabases/meta.yml +++ b/modules/nf-core/pharokka/installdatabases/meta.yml @@ -17,17 +17,19 @@ tools: tool_dev_url: "https://github.com/gbouras13/pharokka" doi: "10.1093/bioinformatics/btac776" licence: ["MIT"] + identifier: biotools:pharokka output: - pharokka_db: - type: directory - description: Directory pointing to Pharokka's database - pattern: "${prefix}/" + - ${prefix}/: + type: directory + description: Directory pointing to Pharokka's database + pattern: "${prefix}/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/pharokka/pharokka/meta.yml b/modules/nf-core/pharokka/pharokka/meta.yml index fbba281b633..c73eb479b58 100644 --- a/modules/nf-core/pharokka/pharokka/meta.yml +++ b/modules/nf-core/pharokka/pharokka/meta.yml @@ -15,56 +15,100 @@ tools: tool_dev_url: "https://github.com/gbouras13/pharokka" doi: "10.1093/bioinformatics/btac776" licence: ["MIT"] + identifier: biotools:pharokka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - phage_fasta: - type: file - description: A FASTA file containing phage sequence(s) - pattern: "*.{fasta,fna,fa}" - - pharokka_db: - type: file - description: Directory containing Pharokka's database - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - phage_fasta: + type: file + description: A FASTA file containing phage sequence(s) + pattern: "*.{fasta,fna,fa}" + - - pharokka_db: + type: file + description: Directory containing Pharokka's database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - log: - type: file - description: Log file containing all logging output - pattern: "*.log" + - cds_final_merged_output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv: + type: file + description: A file containing the final merged output of CDSs + pattern: "*_cds_final_merged_output.tsv" - cds_functions: - type: file - description: A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs - pattern: "*_cds_functions.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_cds_functions.tsv: + type: file + description: A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and + PHROG functions assigned to CDSs + pattern: "*_cds_functions.tsv" + - length_gc_cds_density: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv: + type: file + description: A file containing the length, GC content, and CDS density of + the phage genome + pattern: "*_length_gc_cds_density.tsv" - card: - type: file - description: OPTIONAL - A file containing any CARD database hits - pattern: "*top_hits_card.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_top_hits_card.tsv: + type: file + description: OPTIONAL - A file containing any CARD database hits + pattern: "*top_hits_card.tsv" - vfdb: - type: file - description: OPTIONAL - A file containing any VFDB database hits - pattern: "*top_hits_vfdb.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv: + type: file + description: OPTIONAL - A file containing any VFDB database hits + pattern: "*top_hits_vfdb.tsv" - mash: - type: file - description: OPTIONAL - File containing top hits to INPHARED database - pattern: "*_top_hits_mash_inphared.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv: + type: file + description: OPTIONAL - File containing top hits to INPHARED database + pattern: "*_top_hits_mash_inphared.tsv" - reoriented: - type: file - description: OPTIONAL - FASTA file reoriented to start with the large terminase subunit - pattern: "*_genome_terminase_reoriented.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta: + type: file + description: OPTIONAL - FASTA file reoriented to start with the large terminase + subunit + pattern: "*_genome_terminase_reoriented.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/phispy/meta.yml b/modules/nf-core/phispy/meta.yml index e9c65aeaf30..fd47eb4f561 100644 --- a/modules/nf-core/phispy/meta.yml +++ b/modules/nf-core/phispy/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "phispy" description: Predict prophages in bacterial genomes @@ -17,80 +16,143 @@ tools: tool_dev_url: "https://github.com/linsalrob/PhiSpy/" doi: "10.1093/nar/gks406" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gbk: - type: file - description: Genome file in .gbk or .gbff format. - pattern: "*.{gbk,gbff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gbk: + type: file + description: Genome file in .gbk or .gbff format. + pattern: "*.{gbk,gbff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - coordinates: - type: file - description: | - Coordinates of each prophage identified in the genome, - and their att sites (if found). - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: | + Coordinates of each prophage identified in the genome, + and their att sites (if found). + pattern: "*.{tsv}" - gbk: - type: file - description: | - A duplicate GenBank record that is the same as the input record, - but we have inserted the prophage information, including att - sites into the record. - pattern: "*.{gbk,gbff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.gb*: + type: file + description: | + A duplicate GenBank record that is the same as the input record, + but we have inserted the prophage information, including att + sites into the record. + pattern: "*.{gbk,gbff}" - log: - type: file - description: File containing the PhiSpy execution log - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.log: + type: file + description: File containing the PhiSpy execution log + pattern: "*.{log}" - information: - type: file - description: | - File containing all the genes of the genome, one per line. - The tenth column describes how likely the gene is a phage gene. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage_information.tsv: + type: file + description: | + File containing all the genes of the genome, one per line. + The tenth column describes how likely the gene is a phage gene. + pattern: "*.{tsv}" - bacteria_fasta: - type: file - description: Genome with prophage regions masked with N. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_bacteria.fasta: + type: file + description: Genome with prophage regions masked with N. + pattern: "*.{fasta}" - bacteria_gbk: - type: file - description: Genome sequences identified as bacterial. - pattern: "*.{gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_bacteria.gbk: + type: file + description: Genome sequences identified as bacterial. + pattern: "*.{gbk}" - phage_fasta: - type: file - description: Phage sequences extracted from the genome. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_phage.fasta: + type: file + description: Phage sequences extracted from the genome. + pattern: "*.{fasta}" - phage_gbk: - type: file - description: Phage sequences extracted from the genome. - pattern: "*.{gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_phage.gbk: + type: file + description: Phage sequences extracted from the genome. + pattern: "*.{gbk}" - prophage_gff: - type: file - description: Prophage information in GFF3 format. - pattern: "*.{gff3}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage.gff3: + type: file + description: Prophage information in GFF3 format. + pattern: "*.{gff3}" - prophage_tbl: - type: file - description: | - File containing prophage number and its location in the genome. - pattern: "*.{tbl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage.tbl: + type: file + description: | + File containing prophage number and its location in the genome. + pattern: "*.{tbl}" - prophage_tsv: - type: file - description: | - A file containing simpler version of the coordinates file, - with only prophage number, contig, start and stop. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage.tsv: + type: file + description: | + A file containing simpler version of the coordinates file, + with only prophage number, contig, start and stop. + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvfe" maintainers: diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml index 1b7ab8bec44..5d0c9ad906c 100644 --- a/modules/nf-core/phyloflash/meta.yml +++ b/modules/nf-core/phyloflash/meta.yml @@ -1,49 +1,53 @@ name: phyloflash -description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. +description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore + phylogenetic composition of an illumina (meta)genomic dataset. keywords: - metagenomics - illumina datasets - phylogenetic composition tools: - phyloflash: - description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. + description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and + explore phylogenetic composition of an illumina (meta)genomic dataset. homepage: https://hrgv.github.io/phyloFlash/ documentation: https://hrgv.github.io/phyloFlash/usage.html tool_dev_url: https://github.com/HRGV/phyloFlash doi: "10.1128/mSystems.00920-20" licence: ["GPL v3"] + identifier: biotools:phyloflash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Channel containing single or paired-end reads - pattern: "*.{fastq.gz,fq.gz}" - - sliva_db: - type: directory - description: Folder containing the SILVA database - pattern: "ref" - - univec_db: - type: directory - description: Folder containing UniVec database - pattern: "UniVec" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Channel containing single or paired-end reads + pattern: "*.{fastq.gz,fq.gz}" + - - silva_db: + type: directory + description: Folder containing SILVA database + - - univec_db: + type: directory + description: Folder containing UniVec database + pattern: "UniVec" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Folder containing the results of phyloFlash analysis - pattern: "${prefix}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}*/*: + type: directory + description: Folder containing the results of phyloFlash analysis + pattern: "${prefix}*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index efd5b86dc05..77ce85035f0 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -14,56 +14,71 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Sequence reads file, can be SAM/BAM/CRAM format - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - fasta_index: - type: file - description: Reference genome index file - pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_index: + type: file + description: Reference genome index file + pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Output BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/bedtointervallist/meta.yml b/modules/nf-core/picard/bedtointervallist/meta.yml index 862736d3967..e9e35a29bb1 100644 --- a/modules/nf-core/picard/bedtointervallist/meta.yml +++ b/modules/nf-core/picard/bedtointervallist/meta.yml @@ -15,38 +15,45 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bed: - type: file - description: Input bed file - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - dict: - type: file - description: Sequence dictionary - pattern: "*.dict" - - arguments_file: - type: file - description: File containing command line arguments (optional) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bed: + type: file + description: Input bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: + type: file + description: Sequence dictionary + pattern: "*.dict" output: - interval_list: - type: file - description: gatk interval list file - pattern: "*.interval_list" + - meta: + type: file + description: gatk interval list file + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: gatk interval list file + pattern: "*.interval_list" + - _list: + type: file + description: gatk interval list file + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@matthdsm" diff --git a/modules/nf-core/picard/cleansam/meta.yml b/modules/nf-core/picard/cleansam/meta.yml index a74fe2e100d..ae981700c61 100644 --- a/modules/nf-core/picard/cleansam/meta.yml +++ b/modules/nf-core/picard/cleansam/meta.yml @@ -1,5 +1,6 @@ name: picard_cleansam -description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads +description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments + and setting MAPQ to 0 for unmapped reads keywords: - clean - bam @@ -15,30 +16,33 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Cleaned BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Cleaned BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index 4b6d53b807d..ea6deda3e56 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -17,71 +17,75 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: An aligned BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Optional aligned BAM/CRAM/SAM file index - pattern: "*.{bai,crai,sai}" - - bait_intervals: - type: file - description: An interval file that contains the locations of the baits used. - pattern: "*.{interval_list,bed,bed.gz}" - - target_intervals: - type: file - description: An interval file that contains the locations of the targets. - pattern: "*.{interval_list,bed,bed.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: | - A reference file to calculate dropout metrics measuring reduced representation of reads. - Optional input. - pattern: "*.{fa,fasta,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of FASTA file. Only needed when fasta is supplied. - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied. - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: An aligned BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Optional aligned BAM/CRAM/SAM file index + pattern: "*.{bai,crai,sai}" + - bait_intervals: + type: file + description: An interval file that contains the locations of the baits used. + pattern: "*.{interval_list,bed,bed.gz}" + - target_intervals: + type: file + description: An interval file that contains the locations of the targets. + pattern: "*.{interval_list,bed,bed.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: | + A reference file to calculate dropout metrics measuring reduced representation of reads. + Optional input. + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of FASTA file. Only needed when fasta is supplied. + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of FASTA file. Only needed when bed interval + lists are supplied. + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_metrics": + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@matthdsm" diff --git a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml index e2749cb6217..0947048dc67 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml @@ -13,34 +13,43 @@ tools: documentation: "https://broadinstitute.github.io/picard/" tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pdf: - type: file - description: Histogram plots of the insert size metrics computed by Picard - pattern: "*.pdf" - metrics: - type: file - description: Values used by Picard to generate the insert size histograms - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Values used by Picard to generate the insert size histograms + pattern: "*.txt" + - histogram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: Insert size histogram in PDF format + pattern: "*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FerriolCalvet" maintainers: diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 67bba57b21d..2b7981ac6b3 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -15,55 +15,64 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: SAM/BAM/CRAM file - pattern: "*.{sam,bam,cram}" - - bai: - type: file - description: Optional SAM/BAM/CRAM file index - pattern: "*.{sai,bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fasta: - type: file - description: Genome fasta file - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fai: - type: file - description: Index of FASTA file. Only needed when fasta is supplied. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: SAM/BAM/CRAM file + pattern: "*.{sam,bam,cram}" + - bai: + type: file + description: Optional SAM/BAM/CRAM file index + pattern: "*.{sai,bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fasta: + type: file + description: Genome fasta file + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fai: + type: file + description: Index of FASTA file. Only needed when fasta is supplied. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_metrics": + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" - pdf: - type: file - description: PDF plots of metrics - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: PDF plots of metrics + pattern: "*.{pdf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml index 8a7bd2346ae..15d146baac0 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml @@ -16,45 +16,52 @@ tools: documentation: "https://broadinstitute.github.io/picard/" tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, strandedness:true ] - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" - - ref_flat: - type: file - description: Genome ref_flat file - - gene_pred: - type: file - description: genome gene_pred file as an alternative to the ref_flat file - - fasta: - type: file - description: Genome fasta file - - rrna_intervals: - type: file - description: Interval file of ribosomal RNA regions + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, strandedness:true ] + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - - ref_flat: + type: file + description: Genome ref_flat file + - - fasta: + type: file + description: Genome fasta file + - - rrna_intervals: + type: file + description: Interval file of ribosomal RNA regions output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - metrics: - type: file - description: RNA alignment metrics files generated by picard - pattern: "*.rna_metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rna_metrics": + type: file + description: RNA alignment metrics files generated by picard + pattern: "*.rna_metrics" - pdf: - type: file - description: Plot normalized position vs. coverage in a pdf file generated by picard + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: Plot normalized position vs. coverage in a pdf file generated by + picard - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index 5576ef9287b..bb748080983 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -1,5 +1,6 @@ name: picard_collectwgsmetrics -description: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. +description: Collect metrics about coverage and performance of whole genome sequencing + (WGS) experiments. keywords: - alignment - metrics @@ -14,55 +15,59 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Aligned reads file - pattern: "*.{bam, cram}" - - bai: - type: file - description: (Optional) Aligned reads file index - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome fasta file index - pattern: "*.{fai}" - - intervallist: - type: file - description: Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Aligned reads file + pattern: "*.{bam, cram}" + - bai: + type: file + description: (Optional) Aligned reads file index + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome fasta file index + pattern: "*.{fai}" + - - intervallist: + type: file + description: Picard Interval List. Defines which contigs to include. Can be + generated from a BED file with GATK BedToIntervalList. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_metrics": + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@flowuenne" diff --git a/modules/nf-core/picard/createsequencedictionary/meta.yml b/modules/nf-core/picard/createsequencedictionary/meta.yml index 0cb79cfe5c4..67616703118 100644 --- a/modules/nf-core/picard/createsequencedictionary/meta.yml +++ b/modules/nf-core/picard/createsequencedictionary/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reference_dict: - type: file - description: picard dictionary file - pattern: "*.{dict}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dict": + type: file + description: picard dictionary file + pattern: "*.{dict}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/crosscheckfingerprints/meta.yml b/modules/nf-core/picard/crosscheckfingerprints/meta.yml index 1db3b866f21..898a11a8004 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/meta.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/meta.yml @@ -1,5 +1,6 @@ name: "picard_crosscheckfingerprints" -description: Checks that all data in the set of input files appear to come from the same individual +description: Checks that all data in the set of input files appear to come from the + same individual keywords: - alignment - metrics @@ -15,60 +16,59 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input1: - type: file - description: List containing 1 or more bam/vcf files or a file containing filepaths - pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" - - input1_index: - type: file - description: List containing 1 or more bam/vcf files indexes - pattern: "*.{bai,csi,crai,tbi}" - - input2: - type: file - description: Optional list containing 1 or more bam/vcf files or a file containing filepaths - pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" - - input2_index: - type: file - description: List containing 1 or more bam/vcf files indexes - pattern: "*.{bai,csi,crai,tbi}" - - haplotype_map: - type: file - description: Haplotype map file - pattern: "*.{txt,vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - fasta_index: - type: file - description: Reference genome index file - pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input1: + type: file + description: List containing 1 or more bam/vcf files or a file containing filepaths + pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" + - input1_index: + type: file + description: List containing 1 or more bam/vcf files indexes + pattern: "*.{bai,csi,crai,tbi}" + - input2: + type: file + description: Optional list containing 1 or more bam/vcf files or a file containing + filepaths + pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" + - input2_index: + type: file + description: List containing 1 or more bam/vcf files indexes + pattern: "*.{bai,csi,crai,tbi}" + - haplotype_map: + type: file + description: Haplotype map file + pattern: "*.{txt,vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - crosscheck_metrics: - type: file - description: Metrics created by crosscheckfingerprints - pattern: "*.{crosscheck_metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crosscheck_metrics.txt": + type: file + description: Metrics created by crosscheckfingerprints + pattern: "*.{crosscheck_metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/picard/extractfingerprint/meta.yml b/modules/nf-core/picard/extractfingerprint/meta.yml index 5c6ccb42ccc..d8f6144f54f 100644 --- a/modules/nf-core/picard/extractfingerprint/meta.yml +++ b/modules/nf-core/picard/extractfingerprint/meta.yml @@ -1,5 +1,6 @@ name: "picard_extractfingerprint" -description: Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites. +description: Computes/Extracts the fingerprint genotype likelihoods from the supplied + file. It is given as a list of PLs at the fingerprinting sites. keywords: - picard - extract @@ -14,30 +15,63 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: file - description: | - Input SAM/BAM/CRAM file - - reference: - type: file - description: | - Reference sequence file - - haplotype_map: - type: file - description: | - A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. - See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details. - pattern: "*.{txt,vcf,vcf.gz}" + - - meta: + type: file + description: | + Input SAM/BAM/CRAM file + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - - haplotype_map: + type: file + description: | + A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. + See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details. + pattern: "*.{txt,vcf,vcf.gz}" + - - fasta: + type: file + description: Reference sequence file + pattern: "*.{fasta,fna,fa}" + - - fasta_fai: + type: file + description: Reference sequence index file + pattern: "*.{fai}" + - - sequence_dictionary: + type: file + description: Reference sequence dictionary file output: - - fingerprint: - type: file - description: | - Output fingerprint file (VCF) + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz.tbi": + type: file + description: Tabix index file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@mauro-saporita" diff --git a/modules/nf-core/picard/fastqtosam/meta.yml b/modules/nf-core/picard/fastqtosam/meta.yml index 67391438607..4cf42d855bd 100644 --- a/modules/nf-core/picard/fastqtosam/meta.yml +++ b/modules/nf-core/picard/fastqtosam/meta.yml @@ -13,32 +13,34 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Unaligned bam file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Unaligned bam file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/picard/filtersamreads/meta.yml b/modules/nf-core/picard/filtersamreads/meta.yml index 0be39002ee9..9fe52dec14c 100644 --- a/modules/nf-core/picard/filtersamreads/meta.yml +++ b/modules/nf-core/picard/filtersamreads/meta.yml @@ -1,5 +1,6 @@ name: picard_filtersamreads -description: Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list +description: Filters SAM/BAM files to include/exclude either aligned/unaligned reads + or based on a read list keywords: - bam - filter @@ -14,37 +15,41 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam - pattern: "*.{bam}" - - filter: - type: string - description: Picard filter type - pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList" - - readlist: - type: file - description: Optional text file containing reads IDs to include or exclude + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM files. If filtering without read list must be sorted + by queryname with picard sortsam + pattern: "*.{bam}" + - readlist: + type: file + description: Optional text file containing reads IDs to include or exclude + - - filter: + type: string + description: Picard filter type + pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Filtered BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Filtered BAM file + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/picard/fixmateinformation/meta.yml b/modules/nf-core/picard/fixmateinformation/meta.yml index 35849993c29..ec562e97e1d 100644 --- a/modules/nf-core/picard/fixmateinformation/meta.yml +++ b/modules/nf-core/picard/fixmateinformation/meta.yml @@ -14,30 +14,33 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: mate-pair verified BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: mate-pair verified BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml index 9ccba6d24ad..10fbfc83785 100644 --- a/modules/nf-core/picard/liftovervcf/meta.yml +++ b/modules/nf-core/picard/liftovervcf/meta.yml @@ -11,56 +11,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: dictionary for fasta file - pattern: "*.{dict}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - chain: - type: file - description: The liftover chain file + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: dictionary for fasta file + pattern: "*.{dict}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: fasta file + pattern: "*.fasta" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - chain: + type: file + description: The liftover chain file output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf_lifted: - type: file - description: VCF file containing successfully lifted variants - pattern: "*.{lifted.vcf.gz}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.lifted.vcf.gz": + type: file + description: VCF file containing successfully lifted variants + pattern: "*.{lifted.vcf.gz}" - vcf_unlifted: - type: file - description: VCF file containing unsuccessfully lifted variants - pattern: "*.{unlifted.vcf.gz}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.unlifted.vcf.gz": + type: file + description: VCF file containing unsuccessfully lifted variants + pattern: "*.{unlifted.vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucpen" - "@ramprasadn" diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 1f0ffe16c2f..bcaf916055a 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -15,60 +15,82 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Sequence reads file, can be SAM/BAM/CRAM format - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file, required for CRAM input - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference genome fasta index - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file, required for CRAM input + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference genome fasta index + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be + passed as a flag + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" - metrics: - type: file - description: Duplicate metrics file generated by picard - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by picard + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/mergesamfiles/meta.yml b/modules/nf-core/picard/mergesamfiles/meta.yml index c1ca98cf741..df356b0d41d 100644 --- a/modules/nf-core/picard/mergesamfiles/meta.yml +++ b/modules/nf-core/picard/mergesamfiles/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM files - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: list + description: List of input BAM files to be merged + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Merged BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Merged BAM file + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml b/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml index 7b5dd29fe37..3b19eed3f47 100644 --- a/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml +++ b/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml @@ -1,5 +1,6 @@ name: picard_positionbaseddownsamplesam -description: Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads +description: Samples a SAM/BAM/CRAM file using flowcell position information for the + best approximation of having sequenced fewer reads keywords: - sample - bam @@ -13,39 +14,55 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam,cram,sam}" - - fraction: - type: float - description: Fraction of reads to downsample to + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam,cram,sam}" + - fraction: + type: float + description: Fraction of reads to downsample to output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: A downsampled BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ds*.bam": + type: file + description: A downsampled BAM file + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ds*.bai": + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be + passed as a flag + pattern: "*.{bai}" - num_reads: - type: integer - description: The actual number of downsampled reads + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ACTUAL_NUM_READS: + type: integer + description: The actual number of downsampled reads - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bwlang" diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 528002d07bb..7c279fe1eff 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -13,30 +13,33 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/picard/scatterintervalsbyns/meta.yml b/modules/nf-core/picard/scatterintervalsbyns/meta.yml index c81ed7bf59a..f18bf6a5e1a 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/meta.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "picard_scatterintervalsbyns" -description: Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases +description: Writes an interval list created by splitting a reference at Ns.A Program + for breaking up a reference into intervals of alternating regions of N and ACGT + bases keywords: - interval_list - scatter @@ -15,48 +16,55 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file to derive the intervals from - pattern: "*.{fasta,fa,fna}" - - meta2: - type: map - description: | - Groovy Map containing fai information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of the fasta file - pattern: "*.fai" - - meta3: - type: map - description: | - Groovy Map containing dictionary information - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: Sequence dictionary of the fasta file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file to derive the intervals from + pattern: "*.{fasta,fa,fna}" + - - meta2: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of the fasta file + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing dictionary information + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: Sequence dictionary of the fasta file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - intervals: - type: file - description: The scattered intervals - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interval_list": + type: file + description: The scattered intervals + pattern: "*.interval_list" + - s: + type: file + description: The scattered intervals + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/picard/sortsam/meta.yml b/modules/nf-core/picard/sortsam/meta.yml index 509942f994d..24ea9d37dfe 100644 --- a/modules/nf-core/picard/sortsam/meta.yml +++ b/modules/nf-core/picard/sortsam/meta.yml @@ -13,34 +13,37 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,sam}" - - sort_order: - type: string - description: Picard sort order type - pattern: "unsorted|queryname|coordinate|duplicate|unknown" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,sam}" + - - sort_order: + type: string + description: Picard sort order type + pattern: "unsorted|queryname|coordinate|duplicate|unknown" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/picard/sortvcf/meta.yml b/modules/nf-core/picard/sortvcf/meta.yml index 62507a085dd..6dc28e03fec 100644 --- a/modules/nf-core/picard/sortvcf/meta.yml +++ b/modules/nf-core/picard/sortvcf/meta.yml @@ -6,52 +6,56 @@ keywords: - sortvcf tools: - picard: - description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format + description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF + format homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Reference genome dictionary file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Reference genome dictionary file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Sorted VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_sorted.vcf.gz": + type: file + description: Sorted VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/pigz/compress/meta.yml b/modules/nf-core/pigz/compress/meta.yml index 42efd7351c6..0966e651178 100644 --- a/modules/nf-core/pigz/compress/meta.yml +++ b/modules/nf-core/pigz/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pigz_compress" description: Compresses files with pigz. @@ -12,35 +11,33 @@ tools: homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - raw_file: - type: file - description: File to be compressed - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - raw_file: + type: file + description: File to be compressed + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - archive: - type: file - description: The compressed file - pattern: "*.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $archive: + type: file + description: The compressed file + pattern: "*.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/pigz/uncompress/meta.yml b/modules/nf-core/pigz/uncompress/meta.yml index c2d16cd4e4e..3f583b22698 100644 --- a/modules/nf-core/pigz/uncompress/meta.yml +++ b/modules/nf-core/pigz/uncompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "pigz_uncompress" description: write your description here @@ -12,31 +11,32 @@ tools: homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - zip: - type: file - description: Gzipped file - pattern: "*.{gzip}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - zip: + type: file + description: Gzipped file + pattern: "*.{gzip}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - file: - type: file - description: File to compress - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - ${uncompressed_filename}: + type: file + description: File to compress + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" diff --git a/modules/nf-core/pilon/meta.yml b/modules/nf-core/pilon/meta.yml index 7a11c4dde1a..38d9006db67 100644 --- a/modules/nf-core/pilon/meta.yml +++ b/modules/nf-core/pilon/meta.yml @@ -1,74 +1,111 @@ name: "pilon" -description: Automatically improve draft assemblies and find variation among strains, including large event detection +description: Automatically improve draft assemblies and find variation among strains, + including large event detection keywords: - polishing - assembly - variant calling tools: - "pilon": - description: "Pilon is an automated genome assembly improvement and variant detection tool." + description: "Pilon is an automated genome assembly improvement and variant detection + tool." homepage: "https://github.com/broadinstitute/pilon/wiki" documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage" tool_dev_url: "https://github.com/broadinstitute/pilon" doi: "10.1371/journal.pone.0112963" licence: ["GPL-2.0-or-later"] + identifier: biotools:pilon input: - - meta: - type: map - description: | - Groovy Map containing sample information for the fasta - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA of the input genome - pattern: "*.{fasta}" - - meta2: - type: map - description: | - Groovy Map containing sample information for the bam file - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file of reads aligned to the input genome - pattern: "*.{bam}" - - bai: - type: file - description: BAI file (BAM index) of BAM reads aligned to the input genome - pattern: "*.{bai}" - - pilon_mode: - type: string - description: Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher). - enum: ["frags", "jumps", "unpaired", "bam"] + - - meta: + type: map + description: | + Groovy Map containing sample information for the fasta + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA of the input genome + pattern: "*.{fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information for the bam file + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file of reads aligned to the input genome + pattern: "*.{bam}" + - bai: + type: file + description: BAI file (BAM index) of BAM reads aligned to the input genome + pattern: "*.{bai}" + - - pilon_mode: + type: string + description: Indicates the type of bam file used (frags for paired-end sequencing + of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, + jumps for paired sequencing data of larger insert size, such as Illumina mate + pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing + reads, bam will automatically classify the BAM as one of the three types above + (version 1.17 and higher). + enum: ["frags", "jumps", "unpaired", "bam"] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - improved_assembly: - type: file - description: fasta file, improved assembly - pattern: "*.{fasta}" - - change_record: - type: file - description: file containing a space-delimited record of every change made in the assembly as instructed by the --fix option - pattern: "*.{change}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: fasta file, improved assembly + pattern: "*.{fasta}" - vcf: - type: file - description: Pilon variant output - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Pilon variant output + pattern: "*.{vcf}" + - change_record: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.change": + type: file + description: file containing a space-delimited record of every change made in + the assembly as instructed by the --fix option + pattern: "*.{change}" - tracks_bed: - type: file - description: files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: files that may be viewed in genome browsers such as IGV, GenomeView, + and other applications that support these formats + pattern: "*.{bed}" - tracks_wig: - type: file - description: files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats - pattern: "*.{wig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: files that may be viewed in genome browsers such as IGV, GenomeView, + and other applications that support these formats + pattern: "*.{wig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" maintainers: diff --git a/modules/nf-core/pindel/pindel/meta.yml b/modules/nf-core/pindel/pindel/meta.yml index 6b44f78e150..a4983337d1e 100644 --- a/modules/nf-core/pindel/pindel/meta.yml +++ b/modules/nf-core/pindel/pindel/meta.yml @@ -1,89 +1,150 @@ name: "pindel_pindel" -description: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data +description: Pindel can detect breakpoints of large deletions, medium sized insertions, + inversions, tandem duplications and other structural variants at single-based resolution + from next-gen sequence data keywords: - deletions - insertions - tandem duplications tools: - "pindel": - description: "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data" + description: "Pindel can detect breakpoints of large deletions, medium sized insertions, + inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data" homepage: "https://gmt.genome.wustl.edu/packages/pindel/" documentation: https://gmt.genome.wustl.edu/packages/pindel/user-manual.html licence: ["GPL v3"] + identifier: biotools:pindel input: - - meta: - type: map - description: | - Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics - or a sensible default - setting ext.args2 to either in modules.conf - e.g. [ id:'test', single_end:false, insert_size:500 ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - bed: - type: file - description: BED file containing regions of interest - - fasta: - type: file - description: Input reference genome fasta file - - fai: - type: file - description: Input reference genome fasta index file + - - meta: + type: map + description: | + Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics + or a sensible default - setting ext.args2 to either in modules.conf + e.g. [ id:'test', single_end:false, insert_size:500 ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - fasta: + type: file + description: Input reference genome fasta file + - - fai: + type: file + description: Input reference genome fasta index file + - - bed: + type: file + description: BED file containing regions of interest output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bp: - type: file - description: File containing breakpoints - pattern: "*_{BP}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BP": + type: file + description: File containing breakpoints + pattern: "*_{BP}" - cem: - type: file - description: File containing close end reads - pattern: "*_{CloseEndMapped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_CloseEndMapped": + type: file + description: File containing close end reads + pattern: "*_{CloseEndMapped}" - del: - type: file - description: File containing deletions - pattern: "*_{D}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_D": + type: file + description: File containing deletions + pattern: "*_{D}" - dd: - type: file - description: File containing dispersed duplications - pattern: "*_{DD}" - - int_{final: - type: file - description: File containing interchromosomal events - pattern: "*_{INT_final}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_DD": + type: file + description: File containing dispersed duplications + pattern: "*_{DD}" + - int_final: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_INT_final": + type: file + description: int file + pattern: "*_INT_final" - inv: - type: file - description: File containing inversions - pattern: "*_{INV}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_INV": + type: file + description: File containing inversions + pattern: "*_{INV}" - li: - type: file - description: File containing long insertions - pattern: "*_{LI}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_LI": + type: file + description: File containing long insertions + pattern: "*_{LI}" - rp: - type: file - description: File containing read-pair evidence - pattern: "*_{RP}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_RP": + type: file + description: File containing read-pair evidence + pattern: "*_{RP}" - si: - type: file - description: File containing short insertions - pattern: "*_{SI}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_SI": + type: file + description: File containing short insertions + pattern: "*_{SI}" - td: - type: file - description: File containing tandem duplications - pattern: "*_{TD}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_TD": + type: file + description: File containing tandem duplications + pattern: "*_{TD}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" maintainers: diff --git a/modules/nf-core/pints/caller/meta.yml b/modules/nf-core/pints/caller/meta.yml index ec749b0515d..851ead841ba 100644 --- a/modules/nf-core/pints/caller/meta.yml +++ b/modules/nf-core/pints/caller/meta.yml @@ -20,52 +20,73 @@ tools: tool_dev_url: "https://github.com/hyulab/PINTS" doi: "10.1038/s41587-022-01211-7" licence: ["GPL v3"] + identifier: biotools:pyPINTS input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: One or more BAM files - pattern: "*.{bam}" - - bais: - type: file - description: Corresponding BAM file indexes - pattern: "*.bam.bai" - - assay: - type: string - description: Assay name + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: One or more BAM files + pattern: "*.{bam}" + - bais: + type: file + description: Corresponding BAM file indexes + pattern: "*.bam.bai" + - - assay_type: + type: string + description: Assay type output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - divergent_TREs: - type: file - description: Divergent TREs - pattern: "*_divergent_peaks.bed" - optional: true + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_divergent_peaks.bed": + type: file + description: Divergent TREs + pattern: "*_divergent_peaks.bed" + optional: true - bidirectional_TREs: - type: file - description: Divergent TREs and convergent TREs - pattern: "*_bidirectional_peaks.bed" - optional: true + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bidirectional_peaks.bed": + type: file + description: Divergent TREs and convergent TREs + pattern: "*_bidirectional_peaks.bed" + optional: true - unidirectional_TREs: - type: file - description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs) - pattern: "*_unidirectional_peaks.bed" - optional: true + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_unidirectional_peaks.bed": + type: file + description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs) + pattern: "*_unidirectional_peaks.bed" + optional: true - peakcalling_log: - type: file - description: Peakcalling log for debugging purposes - pattern: "peakcalling_*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peakcalling_*.log: + type: file + description: Peakcalling log for debugging purposes + pattern: "peakcalling_*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/pirate/meta.yml b/modules/nf-core/pirate/meta.yml index 657dc8285e0..b53ca30db29 100644 --- a/modules/nf-core/pirate/meta.yml +++ b/modules/nf-core/pirate/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: https://github.com/SionBayliss/PIRATE doi: "10.1093/gigascience/giz119" licence: ["GPL v3"] + identifier: biotools:PIRATE input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: A set of GFF3 formatted files - pattern: "*.{gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: A set of GFF3 formatted files + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing PIRATE result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing PIRATE result files + pattern: "*/*" - aln: - type: file - description: Core-genome alignment produced by PIRATE (Optional) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/core_alignment.fasta: + type: file + description: Core-genome alignment produced by PIRATE (Optional) + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/plasmidfinder/meta.yml b/modules/nf-core/plasmidfinder/meta.yml index 946d29f0741..6d3a554d4cb 100644 --- a/modules/nf-core/plasmidfinder/meta.yml +++ b/modules/nf-core/plasmidfinder/meta.yml @@ -6,52 +6,80 @@ keywords: - plasmid tools: - "plasmidfinder": - description: "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria." + description: "PlasmidFinder allows identification of plasmids in total or partial + sequenced isolates of bacteria." homepage: "https://cge.cbs.dtu.dk/services/PlasmidFinder/" documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder" tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder" doi: "10.1128/AAC.02412-14" licence: ["Apache-2.0"] + identifier: biotools:PlasmidFinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: Input FASTA or FASTQ formatted genome sequences - pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: Input FASTA or FASTQ formatted genome sequences + pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: The results from analysis in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: The results from analysis in JSON format + pattern: "*.json" - txt: - type: file - description: The summary of results from analysis - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: The summary of results from analysis + pattern: "*.txt" - tsv: - type: file - description: The results from analysis in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The results from analysis in TSV format + pattern: "*.tsv" - genome_seq: - type: file - description: FASTA of sequences in the input with a hit - pattern: "*-hit_in_genome_seq.fsa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-hit_in_genome_seq.fsa": + type: file + description: FASTA of sequences in the input with a hit + pattern: "*-hit_in_genome_seq.fsa" - plasmid_seq: - type: file - description: FASTA of plasmid sequences with a hit against the input - pattern: "*-plasmid_seqs.fsa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-plasmid_seqs.fsa": + type: file + description: FASTA of plasmid sequences with a hit against the input + pattern: "*-plasmid_seqs.fsa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/plasmidid/meta.yml b/modules/nf-core/plasmidid/meta.yml index 664793598ee..5fc9b722aa1 100644 --- a/modules/nf-core/plasmidid/meta.yml +++ b/modules/nf-core/plasmidid/meta.yml @@ -11,62 +11,107 @@ tools: documentation: https://github.com/BU-ISCIII/plasmidID#readme tool_dev_url: https://github.com/BU-ISCIII/plasmidID licence: ["GPL v3"] + identifier: biotools:plasmidid input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - scaffold: - type: file - description: | - Fasta file containing scaffold - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: | + Fasta file containing scaffold + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: html file with results rendered - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*final_results.html: + type: file + description: html file with results rendered + pattern: "*.{html}" - tab: - type: file - description: Results in a tabular file - pattern: "*.{tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*final_results.tab: + type: file + description: Results in a tabular file + pattern: "*.{tab}" - images: - type: directory - description: Directory containing the images produced by plasmidid - pattern: "images" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/images/: + type: directory + description: Directory containing the images produced by plasmidid + pattern: "images" - logs: - type: directory - description: Directory containing the logs produced by plasmidid - pattern: "logs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/logs/: + type: directory + description: Directory containing the logs produced by plasmidid + pattern: "logs" - data: - type: directory - description: Directory containing the data produced by plasmidid - pattern: "data" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/data/: + type: directory + description: Directory containing the data produced by plasmidid + pattern: "data" - database: - type: directory - description: Directory containing the database produced by plasmidid - pattern: "database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/database/: + type: directory + description: Directory containing the database produced by plasmidid + pattern: "database" - fasta_files: - type: directory - description: Directory containing the fasta files produced by plasmidid - pattern: "fasta_files" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/fasta_files/: + type: directory + description: Directory containing the fasta files produced by plasmidid + pattern: "fasta_files" - kmer: - type: directory - description: Directory containing the kmer files produced by plasmidid - pattern: "database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/kmer/: + type: directory + description: Directory containing the kmer files produced by plasmidid + pattern: "database" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/platypus/meta.yml b/modules/nf-core/platypus/meta.yml index ade5de56ba2..5ffeaa2f0db 100644 --- a/modules/nf-core/platypus/meta.yml +++ b/modules/nf-core/platypus/meta.yml @@ -1,5 +1,6 @@ name: platypus -description: Platypus is a tool that efficiently and accurately calling genetic variants from next-generation DNA sequencing data +description: Platypus is a tool that efficiently and accurately calling genetic variants + from next-generation DNA sequencing data keywords: - variant - call @@ -7,68 +8,86 @@ keywords: - genetic tools: - platypus: - description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. + description: Platypus is a tool designed for efficient and accurate variant-detection + in high-throughput sequencing data. homepage: https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data documentation: https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-documentation tool_dev_url: https://github.com/andyrimmer/Platypus doi: "10.1038/ng.3036" licence: ["BSD-3-clause"] + identifier: biotools:platypus input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - tumor_file: - type: file - description: Tumor or metastatic sample, BAM or CRAM file - pattern: "*.{bam,cram}" - - tummor_file_bai: - type: file - description: Index of BAMfile - pattern: "*.{bai,crai}" - - control_file: - type: file - description: Control (or blood) of matching tumor/metastatic sample, BAM or CRAM file - pattern: "*.{bam,cram}" - - control_file_bai: - type: file - description: Index of BAMfile - pattern: "*.{bai,crai}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fa" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - skipregions_file: - type: file - description: File with regions to skip, region as comma-separated list of chr:start-end, or just list of chr, or nothing - pattern: "*.bed|*.txt|*.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - tumor_file: + type: file + description: Tumor or metastatic sample, BAM or CRAM file + pattern: "*.{bam,cram}" + - tumor_file_bai: + type: file + description: Index of BAM file + pattern: "*.{bai,crai}" + - control_file: + type: file + description: Control (or blood) of matching tumor/metastatic sample, BAM or + CRAM file + pattern: "*.{bam,cram}" + - control_file_bai: + type: file + description: Index of BAMfile + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fa" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - skipregions_file: + type: file + description: File with regions to skip, region as comma-separated list of chr:start-end, + or just list of chr, or nothing + pattern: "*.bed|*.txt|*.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - vcf: - type: file - description: Output VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.vcf.gz": + type: file + description: Output VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.vcf.gz.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - log: - type: file - description: Log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.log": + type: file + description: Log file + pattern: "*.log" - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - versions.yml: + type: file + description: File containing software version + pattern: "*.{version.txt}" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/plink/bcf/meta.yml b/modules/nf-core/plink/bcf/meta.yml index c86b6682676..d31239f2f9f 100644 --- a/modules/nf-core/plink/bcf/meta.yml +++ b/modules/nf-core/plink/bcf/meta.yml @@ -8,43 +8,59 @@ keywords: - fam tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bcf: - type: file - description: Binary variant call format file (bcf) - pattern: "*.{bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bcf: + type: file + description: Binary variant call format file (bcf) + pattern: "*.{bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/epistasis/meta.yml b/modules/nf-core/plink/epistasis/meta.yml index 47581bc64d2..eda5dd0bc39 100644 --- a/modules/nf-core/plink/epistasis/meta.yml +++ b/modules/nf-core/plink/epistasis/meta.yml @@ -1,96 +1,118 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plink_epistasis" -description: Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. +description: Epistasis in PLINK, analyzing how the effects of one gene depend on the + presence of others. keywords: - interactions - variants - regression tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to the PLINK native file input - - meta2: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF file input - - meta3: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta3 is associated to BCF file input - - meta4: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta4 is associated to phenotype file input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - bcf: - type: file - description: PLINK variant information + sample ID + genotype call binary file - pattern: "*.{bcf}" - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" - - phe: - type: file - description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option. - pattern: "*.{phe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information + can be read from the third column with the --pheno option or from a specific + column with the --pheno-name option. + pattern: "*.{phe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - epi: - type: file - description: PLINK epistasis file - pattern: "*.{epi.cc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc": + type: file + description: PLINK epistasis file + pattern: "*.{epi.cc}" - episummary: - type: file - description: PLINK epistasis summary file - pattern: "*.{epi.cc.summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc.summary": + type: file + description: PLINK epistasis summary file + pattern: "*.{epi.cc.summary}" - log: - type: file - description: PLINK epistasis log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: PLINK epistasis log file + pattern: "*.{log}" - nosex: - type: file - description: Ambiguous sex ID file - pattern: "*.{nosex}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.nosex": + type: file + description: Ambiguous sex ID file + pattern: "*.{nosex}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidebag" maintainers: diff --git a/modules/nf-core/plink/exclude/meta.yml b/modules/nf-core/plink/exclude/meta.yml index 5f861ce3b0b..462d2f6b9b9 100644 --- a/modules/nf-core/plink/exclude/meta.yml +++ b/modules/nf-core/plink/exclude/meta.yml @@ -6,53 +6,69 @@ keywords: - variant identifiers tools: - plink: - description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + description: Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner. homepage: https://www.cog-genomics.org/plink licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - variants: - type: file - description: A text file containing variant identifiers to remove (one per line) - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - variants: + type: file + description: A text file containing variant identifiers to remove (one per line) + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/extract/meta.yml b/modules/nf-core/plink/extract/meta.yml index 859ea49e52c..2007cf0e3ea 100644 --- a/modules/nf-core/plink/extract/meta.yml +++ b/modules/nf-core/plink/extract/meta.yml @@ -7,53 +7,69 @@ keywords: - bfiles tools: - plink: - description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + description: Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner. homepage: https://www.cog-genomics.org/plink licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - variants: - type: file - description: A text file containing variant identifiers to keep (one per line) - pattern: "*.{keep}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - variants: + type: file + description: A text file containing variant identifiers to keep (one per line) + pattern: "*.{keep}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/plink/fastepistasis/meta.yml b/modules/nf-core/plink/fastepistasis/meta.yml index 0545c66dd61..2d61f21a02a 100644 --- a/modules/nf-core/plink/fastepistasis/meta.yml +++ b/modules/nf-core/plink/fastepistasis/meta.yml @@ -1,96 +1,118 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plink_fastepistasis" -description: Fast Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. +description: Fast Epistasis in PLINK, analyzing how the effects of one gene depend + on the presence of others. keywords: - interactions - variants - regression tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to the PLINK native file input - - meta2: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF file input - - meta3: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta3 is associated to BCF file input - - meta4: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta4 is associated to phenotype file input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - bcf: - type: file - description: PLINK variant information + sample ID + genotype call binary file - pattern: "*.{bcf}" - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" - - phe: - type: file - description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option. - pattern: "*.{phe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information + can be read from the third column with the --pheno option or from a specific + column with the --pheno-name option. + pattern: "*.{phe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fepi: - type: file - description: PLINK fast-epistasis file - pattern: "*.{epi.cc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc": + type: file + description: PLINK fast-epistasis file + pattern: "*.{epi.cc}" - fepisummary: - type: file - description: PLINK fast-epistasis summary file - pattern: "*.{epi.cc.summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc.summary": + type: file + description: PLINK fast-epistasis summary file + pattern: "*.{epi.cc.summary}" - flog: - type: file - description: PLINK fast-epistasis log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: PLINK fast-epistasis log file + pattern: "*.{log}" - fnosex: - type: file - description: Ambiguous sex ID file - pattern: "*.{nosex}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.nosex": + type: file + description: Ambiguous sex ID file + pattern: "*.{nosex}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidebag" maintainers: diff --git a/modules/nf-core/plink/gwas/meta.yml b/modules/nf-core/plink/gwas/meta.yml index 4bdb0ed0f0c..67a62720b45 100644 --- a/modules/nf-core/plink/gwas/meta.yml +++ b/modules/nf-core/plink/gwas/meta.yml @@ -6,85 +6,102 @@ keywords: - case/control tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to the PLINK native file input - - meta2: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF file input - - meta3: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta3 is associated to BCF file input - - meta4: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta4 is associated to phenotype file input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - bcf: - type: file - description: PLINK variant information + sample ID + genotype call binary file - pattern: "*.{bcf}" - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" - - phe: - type: file - description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option - pattern: "*.{phe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information + can be read from the third column with the --pheno option or from a specific + column with the --pheno-name option + pattern: "*.{phe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - assoc: - type: file - description: PLINK GWAS association file - pattern: "*.{assoc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assoc": + type: file + description: PLINK GWAS association file + pattern: "*.{assoc}" - log: - type: file - description: PLINK GWAS association log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: PLINK GWAS association log file + pattern: "*.{log}" - nosex: - type: file - description: PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option --allow-no-sex - pattern: "*.{nosex}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.nosex": + type: file + description: PLINK GWAS association file that retains phenotypes for samples + with ambiguous sex. Produced with the option --allow-no-sex + pattern: "*.{nosex}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LorenzoS96" maintainers: diff --git a/modules/nf-core/plink/hwe/meta.yml b/modules/nf-core/plink/hwe/meta.yml index 5624e24c888..6d9cf2726d7 100644 --- a/modules/nf-core/plink/hwe/meta.yml +++ b/modules/nf-core/plink/hwe/meta.yml @@ -6,65 +6,69 @@ keywords: - hwe equilibrium tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to PLINK native files input - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF files input - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to BCF files input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - vcf: - type: file - description: VCF format input file - pattern: "*.{vcf} | *{vcf.gz}" - - bcf: - type: file - description: BCF format input file - pattern: "*.{bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to PLINK native files input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF files input + - vcf: + type: file + description: VCF format input file + pattern: "*.{vcf} | *{vcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to BCF files input + - bcf: + type: file + description: BCF format input file + pattern: "*.{bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hwe: - type: file - description: | - Summary file containing observed vs expected heterozygous frequencies and the - p-value of the hardy-weinberg statistics + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hwe": + type: file + description: | + Summary file containing observed vs expected heterozygous frequencies and the + p-value of the hardy-weinberg statistics + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/plink/indep/meta.yml b/modules/nf-core/plink/indep/meta.yml index 9d6b7500ec9..d0c6a02e49c 100644 --- a/modules/nf-core/plink/indep/meta.yml +++ b/modules/nf-core/plink/indep/meta.yml @@ -1,5 +1,6 @@ name: plink_indep -description: Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. +description: Produce a pruned subset of markers that are in approximate linkage equilibrium + with each other. keywords: - plink - indep @@ -8,56 +9,70 @@ keywords: - fam tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - window_size: - type: string - description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. - - variant_count: - type: string - description: Variant count to shift the window at the end of each step. - - variance_inflation_factor: - type: string - description: Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - window_size: + type: string + description: Window size in variant count or kilobase (if the 'kb' modifier + is present) units, a variant count to shift the window at the end of each + step, and a variance inflation factor (VIF) threshold. + - - variant_count: + type: string + description: Variant count to shift the window at the end of each step. + - - variance_inflation_factor: + type: string + description: Variance inflation factor (VIF) threshold. At each step, all variants + in the current window with VIF exceeding the threshold are removed. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - prunein: - type: file - description: File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other - pattern: "*.{prune.in}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.in": + type: file + description: File with IDs of pruned subset of markers that are in approximate + linkage equilibrium with each other + pattern: "*.{prune.in}" - pruneout: - type: file - description: File with IDs of excluded variants - pattern: "*.{prune.out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.out": + type: file + description: File with IDs of excluded variants + pattern: "*.{prune.out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/indeppairwise/meta.yml b/modules/nf-core/plink/indeppairwise/meta.yml index 470ce24880e..5ef9d3cd8ee 100644 --- a/modules/nf-core/plink/indeppairwise/meta.yml +++ b/modules/nf-core/plink/indeppairwise/meta.yml @@ -1,5 +1,8 @@ name: plink_indeppairwise -description: Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain. +description: Produce a pruned subset of markers that are in approximate linkage equilibrium + with each other. Pairs of variants in the current window with squared correlation + greater than the threshold are noted and variants are greedily pruned from the window + until no such pairs remain. keywords: - plink - indep pairwise @@ -8,56 +11,71 @@ keywords: - fam tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - window_size: - type: string - description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. - - variant_count: - type: string - description: Variant count to shift the window at the end of each step. - - r2_threshold: - type: string - description: Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - window_size: + type: string + description: Window size in variant count or kilobase (if the 'kb' modifier + is present) units, a variant count to shift the window at the end of each + step, and a variance inflation factor (VIF) threshold. + - - variant_count: + type: string + description: Variant count to shift the window at the end of each step. + - - r2_threshold: + type: string + description: Pairwise r2 threshold. At each step, pairs of variants in the current + window with squared correlation greater than the threshold are noted, and + variants are greedily pruned from the window until no such pairs remain output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - prunein: - type: file - description: File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other - pattern: "*.{prune.in}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.in": + type: file + description: File with IDs of pruned subset of markers that are in approximate + linkage equilibrium with each other + pattern: "*.{prune.in}" - pruneout: - type: file - description: File with IDs of excluded variants - pattern: "*.{prune.out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.out": + type: file + description: File with IDs of excluded variants + pattern: "*.{prune.out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/ld/meta.yml b/modules/nf-core/plink/ld/meta.yml index 3e16ab4b6bc..804feed8494 100644 --- a/modules/nf-core/plink/ld/meta.yml +++ b/modules/nf-core/plink/ld/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plink_ld" description: LD analysis in PLINK examines genetic variant associations within populations @@ -8,86 +7,100 @@ keywords: - variants tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to PLINK native files input - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF files input - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to BCF files input - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to randomly selected snp files input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - vcf: - type: file - description: VCF format input file - pattern: "*.{vcf} | *{vcf.gz}" - - bcf: - type: file - description: BCF format input file - pattern: "*.{bcf}" - - snpfile: - type: file - description: randomly selected snp identifiers, used to calculate linkage disequilibrium - pattern: "*.{txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to PLINK native files input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF files input + - vcf: + type: file + description: VCF format input file + pattern: "*.{vcf} | *{vcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to BCF files input + - bcf: + type: file + description: BCF format input file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to randomly selected snp files input + - snpfile: + type: file + description: randomly selected snp identifiers, used to calculate linkage disequilibrium + pattern: "*.{txt}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ld: - type: file - description: | - The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R². + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.ld": + type: file + description: | + The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R². - log: - type: file - description: | - Log file of the ld process + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: | + Log file of the ld process - nosex: - type: file - description: | - Ambiguous sex ID file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.nosex": + type: file + description: | + Ambiguous sex ID file + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidebag" maintainers: diff --git a/modules/nf-core/plink/recode/meta.yml b/modules/nf-core/plink/recode/meta.yml index 7f2bd053f52..4316bd193d4 100644 --- a/modules/nf-core/plink/recode/meta.yml +++ b/modules/nf-core/plink/recode/meta.yml @@ -7,135 +7,282 @@ keywords: - whole genome association tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ped: - type: file - description: PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default "--recode" or by "--recode 12". - pattern: "*.{ped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ped": + type: file + description: PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced + by the default "--recode" or by "--recode 12". + pattern: "*.{ped}" - map: - type: file - description: PLINK text fileset variant information file. Produced by the default "--recode" or by "--recode 12". - pattern: "*.{map}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.map": + type: file + description: PLINK text fileset variant information file. Produced by the default + "--recode" or by "--recode 12". + pattern: "*.{map}" - txt: - type: file - description: Text file. Produced by "--recode 23". Can only be used in a file with only one sample. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Text file. Produced by "--recode 23". Can only be used in a file + with only one sample. + pattern: "*.{txt}" - raw: - type: file - description: Additive + dominant component file. Produced by "--recode AD" or "--recode A". - pattern: "*.{raw}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.raw": + type: file + description: Additive + dominant component file. Produced by "--recode AD" or + "--recode A". + pattern: "*.{raw}" - traw: - type: file - description: Variant-major additive component file. Produced by "--recode A-transpose". - pattern: "*.{traw}" - - beagle-dat: - type: file - description: Single BEAGLE unphased genotype file. Produced by "--recode beagle" in 'beagle-nomap' mode. - pattern: "*.{beagle.dat}" - - chr-dat: - type: file - description: BEAGLE unphased genotype and variant information files. Produced by "--recode beagle". - pattern: "*.{*.chr-*.dat}" - - chr-map: - type: file - description: BEAGLE variant information files. Produced by "--recode beagle". - pattern: "*.{*chr-*.map}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.traw": + type: file + description: Variant-major additive component file. Produced by "--recode A-transpose". + pattern: "*.{traw}" + - beagledat: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.beagle.dat": + type: file + description: BEAGLE file + pattern: "*.{beagle.dat}" + - chrdat: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chr-*.dat": + type: file + description: chr file + pattern: "*.{chr-*.dat}" + - chrmap: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - .*chr-*.map: + type: file + description: chr map file + pattern: "*.{chr-*.map}" - geno: - type: file - description: BIMBAM genotype file. Produced by "--recode bimbam". - pattern: "*.{recode.geno.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.geno.txt": + type: file + description: BIMBAM genotype file. Produced by "--recode bimbam". + pattern: "*.{recode.geno.txt}" - pheno: - type: file - description: BIMBAM phenotype file. Produced by "--recode bimbam". - pattern: "*.{recode.pheno.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.pheno.txt": + type: file + description: BIMBAM phenotype file. Produced by "--recode bimbam". + pattern: "*.{recode.pheno.txt}" - pos: - type: file - description: BIMBAM variant position file. Produced by "--recode bimbam". - pattern: "*.{recode.pos.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.pos.txt": + type: file + description: BIMBAM variant position file. Produced by "--recode bimbam". + pattern: "*.{recode.pos.txt}" - phase: - type: file - description: fastPHASE format. Produced by "--recode fastphase". - pattern: "*.{recode.phase.inp}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.phase.inp": + type: file + description: fastPHASE format. Produced by "--recode fastphase". + pattern: "*.{recode.phase.inp}" - info: - type: file - description: Haploview map file. Produced by "--recode HV". - pattern: "*.{info}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.info": + type: file + description: Haploview map file. Produced by "--recode HV". + pattern: "*.{info}" - lgen: - type: file - description: PLINK long-format genotype file. Produced by "--recode lgen". - pattern: "*.{lgen}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lgen": + type: file + description: PLINK long-format genotype file. Produced by "--recode lgen". + pattern: "*.{lgen}" - list: - type: file - description: Genotype list file. Produced by "--recode list". - pattern: "*.{list}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list": + type: file + description: Genotype list file. Produced by "--recode list". + pattern: "*.{list}" - gen: - type: file - description: Oxford genotype file format. Produced by "--recode oxford". - pattern: "*.{gen}" - - genz: - type: file - description: Compressed Oxford genotype file format. Produced by "--recode oxford gen-gz". - pattern: "*.{genz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gen": + type: file + description: Oxford genotype file format. Produced by "--recode oxford". + pattern: "*.{gen}" + - gengz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gen.gz": + type: file + description: Compressed Oxford genotype file format + pattern: "*.{gen.gz}" - sample: - type: file - description: Oxford sample information file. Produced by "--recode oxford". - pattern: "*.{sample}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sample": + type: file + description: Oxford sample information file. Produced by "--recode oxford". + pattern: "*.{sample}" - rlist: - type: file - description: Rare genotype list file. Produced by "--recode rlist". - pattern: "*.{rlist}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rlist": + type: file + description: Rare genotype list file. Produced by "--recode rlist". + pattern: "*.{rlist}" - strctin: - type: file - description: Structure-format file. Produced by "--recode structure". - pattern: "*.{strct_in}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.strct_in": + type: file + description: Structure-format file. Produced by "--recode structure". + pattern: "*.{strct_in}" - tped: - type: file - description: Transposed text PED file. Produced by "--recode transpose". - pattern: "*.{tped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tped": + type: file + description: Transposed text PED file. Produced by "--recode transpose". + pattern: "*.{tped}" - tfam: - type: file - description: Transposed text FAM file. Produced by "--recode transpose". - pattern: "*.{tfam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tfam": + type: file + description: Transposed text FAM file. Produced by "--recode transpose". + pattern: "*.{tfam}" - vcf: - type: file - description: Variant calling file (VCF). Produced by "--recode vcf". - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variant calling file (VCF). Produced by "--recode vcf". + pattern: "*.{vcf}" - vcfgz: - type: file - description: Compressed variant calling file (VCF). Produced by "--recode vcf bgz". - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed variant calling file (VCF). Produced by "--recode vcf + bgz". + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/vcf/meta.yml b/modules/nf-core/plink/vcf/meta.yml index 2a3ee4b11be..d6eefd9a4cb 100644 --- a/modules/nf-core/plink/vcf/meta.yml +++ b/modules/nf-core/plink/vcf/meta.yml @@ -13,38 +13,53 @@ tools: homepage: "https://www.cog-genomics.org/plink" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Mxrcon" - "@abhi18av" diff --git a/modules/nf-core/plink2/extract/meta.yml b/modules/nf-core/plink2/extract/meta.yml index aeda84cda9f..0d758817c82 100644 --- a/modules/nf-core/plink2/extract/meta.yml +++ b/modules/nf-core/plink2/extract/meta.yml @@ -13,50 +13,65 @@ tools: documentation: http://www.cog-genomics.org/plink/2.0/general_usage doi: "10.1186/s13742-015-0047-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pgen: - type: file - description: PLINK 2 binary genotype table - pattern: "*.{pgen}" - - psam: - type: file - description: PLINK 2 sample information file - pattern: "*.{psam}" - - pvar: - type: file - description: PLINK 2 variant information file - pattern: "*.{pvar}" - - variants: - type: file - description: A text file containing variant identifiers to keep (one per line) - pattern: "*.{keep}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pgen: + type: file + description: PLINK 2 binary genotype table + pattern: "*.{pgen}" + - psam: + type: file + description: PLINK 2 sample information file + pattern: "*.{psam}" + - pvar: + type: file + description: PLINK 2 variant information file + pattern: "*.{pvar}" + - variants: + type: file + description: A text file containing variant identifiers to keep (one per line) + pattern: "*.{keep}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - extract_pgen: - type: file - description: PLINK 2 binary genotype table, containing extracted variants - pattern: "*.{pgen}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pgen": + type: file + description: PLINK 2 binary genotype table, containing extracted variants + pattern: "*.{pgen}" - extract_psam: - type: file - description: PLINK 2 sample information file associated with the extracted data - pattern: "*.{psam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.psam": + type: file + description: PLINK 2 sample information file associated with the extracted data + pattern: "*.{psam}" - extract_pvar: - type: file - description: PLINK 2 variant information file, containing extracted variants - pattern: "*.{pvar.zst}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvar.zst": + type: file + description: PLINK 2 variant information file, containing extracted variants + pattern: "*.{pvar.zst}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/plink2/score/meta.yml b/modules/nf-core/plink2/score/meta.yml index 9fc7f436161..ea20bb355ee 100644 --- a/modules/nf-core/plink2/score/meta.yml +++ b/modules/nf-core/plink2/score/meta.yml @@ -13,42 +13,45 @@ tools: documentation: http://www.cog-genomics.org/plink/2.0/general_usage doi: "10.1186/s13742-015-0047-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pgen: - type: file - description: PLINK 2 binary genotype table - pattern: "*.{pgen}" - - psam: - type: file - description: PLINK 2 sample information file - pattern: "*.{psam}" - - pvar: - type: file - description: PLINK 2 variant information file - pattern: "*.{pvar}" - - scorefile: - type: file - description: A text file containing variant identifiers and weights - pattern: "*.{scores,txt,scorefile}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pgen: + type: file + description: PLINK 2 binary genotype table + pattern: "*.{pgen}" + - psam: + type: file + description: PLINK 2 sample information file + pattern: "*.{psam}" + - pvar: + type: file + description: PLINK 2 variant information file + pattern: "*.{pvar}" + - - scorefile: + type: file + description: A text file containing variant identifiers and weights + pattern: "*.{scores,txt,scorefile}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - score: - type: file - description: A text file containing sample scores, in plink 2 .sscore format - pattern: "*.{sscore}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sscore": + type: file + description: A text file containing sample scores, in plink 2 .sscore format + pattern: "*.{sscore}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/plink2/vcf/meta.yml b/modules/nf-core/plink2/vcf/meta.yml index 7ea8a8976a2..c745532c747 100644 --- a/modules/nf-core/plink2/vcf/meta.yml +++ b/modules/nf-core/plink2/vcf/meta.yml @@ -12,42 +12,63 @@ tools: homepage: http://www.cog-genomics.org/plink/2.0/ documentation: http://www.cog-genomics.org/plink/2.0/general_usage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}, *.{vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}, *.{vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pgen: - type: file - description: PLINK 2 binary genotype table - pattern: "*.{pgen}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pgen": + type: file + description: PLINK 2 binary genotype table + pattern: "*.{pgen}" - psam: - type: file - description: PLINK 2 sample information file - pattern: "*.{psam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.psam": + type: file + description: PLINK 2 sample information file + pattern: "*.{psam}" - pvar: - type: file - description: PLINK 2 variant information file - pattern: "*.{pvar.zst}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvar": + type: file + description: PLINK 2 variant information file + pattern: "*.{pvar.zst}" - pvar_zst: - type: file - description: PLINK 2 variant information zst file - pattern: "*.pvar.zst" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvar.zst": + type: file + description: PLINK 2 variant information zst file + pattern: "*.pvar.zst" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/pmdtools/filter/meta.yml b/modules/nf-core/pmdtools/filter/meta.yml index 6161b1ffbe6..0a55262789c 100644 --- a/modules/nf-core/pmdtools/filter/meta.yml +++ b/modules/nf-core/pmdtools/filter/meta.yml @@ -13,41 +13,44 @@ tools: tool_dev_url: https://github.com/pontussk/PMDtools doi: "10.1073/pnas.1318934111" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - threshold: - type: float - description: Post-mortem damage score threshold - - reference: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - threshold: + type: float + description: Post-mortem damage score threshold + - - reference: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Filtered BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Filtered BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alexandregilardet" maintainers: diff --git a/modules/nf-core/pneumocat/meta.yml b/modules/nf-core/pneumocat/meta.yml index 8015826add9..e7f885171dd 100644 --- a/modules/nf-core/pneumocat/meta.yml +++ b/modules/nf-core/pneumocat/meta.yml @@ -1,47 +1,57 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "pneumocat" -description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads +description: Determine Streptococcus pneumoniae serotype from Illumina paired-end + reads keywords: - fastq - serotype - Streptococcus pneumoniae tools: - "pneumocat": - description: "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)" + description: "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach + to assign capsular type to S.pneumoniae genomic data (Illumina)" homepage: "https://github.com/ukhsa-collaboration/PneumoCaT" documentation: "https://github.com/ukhsa-collaboration/PneumoCaT" tool_dev_url: "https://github.com/ukhsa-collaboration/PneumoCaT" doi: "10.7717/peerj.2477" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input Illunina paired-end FASTQ files - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input Illunina paired-end FASTQ files + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - xml: - type: file - description: The predicted serotype in XML format - pattern: "*.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.xml": + type: file + description: The predicted serotype in XML format + pattern: "*.xml" - txt: - type: file - description: A detailed description of the predicted serotype - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: A detailed description of the predicted serotype + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/poolsnp/meta.yml b/modules/nf-core/poolsnp/meta.yml index 8de67751c65..36054b58aca 100644 --- a/modules/nf-core/poolsnp/meta.yml +++ b/modules/nf-core/poolsnp/meta.yml @@ -1,97 +1,110 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "poolsnp" -description: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs. +description: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference + genome in FASTA format as inputs. keywords: - poolseq - mpileup - variant-calling tools: - "poolsnp": - description: "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs." + description: "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and + a reference genome in FASTA format as inputs." homepage: "https://github.com/capoony/PoolSNP" documentation: "https://github.com/capoony/PoolSNP/blob/master/README.md" licence: ["Apache-2.0"] args_id: "$args" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. `[ id:'sample1', single_end:false ]` - - - mpileup: - type: file - description: | - MPILEUP file. This file contains the base calls and alignment information - for each position in the reference genome. - It is used as input for variant calling and other downstream analyses. - pattern: "*.mpileup" - - - meta2: - type: map - description: | - Groovy Map containing sample information. - e.g. `[ id:'sample1' ]` - - - reference: - type: file - description: | - Reference genome in FASTA format. - May NOT contain any special characters such as "/|,:" - pattern: "*.{fasta,fa}" - - - max_cov: - type: float - description: | - Maximum coverage is calculated for every library and chromosomal arm - as the percentile of a coverage distribution, - e.g. max-cov=0.98 will only consider positions within the 98% coverage percentile - for a given sample and chromosomal arm. - Note: Provide `max_cov` or `max_cov_file` but not both. - Read more: https://github.com/capoony/PoolSNP - - - max_cov_file: - type: file - description: | - File containing the maximum coverage thresholds for all chromosomal arms and libraries. - This file needs to be tab-delimited with two columns: - 1. Chromosomal name - 2. Comma-separated list of coverage thresholds for each sample in the mpileup file. - e.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples - and 200 for the last two samples on chromosomal arm 2L. - Note: Provide `max_cov` or `max_cov_file` but not both. - Read more: https://github.com/capoony/PoolSNP - + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1', single_end:false ]` + - mpileup: + type: file + description: | + MPILEUP file. This file contains the base calls and alignment information + for each position in the reference genome. + It is used as input for variant calling and other downstream analyses. + pattern: "*.mpileup" + - - meta2: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1' ]` + - reference: + type: file + description: | + Reference genome in FASTA format. + May NOT contain any special characters such as "/|,:" + pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1', single_end:false ]` + - max_cov: + type: float + description: | + Maximum coverage is calculated for every library and chromosomal arm + as the percentile of a coverage distribution, + e.g. max-cov=0.98 will only consider positions within the 98% coverage percentile + for a given sample and chromosomal arm. + Note: Provide `max_cov` or `max_cov_file` but not both. + Read more: https://github.com/capoony/PoolSNP + - max_cov_file: + type: file + description: | + File containing the maximum coverage thresholds for all chromosomal arms and libraries. + This file needs to be tab-delimited with two columns: + 1. Chromosomal name + 2. Comma-separated list of coverage thresholds for each sample in the mpileup file. + e.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples + and 200 for the last two samples on chromosomal arm 2L. + Note: Provide `max_cov` or `max_cov_file` but not both. + Read more: https://github.com/capoony/PoolSNP output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: Gzipped VCF file containing allele counts and frequencies for every position and library - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Gzipped VCF file containing allele counts and frequencies for every + position and library + pattern: "*.vcf.gz" - max_cov: - type: file - description: File containing the maximum coverage thresholds for all chromosomal arms and libraries - pattern: "*cov-*.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*cov-*.txt": + type: file + description: File containing the maximum coverage thresholds for all chromosomal + arms and libraries + pattern: "*cov-*.txt" - bad_sites: - type: file - description: File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria - pattern: "*BS.txt.gz" - optional: true - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*BS.txt.gz": + type: file + description: File containing a list of sites (variable and invariable) that + did not pass the SNP calling criteria + pattern: "*BS.txt.gz" + optional: true - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhilesh" maintainers: diff --git a/modules/nf-core/popscle/demuxlet/meta.yml b/modules/nf-core/popscle/demuxlet/meta.yml index 56224512d5f..3ffb07b9f6e 100644 --- a/modules/nf-core/popscle/demuxlet/meta.yml +++ b/modules/nf-core/popscle/demuxlet/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "popscle_demuxlet" -description: Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available. +description: Software to deconvolute sample identity and identify multiplets when + multiple samples are pooled by barcoded single cell sequencing and external genotyping + data for each sample is available. keywords: - popscle - demultiplexing @@ -9,51 +10,53 @@ keywords: - single cell tools: - "popscle": - description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" + description: "A suite of population scale analysis tools for single-cell genomics + data including implementation of Demuxlet / Freemuxlet methods and auxilary + tools" homepage: "https://github.com/statgen/popscle" documentation: "https://github.com/statgen/popscle" tool_dev_url: "https://github.com/statgen/popscle" doi: "10.1038/nbt.4042" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - plp_prefix: - type: string - description: Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. - - - bam: - type: file - description: Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed. - pattern: "*.{bam,cram,sam}" - - - donor_genotype: - type: file - description: Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file. - pattern: "*.{vcf,bcf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - plp_prefix: + type: string + description: Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. + - bam: + type: file + description: Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must + be sorted by coordinates and indexed. + pattern: "*.{bam,cram,sam}" + - donor_genotype: + type: file + description: Input VCF/BCF file, containing the individual genotypes (GT), posterior + probability (GP), or genotype likelihood (PL) to assign each barcode to a + specific sample (or a pair of samples) in the VCF file. + pattern: "*.{vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - demuxlet_result: - type: file - description: Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess. - pattern: "*.best" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.best": + type: file + description: Result of demuxlet containing the best guess of the sample identity, + with detailed statistics to reach to the best guess. + pattern: "*.best" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/popscle/dscpileup/meta.yml b/modules/nf-core/popscle/dscpileup/meta.yml index 234a1830759..70442d830f0 100644 --- a/modules/nf-core/popscle/dscpileup/meta.yml +++ b/modules/nf-core/popscle/dscpileup/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "popscle_dscpileup" -description: Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode. +description: Software to pileup reads and corresponding base quality for each overlapping + SNPs and each barcode. keywords: - popscle - demultiplexing @@ -10,62 +10,81 @@ keywords: - pile up tools: - "popscle": - description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" + description: "A suite of population scale analysis tools for single-cell genomics + data including implementation of Demuxlet / Freemuxlet methods and auxilary + tools" homepage: "https://github.com/statgen/popscle" documentation: "https://github.com/statgen/popscle" tool_dev_url: "https://github.com/statgen/popscle" doi: "10.1038/nbt.4042" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - bam: - type: file - description: Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq. - pattern: "*.{bam,cram,sam}" - - - vcf: - type: file - description: Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g). - pattern: "*.{vcf,bcf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - bam: + type: file + description: Input SAM/BAM/CRAM file produced by the standard 10x sequencing + platform, or any other barcoded single cell RNA-seq. + pattern: "*.{bam,cram,sam}" + - vcf: + type: file + description: Input VCF/BCF file files containing (AC) and (AN) from referenced + population (e.g. 1000g). + pattern: "*.{vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - cel: - type: file - description: Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet. - pattern: "*.cel.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.cel.gz": + type: file + description: Contains the relation between numerated barcode ID and barcode + and the number of SNP and number of UMI for each barcoded droplet. + pattern: "*.cel.gz" - plp: - type: file - description: Contains the overlapping SNP and the corresponding read and base quality for each barcode ID. - pattern: "*.plp.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.plp.gz": + type: file + description: Contains the overlapping SNP and the corresponding read and base + quality for each barcode ID. + pattern: "*.plp.gz" - var: - type: file - description: Contains the position, reference allele and allele frequency for each SNP. - pattern: "*.var.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.var.gz": + type: file + description: Contains the position, reference allele and allele frequency for + each SNP. + pattern: "*.var.gz" - umi: - type: file - description: Contains the position covered by each umi. - pattern: "*.umi.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.umi.gz": + type: file + description: Contains the position covered by each umi. + pattern: "*.umi.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/popscle/freemuxlet/meta.yml b/modules/nf-core/popscle/freemuxlet/meta.yml index 34eaaa59dc9..dffcd3431dc 100644 --- a/modules/nf-core/popscle/freemuxlet/meta.yml +++ b/modules/nf-core/popscle/freemuxlet/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "popscle_freemuxlet" -description: Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available. +description: Software to deconvolute sample identity and identify multiplets when + multiple samples are pooled by barcoded single cell sequencing and external genotyping + data for each sample is not available. keywords: - popscle - demultiplexing @@ -9,64 +10,88 @@ keywords: - single cell tools: - "popscle": - description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" + description: "A suite of population scale analysis tools for single-cell genomics + data including implementation of Demuxlet / Freemuxlet methods and auxilary + tools" homepage: "https://github.com/statgen/popscle" documentation: "https://github.com/statgen/popscle" tool_dev_url: "https://github.com/statgen/popscle" doi: "10.1038/nbt.4042" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - plp: - type: directory - description: Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. - - n_sample: - type: integer - description: Number of samples multiplexed together. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - plp: + type: directory + description: Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. + - n_sample: + type: integer + description: Number of samples multiplexed together. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - result: - type: file - description: Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess. - pattern: "*.clust1.samples.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust1.samples.gz": + type: file + description: Output file contains the best guess of the sample identity, with + detailed statistics to reach to the best guess. + pattern: "*.clust1.samples.gz" - vcf: - type: file - description: Output vcf file for each sample inferred and clustered from freemuxlet. - pattern: "*.clust1.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust1.vcf.gz": + type: file + description: Output vcf file for each sample inferred and clustered from freemuxlet. + pattern: "*.clust1.vcf.gz" - lmix: - type: file - description: Output file contains basic statistics for each barcode. - pattern: "*.lmix" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.lmix": + type: file + description: Output file contains basic statistics for each barcode. + pattern: "*.lmix" - singlet_result: - type: file - description: Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on. - pattern: "*.clust0.samples.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust0.samples.gz": + type: file + description: Optional output file contains the best sample identity assuming + all droplets are singlets when writing auxiliary output files is turned on. + pattern: "*.clust0.samples.gz" - singlet_vcf: - type: file - description: Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on. - pattern: "*.clust0.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust0.vcf.gz": + type: file + description: Optional output vcf file for each sample inferred and clustered + from freemuxlet assuming all droplets are singlets when writing auxiliary + output files is turned on. + pattern: "*.clust0.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@wxicu" maintainers: diff --git a/modules/nf-core/porechop/abi/meta.yml b/modules/nf-core/porechop/abi/meta.yml index a856ffbe65c..6016da7560f 100644 --- a/modules/nf-core/porechop/abi/meta.yml +++ b/modules/nf-core/porechop/abi/meta.yml @@ -1,45 +1,56 @@ name: "porechop_abi" -description: Extension of Porechop whose purpose is to process adapter sequences in ONT reads. +description: Extension of Porechop whose purpose is to process adapter sequences in + ONT reads. keywords: - porechop_abi - adapter - nanopore tools: - "porechop_abi": - description: Extension of Porechop whose purpose is to process adapter sequences in ONT reads. + description: Extension of Porechop whose purpose is to process adapter sequences + in ONT reads. homepage: "https://github.com/bonsai-team/Porechop_ABI" documentation: "https://github.com/bonsai-team/Porechop_ABI" tool_dev_url: "https://github.com/bonsai-team/Porechop_ABI" doi: "10.1101/2022.07.07.499093" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: fastq/fastq.gz file - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq/fastq.gz file + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Adapter-trimmed fastq.gz file - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Adapter-trimmed fastq.gz file + pattern: "*.fastq.gz" - log: - type: file - description: Log file containing stdout information - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stdout information + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "LilyAnderssonLee" diff --git a/modules/nf-core/porechop/porechop/meta.yml b/modules/nf-core/porechop/porechop/meta.yml index 13be76f26bb..9e61c05421b 100644 --- a/modules/nf-core/porechop/porechop/meta.yml +++ b/modules/nf-core/porechop/porechop/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: "https://github.com/rrwick/Porechop" doi: "10.1099/mgen.0.000132" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: fastq/fastq.gz file - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq/fastq.gz file + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Demultiplexed and/or adapter-trimmed fastq.gz file - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Demultiplexed and/or adapter-trimmed fastq.gz file + pattern: "*.{fastq.gz}" - log: - type: file - description: Log file containing stdout information - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stdout information + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ggabernet" - "@jasmezz" diff --git a/modules/nf-core/preseq/ccurve/meta.yml b/modules/nf-core/preseq/ccurve/meta.yml index f804b0669b9..39fb249128f 100644 --- a/modules/nf-core/preseq/ccurve/meta.yml +++ b/modules/nf-core/preseq/ccurve/meta.yml @@ -1,44 +1,55 @@ name: preseq_ccurve -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq licence: ["GPL"] + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - ccurve: - type: file - description: File containing output of Preseq c curve - pattern: "*.{c_curve.txt}" + - c_curve: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.c_curve.txt": + type: file + description: Preseq c_curve output file + pattern: "*.{c_curve.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/preseq/lcextrap/meta.yml b/modules/nf-core/preseq/lcextrap/meta.yml index c00fa8eef31..28fb449ca92 100644 --- a/modules/nf-core/preseq/lcextrap/meta.yml +++ b/modules/nf-core/preseq/lcextrap/meta.yml @@ -1,44 +1,55 @@ name: preseq_lcextrap -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq licence: ["GPL"] + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lc_extrap: - type: file - description: File containing output of Preseq lcextrap - pattern: "*.{lc_extrap.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lc_extrap.txt": + type: file + description: File containing output of Preseq lcextrap + pattern: "*.{lc_extrap.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/president/meta.yml b/modules/nf-core/president/meta.yml index 7d6d3c9bcb9..0162ab53123 100644 --- a/modules/nf-core/president/meta.yml +++ b/modules/nf-core/president/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "president" description: "Calculate pairwise nucleotide identity with respect to a reference sequence" @@ -9,53 +8,92 @@ keywords: - nucleotides tools: - "president": - description: "Calculate pairwise nucleotide identity with respect to a reference sequence" + description: "Calculate pairwise nucleotide identity with respect to a reference + sequence" homepage: "https://github.com/rki-mf1/president" documentation: "https://github.com/rki-mf1/president" tool_dev_url: "https://github.com/rki-mf1/president" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: Groovy Map containing information, e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed! - pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" - - meta2: - type: map - description: Groovy Map containing information about the reference genome - - reference: - type: file - description: Fasta of a reference genome. Has to be uncompressed! - pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" - - compress: - type: boolean - description: Set to "true" if fasta output should be compressed - + - - meta: + type: map + description: Groovy Map containing information, e.g. [ id:'test', single_end:false + ] + - fasta: + type: file + description: One fasta file or a list of multiple fasta files to perform president + on. Has to be uncompressed! + pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" + - - meta2: + type: map + description: Groovy Map containing information about the reference genome + - reference: + type: file + description: Fasta of a reference genome. Has to be uncompressed! + pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" + - - compress: + type: boolean + description: Set to "true" if fasta output should be compressed output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - valid_fasta: - type: file - description: Fasta file containing sequences which passed the qc ("valid.fasta"). If true is set on the "compress" input value, the file is gz-compressed. - pattern: "*.{fasta.gz, fasta}" + - meta: + type: file + description: Fasta file containing sequences which passed the qc ("valid.fasta"). + If true is set on the "compress" input value, the file is gz-compressed. + pattern: "*.{fasta.gz, fasta}" + - ${prefix}_valid.fasta*: + type: file + description: Fasta file containing sequences which passed the qc ("valid.fasta"). + If true is set on the "compress" input value, the file is gz-compressed. + pattern: "*.{fasta.gz, fasta}" + - id_fasta: + type: file + description: Fasta file containing sequences which passed the qc ("valid.fasta"). + If true is set on the "compress" input value, the file is gz-compressed. + pattern: "*.{fasta.gz, fasta}" - invalid_fasta: - type: file - description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). If true is set on the "compress" input value, the files are gz-compressed. - pattern: "*_invalid.{fasta.gz, fasta}" + - meta: + type: file + description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). + If true is set on the "compress" input value, the files are gz-compressed. + pattern: "*_invalid.{fasta.gz, fasta}" + - ${prefix}_invalid.fasta*: + type: file + description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). + If true is set on the "compress" input value, the files are gz-compressed. + pattern: "*_invalid.{fasta.gz, fasta}" + - id_fasta: + type: file + description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). + If true is set on the "compress" input value, the files are gz-compressed. + pattern: "*_invalid.{fasta.gz, fasta}" - report: - type: file - description: Report with some information for every sample, like statistic values. See docs for details - pattern: "*.tsv" + - meta: + type: file + description: Report with some information for every sample, like statistic values. + See docs for details + pattern: "*.tsv" + - "*.tsv": + type: file + description: Report with some information for every sample, like statistic values. + See docs for details + pattern: "*.tsv" - log: - type: file - description: Log file of president - pattern: "*.log" - + - meta: + type: file + description: Log file of president + pattern: "*.log" + - "*.log": + type: file + description: Log file of president + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@paulwolk" maintainers: diff --git a/modules/nf-core/presto/filterseq/meta.yml b/modules/nf-core/presto/filterseq/meta.yml index 6b0b6c85e5c..32e13e03aa1 100644 --- a/modules/nf-core/presto/filterseq/meta.yml +++ b/modules/nf-core/presto/filterseq/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "presto_filterseq" description: Filter reads by quality score. @@ -9,46 +8,50 @@ keywords: - immunoinformatics tools: - "presto": - description: "A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data." + description: "A bioinformatics toolkit for processing high-throughput lymphocyte + receptor sequencing data." homepage: "https://immcantation.readthedocs.io" documentation: "https://presto.readthedocs.io" tool_dev_url: "https://bitbucket.org/kleinstein/presto" doi: "10.1093/bioinformatics/btu138" licence: ["AGPL v3"] + identifier: biotools:presto-measure input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq file - pattern: "*.{fastq}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: fastq file + pattern: "*.{fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: filtered fastq file - pattern: "*.{fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_quality-pass.fastq": + type: file + description: filtered fastq file + pattern: "*.{fastq}" - logs: - type: file - description: command logs - pattern: "*.txt" + - "*_command_log.txt": + type: file + description: command logs + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log_tab: - type: file - description: parsed log table - pattern: "*.tab" - + - "*.tab": + type: file + description: parsed log table + pattern: "*.tab" authors: - "@ggabernet" diff --git a/modules/nf-core/pretextmap/meta.yml b/modules/nf-core/pretextmap/meta.yml index 97158cda0d5..d79295cd723 100644 --- a/modules/nf-core/pretextmap/meta.yml +++ b/modules/nf-core/pretextmap/meta.yml @@ -6,47 +6,51 @@ keywords: - map tools: - "pretextmap": - description: "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps." + description: "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into + genome contact maps." homepage: "https://github.com/wtsi-hpag/PretextMap" documentation: "https://github.com/wtsi-hpag/PretextMap/blob/master/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file or pairs formatted reads file - pattern: "*.{bam,cram,sam,pairs.gz}" - - input: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test2', single_end:false ] - - input: - type: file - description: FASTA file - pattern: "*.{fasta,fa,fna}" - - input: - type: file - description: Fasta index - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file or pairs formatted reads file + pattern: "*.{bam,cram,sam,pairs.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference sequence file + pattern: "*.{fasta,fna,fa}" + - fai: + type: file + description: Reference sequence index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pretext: - type: file - description: pretext map - pattern: "*.pretext" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pretext": + type: file + description: pretext map + pattern: "*.pretext" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" - "@getrudeln" diff --git a/modules/nf-core/pretextsnapshot/meta.yml b/modules/nf-core/pretextsnapshot/meta.yml index 59e3862be24..434da68e420 100644 --- a/modules/nf-core/pretextsnapshot/meta.yml +++ b/modules/nf-core/pretextsnapshot/meta.yml @@ -14,30 +14,33 @@ tools: homepage: "https://github.com/wtsi-hpag/PretextSnapshot" tool_dev_url: "https://github.com/wtsi-hpag/PretextSnapshot" licence: ["https://github.com/wtsi-hpag/PretextSnapshot/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pretext_map: - type: file - description: pretext hic map - pattern: "*.pretext" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pretext_map: + type: file + description: pretext hic map + pattern: "*.pretext" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - image: - type: file - description: image of a hic contact map - pattern: "*.{png,jpg,bmp}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{jpeg,png,bmp}": + type: file + description: image of a hic contact map + pattern: "*.{png,jpg,bmp}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@epaule" maintainers: diff --git a/modules/nf-core/prinseqplusplus/meta.yml b/modules/nf-core/prinseqplusplus/meta.yml index a978be4a5cd..5e09ba4546c 100644 --- a/modules/nf-core/prinseqplusplus/meta.yml +++ b/modules/nf-core/prinseqplusplus/meta.yml @@ -1,5 +1,6 @@ name: "prinseqplusplus" -description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data +description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It + can be used to filter, reformat or trim genomic and metagenomic sequence data keywords: - fastq - fasta @@ -13,46 +14,67 @@ tools: tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus" doi: "10.7287/peerj.preprints.27553v1" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end - data, respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - good_reads: - type: file - description: Reads passing filter(s) in gzipped FASTQ format - pattern: "*_good_out_{R1,R2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_good_out*.fastq.gz": + type: file + description: Reads passing filter(s) in gzipped FASTQ format + pattern: "*_good_out_{R1,R2}.fastq.gz" - single_reads: - type: file - description: | - Single reads without the pair passing filter(s) in gzipped FASTQ format - pattern: "*_single_out_{R1,R2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_single_out*.fastq.gz": + type: file + description: | + Single reads without the pair passing filter(s) in gzipped FASTQ format + pattern: "*_single_out_{R1,R2}.fastq.gz" - bad_reads: - type: file - description: | - Reads without not passing filter(s) in gzipped FASTQ format - pattern: "*_bad_out_{R1,R2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bad_out*.fastq.gz": + type: file + description: | + Reads without not passing filter(s) in gzipped FASTQ format + pattern: "*_bad_out_{R1,R2}.fastq.gz" - log: - type: file - description: | - Verbose level 2 STDOUT information in a log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: | + Verbose level 2 STDOUT information in a log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/prodigal/meta.yml b/modules/nf-core/prodigal/meta.yml index a5d15d58e5e..7d3d459ee69 100644 --- a/modules/nf-core/prodigal/meta.yml +++ b/modules/nf-core/prodigal/meta.yml @@ -1,55 +1,78 @@ name: prodigal -description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program +description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a + microbial (bacterial and archaeal) gene finding program keywords: - prokaryotes - gene finding - microbial tools: - prodigal: - description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program + description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program homepage: https://github.com/hyattpd/Prodigal documentation: https://github.com/hyattpd/prodigal/wiki tool_dev_url: https://github.com/hyattpd/Prodigal doi: "10.1186/1471-2105-11-119" licence: ["GPL v3"] + identifier: biotools:prodigal input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genome: - type: file - description: fasta/fasta.gz file - - output_format: - type: string - description: Output format ("gbk"/"gff"/"sqn"/"sco") + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: fasta/fasta.gz file + - - output_format: + type: string + description: Output format ("gbk"/"gff"/"sqn"/"sco") output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - gene_annotations: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${output_format}.gz: + type: file + description: gene annotations in output_format given as input + pattern: "*.{output_format}" - nucleotide_fasta: - type: file - description: nucleotide sequences file - pattern: "*.{fna}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fna.gz: + type: file + description: nucleotide sequences file + pattern: "*.{fna}" - amino_acid_fasta: - type: file - description: protein translations file - pattern: "*.{faa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.faa.gz: + type: file + description: protein translations file + pattern: "*.{faa}" - all_gene_annotations: - type: file - description: complete starts file - pattern: "*.{_all.txt}" - - gene_annotations: - type: file - description: gene annotations in output_format given as input - pattern: "*.{output_format}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_all.txt.gz: + type: file + description: complete starts file + pattern: "*.{_all.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/prokka/meta.yml b/modules/nf-core/prokka/meta.yml index 9d82ffac720..907457355e5 100644 --- a/modules/nf-core/prokka/meta.yml +++ b/modules/nf-core/prokka/meta.yml @@ -10,80 +10,151 @@ tools: homepage: https://github.com/tseemann/prokka doi: "10.1093/bioinformatics/btu153" licence: ["GPL v2"] + identifier: biotools:prokka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - FASTA file to be annotated. Has to contain at least a non-empty string dummy value. - - proteins: - type: file - description: FASTA file of trusted proteins to first annotate from (optional) - - prodigal_tf: - type: file - description: Training file to use for Prodigal (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + FASTA file to be annotated. Has to contain at least a non-empty string dummy value. + - - proteins: + type: file + description: FASTA file of trusted proteins to first annotate from (optional) + - - prodigal_tf: + type: file + description: Training file to use for Prodigal (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: annotation in GFF3 format, containing both sequences and annotations - pattern: "*.{gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.gff: + type: file + description: annotation in GFF3 format, containing both sequences and annotations + pattern: "*.{gff}" - gbk: - type: file - description: annotation in GenBank format, containing both sequences and annotations - pattern: "*.{gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.gbk: + type: file + description: annotation in GenBank format, containing both sequences and annotations + pattern: "*.{gbk}" - fna: - type: file - description: nucleotide FASTA file of the input contig sequences - pattern: "*.{fna}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.fna: + type: file + description: nucleotide FASTA file of the input contig sequences + pattern: "*.{fna}" - faa: - type: file - description: protein FASTA file of the translated CDS sequences - pattern: "*.{faa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.faa: + type: file + description: protein FASTA file of the translated CDS sequences + pattern: "*.{faa}" - ffn: - type: file - description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) - pattern: "*.{ffn}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.ffn: + type: file + description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, + tRNA, tmRNA, misc_RNA) + pattern: "*.{ffn}" - sqn: - type: file - description: an ASN1 format "Sequin" file for submission to Genbank - pattern: "*.{sqn}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.sqn: + type: file + description: an ASN1 format "Sequin" file for submission to Genbank + pattern: "*.{sqn}" - fsa: - type: file - description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file - pattern: "*.{fsa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.fsa: + type: file + description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" + to create the .sqn file + pattern: "*.{fsa}" - tbl: - type: file - description: feature Table file, used by "tbl2asn" to create the .sqn file - pattern: "*.{tbl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.tbl: + type: file + description: feature Table file, used by "tbl2asn" to create the .sqn file + pattern: "*.{tbl}" - err: - type: file - description: unacceptable annotations - the NCBI discrepancy report. - pattern: "*.{err}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.err: + type: file + description: unacceptable annotations - the NCBI discrepancy report. + pattern: "*.{err}" - log: - type: file - description: contains all the output that Prokka produced during its run - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.log: + type: file + description: contains all the output that Prokka produced during its run + pattern: "*.{log}" - txt: - type: file - description: statistics relating to the annotated features found - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.txt: + type: file + description: statistics relating to the annotated features found + pattern: "*.{txt}" - tsv: - type: file - description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product) - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.tsv: + type: file + description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product) + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/propr/grea/meta.yml b/modules/nf-core/propr/grea/meta.yml index d78d7c8b33f..58f73fc4d86 100644 --- a/modules/nf-core/propr/grea/meta.yml +++ b/modules/nf-core/propr/grea/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "propr_grea" description: Perform Gene Ratio Enrichment Analysis @@ -17,44 +16,49 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.2202/1544-6115.1175" licence: ["GPL-2"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the knowledge database - - adj: - type: file - description: adjacency matrix for gene ratio proportionality/differential proportionality - pattern: "*.{csv,tsv}" - - gmt: - type: file - description: relational database containing genes and GO terms (generated by mygene module) - pattern: "*.{gmt}" + - - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - adj: + type: file + description: adjacency matrix for gene ratio proportionality/differential proportionality + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the knowledge database + - gmt: + type: file + description: relational database containing genes and GO terms (generated by + mygene module) + pattern: "*.{gmt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - enrichedGO: - type: file - description: File containing GO terms and their enrichment values - pattern: "*.{csv}" - - session_info: - type: file - description: R session log - pattern: "*.R_sessionInfo.log" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.go.tsv": + type: file + description: File containing GO terms and their enrichment values + pattern: "*.{csv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - session_info: + - "*.R_sessionInfo.log": + type: file + description: R session log + pattern: "*.R_sessionInfo.log" authors: - "@caraiz2001" maintainers: diff --git a/modules/nf-core/propr/logratio/meta.yml b/modules/nf-core/propr/logratio/meta.yml index 77d6438254e..30f8ac887ff 100644 --- a/modules/nf-core/propr/logratio/meta.yml +++ b/modules/nf-core/propr/logratio/meta.yml @@ -1,5 +1,6 @@ name: "propr_logratio" -description: Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR) +description: Transform the data matrix using centered logratio transformation (CLR) + or additive logratio transformation (ALR) keywords: - alr - clr @@ -15,39 +16,44 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" licence: ["GPL-2"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing additional information. - meta.id can be used to name the output files. - [id: 'test', ...] - - count: - type: file - description: | - Count matrix, where rows = variables or genes, columns = samples or cells. - This matrix should not contain zeros. Otherwise, they will be first replaced by the minimun value. - You may want to handle the zeros with a different method beforehand. - pattern: "*.{csv,tsv}" + - - meta: + type: map + description: | + Groovy Map containing additional information. + meta.id can be used to name the output files. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. Otherwise, they will be first replaced by the minimun value. + You may want to handle the zeros with a different method beforehand. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing additional information. - meta.id can be used to name the output files. - [id: 'test', ...] - logratio: - type: file - description: ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells. - pattern: "*.logratio.tsv" + - meta: + type: map + description: | + Groovy Map containing additional information. + meta.id can be used to name the output files. + [id: 'test', ...] + - "*.logratio.tsv": + type: file + description: ALR/CLR transformed data matrix. With rows = variables or genes, + columns = samples or cells. + pattern: "*.logratio.tsv" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.R_sessionInfo.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" - "@oprana22" diff --git a/modules/nf-core/propr/propd/meta.yml b/modules/nf-core/propr/propd/meta.yml index 7dcb46259bf..261e80ed216 100644 --- a/modules/nf-core/propr/propd/meta.yml +++ b/modules/nf-core/propr/propd/meta.yml @@ -14,62 +14,88 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" licence: ["GPL-2"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing additional information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - - count: - type: file - description: | - Count matrix, where rows = variables or genes, columns = samples or cells. - This matrix should not contain zeros. One should plug this module after another one that handles the zeros. - pattern: "*.{csv,tsv}" - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata + - - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. One should plug this module after another one that handles the zeros. + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata output: - - meta: - type: map - description: | - Groovy Map containing additional information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - propd: - type: file - description: R propd object - pattern: "*.propd.rds" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propd.rds": + type: file + description: R propd object + pattern: "*.propd.rds" - results: - type: file - description: Results table - pattern: "*.propd.tsv" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propd.tsv": + type: file + description: Results table + pattern: "*.propd.tsv" - fdr: - type: file - description: (optional) propd fdr table - pattern: "*.fdr.tsv" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.fdr.tsv": + type: file + description: (optional) propd fdr table + pattern: "*.fdr.tsv" - adj: - type: file - description: (optional) propd adj table - pattern: "*.adj.csv" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.adj.csv": + type: file + description: (optional) propd adj table + pattern: "*.adj.csv" - warnings: - type: file - description: propd warnings - pattern: "*.warnings.txt" + - "*.warnings.log": + type: file + description: propd warnings + pattern: "*.warnings.txt" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.R_sessionInfo.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" maintainers: diff --git a/modules/nf-core/propr/propr/meta.yml b/modules/nf-core/propr/propr/meta.yml index 206565168cc..cdfc5982b72 100644 --- a/modules/nf-core/propr/propr/meta.yml +++ b/modules/nf-core/propr/propr/meta.yml @@ -18,63 +18,88 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" licence: ["GPL-2"] + identifier: biotools:propr - "corpcor": description: "Efficient Estimation of Covariance and (Partial) Correlation" homepage: "https://cran.r-project.org/web/packages/corpcor/index.html" documentation: "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf" doi: "10.2202/1544-6115.1175" licence: ["GPL >=3"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - - count: - type: file - description: | - Count matrix, where rows = variables or genes, columns = samples or cells. - This matrix should not contain zeros. Otherwise, they will be replaced by the minimun number. - It is recommended to handle the zeros beforehand with the method of preference. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. Otherwise, they will be replaced by the minimun number. + It is recommended to handle the zeros beforehand with the method of preference. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - propr: - type: file - description: R propr object - pattern: "*.propr.rds" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propr.rds": + type: file + description: R propr object + pattern: "*.propr.rds" - matrix: - type: file - description: Coefficient matrix - pattern: "*.propr.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propr.tsv": + type: file + description: Coefficient matrix + pattern: "*.propr.tsv" - fdr: - type: file - description: (optional) propr fdr table - pattern: "*.fdr.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.fdr.tsv": + type: file + description: (optional) propr fdr table + pattern: "*.fdr.tsv" - adj: - type: file - description: (optional) propr adjacency table - pattern: "*.adj.csv" - - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.R_sessionInfo.log" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.adj.csv": + type: file + description: (optional) propr adjacency table + pattern: "*.adj.csv" - warnings: - type: file - description: Warnings - pattern: "*.warnings.log" + - "*.warnings.log": + type: file + description: Warnings + pattern: "*.warnings.log" + - session_info: + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" diff --git a/modules/nf-core/proteinortho/meta.yml b/modules/nf-core/proteinortho/meta.yml index 58e8eefd4c9..b54e84f2600 100644 --- a/modules/nf-core/proteinortho/meta.yml +++ b/modules/nf-core/proteinortho/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "proteinortho" description: Proteinortho is a tool to detect orthologous genes within different species. @@ -12,42 +11,59 @@ keywords: - genomics tools: - "proteinortho": - description: "Proteinortho is a tool to detect orthologous genes within different species." + description: "Proteinortho is a tool to detect orthologous genes within different + species." homepage: "https://gitlab.com/paulklemm_PHD/proteinortho" documentation: "https://gitlab.com/paulklemm_PHD/proteinortho#proteinortho" tool_dev_url: "https://gitlab.com/paulklemm_PHD/proteinortho" doi: "10.3389/fbinf.2023.1322477" licence: ["GPL v3"] + identifier: biotools:proteinortho input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - fasta_files: - type: file - description: Input fasta files (proteomes or transcriptomes), at least 2 are needed - pattern: "*.{fa,fasta,faa,fna,fn}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fasta_files: + type: file + description: Input fasta files (proteomes or transcriptomes), at least 2 are + needed + pattern: "*.{fa,fasta,faa,fna,fn}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - orthologgroups: - type: file - description: Orthology table - pattern: "*.proteinortho.tsv" + - meta: + type: file + description: Orthology table + pattern: "*.proteinortho.tsv" + - ${meta.id}.proteinortho.tsv: + type: file + description: Orthology table + pattern: "*.proteinortho.tsv" - orthologgraph: - type: file - description: Orthology graph - pattern: "*.proteinortho-graph" + - meta: + type: file + description: Orthology graph + pattern: "*.proteinortho-graph" + - ${meta.id}.proteinortho-graph: + type: file + description: Orthology graph + pattern: "*.proteinortho-graph" - blastgraph: - type: file - description: BLAST graph - pattern: "*.blast-graph" - + - meta: + type: file + description: BLAST graph + pattern: "*.blast-graph" + - ${meta.id}.blast-graph: + type: file + description: BLAST graph + pattern: "*.blast-graph" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pmjklemm" maintainers: diff --git a/modules/nf-core/proteus/readproteingroups/environment.yml b/modules/nf-core/proteus/readproteingroups/environment.yml index 47fc6415956..986db59603a 100644 --- a/modules/nf-core/proteus/readproteingroups/environment.yml +++ b/modules/nf-core/proteus/readproteingroups/environment.yml @@ -1,9 +1,10 @@ channels: - conda-forge - bioconda + dependencies: - - conda-forge::r-base=4.2.1 - - bioconda::r-proteus-bartongroup=0.2.16 - - conda-forge::r-plotly=4.10.2 - bioconda::bioconductor-limma=3.54.0 + - bioconda::r-proteus-bartongroup=0.2.16 + - conda-forge::r-base=4.2.1 - conda-forge::r-ggplot2=3.4.4 + - conda-forge::r-plotly=4.10.2 diff --git a/modules/nf-core/proteus/readproteingroups/meta.yml b/modules/nf-core/proteus/readproteingroups/meta.yml index 4e67cf0c289..d1d7e8c9f5e 100644 --- a/modules/nf-core/proteus/readproteingroups/meta.yml +++ b/modules/nf-core/proteus/readproteingroups/meta.yml @@ -12,68 +12,107 @@ tools: tool_dev_url: "https://github.com/bartongroup/Proteus" doi: "10.1101/416511" licence: ["GPL v2"] + identifier: biotools:proteus-engineering input: - - meta: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html - - intensities: - type: file - description: | - proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html - - meta2: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for comparison + - - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html + - intensities: + type: file + description: | + proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html output: - dendro_plot: - type: file - description: | - PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities + - meta: + type: file + description: | + PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities + - "*dendrogram.png": + type: file + description: | + PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities - mean_var_plot: - type: file - description: | - PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples + - meta: + type: file + description: | + PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples + - "*mean_variance_relationship.png": + type: file + description: | + PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples - raw_dist_plot: - type: file - description: | - PNG file; plot of the intensity/ratio distributions of the raw samples + - meta: + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the raw samples + - "*raw_distributions.png": + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the raw samples - norm_dist_plot: - type: file - description: | - PNG file; plot of the intensity/ratio distributions of the normalized samples + - meta: + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the normalized samples + - "*normalized_distributions.png": + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the normalized samples - raw_rdata: - type: file - description: | - RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info + - meta: + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info + - "*raw_proteingroups.rds": + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info - norm_rdata: - type: file - description: | - RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info + - meta: + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info + - "*normalized_proteingroups.rds": + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info - raw_tab: - type: file - description: | - TSV-format intensities table from Proteus, contains raw protein intensities + - meta: + type: file + description: | + TSV-format intensities table from Proteus, contains raw protein intensities + - "*raw_proteingroups_tab.tsv": + type: file + description: | + TSV-format intensities table from Proteus, contains raw protein intensities - norm_tab: - type: file - description: | - TSV-format intensities table from Proteus, contains normalized protein intensities + - meta: + type: file + description: | + TSV-format intensities table from Proteus, contains normalized protein intensities + - "*normalized_proteingroups_tab.tsv": + type: file + description: | + TSV-format intensities table from Proteus, contains normalized protein intensities - session_info: - type: file - description: | - LOG file of the R sessionInfo from the module run + - meta: + type: file + description: | + LOG file of the R sessionInfo from the module run + - "*R_sessionInfo.log": + type: file + description: | + LOG file of the R sessionInfo from the module run - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@WackerO" maintainers: diff --git a/modules/nf-core/pureclip/meta.yml b/modules/nf-core/pureclip/meta.yml index 48308ce6344..ceec2106718 100644 --- a/modules/nf-core/pureclip/meta.yml +++ b/modules/nf-core/pureclip/meta.yml @@ -1,70 +1,85 @@ ---- name: "pureclip" -description: PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. +description: PureCLIP is a tool to detect protein-RNA interaction footprints from + single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. keywords: - iCLIP - eCLIP - CLIP tools: - "pureclip": - description: "PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP." + description: "PureCLIP is a tool to detect protein-RNA interaction footprints + from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP." homepage: "https://github.com/skrakau/PureCLIP" documentation: "https://pureclip.readthedocs.io/en/latest/GettingStarted/index.html" tool_dev_url: "https://github.com/skrakau/PureCLIP" doi: "10.1186/s13059-017-1364-2" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - ipbam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - controlbam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - ipbai: - type: file - description: BAM index - pattern: "*.{bai}" - - controlbai: - type: file - description: BAM index - pattern: "*.{bai}" - - input_control: - type: boolean - description: Whether to run PureCLIP with an input control - - genome_fasta: - type: file - description: FASTA file of reference genome - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ipbam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - controlbam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ipbai: + type: file + description: BAM index + pattern: "*.{bai}" + - controlbai: + type: file + description: BAM index + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - genome_fasta: + type: file + description: FASTA file of reference genome + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - input_control: + type: boolean + description: Whether to run PureCLIP with an input control output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - crosslinks: - type: file - description: Bed file of crosslinks - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${crosslinks_output_name}: + type: file + description: Bed file of crosslinks + pattern: "*.{bed}" - peaks: - type: file - description: Bed file of peaks - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${peaks_output_name}: + type: file + description: Bed file of peaks + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charlotteanne" - "@marcjones" diff --git a/modules/nf-core/purecn/coverage/environment.yml b/modules/nf-core/purecn/coverage/environment.yml index cbd210aa496..ffb69fe35cc 100644 --- a/modules/nf-core/purecn/coverage/environment.yml +++ b/modules/nf-core/purecn/coverage/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: + - bioconda::bioconductor-org.hs.eg.db=3.16.0 - bioconda::bioconductor-purecn=2.4.0 - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 - - bioconda::bioconductor-org.hs.eg.db=3.16.0 diff --git a/modules/nf-core/purecn/coverage/meta.yml b/modules/nf-core/purecn/coverage/meta.yml index e88bb21a148..aba8770dbc2 100644 --- a/modules/nf-core/purecn/coverage/meta.yml +++ b/modules/nf-core/purecn/coverage/meta.yml @@ -1,5 +1,6 @@ name: "purecn_coverage" -description: Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to 'link'. +description: Calculate intervals coverage for each sample. N.B. the tool can not handle + staging files with symlinks, stageInMode should be set to 'link'. keywords: - copy number alteration calling - intervals coverage @@ -8,63 +9,85 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" license: ["Artistic-2.0"] args_id: "$args" + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bai}" - - intervals: - type: file - description: Annotated targets optimized for copy number calling - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - - intervals: + type: file + description: Annotated targets optimized for copy number calling + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Intervals coverage file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Intervals coverage file + pattern: "*.txt.gz" - png: - type: file - description: | - GC-normalized intervals coverage plot. - Generated only when GC-normalization is enabled. - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: | + GC-normalized intervals coverage plot. + Generated only when GC-normalization is enabled. + pattern: "*.png" - loess_qc_txt: - type: file - description: | - GC-normalized intervals coverage metrics. - Generated only when GC-normalization is enabled. - pattern: "*_loess_qc.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_loess_qc.txt": + type: file + description: | + GC-normalized intervals coverage metrics. + Generated only when GC-normalization is enabled. + pattern: "*_loess_qc.txt" - loess_txt: - type: file - description: | - GC-normalized intervals coverage file. - Generated only when GC-normalization is enabled. - pattern: "*_loess.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_loess.txt.gz": + type: file + description: | + GC-normalized intervals coverage file. + Generated only when GC-normalization is enabled. + pattern: "*_loess.txt.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purecn/intervalfile/meta.yml b/modules/nf-core/purecn/intervalfile/meta.yml index 489fed1cd07..0965574e221 100644 --- a/modules/nf-core/purecn/intervalfile/meta.yml +++ b/modules/nf-core/purecn/intervalfile/meta.yml @@ -8,56 +8,66 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z." licence: ["Artistic-2.0"] + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - target_bed: - type: file - description: BED file of target intervals - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: FASTA reference sequence of the genome being used - pattern: "*.fasta" - - genome: - type: string - description: Genome used for the BED file (e.g., "hg38", "mm10"...) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - target_bed: + type: file + description: BED file of target intervals + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: FASTA reference sequence of the genome being used + pattern: "*.fasta" + - - genome: + type: string + description: Genome used for the BED file (e.g., "hg38", "mm10"...) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - pattern: "*.txt" - description: | - Annotated targets optimized for copy number calling + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + pattern: "*.txt" + description: | + Annotated targets optimized for copy number calling - bed: - type: file - pattern: "*.bed" - description: | - Modified and optimized targets exported as a BED file. - Generate the file using the --export command-line switch - IntervalFile.R. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + pattern: "*.bed" + description: | + Modified and optimized targets exported as a BED file. + Generate the file using the --export command-line switch + IntervalFile.R. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purecn/normaldb/meta.yml b/modules/nf-core/purecn/normaldb/meta.yml index cddabe9f0e1..4fbe29d643c 100644 --- a/modules/nf-core/purecn/normaldb/meta.yml +++ b/modules/nf-core/purecn/normaldb/meta.yml @@ -1,5 +1,9 @@ name: "purecn_normaldb" -description: Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes. +description: Build a normal database for coverage normalization from all the (GC-normalized) + normal coverage files. N.B. as reported in + https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, + it is advised to provide a normal panel (VCF format) to precompute mapping bias + for faster runtimes. keywords: - copy number alteration calling - normal database @@ -9,62 +13,96 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" licence: ["Artistic-2.0"] args_id: "$args" + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_files: - type: file - description: Coverage files from normal samples - pattern: "*.txt.gz" - - normal_vcf: - type: file - description: | - Normal panel in VCF format, used to precompute mapping bias - for faster runtimes. Optional. - pattern: "*.vcf.gz" - - genome: - type: string - description: Genome build - - assay: - type: string - description: Assay name + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_files: + type: file + description: Coverage files from normal samples + pattern: "*.txt.gz" + - normal_vcf: + type: file + description: | + Normal panel in VCF format, used to precompute mapping bias + for faster runtimes. Optional. + pattern: "*.vcf.gz" + - normal_vcf_tbi: + type: file + description: Normal panel in VCF format + pattern: "*.vcf.gz.tbi" + - - genome: + type: string + description: Genome build + - - assay: + type: string + description: Assay name output: - rds: - type: file - description: File containing the generated panel of normals - pattern: "normalDB*.rds" + - meta: + type: file + description: File containing the generated panel of normals + pattern: "normalDB*.rds" + - normalDB*.rds: + type: file + description: File containing the generated panel of normals + pattern: "normalDB*.rds" - png: - type: file - description: Plot of interval weights calculated from the panel of normals - pattern: "interval_weights*.png" + - meta: + type: file + description: Plot of interval weights calculated from the panel of normals + pattern: "interval_weights*.png" + - interval_weights*.png: + type: file + description: Plot of interval weights calculated from the panel of normals + pattern: "interval_weights*.png" - bias_rds: - type: file - description: Calculated mapping bias from the normal files - pattern: "mapping_bias*.rds" + - meta: + type: file + description: Calculated mapping bias from the normal files + pattern: "mapping_bias*.rds" + - mapping_bias*.rds: + type: file + description: Calculated mapping bias from the normal files + pattern: "mapping_bias*.rds" - bias_bed: - type: file - description: Calculated mapping bias sites from the normal files - pattern: "mapping_bias_hq_sites*.bed" + - meta: + type: file + description: Calculated mapping bias sites from the normal files + pattern: "mapping_bias_hq_sites*.bed" + - mapping_bias_hq_sites*.bed: + type: file + description: Calculated mapping bias sites from the normal files + pattern: "mapping_bias_hq_sites*.bed" - low_cov_bed: - type: file - description: | - BED with possibly low coverage targets identified, only - generated if there are low coverage targets - pattern: "low_coverage_targets*.bed" + - meta: + type: file + description: | + BED with possibly low coverage targets identified, only + generated if there are low coverage targets + pattern: "low_coverage_targets*.bed" + - low_coverage_targets*.bed: + type: file + description: | + BED with possibly low coverage targets identified, only + generated if there are low coverage targets + pattern: "low_coverage_targets*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purecn/run/environment.yml b/modules/nf-core/purecn/run/environment.yml index cbd210aa496..ffb69fe35cc 100644 --- a/modules/nf-core/purecn/run/environment.yml +++ b/modules/nf-core/purecn/run/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: + - bioconda::bioconductor-org.hs.eg.db=3.16.0 - bioconda::bioconductor-purecn=2.4.0 - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 - - bioconda::bioconductor-org.hs.eg.db=3.16.0 diff --git a/modules/nf-core/purecn/run/meta.yml b/modules/nf-core/purecn/run/meta.yml index f70f780e869..6817837fbb5 100644 --- a/modules/nf-core/purecn/run/meta.yml +++ b/modules/nf-core/purecn/run/meta.yml @@ -7,96 +7,167 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" license: ["Artistic-2.0"] args_id: "$args" + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - intervals: - type: file - description: | - BED file of target intervals, generated from IntervalFile.R - pattern: "{*.bed,*.txt}" - - coverage: - type: file - description: Coverage file generated from Coverage.R - pattern: "*.txt" - - normaldb: - type: file - description: | - Normal panel in RDS format, generated from NormalDB.R - pattern: "*.rds" - - genome: - type: string - description: Genome build + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - intervals: + type: file + description: | + BED file of target intervals, generated from IntervalFile.R + pattern: "{*.bed,*.txt}" + - coverage: + type: file + description: Coverage file generated from Coverage.R + pattern: "*.txt" + - - normal_db: + type: file + description: normal pannel database + - - genome: + type: string + description: Genome build output: - pdf: - type: file - description: | - PDF file containing copy number plots - pattern: "*.pdf" + - meta: + type: file + description: | + PDF file containing copy number plots + pattern: "*.pdf" + - "*.pdf": + type: file + description: | + PDF file containing copy number plots + pattern: "*.pdf" - local_optima_pdf: - type: file - description: | - PDF file containing local optima plots - pattern: "*_local_optima.pdf" + - meta: + type: file + description: | + PDF file containing local optima plots + pattern: "*_local_optima.pdf" + - "*_local_optima.pdf": + type: file + description: | + PDF file containing local optima plots + pattern: "*_local_optima.pdf" - seg: - type: file - description: | - Tab-delimited file containing segmentation results - pattern: "*_dnacopy.seg" + - meta: + type: file + description: | + Tab-delimited file containing segmentation results + pattern: "*_dnacopy.seg" + - "*_dnacopy.seg": + type: file + description: | + Tab-delimited file containing segmentation results + pattern: "*_dnacopy.seg" - genes_csv: - type: file - description: | - CSV file containing gene copy number calls. Optional - pattern: "*_genes.csv" + - meta: + type: file + description: | + CSV file containing gene copy number calls. Optional + pattern: "*_genes.csv" + - "*_genes.csv": + type: file + description: | + CSV file containing gene copy number calls. Optional + pattern: "*_genes.csv" - amplification_pvalues_csv: - type: file - description: | - CSV file containing amplification p-values. Optional - pattern: "*_amplification_pvalues.csv" + - meta: + type: file + description: | + CSV file containing amplification p-values. Optional + pattern: "*_amplification_pvalues.csv" + - "*_amplification_pvalues.csv": + type: file + description: | + CSV file containing amplification p-values. Optional + pattern: "*_amplification_pvalues.csv" + - ues_csv: + type: file + description: | + CSV file containing amplification p-values. Optional + pattern: "*_amplification_pvalues.csv" - vcf_gz: - type: file - description: | - GZipped VCF file containing SNV calls. Optional - pattern: "*.vcf.gz" + - meta: + type: file + description: | + GZipped VCF file containing SNV calls. Optional + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: | + GZipped VCF file containing SNV calls. Optional + pattern: "*.vcf.gz" - variants_csv: - type: file - description: | - CSV file containing SNV calls. Optional - pattern: "*_variants.csv" + - meta: + type: file + description: | + CSV file containing SNV calls. Optional + pattern: "*_variants.csv" + - "*_variants.csv": + type: file + description: | + CSV file containing SNV calls. Optional + pattern: "*_variants.csv" - loh_csv: - type: file - description: | - CSV file containing LOH calls. Optional - pattern: "*_loh.csv" + - meta: + type: file + description: | + CSV file containing LOH calls. Optional + pattern: "*_loh.csv" + - "*_loh.csv": + type: file + description: | + CSV file containing LOH calls. Optional + pattern: "*_loh.csv" - chr_pdf: - type: file - description: | - PDF file containing chromosome plots. Optional - pattern: "*_chromosomes.pdf" + - meta: + type: file + description: | + PDF file containing chromosome plots. Optional + pattern: "*_chromosomes.pdf" + - "*_chromosomes.pdf": + type: file + description: | + PDF file containing chromosome plots. Optional + pattern: "*_chromosomes.pdf" - segmentation_pdf: - type: file - description: | - PDF file containing segmentation plots. Optional - pattern: "*_segmentation.pdf" - - multisample.seg: - type: file - description: | - Tab-delimited file containing segmentation data from multiple samples. Optional - pattern: "*_multisample.seg" + - meta: + type: file + description: | + PDF file containing segmentation plots. Optional + pattern: "*_segmentation.pdf" + - "*_segmentation.pdf": + type: file + description: | + PDF file containing segmentation plots. Optional + pattern: "*_segmentation.pdf" + - multisample_seg: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_multisample.seg": + type: file + description: multisample segmentation results + pattern: "*_multisample.seg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purgedups/calcuts/meta.yml b/modules/nf-core/purgedups/calcuts/meta.yml index 94fcec79502..4c236d65227 100644 --- a/modules/nf-core/purgedups/calcuts/meta.yml +++ b/modules/nf-core/purgedups/calcuts/meta.yml @@ -6,40 +6,50 @@ keywords: - purge duplications tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stat: - type: file - description: Histogram of coverage - pattern: "*.stat" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stat: + type: file + description: Histogram of coverage + pattern: "*.stat" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cutoff: - type: file - description: Cutoff file - pattern: "*.cutoffs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cutoffs": + type: file + description: Cutoff file + pattern: "*.cutoffs" - log: - type: file - description: Log file - pattern: ".calcuts.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.calcuts.log": + type: file + description: Log file + pattern: ".calcuts.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/getseqs/meta.yml b/modules/nf-core/purgedups/getseqs/meta.yml index 2b759ce4f02..41d85b64970 100644 --- a/modules/nf-core/purgedups/getseqs/meta.yml +++ b/modules/nf-core/purgedups/getseqs/meta.yml @@ -7,44 +7,54 @@ keywords: - assembly curation tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly in fasta format - pattern: "*.fasta" - - bed: - type: file - description: Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly in fasta format + pattern: "*.fasta" + - bed: + type: file + description: Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - haplotigs: - type: file - description: Fasta file containing purged haplotigs - pattern: "*.hap.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap.fa": + type: file + description: Fasta file containing purged haplotigs + pattern: "*.hap.fa" - purged: - type: file - description: Fasta file purged of duplicated haplotigs - pattern: "*.purged.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.purged.fa": + type: file + description: Fasta file purged of duplicated haplotigs + pattern: "*.purged.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/histplot/meta.yml b/modules/nf-core/purgedups/histplot/meta.yml index 47596104f21..f4215c49769 100644 --- a/modules/nf-core/purgedups/histplot/meta.yml +++ b/modules/nf-core/purgedups/histplot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "purgedups_histplot" description: Plots the read coverage from a purge dups statistics file and cutoffs. @@ -8,40 +7,44 @@ keywords: - Read depth tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - statfile: - type: file - description: A Purge dups statistic file - pattern: "*.stat" - - cutoff: - type: file - description: A Purge dups cutoff file - pattern: "*.cutoffs" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - statfile: + type: file + description: A Purge dups statistic file + pattern: "*.stat" + - cutoff: + type: file + description: A Purge dups cutoff file + pattern: "*.cutoffs" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: A png file of the read depth coverage. - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.png": + type: file + description: A png file of the read depth coverage. + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/pbcstat/meta.yml b/modules/nf-core/purgedups/pbcstat/meta.yml index 875de168cf8..db635a23fe3 100644 --- a/modules/nf-core/purgedups/pbcstat/meta.yml +++ b/modules/nf-core/purgedups/pbcstat/meta.yml @@ -1,5 +1,6 @@ name: "purgedups_pbcstat" -description: Create read depth histogram and base-level read depth for an assembly based on pacbio data +description: Create read depth histogram and base-level read depth for an assembly + based on pacbio data keywords: - sort - genome assembly @@ -7,40 +8,50 @@ keywords: - read depth tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf_alignment: - type: file - description: PAF alignment file - pattern: "*.paf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - paf_alignment: + type: file + description: PAF alignment file + pattern: "*.paf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stat: - type: file - description: PacBio Statistic file - pattern: "*.PB.stat" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.PB.stat": + type: file + description: PacBio Statistic file + pattern: "*.PB.stat" - basecov: - type: file - description: PacBio Base coverage file - pattern: "*.PB.base.cov" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.PB.base.cov": + type: file + description: PacBio Base coverage file + pattern: "*.PB.base.cov" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/purgedups/meta.yml b/modules/nf-core/purgedups/purgedups/meta.yml index d79ab58ed93..ecee7b80548 100644 --- a/modules/nf-core/purgedups/purgedups/meta.yml +++ b/modules/nf-core/purgedups/purgedups/meta.yml @@ -8,48 +8,58 @@ keywords: - Read depth tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - basecov: - type: file - description: A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT - pattern: "*.PB.base.cov" - - cutoff: - type: file - description: A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS - pattern: "*.cutoffs" - - paf: - type: file - description: A file of assembly alignments to itself - pattern: "*.paf(.gz)?" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - basecov: + type: file + description: A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT + pattern: "*.PB.base.cov" + - cutoff: + type: file + description: A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS + pattern: "*.cutoffs" + - paf: + type: file + description: A file of assembly alignments to itself + pattern: "*.paf(.gz)?" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: A bed file of sequences purged of false duplications - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dups.bed": + type: file + description: A bed file of sequences purged of false duplications + pattern: "*.bed" - log: - type: file - description: A log of the tool output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.purge_dups.log": + type: file + description: A log of the tool output + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/splitfa/meta.yml b/modules/nf-core/purgedups/splitfa/meta.yml index 938cc225f0c..a3a9eeaa4b7 100644 --- a/modules/nf-core/purgedups/splitfa/meta.yml +++ b/modules/nf-core/purgedups/splitfa/meta.yml @@ -7,36 +7,40 @@ keywords: - purging tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_fasta: - type: file - description: Fasta split by N's - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.split.fasta.gz": + type: file + description: Fasta split by N's + pattern: "*.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/pycoqc/meta.yml b/modules/nf-core/pycoqc/meta.yml index cfbd8516337..c535c56469e 100644 --- a/modules/nf-core/pycoqc/meta.yml +++ b/modules/nf-core/pycoqc/meta.yml @@ -7,39 +7,49 @@ keywords: - nanopore tools: - pycoqc: - description: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data + description: PycoQC computes metrics and generates interactive QC plots for Oxford + Nanopore technologies sequencing data homepage: https://github.com/tleonardi/pycoQC documentation: https://tleonardi.github.io/pycoQC/ tool_dev_url: https://github.com/tleonardi/pycoQC doi: "10.21105/joss.01236" licence: ["GNU General Public v3 (GPL v3)"] + identifier: biotools:pycoqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - summary: - type: file - description: sequencing summary file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - summary: + type: file + description: sequencing summary file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: Results in HTML format + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format - json: - type: file - description: Results in JSON format - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.{json}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/pydamage/analyze/meta.yml b/modules/nf-core/pydamage/analyze/meta.yml index fd6aa513e6c..d862fd3d42d 100644 --- a/modules/nf-core/pydamage/analyze/meta.yml +++ b/modules/nf-core/pydamage/analyze/meta.yml @@ -20,34 +20,37 @@ tools: documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: PyDamage results as csv files - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pydamage_results/pydamage_results.csv: + type: file + description: PyDamage results as csv files + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/pydamage/filter/meta.yml b/modules/nf-core/pydamage/filter/meta.yml index 6b1b0bb8753..eb20375440f 100644 --- a/modules/nf-core/pydamage/filter/meta.yml +++ b/modules/nf-core/pydamage/filter/meta.yml @@ -20,30 +20,33 @@ tools: documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: csv file from pydamage analyze - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: csv file from pydamage analyze + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: PyDamage filtered results as csv file - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pydamage_results/pydamage_filtered_results.csv: + type: file + description: PyDamage filtered results as csv file + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/pyrodigal/meta.yml b/modules/nf-core/pyrodigal/meta.yml index 0967606f34d..d8394d07069 100644 --- a/modules/nf-core/pyrodigal/meta.yml +++ b/modules/nf-core/pyrodigal/meta.yml @@ -1,5 +1,6 @@ name: "pyrodigal" -description: Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes. +description: Pyrodigal is a Python module that provides bindings to Prodigal, a fast, + reliable protein-coding gene prediction for prokaryotic genomes. keywords: - sort - annotation @@ -7,52 +8,75 @@ keywords: - prokaryote tools: - "pyrodigal": - description: "Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython." + description: "Pyrodigal is a Python module that provides bindings to Prodigal + (ORF finder for microbial sequences) using Cython." homepage: "https://pyrodigal.readthedocs.org/" documentation: "https://pyrodigal.readthedocs.org/" tool_dev_url: "https://github.com/althonos/pyrodigal/" doi: "10.21105/joss.04296" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta.gz,fa.gz,fna.gz}" - - output_format: - type: string - description: Output format - pattern: "{gbk,gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta.gz,fa.gz,fna.gz}" + - - output_format: + type: string + description: Output format + pattern: "{gbk,gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotations: - type: file - description: Gene annotations. The file format is specified via input channel "output_format". - pattern: "*.{gbk,gff}.gz" - - faa: - type: file - description: protein translations file - pattern: "*.{faa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${output_format}.gz": + type: file + description: Gene annotations. The file format is specified via input channel + "output_format". + pattern: "*.{gbk,gff}.gz" - fna: - type: file - description: nucleotide sequences file - pattern: "*.{fna.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fna.gz": + type: file + description: nucleotide sequences file + pattern: "*.{fna.gz}" + - faa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.faa.gz": + type: file + description: protein translations file + pattern: "*.{faa.gz}" - score: - type: file - description: all potential genes (with scores) - pattern: "*.{score.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.score.gz": + type: file + description: all potential genes (with scores) + pattern: "*.{score.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/qcat/meta.yml b/modules/nf-core/qcat/meta.yml index c00a21eef45..81bf47b8bfd 100644 --- a/modules/nf-core/qcat/meta.yml +++ b/modules/nf-core/qcat/meta.yml @@ -11,30 +11,36 @@ tools: homepage: https://github.com/nanoporetech/qcat documentation: https://github.com/nanoporetech/qcat#qcat licence: ["MPL-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Non-demultiplexed fastq files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Non-demultiplexed fastq files + - - barcode_kit: + type: string + description: Barcode kit used for demultiplexing output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Demultiplexed fastq samples - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq/*.fastq.gz: + type: file + description: Demultiplexed fastq samples + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml index 7756d4975b6..8be33c00a58 100644 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -15,34 +15,37 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/qualimap/bamqccram/meta.yml b/modules/nf-core/qualimap/bamqccram/meta.yml index ec388b309ae..4b7225a595b 100644 --- a/modules/nf-core/qualimap/bamqccram/meta.yml +++ b/modules/nf-core/qualimap/bamqccram/meta.yml @@ -15,38 +15,49 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bacramm: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" - - fasta: - type: file - description: Reference file of cram file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: Input cram file + pattern: "*.{cram}" + - crai: + type: file + description: Index file for cram file + pattern: "*.{crai}" + - - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" + - - fasta: + type: file + description: Reference file of cram file + pattern: "*.{fasta,fa,fna}" + - - fasta_fai: + type: file + description: Index file for reference file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml index 6f766e4f503..a730261b596 100644 --- a/modules/nf-core/qualimap/rnaseq/meta.yml +++ b/modules/nf-core/qualimap/rnaseq/meta.yml @@ -15,39 +15,42 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/quartonotebook/meta.yml b/modules/nf-core/quartonotebook/meta.yml index 5d95e8b6630..e3c3c1cfedd 100644 --- a/modules/nf-core/quartonotebook/meta.yml +++ b/modules/nf-core/quartonotebook/meta.yml @@ -13,70 +13,96 @@ tools: documentation: https://quarto.org/docs/reference/ tool_dev_url: https://github.com/quarto-dev/quarto-cli licence: ["MIT"] + identifier: "" - papermill: description: Parameterize, execute, and analyze notebooks homepage: https://github.com/nteract/papermill documentation: http://papermill.readthedocs.io/en/latest/ tool_dev_url: https://github.com/nteract/papermill licence: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]`. - - notebook: - type: file - description: The Quarto notebook to be rendered. - pattern: "*.{qmd}" - - parameters: - type: map - description: | - Groovy map with notebook parameters which will be passed to Quarto to - generate parametrized reports. - - input_files: - type: file - description: One or multiple files serving as input data for the notebook. - pattern: "*" - - extensions: - type: file - description: | - A quarto `_extensions` directory with custom template(s) to be - available for rendering. - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - notebook: + type: file + description: The Quarto notebook to be rendered. + pattern: "*.{qmd}" + - - parameters: + type: map + description: | + Groovy map with notebook parameters which will be passed to Quarto to + generate parametrized reports. + - - input_files: + type: file + description: One or multiple files serving as input data for the notebook. + pattern: "*" + - - extensions: + type: file + description: | + A quarto `_extensions` directory with custom template(s) to be + available for rendering. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]`. - html: - type: file - description: HTML report generated by Quarto. - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - "*.html": + type: file + description: HTML report generated by Quarto. + pattern: "*.html" - notebook: - type: file - description: The original, un-rendered notebook. - pattern: "*.[qmd,ipynb,rmd]" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - ${notebook}: + type: file + description: The original, un-rendered notebook. + pattern: "*.[qmd,ipynb,rmd]" - artifacts: - type: file - description: Artifacts generated during report rendering. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - artifacts/*: + type: file + description: Artifacts generated during report rendering. + pattern: "*" - params_yaml: - type: file - description: Parameters used during report rendering. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - params.yml: + type: file + description: Parameters used during report rendering. + pattern: "*" - extensions: - type: file - description: Quarto extensions used during report rendering. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - _extensions: + type: file + description: Quarto extensions used during report rendering. + pattern: "*" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@fasterius" maintainers: diff --git a/modules/nf-core/quast/meta.yml b/modules/nf-core/quast/meta.yml index 5850ff98c86..ea4924bdfc6 100644 --- a/modules/nf-core/quast/meta.yml +++ b/modules/nf-core/quast/meta.yml @@ -13,46 +13,94 @@ tools: homepage: http://bioinf.spbau.ru/quast doi: 10.1093/bioinformatics/btt086 licence: ["GPL-2.0-only"] + identifier: biotools:quast input: - - consensus: - type: file - description: | - Fasta file containing the assembly of interest - - fasta: - type: file - description: | - The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value. - - gff: - type: file - description: The genome GFF file. Has to contain at least a non-empty string dummy value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - consensus: + type: file + description: | + Fasta file containing the assembly of interest + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value. + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: The genome GFF file. Has to contain at least a non-empty string + dummy value. output: - - quast: - type: directory - description: Directory containing complete quast report - pattern: "{prefix}/" - - report: - type: file - description: tab-separated version of the summary, suitable for spreadsheets and mqc - pattern: "${prefix}.tsv" - - misassemblies: - type: file - description: | - Report containing misassemblies, only when a reference fasta is provided - pattern: "${prefix}_misassemblies.tsv" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: | + Directory containing the results of the QUAST analysis + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: TSV file + pattern: "${prefix}.tsv" - transcriptome: - type: file - description: | - Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided - pattern: "${prefix}_transcriptome.tsv" + - meta: + type: file + description: | + Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided + pattern: "${prefix}_transcriptome.tsv" + - ${prefix}_transcriptome.tsv: + type: file + description: | + Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided + pattern: "${prefix}_transcriptome.tsv" + - misassemblies: + - meta: + type: file + description: | + Report containing misassemblies, only when a reference fasta is provided + pattern: "${prefix}_misassemblies.tsv" + - ${prefix}_misassemblies.tsv: + type: file + description: | + Report containing misassemblies, only when a reference fasta is provided + pattern: "${prefix}_misassemblies.tsv" - unaligned: - type: file - description: | - Report containing unaligned contigs, only when a reference fasta is provided - pattern: "${prefix}_unaligned.tsv" + - meta: + type: file + description: | + Report containing unaligned contigs, only when a reference fasta is provided + pattern: "${prefix}_unaligned.tsv" + - ${prefix}_unaligned.tsv: + type: file + description: | + Report containing unaligned contigs, only when a reference fasta is provided + pattern: "${prefix}_unaligned.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/quilt/quilt/meta.yml b/modules/nf-core/quilt/quilt/meta.yml index e4653983217..90dbb4caf52 100644 --- a/modules/nf-core/quilt/quilt/meta.yml +++ b/modules/nf-core/quilt/quilt/meta.yml @@ -1,5 +1,6 @@ name: "quilt_quilt" -description: QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel. +description: QUILT is an R and C++ program for rapid genotype imputation from low-coverage + sequence using a large reference panel. keywords: - imputation - low-coverage @@ -8,99 +9,143 @@ keywords: - vcf tools: - "quilt": - description: "Read aware low coverage whole genome sequence imputation from a reference panel" + description: "Read aware low coverage whole genome sequence imputation from a + reference panel" homepage: "https://github.com/rwdavies/quilt" documentation: "https://github.com/rwdavies/quilt" tool_dev_url: "https://github.com/rwdavies/quilt" doi: "10.1038/s41588-021-00877-0" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: (Mandatory) BAM/CRAM files - pattern: "*.{bam,cram,sam}" - - bais: - type: file - description: (Mandatory) BAM/CRAM index files - pattern: "*.{bai}" - - reference_haplotype_file: - type: file - description: (Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1) - pattern: "*.{hap.gz}" - - reference_legend_file: - type: file - description: (Mandatory) Reference haplotype legend file in IMPUTE format (file with one row per SNP, and a header including position for the physical position in 1 based coordinates, a0 for the reference allele, and a1 for the alternate allele). - pattern: "*.{legend.gz}" - - chr: - type: string - description: (Mandatory) What chromosome to run. Should match BAM headers. - - regions_start: - type: integer - description: (Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd. - - regions_end: - type: integer - description: (Mandatory) When running imputation, where to stop. - - buffer: - type: integer - description: Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd. - - ngen: - type: integer - description: Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure. - - genetic_map_file: - type: file - description: (Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate). - pattern: "*.{txt.gz}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - posfile: - type: file - description: (Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab seperated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized. - pattern: "*.{txt}" - - phasefile: - type: file - description: (Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header. - pattern: "*.{txt}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: (Optional) File with reference genome. - pattern: "*.{txt.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: (Mandatory) BAM/CRAM files + pattern: "*.{bam,cram,sam}" + - bais: + type: file + description: (Mandatory) BAM/CRAM index files + pattern: "*.{bai}" + - reference_haplotype_file: + type: file + description: (Mandatory) Reference haplotype file in IMPUTE format (file with + no header and no rownames, one row per SNP, one column per reference haplotype, + space separated, values must be 0 or 1) + pattern: "*.{hap.gz}" + - reference_legend_file: + type: file + description: (Mandatory) Reference haplotype legend file in IMPUTE format (file + with one row per SNP, and a header including position for the physical position + in 1 based coordinates, a0 for the reference allele, and a1 for the alternate + allele). + pattern: "*.{legend.gz}" + - chr: + type: string + description: (Mandatory) What chromosome to run. Should match BAM headers. + - regions_start: + type: integer + description: (Mandatory) When running imputation, where to start from. The 1-based + position x is kept if regionStart <= x <= regionEnd. + - regions_end: + type: integer + description: (Mandatory) When running imputation, where to stop. + - ngen: + type: integer + description: Number of generations since founding or mixing. Note that the algorithm + is relatively robust to this. Use nGen = 4 * Ne / K if unsure. + - buffer: + type: integer + description: Buffer of region to perform imputation over. So imputation is run + form regionStart-buffer to regionEnd+buffer, and reported for regionStart + to regionEnd, including the bases of regionStart and regionEnd. + - genetic_map_file: + type: file + description: (Optional) File with genetic map information, a file with 3 white-space + delimited entries giving position (1-based), genetic rate map in cM/Mbp, and + genetic map in cM. If no file included, rate is based on physical distance + and expected rate (expRate). + pattern: "*.{txt.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - posfile: + type: file + description: (Optional) File with positions of where to impute, lining up one-to-one + with genfile. File is tab seperated with no header, one row per SNP, with + col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), + col 3 = reference base, col 4 = alternate base. Bases are capitalized. + pattern: "*.{txt}" + - phasefile: + type: file + description: (Optional) File with truth phasing results. Supersedes genfile + if both options given. File has a header row with a name for each sample, + matching what is found in the bam file. Each subject is then a tab seperated + column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 + or 0|1. Note therefore this file has one more row than posfile which has no + header. + pattern: "*.{txt}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: (Optional) File with reference genome. + pattern: "*.{txt.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with both SNP annotation information and per-sample genotype information. - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file with both SNP annotation information and per-sample genotype + information. + pattern: "*.{vcf.gz}" - tbi: - type: file - description: TBI file of the VCF. - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: TBI file of the VCF. + pattern: "*.{vcf.gz.tbi}" - rdata: - type: directory - description: Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE). + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - 'RData", type: "dir': + type: directory + description: Optional directory path to prepared RData file with reference objects + (useful with --save_prepared_reference=TRUE). - plots: - type: directory - description: Optional directory path to save plots. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - 'plots", type: "dir': + type: directory + description: Optional directory path to save plots. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/racon/meta.yml b/modules/nf-core/racon/meta.yml index 9698c0a8aee..360a578d4ee 100644 --- a/modules/nf-core/racon/meta.yml +++ b/modules/nf-core/racon/meta.yml @@ -7,44 +7,48 @@ keywords: - polish tools: - racon: - description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. + description: Ultrafast consensus module for raw de novo genome assembly of long + uncorrected reads. homepage: https://github.com/lbcb-sci/racon documentation: https://github.com/lbcb-sci/racon tool_dev_url: https://github.com/lbcb-sci/racon doi: 10.1101/gr.214270.116 licence: ["MIT"] + identifier: biotools:Racon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files. Racon expects single end reads - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" - - assembly: - type: file - description: Genome assembly to be improved - pattern: "*.{fasta,fa}" - - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files. Racon expects single end reads + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - assembly: + type: file + description: Genome assembly to be improved + pattern: "*.{fasta,fa}" + - paf: + type: file + description: Alignment in PAF format + pattern: "*.paf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - improved_assembly: - type: file - description: Improved genome assembly - pattern: "*_assembly_consensus.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_assembly_consensus.fasta.gz": + type: file + description: Improved genome assembly + pattern: "*_assembly_consensus.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/rapidnj/meta.yml b/modules/nf-core/rapidnj/meta.yml index 0e54b61f103..84b9a617bdc 100644 --- a/modules/nf-core/rapidnj/meta.yml +++ b/modules/nf-core/rapidnj/meta.yml @@ -1,35 +1,43 @@ name: rapidnj -description: Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments. +description: Produces a Newick format phylogeny from a multiple sequence alignment + using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments. keywords: - phylogeny - newick - neighbour-joining tools: - rapidnj: - description: RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. + description: RapidNJ is an algorithmic engineered implementation of canonical + neighbour-joining. It uses an efficient search heuristic to speed-up the core + computations of the neighbour-joining method that enables RapidNJ to outperform + other state-of-the-art neighbour-joining implementations. homepage: https://birc.au.dk/software/rapidnj documentation: https://birc.au.dk/software/rapidnj tool_dev_url: https://github.com/somme89/rapidNJ doi: "10.1007/978-3-540-87361-7_10" licence: ["GPL v2"] + identifier: biotools:rapidnj input: - - alignment: - type: file - description: A FASTA format multiple sequence alignment file - pattern: "*.{fasta,fas,fa,mfa}" + - - alignment: + type: file + description: A FASTA format multiple sequence alignment file + pattern: "*.{fasta,fas,fa,mfa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{tre}" - stockholm_alignment: - type: file - description: An alignment in Stockholm format - pattern: "*.{sth}" + - "*.sth": + type: file + description: An alignment in Stockholm format + pattern: "*.{sth}" + - phylogeny: + - "*.tre": + type: file + description: A phylogeny in Newick format + pattern: "*.{tre}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aunderwo" - "@avantonder" diff --git a/modules/nf-core/rasusa/meta.yml b/modules/nf-core/rasusa/meta.yml index 8d80563af6b..abda9a394a8 100644 --- a/modules/nf-core/rasusa/meta.yml +++ b/modules/nf-core/rasusa/meta.yml @@ -12,35 +12,38 @@ tools: tool_dev_url: https://github.com/mbhall88/rasusa doi: "10.5281/zenodo.3731394" licence: ["MIT"] + identifier: biotools:rasusa input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input paired-end FastQ files - - genome_size: - type: string - description: Genome size of the species - - depth_cutoff: - type: integer - description: Depth of coverage cutoff + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input paired-end FastQ files + - genome_size: + type: string + description: Genome size of the species + - - depth_cutoff: + type: integer + description: Depth of coverage cutoff output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Reads with subsampled coverage - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Reads with subsampled coverage + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@thanhleviet" maintainers: diff --git a/modules/nf-core/raven/meta.yml b/modules/nf-core/raven/meta.yml index cd962ec3caa..a017c4f2442 100644 --- a/modules/nf-core/raven/meta.yml +++ b/modules/nf-core/raven/meta.yml @@ -14,34 +14,43 @@ tools: tool_dev_url: https://github.com/lbcb-sci/raven doi: 10.1038/s43588-021-00073-4 licence: ["MIT"] + identifier: biotools:raven input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', suffix:'bacteria' ] - - reads: - type: file - description: Input file in FASTA/FASTQ format. - pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', suffix:'bacteria' ] + - reads: + type: file + description: Input file in FASTA/FASTQ format. + pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', suffix:'bacteria' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Assembled FASTA file - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', suffix:'bacteria' ] + - "*.fasta.gz": + type: file + description: Assembled FASTA file + pattern: "*.fasta.gz" - gfa: - type: file - description: Repeat graph - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', suffix:'bacteria' ] + - "*.gfa.gz": + type: file + description: Repeat graph + pattern: "*.gfa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" maintainers: diff --git a/modules/nf-core/raxmlng/meta.yml b/modules/nf-core/raxmlng/meta.yml index f70bfa62e30..9472081ce58 100644 --- a/modules/nf-core/raxmlng/meta.yml +++ b/modules/nf-core/raxmlng/meta.yml @@ -1,35 +1,41 @@ name: raxmlng -description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. +description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood + (ML) optimality criterion. keywords: - phylogeny - newick - maximum likelihood tools: - raxmlng: - description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. + description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood + (ML) optimality criterion. homepage: https://github.com/amkozlov/raxml-ng documentation: https://github.com/amkozlov/raxml-ng/wiki tool_dev_url: https://github.com/amkozlov/raxml-ng doi: 10.1093/bioinformatics/btz305 licence: ["GPL v2-or-later"] + identifier: "" input: - - alignment: - type: file - description: A FASTA format multiple sequence alignment file - pattern: "*.{fasta,fas,fa,mfa}" + - - alignment: + type: file + description: A FASTA format multiple sequence alignment file + pattern: "*.{fasta,fas,fa,mfa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{raxml.bestTree}" + - "*.raxml.bestTree": + type: file + description: A phylogeny in Newick format + pattern: "*.{raxml.bestTree}" - phylogeny_bootstrapped: - type: file - description: A phylogeny in Newick format with bootstrap values - pattern: "*.{raxml.support}" + - "*.raxml.support": + type: file + description: A phylogeny in Newick format with bootstrap values + pattern: "*.{raxml.support}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" - "@aunderwo" diff --git a/modules/nf-core/repeatmodeler/builddatabase/meta.yml b/modules/nf-core/repeatmodeler/builddatabase/meta.yml index d3aa9310fb5..cc78cf0f1b4 100644 --- a/modules/nf-core/repeatmodeler/builddatabase/meta.yml +++ b/modules/nf-core/repeatmodeler/builddatabase/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "repeatmodeler_builddatabase" description: Create a database for RepeatModeler @@ -8,36 +7,40 @@ keywords: - repeat tools: - "repeatmodeler": - description: "RepeatModeler is a de-novo repeat family identification and modeling package." + description: "RepeatModeler is a de-novo repeat family identification and modeling + package." homepage: "https://github.com/Dfam-consortium/RepeatModeler" documentation: "https://github.com/Dfam-consortium/RepeatModeler" tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler" licence: ["Open Software License v2.1"] + identifier: biotools:repeatmodeler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta,fsa,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Fasta file + pattern: "*.{fasta,fsa,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - db: - type: file - description: Database files for repeatmodeler - pattern: "`${prefix}.*`" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Database files for repeatmodeler + pattern: "`${prefix}.*`" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml index 29bb795bf35..6693ae9a192 100644 --- a/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml +++ b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "repeatmodeler_repeatmodeler" -description: Performs de novo transposable element (TE) family identification with RepeatModeler +description: Performs de novo transposable element (TE) family identification with + RepeatModeler keywords: - genomics - fasta @@ -9,43 +9,59 @@ keywords: - transposable element tools: - "repeatmodeler": - description: "RepeatModeler is a de-novo repeat family identification and modeling package." + description: "RepeatModeler is a de-novo repeat family identification and modeling + package." homepage: "https://github.com/Dfam-consortium/RepeatModeler" documentation: "https://github.com/Dfam-consortium/RepeatModeler" tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler" licence: ["Open Software License v2.1"] + identifier: biotools:repeatmodeler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - db: - type: file - description: RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - db: + type: file + description: RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fasta: - type: file - description: Consensus repeat sequences - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.fa": + type: file + description: Consensus repeat sequences + pattern: "*.fa" - stk: - type: file - description: Seed alignments - pattern: "*.stk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.stk": + type: file + description: Seed alignments + pattern: "*.stk" - log: - type: file - description: A summarized log of the run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: A summarized log of the run + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/resfinder/run/meta.yml b/modules/nf-core/resfinder/run/meta.yml index aa9ad76b864..7e81dc15274 100644 --- a/modules/nf-core/resfinder/run/meta.yml +++ b/modules/nf-core/resfinder/run/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "resfinder_run" -description: ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria +description: ResFinder identifies acquired antimicrobial resistance genes in total + or partial sequenced isolates of bacteria keywords: - blastn - kma @@ -10,125 +10,195 @@ keywords: - resistance genes tools: - "resfinder": - description: "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria" + description: "ResFinder identifies acquired antimicrobial resistance genes in + total or partial sequenced isolates of bacteria" homepage: "https://bitbucket.org/genomicepidemiology/resfinder.git/src" documentation: "https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md" tool_dev_url: "https://bitbucket.org/genomicepidemiology/resfinder.git/src" doi: "10.1099/mgen.0.000748" licence: ["APACHE-2.0"] + identifier: biotools:resfinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fastq: - type: file - description: fastq file(s) - pattern: "*.{fastq,fq}{.gz}" - - - fasta: - type: file - description: fasta file - pattern: "*.{fa,fna}" - - - db_point: - type: directory - description: database directory containing known point mutations - - - db_res: - type: directory - description: database directory containing known resistance genes - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: fastq file(s) + pattern: "*.{fastq,fq}{.gz}" + - fasta: + type: file + description: fasta file + pattern: "*.{fa,fna}" + - - db_point: + type: directory + description: database directory containing known point mutations + - - db_res: + type: directory + description: database directory containing known resistance genes output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - json: - type: file - description: CGE standardized json file - pattern: "*.json" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: CGE standardized json file + pattern: "*.json" - disinfinder_kma: - type: directory - description: directory holding kma results - pattern: "disinfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - disinfinder_kma: + type: directory + description: directory holding kma results + pattern: "disinfinder_kma" - pheno_table_species: - type: file - description: table with species specific AMR phenotypes - pattern: "pheno_table_species.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pheno_table_species.txt: + type: file + description: table with species specific AMR phenotypes + pattern: "pheno_table_species.tsv" - pheno_table: - type: file - description: table with all AMR phenotypes - pattern: "pheno_table.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pheno_table.txt: + type: file + description: table with all AMR phenotypes + pattern: "pheno_table.tsv" - pointfinder_kma: - type: directory - description: directory holding kma results - pattern: "pointfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pointfinder_kma: + type: directory + description: directory holding kma results + pattern: "pointfinder_kma" - pointfinder_prediction: - type: file - description: tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected - pattern: "PointFinder_prediction.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - PointFinder_prediction.txt: + type: file + description: tab separated table; 1 is given to a predicted resistance against + an antibiotic class, 0 is given to not resistance detected + pattern: "PointFinder_prediction.txt" - pointfinder_results: - type: file - description: tab separated table with predicted point mutations leading to antibiotic resistance - pattern: "PointFinder_results.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - PointFinder_results.txt: + type: file + description: tab separated table with predicted point mutations leading to antibiotic + resistance + pattern: "PointFinder_results.txt" - pointfinder_table: - type: file - description: predicted point mutations grouped into genes to which they belong - pattern: "PointFinder_table.txt" - - - resfinder_blast: - type: directory - description: directory holding blast results - pattern: "resfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - PointFinder_table.txt: + type: file + description: predicted point mutations grouped into genes to which they belong + pattern: "PointFinder_table.txt" - resfinder_hit_in_genome_seq: - type: file - description: fasta sequence of resistance gene hits found in the input data (query) - pattern: "ResFinder_Hit_in_genome_seq.fsa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_Hit_in_genome_seq.fsa: + type: file + description: fasta sequence of resistance gene hits found in the input data + (query) + pattern: "ResFinder_Hit_in_genome_seq.fsa" + - resfinder_blast: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - resfinder_blast: + type: directory + description: directory holding blast results + pattern: "resfinder_kma" - resfinder_kma: - type: directory - description: directory holding kma results - pattern: "resfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - resfinder_kma: + type: directory + description: directory holding kma results + pattern: "resfinder_kma" - resfinder_resistance_gene_seq: - type: file - description: fasta sequence of resistance gene hits found in the database (reference) - pattern: "ResFinder_Resistance_gene_seq.fsa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_Resistance_gene_seq.fsa: + type: file + description: fasta sequence of resistance gene hits found in the database (reference) + pattern: "ResFinder_Resistance_gene_seq.fsa" - resfinder_results_table: - type: file - description: predicted resistance genes grouped by antibiotic class - pattern: "ResFinder_results_table.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_results_table.txt: + type: file + description: predicted resistance genes grouped by antibiotic class + pattern: "ResFinder_results_table.txt" - resfinder_results_tab: - type: file - description: tab separated table with predicted resistance genes - pattern: "ResFinder_results_tab.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_results_tab.txt: + type: file + description: tab separated table with predicted resistance genes + pattern: "ResFinder_results_tab.txt" - resfinder_results: - type: file - description: predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes - pattern: "ResFinder_results.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_results.txt: + type: file + description: predicted resistance genes grouped by antibiotic class and hit + alignments to reference resistance genes + pattern: "ResFinder_results.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" maintainers: diff --git a/modules/nf-core/rgi/cardannotation/meta.yml b/modules/nf-core/rgi/cardannotation/meta.yml index 97e6911da6a..8aff020f952 100644 --- a/modules/nf-core/rgi/cardannotation/meta.yml +++ b/modules/nf-core/rgi/cardannotation/meta.yml @@ -1,37 +1,46 @@ name: rgi_cardannotation -description: Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data +description: Preprocess the CARD database for RGI to predict antibiotic resistance + from protein or nucleotide data keywords: - bacteria - fasta - antibiotic resistance tools: - rgi: - description: This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI. + description: This module preprocesses the downloaded Comprehensive Antibiotic + Resistance Database (CARD) which can then be used as input for RGI. homepage: https://card.mcmaster.ca documentation: https://github.com/arpcard/rgi tool_dev_url: https://github.com/arpcard/rgi doi: "10.1093/nar/gkz935" licence: ["https://card.mcmaster.ca/about"] + identifier: "" input: - - card: - type: directory - description: Directory containing the CARD database - pattern: "*/" + - - card: + type: directory + description: Directory containing the CARD database + pattern: "*/" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: Directory containing the processed CARD database files - pattern: "*/" + - card_database_processed: + type: directory + description: Directory containing the processed CARD database files + pattern: "*/" - tool_version: - type: string - description: The version of the tool in string format (useful for downstream tools such as hAMRronization) + - RGI_VERSION: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) - db_version: - type: string - description: The version of the used database in string format (useful for downstream tools such as hAMRronization) + - DB_VERSION: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" - "@jfy133" diff --git a/modules/nf-core/rgi/main/meta.yml b/modules/nf-core/rgi/main/meta.yml index 7e444c8bbfe..9d9836c0d65 100644 --- a/modules/nf-core/rgi/main/meta.yml +++ b/modules/nf-core/rgi/main/meta.yml @@ -6,59 +6,86 @@ keywords: - antibiotic resistance tools: - rgi: - description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website + description: This tool provides a preliminary annotation of your DNA sequence(s) + based upon the data available in The Comprehensive Antibiotic Resistance Database + (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will + be highlighted. As CARD expands to include more pathogens, genomes, plasmids, + and ontology terms this tool will grow increasingly powerful in providing first-pass + detection of antibiotic resistance associated genes. See license at CARD website homepage: https://card.mcmaster.ca documentation: https://github.com/arpcard/rgi tool_dev_url: https://github.com/arpcard/rgi doi: "10.1093/nar/gkz935" licence: ["https://card.mcmaster.ca/about"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide or protein sequences in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - - card: - type: directory - description: Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions). - pattern: "*/" - - wildcard: - type: directory - description: Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions). - pattern: "*/" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide or protein sequences in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - card: + type: directory + description: Directory containing the CARD database. This is expected to be + the unarchived but otherwise unaltered download folder (see RGI documentation + for download instructions). + pattern: "*/" + - - wildcard: + type: directory + description: Directory containing the WildCARD database (optional). This is + expected to be the unarchived but otherwise unaltered download folder (see + RGI documentation for download instructions). + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON formatted file with RGI results - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON formatted file with RGI results + pattern: "*.{json}" - tsv: - type: file - description: Tab-delimited file with RGI results - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab-delimited file with RGI results + pattern: "*.{txt}" - tmp: - type: directory - description: Directory containing various intermediate files - pattern: "temp/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp/: + type: directory + description: Directory containing various intermediate files + pattern: "temp/" - tool_version: - type: string - description: The version of the tool in string format (useful for downstream tools such as hAMRronization) + - RGI_VERSION: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) - db_version: - type: string - description: The version of the used database in string format (useful for downstream tools such as hAMRronization) + - DB_VERSION: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" - "@jfy133" diff --git a/modules/nf-core/rhocall/annotate/meta.yml b/modules/nf-core/rhocall/annotate/meta.yml index 09a64d2591f..fb041cae88a 100644 --- a/modules/nf-core/rhocall/annotate/meta.yml +++ b/modules/nf-core/rhocall/annotate/meta.yml @@ -11,47 +11,50 @@ tools: documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: vcf file - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: vcf index file - pattern: "*.{tbi}" - - roh: - type: file - description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL - pattern: "*.{roh}" - - bed: - type: file - description: BED file with AZ windows. - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: vcf file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: vcf index file + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - roh: + type: file + description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL + pattern: "*.{roh}" + - - bed: + type: file + description: BED file with AZ windows. + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: vcf file - pattern: "*.{vcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rhocall.vcf": + type: file + description: vcf file + pattern: "*.{vcf,vcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/rhocall/viz/meta.yml b/modules/nf-core/rhocall/viz/meta.yml index bbcad9ba970..7efcab02a9b 100644 --- a/modules/nf-core/rhocall/viz/meta.yml +++ b/modules/nf-core/rhocall/viz/meta.yml @@ -11,41 +11,53 @@ tools: documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: VCF file - pattern: "*.{vcf}" - - roh: - type: file - description: Input RHO file produced from rhocall - pattern: "*.{roh}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: VCF file + pattern: "*.{vcf}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - roh: + type: file + description: Input RHO file produced from rhocall + pattern: "*.{roh}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Bed file containing roh calls - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/${prefix}.bed: + type: file + description: Bed file containing roh calls + pattern: "*.{bed}" - wig: - type: file - description: Wig file containing roh calls - pattern: "*.{wig}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/${prefix}.wig: + type: file + description: Wig file containing roh calls + pattern: "*.{wig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ribotish/predict/meta.yml b/modules/nf-core/ribotish/predict/meta.yml index f1a84467741..e8016a2c9d8 100644 --- a/modules/nf-core/ribotish/predict/meta.yml +++ b/modules/nf-core/ribotish/predict/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribotish_predict" description: Quality control of riboseq bam data @@ -8,113 +7,127 @@ keywords: - bam tools: - "ribotish": - description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data." + description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using + ribosome profiling data." homepage: "https://github.com/zhpn1024/ribotish" documentation: "https://github.com/zhpn1024/ribotish" tool_dev_url: "https://github.com/zhpn1024/ribotish" doi: "10.1038/s41467-017-01981-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing riboseq sample information - e.g. `[ id:'sample1', single_end:false ] - - bam_ribo: - type: file - description: Sorted riboseq BAM file(s) - pattern: "*.{bam}" - - bai_ribo: - type: file - description: Index for sorted riboseq bam file(s) - pattern: "*.{bai}" - - meta2: - type: map - description: | - Groovy Map containing TI-Seq sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam_ti: - type: file - description: Sorted TI-Seq BAM file(s) - pattern: "*.{bam}" - - bai_ti: - type: file - description: Index for sorted TI-Seq BAM file(s) - pattern: "*.{bai}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - - fasta: - type: file - description: | - Fasta-format sequence file for reference sequences used in the bam file - pattern: "*.gtf" - - gtf: - type: file - description: | - GTF-format annotation file for reference sequences used in the bam file - pattern: "*.gtf" - - meta4: - type: map - description: | - Groovy Map containing information on candidate ORFs - - candidate_orfs: - type: file - description: | - 3-column (transIDstarttstop) candidate ORFs file - pattern: "*.txt" - - meta5: - type: map - description: | - Groovy Map containing information on riboseq P-site offfset parameter - files - - para_ribo: - type: file - description: | - Input P-site offset parameter files for riboseq bam files - pattern: "*.py" - - meta6: - type: map - description: | - Groovy Map containing information on TI-seq P-site offfset parameter - files - - para_ribo: - type: file - description: | - Input P-site offset parameter files for TI-seq bam files - pattern: "*.py" - + - - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - bam_ribo: + type: file + description: Sorted riboseq BAM file(s) + pattern: "*.{bam}" + - bai_ribo: + type: file + description: Index for sorted riboseq bam file(s) + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing TI-Seq sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam_ti: + type: file + description: Sorted TI-Seq BAM file(s) + pattern: "*.{bam}" + - bai_ti: + type: file + description: Index for sorted TI-Seq BAM file(s) + pattern: "*.{bai}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - fasta: + type: file + description: | + Fasta-format sequence file for reference sequences used in the bam file + pattern: "*.gtf" + - gtf: + type: file + description: | + GTF-format annotation file for reference sequences used in the bam file + pattern: "*.gtf" + - - meta4: + type: map + description: | + Groovy Map containing information on candidate ORFs + - candidate_orfs: + type: file + description: | + 3-column (transIDstarttstop) candidate ORFs file + pattern: "*.txt" + - - meta5: + type: map + description: | + Groovy Map containing information on riboseq P-site offfset parameter + files + - para_ribo: + type: file + description: | + Input P-site offset parameter files for riboseq bam files + pattern: "*.py" + - - meta6: + type: map + description: | + Groovy Map containing information on TI-seq P-site offfset parameter + files + - para_ti: + type: file + description: | + Input P-site offset parameter files for TI-seq bam files + pattern: "*.py" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - predictions: - type: file - description: | - txt file all possible ORF results that fit the thresholds - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_pred.txt": + type: file + description: | + txt file all possible ORF results that fit the thresholds + pattern: "*.{txt}" - all: - type: file - description: | - txt file similar to the predictions but do not use FDR (q-value) cutoff - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_all.txt": + type: file + description: | + txt file similar to the predictions but do not use FDR (q-value) cutoff + pattern: "*.{txt}" - transprofile: - type: file - description: | - Output RPF P-site profile for each transcript. The profile data is in - python dict format, recording non-zero read counts at different - positions on transcript. - pattern: "*.{py}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_transprofile.py": + type: file + description: | + Output RPF P-site profile for each transcript. The profile data is in + python dict format, recording non-zero read counts at different + positions on transcript. + pattern: "*.{py}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribotish/quality/meta.yml b/modules/nf-core/ribotish/quality/meta.yml index 29cf468787c..99bec9d3f79 100644 --- a/modules/nf-core/ribotish/quality/meta.yml +++ b/modules/nf-core/ribotish/quality/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribotish_quality" description: Quality control of riboseq bam data @@ -8,67 +7,79 @@ keywords: - bam tools: - "ribotish": - description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data." + description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using + ribosome profiling data." homepage: "https://github.com/zhpn1024/ribotish" documentation: "https://github.com/zhpn1024/ribotish" tool_dev_url: "https://github.com/zhpn1024/ribotish" doi: "10.1038/s41467-017-01981-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam}" - - bai: - type: file - description: Index for sorted BAM/CRAM/SAM file - pattern: "*.{bai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - - gtf: - type: file - description: | - GTF-format annotation file for reference sequences used in the bam file - pattern: "*.gtf" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam}" + - bai: + type: file + description: Index for sorted BAM/CRAM/SAM file + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - gtf: + type: file + description: | + GTF-format annotation file for reference sequences used in the bam file + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - txt: - type: file - description: | - txt file recording all distribution data in python format for each - group of reads - pattern: "*.{txt}" + - distribution: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.txt": + type: file + description: file containing distribution + pattern: "*.{txt}" - pdf: - type: file - description: | - Pdf figure file is plot of all the distributions and illustration of - quality and P-site offset - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.pdf": + type: file + description: | + Pdf figure file is plot of all the distributions and illustration of + quality and P-site offset + pattern: "*.{pdf}" - offset: - type: file - description: | - This file saves P-site offsets for different reads lengths in python - code dict format, and can be used in further analysis - pattern: "*.{para.py}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.para.py": + type: file + description: | + This file saves P-site offsets for different reads lengths in python + code dict format, and can be used in further analysis + pattern: "*.{para.py}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribotricer/detectorfs/meta.yml b/modules/nf-core/ribotricer/detectorfs/meta.yml index 430f232d001..6daab6c84eb 100644 --- a/modules/nf-core/ribotricer/detectorfs/meta.yml +++ b/modules/nf-core/ribotricer/detectorfs/meta.yml @@ -13,86 +13,142 @@ tools: tool_dev_url: "https://github.com/smithlabcode/ribotricer" doi: "10.1093/bioinformatics/btz878" licence: ["GNU General Public v3 (GPL v3)"] + identifier: biotools:ribotricer input: - - meta: - type: map - description: | - Map containing riboseq sample information - e.g. `[ id:'sample1', single_end:false, strandedness: 'single' ] - - bam_ribo: - type: file - description: Sorted riboseq BAM file(s) - pattern: "*.{bam}" - - bai_ribo: - type: file - description: Index for sorted riboseq bam file(s) - pattern: "*.{bai}" - - meta2: - type: map - description: | - Map containing reference information for the candidate ORFs - e.g. `[ id:'Ensembl human v.111' ]` - - candidate_orfs: - type: file - description: "TSV file with candidate ORFs from 'ribotricer prepareorfs'" - pattern: "*.tsv" - + - - meta: + type: map + description: | + Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false, strandedness: 'single' ] + - bam: + type: file + description: "BAM/CRAM/SAM file" + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: "Index for sorted BAM/CRAM/SAM file" + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Map containing reference information for the candidate ORFs + e.g. `[ id:'Ensembl human v.111' ]` + - candidate_orfs: + type: file + description: "TSV file with candidate ORFs from 'ribotricer prepareorfs'" + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing riboseq sample information - e.g. `[ id:'sample1', single_end:false ] - protocol: - type: file - description: "txt file containing inferred protocol if it was inferred (not supplied as input)" - pattern: "*_protocol.txt" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_protocol.txt": + type: file + description: "txt file containing inferred protocol if it was inferred (not + supplied as input)" + pattern: "*_protocol.txt" - bam_summary: - type: file - description: "Text summary of reads found in the BAM" - pattern: "*_bam_summary.txt" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_bam_summary.txt": + type: file + description: "Text summary of reads found in the BAM" + pattern: "*_bam_summary.txt" - read_length_dist: - type: file - description: "PDF-format read length distribution as quality control" - pattern: "*_read_length_dist.pdf" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_read_length_dist.pdf": + type: file + description: "PDF-format read length distribution as quality control" + pattern: "*_read_length_dist.pdf" - metagene_profile_5p: - type: file - description: "Metagene profile aligning with the start codon" - pattern: "*_metagene_profiles_5p.tsv" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_metagene_profiles_5p.tsv": + type: file + description: "Metagene profile aligning with the start codon" + pattern: "*_metagene_profiles_5p.tsv" - metagene_profile_3p: - type: file - description: "Metagene profile aligning with the stop codon" - pattern: "*_metagene_profiles_3p.tsv" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_metagene_profiles_3p.tsv": + type: file + description: "Metagene profile aligning with the stop codon" + pattern: "*_metagene_profiles_3p.tsv" - metagene_plots: - type: file - description: "Metagene plots for quality control" - pattern: "*_metagene_plots.pdf" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_metagene_plots.pdf": + type: file + description: "Metagene plots for quality control" + pattern: "*_metagene_plots.pdf" - psite_offsets: - type: file - description: | - "If the P-site offsets are not provided, txt file containing the - derived relative offsets" - pattern: "*_psite_offsets.txt" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_psite_offsets.txt": + type: file + description: | + "If the P-site offsets are not provided, txt file containing the + derived relative offsets" + pattern: "*_psite_offsets.txt" - pos_wig: - type: file - description: "Positive strand WIG file for visualization in Genome Browser" - pattern: "*_pos.wig" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_pos.wig": + type: file + description: "Positive strand WIG file for visualization in Genome Browser" + pattern: "*_pos.wig" - neg_wig: - type: file - description: "Negative strand WIG file for visualization in Genome Browser" - pattern: "*_neg.wig" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_neg.wig": + type: file + description: "Negative strand WIG file for visualization in Genome Browser" + pattern: "*_neg.wig" - orfs: - type: file - description: | - "TSV with ORFs assessed as translating in this BAM file. You can output - all ORFs regardless of the translation status with option --report_all" - pattern: "*_translating_ORFs.tsv" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_translating_ORFs.tsv": + type: file + description: | + "TSV with ORFs assessed as translating in this BAM file. You can output + all ORFs regardless of the translation status with option --report_all" + pattern: "*_translating_ORFs.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribotricer/prepareorfs/meta.yml b/modules/nf-core/ribotricer/prepareorfs/meta.yml index 005edd57720..6b92b7dff19 100644 --- a/modules/nf-core/ribotricer/prepareorfs/meta.yml +++ b/modules/nf-core/ribotricer/prepareorfs/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribotricer_prepareorfs" description: "Accurate detection of short and long active ORFs using Ribo-seq data" @@ -14,39 +13,40 @@ tools: tool_dev_url: "https://github.com/smithlabcode/ribotricer" doi: "10.1093/bioinformatics/btz878" licence: ["GNU General Public v3 (GPL v3)"] + identifier: biotools:ribotricer input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - - fasta: - type: file - description: | - Fasta-format sequence file for reference sequences used in the bam file - pattern: "*.gtf" - - gtf: - type: file - description: | - GTF-format annotation file for reference sequences used in the bam file - pattern: "*.gtf" - + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - fasta: + type: file + description: | + Fasta-format sequence file for reference sequences used in the bam file + pattern: "*.gtf" + - gtf: + type: file + description: | + GTF-format annotation file for reference sequences used in the bam file + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - candidate_orfs: - type: file - description: "TSV file with candidate ORFs" - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - "*_candidate_orfs.tsv": + type: file + description: "TSV file with candidate ORFs" + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribowaltz/meta.yml b/modules/nf-core/ribowaltz/meta.yml index 334615984cf..39f4d836a02 100644 --- a/modules/nf-core/ribowaltz/meta.yml +++ b/modules/nf-core/ribowaltz/meta.yml @@ -1,96 +1,153 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribowaltz" -description: Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data +description: Calculation of optimal P-site offsets, diagnostic analysis and visual + inspection of ribosome profiling data keywords: - sort - example - genomics tools: - "ribowaltz": - description: "Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data." + description: "Calculation of optimal P-site offsets, diagnostic analysis and visual + inspection of ribosome profiling data." homepage: "https://github.com/LabTranslationalArchitectomics/riboWaltz" documentation: "https://github.com/LabTranslationalArchitectomics/riboWaltz" tool_dev_url: "https://github.com/LabTranslationalArchitectomics/riboWaltz" doi: "10.1371/journal.pcbi.1006169" licence: ["MIT"] + identifier: biotools:ribowaltz input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - meta2: - type: map - description: | - Map containing reference information for the reference genome GTF file - e.g. `[ id:'Ensembl human v.111' ]` - - meta3: - type: map - description: | - Map containing reference information for the reference genome FASTA file - e.g. `[ id:'Ensembl human v.111' ]` - - bam: - type: file - description: Transcriptome BAM file - pattern: "*.{bam}" - - gtf: - type: file - description: GTF file of reference genome - pattern: "*.{gtf.gz,gtf}" - - fasta: - type: file - description: FASTA file of reference genome - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Transcriptome BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Map containing reference information for the reference genome GTF file + e.g. `[ id:'Ensembl human v.111' ]` + - gtf: + type: file + description: GTF file of reference genome + pattern: "*.{gtf.gz,gtf}" + - - meta3: + type: map + description: | + Map containing reference information for the reference genome FASTA file + e.g. `[ id:'Ensembl human v.111' ]` + - fasta: + type: file + description: FASTA file of reference genome + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - best_offset: - type: file - description: Text file with the extremity used for the offset correction step and the best offset for each sample (optional, in case no offsets could be determined, usually because no reads pass filtering criteria) - pattern: "*.best_offset.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.best_offset.txt": + type: file + description: Text file with the extremity used for the offset correction step + and the best offset for each sample (optional, in case no offsets could be + determined, usually because no reads pass filtering criteria) + pattern: "*.best_offset.txt" - offset: - type: file - description: TSV file containing P-site offsets for each read length (optional, in case no offsets could be determined, usually because no reads pass filtering criteria) - pattern: "*.psite_offset.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.psite_offset.tsv{,.gz}": + type: file + description: TSV file containing P-site offsets for each read length (optional, + in case no offsets could be determined, usually because no reads pass filtering + criteria) + pattern: "*.psite_offset.tsv.gz" - offset_plot: - type: file - description: P-site offset plots for each read length (otional) - pattern: "offset_plot/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - offset_plot/*: + type: file + description: P-site offset plots for each read length (otional) + pattern: "offset_plot/*" - psites: - type: file - description: TSV file containing P-site transcriptomic coordinates and information for each alignment (optional) - pattern: "*.psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.psite.tsv{,.gz}": + type: file + description: TSV file containing P-site transcriptomic coordinates and information + for each alignment (optional) + pattern: "*.psite.tsv.gz" - codon_coverage_rpf: - type: file - description: TSV file with codon-level RPF coverage for each transcript (optional) - pattern: "*.codon_coverage_rpf.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.codon_coverage_rpf.tsv{,.gz}": + type: file + description: TSV file with codon-level RPF coverage for each transcript (optional) + pattern: "*.codon_coverage_rpf.tsv.gz" - codon_coverage_psite: - type: file - description: TSV file with codon-level P-site coverage for each transcript (optional) - pattern: "*.codon_coverage_psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.codon_coverage_psite.tsv{,.gz}": + type: file + description: TSV file with codon-level P-site coverage for each transcript (optional) + pattern: "*.codon_coverage_psite.tsv.gz" - cds_coverage: - type: file - description: TSV file with CDS P-site in-frame counts for each transcript (optional) - pattern: "*.cds_coverage_psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.cds_coverage_psite.tsv{,.gz}": + type: file + description: TSV file with CDS P-site in-frame counts for each transcript (optional) + pattern: "*.cds_coverage_psite.tsv.gz" - cds_window_coverage: - type: file - description: TSV file with CDS P-site in-frame counts for each transcript, excluding P-sites within defined distances to start and stop codons (defined by passing --exclude_start and --exclude_stop with the number of nucleotides) (optional) - pattern: "*nt_coverage_psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*nt_coverage_psite.tsv{,.gz}": + type: file + description: TSV file with CDS P-site in-frame counts for each transcript, excluding + P-sites within defined distances to start and stop codons (defined by passing + --exclude_start and --exclude_stop with the number of nucleotides) (optional) + pattern: "*nt_coverage_psite.tsv.gz" - ribowaltz_qc: - type: file - description: riboWaltz diagnostic plots (optional) - pattern: "ribowaltz_qc/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ribowaltz_qc/*.pdf: + type: file + description: riboWaltz diagnostic plots (optional) + pattern: "ribowaltz_qc/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@iraiosub" maintainers: diff --git a/modules/nf-core/rmarkdownnotebook/meta.yml b/modules/nf-core/rmarkdownnotebook/meta.yml index 379690f7528..eeb0eb362c0 100644 --- a/modules/nf-core/rmarkdownnotebook/meta.yml +++ b/modules/nf-core/rmarkdownnotebook/meta.yml @@ -11,6 +11,7 @@ tools: documentation: https://rmarkdown.rstudio.com/lesson-1.html tool_dev_url: https://github.com/rstudio/rmarkdown licence: ["GPL-3"] + identifier: "" params: - parametrize: type: boolean @@ -28,42 +29,70 @@ params: If true, include a parameter `meta` which contains the information specified via the `meta` input channel. input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - notebook: - type: file - description: Rmarkdown file - pattern: "*.{Rmd}" - - parameters: - type: map - description: | - Groovy map with notebook parameters which will be passed to - rmarkdown to generate parametrized reports. - - input_files: - type: file - description: One or multiple files serving as input data for the notebook. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - notebook: + type: file + description: Rmarkdown file + pattern: "*.{Rmd}" + - - parameters: + type: map + description: | + Groovy map with notebook parameters which will be passed to + rmarkdown to generate parametrized reports. + - - input_files: + type: file + description: One or multiple files serving as input data for the notebook. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: HTML report generated from Rmarkdown - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: HTML report generated from Rmarkdown + pattern: "*.html" + - parameterised_notebook: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.parameterised.Rmd": + type: file + description: Parameterised Rmarkdown file + pattern: "*.parameterised.Rmd" + - artifacts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - artifacts/*: + type: file + description: Artifacts generated by the notebook + pattern: "artifacts/*" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - session_info.log: + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/roary/meta.yml b/modules/nf-core/roary/meta.yml index b6c4d124141..ece578df262 100644 --- a/modules/nf-core/roary/meta.yml +++ b/modules/nf-core/roary/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: https://github.com/sanger-pathogens/Roary/ doi: "10.1093/bioinformatics/btv421" licence: ["GPL v3"] + identifier: biotools:roary input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: A set of GFF3 formatted files - pattern: "*.{gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: A set of GFF3 formatted files + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing Roary result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing Roary result files + pattern: "*/*" - aln: - type: file - description: Core-genome alignment produced by Roary (Optional) - pattern: "*.{aln}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.aln: + type: file + description: Core-genome alignment produced by Roary (Optional) + pattern: "*.{aln}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/rrnatranscripts/meta.yml b/modules/nf-core/rrnatranscripts/meta.yml index 145506011b2..93f6a10ef4a 100644 --- a/modules/nf-core/rrnatranscripts/meta.yml +++ b/modules/nf-core/rrnatranscripts/meta.yml @@ -10,21 +10,24 @@ tools: Extraction of ribosomal RNA homepage: https://github.com/nf-core/rnafusion licence: ["GPL-3.0-or-later"] + identifier: "" input: - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" + - - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" output: # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rrna_gtf: - type: file - description: GTF file with ribosomal RNA only - pattern: "*.{gtf}" + - "*rrna_intervals.gtf": + type: file + description: GTF file with ribosomal RNA only + pattern: "*.{gtf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/rsem/calculateexpression/meta.yml b/modules/nf-core/rsem/calculateexpression/meta.yml index e6d580e9b35..0a7fbe1b3cf 100644 --- a/modules/nf-core/rsem/calculateexpression/meta.yml +++ b/modules/nf-core/rsem/calculateexpression/meta.yml @@ -12,53 +12,97 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input reads for quantification - pattern: "*.fastq.gz" - - index: - type: file - description: RSEM index - pattern: "rsem/*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input reads for quantification + pattern: "*.fastq.gz" + - - index: + type: file + description: RSEM index + pattern: "rsem/*" output: - counts_gene: - type: file - description: Expression counts on gene level - pattern: "*.genes.results" - - counts_transctips: - type: file - description: Expression counts on transcript level - pattern: "*.isoforms.results" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.genes.results": + type: file + description: Expression counts on gene level + pattern: "*.genes.results" + - counts_transcript: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.isoforms.results": + type: file + description: Expression counts on transcript level + pattern: "*.isoforms.results" - stat: - type: file - description: RSEM statistics - pattern: "*.stat" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.stat": + type: file + description: RSEM statistics + pattern: "*.stat" - logs: - type: file - description: RSEM logs - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: RSEM logs + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - bam_star: - type: file - description: BAM file generated by STAR (optional) - pattern: "*.STAR.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.STAR.genome.bam": + type: file + description: BAM file generated by STAR (optional) + pattern: "*.STAR.genome.bam" - bam_genome: - type: file - description: Genome BAM file (optional) - pattern: "*.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.genome.bam: + type: file + description: Genome BAM file (optional) + pattern: "*.genome.bam" - bam_transcript: - type: file - description: Transcript BAM file (optional) - pattern: "*.transcript.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.transcript.bam: + type: file + description: Transcript BAM file (optional) + pattern: "*.transcript.bam" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rsem/preparereference/meta.yml b/modules/nf-core/rsem/preparereference/meta.yml index 05aa44fe6ca..e95f4a2ae78 100644 --- a/modules/nf-core/rsem/preparereference/meta.yml +++ b/modules/nf-core/rsem/preparereference/meta.yml @@ -12,28 +12,32 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - fasta: - type: file - description: The Fasta file of the reference genome - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: The GTF file of the reference genome - pattern: "*.gtf" + - - fasta: + type: file + description: The Fasta file of the reference genome + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: The GTF file of the reference genome + pattern: "*.gtf" output: - - rsem: - type: directory - description: RSEM index directory - pattern: "rsem" + - index: + - rsem: + type: directory + description: RSEM index directory + pattern: "rsem" - transcript_fasta: - type: file - description: Fasta file of transcripts - pattern: "rsem/*transcripts.fa" + - "*transcripts.fa": + type: file + description: Fasta file of transcripts + pattern: "rsem/*transcripts.fa" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/bamstat/meta.yml b/modules/nf-core/rseqc/bamstat/meta.yml index 72745310cf7..d69f054428b 100644 --- a/modules/nf-core/rseqc/bamstat/meta.yml +++ b/modules/nf-core/rseqc/bamstat/meta.yml @@ -13,25 +13,32 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" output: - txt: - type: file - description: bam statistics report - pattern: "*.bam_stat.txt" + - meta: + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" + - "*.bam_stat.txt": + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/inferexperiment/meta.yml b/modules/nf-core/rseqc/inferexperiment/meta.yml index d9b9ff63eae..3ac75728946 100644 --- a/modules/nf-core/rseqc/inferexperiment/meta.yml +++ b/modules/nf-core/rseqc/inferexperiment/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: infer_experiment results report - pattern: "*.infer_experiment.txt" + - meta: + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" + - "*.infer_experiment.txt": + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/innerdistance/meta.yml b/modules/nf-core/rseqc/innerdistance/meta.yml index d0a5bf18191..358e4d16080 100644 --- a/modules/nf-core/rseqc/innerdistance/meta.yml +++ b/modules/nf-core/rseqc/innerdistance/meta.yml @@ -13,45 +13,72 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - distance: - type: file - description: the inner distances - pattern: "*.inner_distance.txt" + - meta: + type: file + description: the inner distances + pattern: "*.inner_distance.txt" + - "*distance.txt": + type: file + description: the inner distances + pattern: "*.inner_distance.txt" - freq: - type: file - description: frequencies of different insert sizes - pattern: "*.inner_distance_freq.txt" + - meta: + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" + - "*freq.txt": + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" - mean: - type: file - description: mean/median values of inner distances - pattern: "*.inner_distance_mean.txt" + - meta: + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" + - "*mean.txt": + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" - pdf: - type: file - description: distribution plot of inner distances - pattern: "*.inner_distance_plot.pdf" + - meta: + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" + - "*.pdf": + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.inner_distance_plot.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionannotation/meta.yml b/modules/nf-core/rseqc/junctionannotation/meta.yml index a88aa2db36f..0622ee43bd3 100644 --- a/modules/nf-core/rseqc/junctionannotation/meta.yml +++ b/modules/nf-core/rseqc/junctionannotation/meta.yml @@ -13,53 +13,90 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: + - xls: + - meta: + type: file + description: xls file with junction information + pattern: "*.xls" + - "*.xls": + type: file + description: xls file with junction information + pattern: "*.xls" + - rscript: + - meta: + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - "*.r": + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - log: + - meta: + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" + - "*.log": + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" - bed: - type: file - description: bed file of annotated junctions - pattern: "*.junction.bed" + - meta: + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" + - "*.junction.bed": + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" - interact_bed: - type: file - description: Interact bed file - pattern: "*.Interact.bed" - - xls: - type: file - description: xls file with junction information - pattern: "*.xls" + - meta: + type: file + description: Interact bed file + pattern: "*.Interact.bed" + - "*.Interact.bed": + type: file + description: Interact bed file + pattern: "*.Interact.bed" - pdf: - type: file - description: junction plot - pattern: "*.junction.pdf" + - meta: + type: file + description: junction plot + pattern: "*.junction.pdf" + - "*junction.pdf": + type: file + description: junction plot + pattern: "*.junction.pdf" - events_pdf: - type: file - description: events plot - pattern: "*.events.pdf" - - rscript: - type: file - description: Rscript to reproduce the plots - pattern: "*.r" - - log: - type: file - description: Log file of execution - pattern: "*.junction_annotation.log" + - meta: + type: file + description: events plot + pattern: "*.events.pdf" + - "*events.pdf": + type: file + description: events plot + pattern: "*.events.pdf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionsaturation/meta.yml b/modules/nf-core/rseqc/junctionsaturation/meta.yml index 19ae3f52d92..b6f422dc739 100644 --- a/modules/nf-core/rseqc/junctionsaturation/meta.yml +++ b/modules/nf-core/rseqc/junctionsaturation/meta.yml @@ -13,33 +13,45 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - pdf: - type: file - description: Junction saturation report - pattern: "*.pdf" + - meta: + type: file + description: Junction saturation report + pattern: "*.pdf" + - "*.pdf": + type: file + description: Junction saturation report + pattern: "*.pdf" - rscript: - type: file - description: Junction saturation R-script - pattern: "*.r" + - meta: + type: file + description: Junction saturation R-script + pattern: "*.r" + - "*.r": + type: file + description: Junction saturation R-script + pattern: "*.r" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readdistribution/meta.yml b/modules/nf-core/rseqc/readdistribution/meta.yml index 989792faa20..578200abb24 100644 --- a/modules/nf-core/rseqc/readdistribution/meta.yml +++ b/modules/nf-core/rseqc/readdistribution/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: the read distribution report - pattern: "*.read_distribution.txt" + - meta: + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" + - "*.read_distribution.txt": + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readduplication/meta.yml b/modules/nf-core/rseqc/readduplication/meta.yml index 4b24d30327d..ef94122e901 100644 --- a/modules/nf-core/rseqc/readduplication/meta.yml +++ b/modules/nf-core/rseqc/readduplication/meta.yml @@ -14,41 +14,59 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" output: - seq_xls: - type: file - description: Read duplication rate determined from mapping position of read - pattern: "*seq.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" + - "*seq.DupRate.xls": + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" - pos_xls: - type: file - description: Read duplication rate determined from sequence of read - pattern: "*pos.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" + - "*pos.DupRate.xls": + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" - pdf: - type: file - description: plot of duplication rate - pattern: "*.pdf" + - meta: + type: file + description: plot of duplication rate + pattern: "*.pdf" + - "*.pdf": + type: file + description: plot of duplication rate + pattern: "*.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/tin/meta.yml b/modules/nf-core/rseqc/tin/meta.yml index f760bb2f4b9..6e363ecd83e 100644 --- a/modules/nf-core/rseqc/tin/meta.yml +++ b/modules/nf-core/rseqc/tin/meta.yml @@ -13,37 +13,49 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - bai: - type: file - description: Index for input BAM file - pattern: "*.{bai}" - - bed: - type: file - description: BED file containing the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Index for input BAM file + pattern: "*.{bai}" + - - bed: + type: file + description: BED file containing the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: TXT file containing tin.py results summary - pattern: "*.txt" + - meta: + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" + - "*.txt": + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" - xls: - type: file - description: XLS file containing tin.py results - pattern: "*.xls" + - meta: + type: file + description: XLS file containing tin.py results + pattern: "*.xls" + - "*.xls": + type: file + description: XLS file containing tin.py results + pattern: "*.xls" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index 1991b807d01..e09aff3af67 100644 --- a/modules/nf-core/rtgtools/format/meta.yml +++ b/modules/nf-core/rtgtools/format/meta.yml @@ -1,5 +1,6 @@ name: "rtgtools_format" -description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into the RTG Sequence Data File (SDF) format. +description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into + the RTG Sequence Data File (SDF) format. keywords: - rtg - fasta @@ -8,43 +9,49 @@ keywords: - sam tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input1: - type: file - description: FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data - pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" - - input2: - type: file - description: The right input file when using paired end FASTQ/FASTA data - pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" - - sam_rg: - type: file - description: A file containing a single readgroup header as a SAM header. This can also be supplied as a string in `task.ext.args` as `--sam-rg `. - pattern: "*.{txt,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input1: + type: file + description: FASTA, FASTQ, BAM or SAM file. This should be the left input file + when using paired end FASTQ/FASTA data + pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" + - input2: + type: file + description: The right input file when using paired end FASTQ/FASTA data + pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" + - sam_rg: + type: file + description: A file containing a single readgroup header as a SAM header. This + can also be supplied as a string in `task.ext.args` as `--sam-rg `. + pattern: "*.{txt,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sdf: - type: directory - description: The sequence dictionary format folder created from the input file(s) - pattern: "*.sdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sdf": + type: directory + description: The sequence dictionary format folder created from the input file(s) + pattern: "*.sdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/pedfilter/meta.yml b/modules/nf-core/rtgtools/pedfilter/meta.yml index 4e90fd7bf98..c8eee99d061 100644 --- a/modules/nf-core/rtgtools/pedfilter/meta.yml +++ b/modules/nf-core/rtgtools/pedfilter/meta.yml @@ -7,37 +7,41 @@ keywords: - ped tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: The input file, can be either a PED or a VCF file - pattern: "*.{vcf,vcf.gz,ped}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file, can be either a PED or a VCF file + pattern: "*.{vcf,vcf.gz,ped}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: | - The output file, can be either a filtered PED file - or a VCF file containing the PED headers (needs --vcf as argument) - pattern: "*.{vcf.gz,ped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf.gz,ped}": + type: file + description: | + The output file, can be either a filtered PED file + or a VCF file containing the PED headers (needs --vcf as argument) + pattern: "*.{vcf.gz,ped}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/rocplot/meta.yml b/modules/nf-core/rtgtools/rocplot/meta.yml index 2b4d43d7c91..8fccb3181cb 100644 --- a/modules/nf-core/rtgtools/rocplot/meta.yml +++ b/modules/nf-core/rtgtools/rocplot/meta.yml @@ -1,5 +1,6 @@ name: "rtgtools_rocplot" -description: Plot ROC curves from vcfeval ROC data files, either to an image, or an interactive GUI. The interactive GUI isn't possible for nextflow. +description: Plot ROC curves from vcfeval ROC data files, either to an image, or an + interactive GUI. The interactive GUI isn't possible for nextflow. keywords: - rtgtools - rocplot @@ -7,39 +8,49 @@ keywords: - vcf tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input TSV ROC files created with RTGTOOLS_VCFEVAL - pattern: "*.tsv.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input TSV ROC files created with RTGTOOLS_VCFEVAL + pattern: "*.tsv.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: The resulting rocplot in PNG format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: The resulting rocplot in PNG format + pattern: "*.png" - svg: - type: file - description: The resulting rocplot in SVG format - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: The resulting rocplot in SVG format + pattern: "*.svg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index 5023ac91822..9814124ee79 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -1,111 +1,196 @@ name: "rtgtools_vcfeval" -description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set +description: The VCFeval tool of RTG tools. It is used to evaluate called variants + for agreement with a baseline variant set keywords: - benchmarking - vcf - rtg-tools tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query_vcf: - type: file - description: A VCF with called variants to benchmark against the standard - pattern: "*.{vcf,vcf.gz}" - - query_vcf_index: - type: file - description: The index of the called VCF (optional) - pattern: "*.tbi" - - truth_vcf: - type: file - description: A standard VCF to compare against - pattern: "*.{vcf,vcf.gz}" - - truth_vcf_index: - type: file - description: The index of the standard VCF (optional) - pattern: "*.tbi" - - truth_bed: - type: file - description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) - pattern: "*.bed" - - evaluation_bed: - type: file - description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) - pattern: "*.bed" - - sdf: - type: file - description: The SDF (RTG Sequence Data File) folder of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_vcf: + type: file + description: A VCF with called variants to benchmark against the standard + pattern: "*.{vcf,vcf.gz}" + - query_vcf_tbi: + type: file + description: The index of the VCF file with called variants to benchmark against the standard + pattern: "*.{vcf.gz.tbi, vcf.tbi}" + - truth_vcf: + type: file + description: A standard VCF to compare against + pattern: "*.{vcf,vcf.gz}" + - truth_vcf_tbi: + type: file + description: The index of the standard VCF to compare against + pattern: "*.{vcf.gz.tbi, vcf.tbi}" + - truth_bed: + type: file + description: A BED file containining the strict regions where VCFeval should + only evaluate the fully overlapping variants (optional) + pattern: "*.bed" + - evaluation_bed: + type: file + description: A BED file containing the regions where VCFeval will evaluate every + fully and partially overlapping variant (optional) + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sdf: + type: file + description: The SDF (RTG Sequence Data File) folder of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tp_vcf: - type: file - description: A VCF file for the true positive variants - pattern: "*.tp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp.vcf.gz": + type: file + description: A VCF file for the true positive variants + pattern: "*.tp.vcf.gz" - tp_tbi: - type: file - description: The index of the VCF file for the true positive variants - pattern: "*.tp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp.vcf.gz.tbi": + type: file + description: The index of the VCF file for the true positive variants + pattern: "*.tp.vcf.gz.tbi" - fn_vcf: - type: file - description: A VCF file for the false negative variants - pattern: "*.fn.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fn.vcf.gz": + type: file + description: A VCF file for the false negative variants + pattern: "*.fn.vcf.gz" - fn_tbi: - type: file - description: The index of the VCF file for the false negative variants - pattern: "*.fn.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fn.vcf.gz.tbi": + type: file + description: The index of the VCF file for the false negative variants + pattern: "*.fn.vcf.gz.tbi" - fp_vcf: - type: file - description: A VCF file for the false positive variants - pattern: "*.fp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fp.vcf.gz": + type: file + description: A VCF file for the false positive variants + pattern: "*.fp.vcf.gz" - fp_tbi: - type: file - description: The index of the VCF file for the false positive variants - pattern: "*.fp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fp.vcf.gz.tbi": + type: file + description: The index of the VCF file for the false positive variants + pattern: "*.fp.vcf.gz.tbi" - baseline_vcf: - type: file - description: A VCF file for the true positive variants from the baseline - pattern: "*.tp-baseline.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp-baseline.vcf.gz": + type: file + description: A VCF file for the true positive variants from the baseline + pattern: "*.tp-baseline.vcf.gz" - baseline_tbi: - type: file - description: The index of the VCF file for the true positive variants from the baseline - pattern: "*.tp-baseline.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp-baseline.vcf.gz.tbi": + type: file + description: The index of the VCF file for the true positive variants from the + baseline + pattern: "*.tp-baseline.vcf.gz.tbi" - snp_roc: - type: file - description: TSV files containing ROC data for the SNPs - pattern: "*.snp_roc.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.snp_roc.tsv.gz": + type: file + description: TSV files containing ROC data for the SNPs + pattern: "*.snp_roc.tsv.gz" - non_snp_roc: - type: file - description: TSV files containing ROC data for all variants except SNPs - pattern: "*.non_snp_roc.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.non_snp_roc.tsv.gz": + type: file + description: TSV files containing ROC data for all variants except SNPs + pattern: "*.non_snp_roc.tsv.gz" - weighted_roc: - type: file - description: TSV files containing weighted ROC data for all variants - pattern: "*.weighted_snp_roc.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.weighted_roc.tsv.gz": + type: file + description: TSV files containing weighted ROC data for all variants + pattern: "*.weighted_snp_roc.tsv.gz" - summary: - type: file - description: A TXT file containing the summary of the evaluation - pattern: "*.summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.txt": + type: file + description: A TXT file containing the summary of the evaluation + pattern: "*.summary.txt" - phasing: - type: file - description: A TXT file containing the data on the phasing - pattern: "*.phasing.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.phasing.txt": + type: file + description: A TXT file containing the data on the phasing + pattern: "*.phasing.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtn/tni/meta.yml b/modules/nf-core/rtn/tni/meta.yml index b60300bd9e5..1057cf3d9e1 100644 --- a/modules/nf-core/rtn/tni/meta.yml +++ b/modules/nf-core/rtn/tni/meta.yml @@ -1,48 +1,76 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "rtn_tni" -description: Uses the RTN R package for transcriptional regulatory network inference (TNI). +description: Uses the RTN R package for transcriptional regulatory network inference + (TNI). keywords: - regulatory network - transcriptomics - transcription factors tools: - "rtn": - description: "RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons" + description: "RTN: Reconstruction of Transcriptional regulatory Networks and analysis + of regulons" homepage: "https://www.bioconductor.org/packages/release/bioc/html/RTN.html" documentation: "https://www.bioconductor.org/packages/release/bioc/vignettes/RTN/inst/doc/RTN.html" tool_dev_url: "https://www.bioconductor.org/packages/release/bioc/html/RTN.html" doi: "10.1038/ncomms3464" licence: ["Artistic-2.0"] + identifier: biotools:rtn input: - - expression_matrix: - type: file - description: expression matrix in TSV format - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - expression_matrix: + type: file + description: expression matrix in TSV format + pattern: "*.tsv" output: - tni: - type: file - description: RDS R Object with the TNI object - pattern: "tni.rds" + - meta: + type: file + description: RDS R Object with the TNI object + pattern: "tni.rds" + - tni.rds: + type: file + description: RDS R Object with the TNI object + pattern: "tni.rds" - tni_perm: - type: file - description: RDS R Object with the TNI object after permutation - pattern: "tni_permutated.rds" + - meta: + type: file + description: RDS R Object with the TNI object after permutation + pattern: "tni_permutated.rds" + - tni_permutated.rds: + type: file + description: RDS R Object with the TNI object after permutation + pattern: "tni_permutated.rds" - tni_bootstrap: - type: file - description: RDS R Object with the TNI object after permutation and bootstrap - pattern: "tni_bootstrapped.rds" + - meta: + type: file + description: RDS R Object with the TNI object after permutation and bootstrap + pattern: "tni_bootstrapped.rds" + - tni_bootstrapped.rds: + type: file + description: RDS R Object with the TNI object after permutation and bootstrap + pattern: "tni_bootstrapped.rds" - tni_filtered: - type: file - description: RDS R Object with the TNI object after permutation, bootstrap and filtering - pattern: "tni_filtered.rds" + - meta: + type: file + description: RDS R Object with the TNI object after permutation, bootstrap and + filtering + pattern: "tni_filtered.rds" + - tni_filtered.rds: + type: file + description: RDS R Object with the TNI object after permutation, bootstrap and + filtering + pattern: "tni_filtered.rds" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mribeirodantas" maintainers: diff --git a/modules/nf-core/sageproteomics/sage/meta.yml b/modules/nf-core/sageproteomics/sage/meta.yml index a62e65c4930..69bc1f8653a 100644 --- a/modules/nf-core/sageproteomics/sage/meta.yml +++ b/modules/nf-core/sageproteomics/sage/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "sageproteomics_sage" description: sage is a search software for proteomics data @@ -14,67 +13,92 @@ tools: tool_dev_url: "https://github.com/lazear/sage" doi: "10.1021/acs.jproteome.3c00486" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - '"*.mzML"': - type: file - description: mzML open source mass spectrometry raw data format - pattern: "*.{mzML, mzML.gz}" - - meta2: - type: map - description: | - Groovy Map containing information about fasta_proteome - e.g. `[ id:'sample1']` - - fasta_proteome: - type: file - description: proteome database in fasta format - pattern: "*.{fasta, fasta.gz}" - - meta3: - type: map - description: | - Groovy Map containing information about base_config - e.g. `[ id:'sample1']` - - base_config: - type: file - description: sage configuration json - pattern: "*.{json}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - '"*.mzML"': + type: file + description: mzML open source mass spectrometry raw data format + pattern: "*.{mzML, mzML.gz}" + - - meta2: + type: map + description: | + Groovy Map containing information about fasta_proteome + e.g. `[ id:'sample1']` + - fasta_proteome: + type: file + description: proteome database in fasta format + pattern: "*.{fasta, fasta.gz}" + - - meta3: + type: map + description: | + Groovy Map containing information about base_config + e.g. `[ id:'sample1']` + - base_config: + type: file + description: sage configuration json + pattern: "*.{json}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results_tsv: - type: file - description: tsv output results - pattern: "results.sage.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - results.sage.tsv: + type: file + description: tsv output results + pattern: "results.sage.tsv" - results_json: - type: file - description: json output results - pattern: "results.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - results.json: + type: file + description: json output results + pattern: "results.json" - results_pin: - type: file - description: pin format output results - pattern: "results.sage.pin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - results.sage.pin: + type: file + description: pin format output results + pattern: "results.sage.pin" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - tmt_tsv: - type: file - description: tandem mass tag quantification - pattern: "tmt.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - tmt.tsv: + type: file + description: tandem mass tag quantification + pattern: "tmt.tsv" - lfq_tsv: - type: file - description: label free quantification - pattern: "lfq.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - lfq.tsv: + type: file + description: label free quantification + pattern: "lfq.tsv" authors: - "@dgemperline-lilly" maintainers: diff --git a/modules/nf-core/salmon/index/meta.yml b/modules/nf-core/salmon/index/meta.yml index fd94dd27472..48486a2bbf0 100644 --- a/modules/nf-core/salmon/index/meta.yml +++ b/modules/nf-core/salmon/index/meta.yml @@ -13,22 +13,25 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - genome_fasta: - type: file - description: Fasta file of the reference genome - - transcriptome_fasta: - type: file - description: Fasta file of the reference transcriptome + - - genome_fasta: + type: file + description: Fasta file of the reference genome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome output: - index: - type: directory - description: Folder containing the star index files - pattern: "salmon" + - salmon: + type: directory + description: Folder containing the star index files + pattern: "salmon" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml index a2faf589a79..4cacde0f0a7 100644 --- a/modules/nf-core/salmon/quant/meta.yml +++ b/modules/nf-core/salmon/quant/meta.yml @@ -13,47 +13,69 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files for single-end or paired-end data. - Multiple single-end fastqs or pairs of paired-end fastqs are - handled. - - index: - type: directory - description: Folder containing the star index files - - gtf: - type: file - description: GTF of the reference transcriptome - - transcript_fasta: - type: file - description: Fasta file of the reference transcriptome - - alignment_mode: - type: boolean - description: whether to run salmon in alignment mode - - lib_type: - type: string - description: | - Override library type inferred based on strandedness defined in meta object + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files for single-end or paired-end data. + Multiple single-end fastqs or pairs of paired-end fastqs are + handled. + - - index: + type: directory + description: Folder containing the star index files + - - gtf: + type: file + description: GTF of the reference transcriptome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome + - - alignment_mode: + type: boolean + description: whether to run salmon in alignment mode + - - lib_type: + type: string + description: | + Override library type inferred based on strandedness defined in meta object output: - results: - type: directory - description: Folder containing the quantification results for a specific sample - pattern: "${prefix}" + - meta: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" + - ${prefix}: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" - json_info: - type: file - description: File containing meta information from Salmon quant - pattern: "*info.json" + - meta: + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - "*info.json": + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - lib_format_counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*lib_format_counts.json": + type: file + description: File containing the library format counts + pattern: "*lib_format_counts.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salsa2/meta.yml b/modules/nf-core/salsa2/meta.yml index 8729ce06443..7232d1da1a0 100644 --- a/modules/nf-core/salsa2/meta.yml +++ b/modules/nf-core/salsa2/meta.yml @@ -15,46 +15,73 @@ tools: tool_dev_url: "https://github.com/marbl/SALSA" doi: "10.1186/s12864-017-3879-z" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of assembly. Headers must not contain ':' - pattern: "*.{fa, fasta}" - - index: - type: file - description: Fasta index file of assembly containing the length of contigs. - pattern: "*.{fa.fai, fasta.fai}" - - bed: - type: file - description: BED file of alignments sorted by read names, e.g., from HiC-Pro - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of assembly. Headers must not contain ':' + pattern: "*.{fa, fasta}" + - index: + type: file + description: Fasta index file of assembly containing the length of contigs. + pattern: "*.{fa.fai, fasta.fai}" + - - bed: + type: file + description: BED file of alignments sorted by read names, e.g., from HiC-Pro + pattern: "*.{bed}" + - - gfa: + type: file + description: GFA file of the assembly graph + - - dup: + type: file + description: File containing the duplicated contigs + - - filter_bed: + type: file + description: BED file of the filtered alignments + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Sequences for the scaffolds generated by the algorithm - pattern: "*_scaffolds_FINAL.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_scaffolds_FINAL.fasta": + type: file + description: Sequences for the scaffolds generated by the algorithm + pattern: "*_scaffolds_FINAL.fasta" - agp: - type: file - description: AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds - pattern: "*_scaffolds_FINAL.agp" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_scaffolds_FINAL.agp": + type: file + description: AGP style output for the scaffolds describing the assignment, orientation + and ordering of contigs along the scaffolds + pattern: "*_scaffolds_FINAL.agp" - agp_original_coordinates: - type: file - description: Secondary output AGP file with names and coordinates matching the original input assembly (optional) - pattern: "*scaffolds_FINAL.original-coordinates.agp" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*scaffolds_FINAL.original-coordinates.agp": + type: file + description: Secondary output AGP file with names and coordinates matching the + original input assembly (optional) + pattern: "*scaffolds_FINAL.original-coordinates.agp" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" maintainers: diff --git a/modules/nf-core/sam2lca/analyze/meta.yml b/modules/nf-core/sam2lca/analyze/meta.yml index aa4f9e310d9..c3152c780d3 100644 --- a/modules/nf-core/sam2lca/analyze/meta.yml +++ b/modules/nf-core/sam2lca/analyze/meta.yml @@ -1,5 +1,6 @@ name: "sam2lca_analyze" -description: Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files +description: Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM + files keywords: - LCA - alignment @@ -14,46 +15,62 @@ tools: documentation: "https://sam2lca.readthedocs.io" doi: "10.21105/joss.04360" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM/CRAM/SAM index - pattern: "*.{bai,.crai}" - - database: - type: file - description: Directory containing the sam2lca database - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index + pattern: "*.{bai,.crai}" + - - database: + type: file + description: Directory containing the sam2lca database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: CSV file containing the sam2lca results - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: CSV file containing the sam2lca results + pattern: "*.csv" - json: - type: file - description: JSON file containing the sam2lca results - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file containing the sam2lca results + pattern: "*.json" - bam: - type: file - description: Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic informations - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic + informations + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/sambamba/flagstat/meta.yml b/modules/nf-core/sambamba/flagstat/meta.yml index 3e68823a5c7..8194d6df143 100644 --- a/modules/nf-core/sambamba/flagstat/meta.yml +++ b/modules/nf-core/sambamba/flagstat/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html" tool_dev_url: "https://github.com/biod/sambamba" licence: ["GPL v2"] + identifier: biotools:sambamba input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Stats file - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: Stats file + pattern: "*.{stats}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/sambamba/markdup/meta.yml b/modules/nf-core/sambamba/markdup/meta.yml index 51b65bd7847..eeebe38b602 100644 --- a/modules/nf-core/sambamba/markdup/meta.yml +++ b/modules/nf-core/sambamba/markdup/meta.yml @@ -11,34 +11,43 @@ tools: documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html" tool_dev_url: "https://github.com/biod/sambamba" licence: ["GPL v2"] + identifier: biotools:sambamba input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" - bai: - type: file - description: An optional BAM index file. - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file. + pattern: "*.{bai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BioInf2305" maintainers: diff --git a/modules/nf-core/samblaster/meta.yml b/modules/nf-core/samblaster/meta.yml index 5c1e5a97002..5faf3a6c3ac 100644 --- a/modules/nf-core/samblaster/meta.yml +++ b/modules/nf-core/samblaster/meta.yml @@ -23,30 +23,33 @@ tools: tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" licence: ["MIT"] + identifier: biotools:samblaster input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Tagged or filtered BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Tagged or filtered BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/ampliconclip/environment.yml +++ b/modules/nf-core/samtools/ampliconclip/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/ampliconclip/meta.yml b/modules/nf-core/samtools/ampliconclip/meta.yml index 27452f30f67..fa1e96bd890 100644 --- a/modules/nf-core/samtools/ampliconclip/meta.yml +++ b/modules/nf-core/samtools/ampliconclip/meta.yml @@ -15,48 +15,63 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bed: - type: file - description: BED file of regions to be removed (e.g. amplicon primers) - pattern: "*.{bed}" - - save_cliprejects: - type: boolean - description: Save filtered reads to a file - - save_clipstats: - type: boolean - description: Save clipping stats to a file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - bed: + type: file + description: BED file of regions to be removed (e.g. amplicon primers) + pattern: "*.{bed}" + - - save_cliprejects: + type: boolean + description: Save filtered reads to a file + - - save_clipstats: + type: boolean + description: Save clipping stats to a file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Clipped reads BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clipallowed.bam": + type: file + description: Clipped reads BAM file + pattern: "*.{bam}" - stats: - type: file - description: Clipping statistics text file - pattern: "*.{clipstats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clipstats.txt": + type: file + description: Clipping statistics text file + pattern: "*.{clipstats.txt}" - rejects_bam: - type: file - description: Filtered reads BAM file - pattern: "*.{cliprejects.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cliprejects.bam": + type: file + description: Filtered reads BAM file + pattern: "*.{cliprejects.bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/bam2fq/meta.yml b/modules/nf-core/samtools/bam2fq/meta.yml index 7769046b54a..b17ed608d0c 100644 --- a/modules/nf-core/samtools/bam2fq/meta.yml +++ b/modules/nf-core/samtools/bam2fq/meta.yml @@ -11,40 +11,43 @@ tools: description: Tools for dealing with SAM, BAM and CRAM files documentation: http://www.htslib.org/doc/1.1/samtools.html licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputbam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - split: - type: boolean - description: | - TRUE/FALSE value to indicate if reads should be separated into - /1, /2 and if present other, or singleton. - Note: choosing TRUE will generate 4 different files. - Choosing FALSE will produce a single file, which will be interleaved in case - the input contains paired reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputbam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - split: + type: boolean + description: | + TRUE/FALSE value to indicate if reads should be separated into + /1, /2 and if present other, or singleton. + Note: choosing TRUE will generate 4 different files. + Choosing FALSE will produce a single file, which will be interleaved in case + the input contains paired reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: | - FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) - or a single interleaved .fq.gz file if the user chooses not to split the reads. - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: | + FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) + or a single interleaved .fq.gz file if the user chooses not to split the reads. + pattern: "*.fq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/calmd/environment.yml +++ b/modules/nf-core/samtools/calmd/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/calmd/meta.yml b/modules/nf-core/samtools/calmd/meta.yml index 857f9b80d39..c34e1f777b6 100644 --- a/modules/nf-core/samtools/calmd/meta.yml +++ b/modules/nf-core/samtools/calmd/meta.yml @@ -15,34 +15,42 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: FASTA ref file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA ref file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JackCurragh" maintainers: diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/cat/environment.yml +++ b/modules/nf-core/samtools/cat/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/cat/meta.yml b/modules/nf-core/samtools/cat/meta.yml index 3541e0c3891..dfb0f78c4cd 100644 --- a/modules/nf-core/samtools/cat/meta.yml +++ b/modules/nf-core/samtools/cat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: samtools_cat description: Concatenate BAM or CRAM file @@ -17,34 +16,43 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_files: - type: file - description: BAM/CRAM files - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_files: + type: file + description: BAM/CRAM files + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Concatenated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Concatenated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Concatenated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: Concatenated CRAM file + pattern: "*.{cram}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/collate/environment.yml +++ b/modules/nf-core/samtools/collate/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml index f0aed28a214..cc54583eea8 100644 --- a/modules/nf-core/samtools/collate/meta.yml +++ b/modules/nf-core/samtools/collate/meta.yml @@ -13,32 +13,64 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA ref file + pattern: "*.fasta" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM + pattern: "*.{bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM + pattern: "*.{cram}" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Sorted SAM + pattern: "*.{sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Collated BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index 2bcd47ee161..b98cbb99092 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/collatefastq/meta.yml b/modules/nf-core/samtools/collatefastq/meta.yml index 898cdbdad79..5bc912496e4 100644 --- a/modules/nf-core/samtools/collatefastq/meta.yml +++ b/modules/nf-core/samtools/collatefastq/meta.yml @@ -11,61 +11,90 @@ tools: description: Tools for dealing with SAM, BAM and CRAM files documentation: http://www.htslib.org/doc/1.1/samtools.html licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - interleave: - type: boolean - description: | - If true, the output is a single interleaved paired-end FASTQ - If false, the output split paired-end FASTQ - default: false + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" + - - interleave: + type: boolean + description: | + If true, the output is a single interleaved paired-end FASTQ + If false, the output split paired-end FASTQ + default: false output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: | - R1 and R2 FASTQ files - pattern: "*_{1,2}.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_{1,2}.fq.gz" + - "*_{1,2}.fq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_{1,2}.fq.gz" - fastq_interleaved: - type: file - description: | - Interleaved paired end FASTQ files - pattern: "*_interleaved.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_interleaved.fq.gz" + - "*_interleaved.fq": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_interleaved.fq.gz" - fastq_other: - type: file - description: | - FASTQ files with reads where the READ1 and READ2 FLAG bits set are either both set or both unset. - pattern: "*_other.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_other.fq.gz" + - "*_other.fq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_other.fq.gz" - fastq_singleton: - type: file - description: | - FASTQ files with singleton reads. - pattern: "*_singleton.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_singleton.fq.gz" + - "*_singleton.fq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_singleton.fq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" - "@maxulysse" diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml index 699c05ce8b6..5a85438e08a 100644 --- a/modules/nf-core/samtools/consensus/environment.yml +++ b/modules/nf-core/samtools/consensus/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - "bioconda::samtools=1.20" diff --git a/modules/nf-core/samtools/consensus/meta.yml b/modules/nf-core/samtools/consensus/meta.yml index 71b96bf368f..43b993dd615 100644 --- a/modules/nf-core/samtools/consensus/meta.yml +++ b/modules/nf-core/samtools/consensus/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "samtools_consensus" description: Produces a consensus FASTA/FASTQ/PILEUP @@ -19,35 +18,54 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fasta": + type: file + description: Consensus FASTA file + pattern: "*.{fasta}" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq": + type: file + description: Consensus FASTQ file + pattern: "*.{fastq}" + - pileup: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.pileup": + type: file + description: Consensus PILEUP file + pattern: "*.{pileup}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Consensus sequences - pattern: "*.{fasta,fastq,pileup}" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml index 558289715cb..d5bfa161ba7 100644 --- a/modules/nf-core/samtools/convert/meta.yml +++ b/modules/nf-core/samtools/convert/meta.yml @@ -15,50 +15,85 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Reference file to create the CRAM file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file to create the CRAM file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference index file to create the CRAM file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: filtered/converted BAM file - pattern: "*{.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: filtered/converted BAM file + pattern: "*{.bam}" - cram: - type: file - description: filtered/converted CRAM file - pattern: "*{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: filtered/converted CRAM file + pattern: "*{cram}" - bai: - type: file - description: filtered/converted BAM index - pattern: "*{.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: filtered/converted BAM index + pattern: "*{.bai}" - crai: - type: file - description: filtered/converted CRAM index - pattern: "*{.crai}" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: filtered/converted CRAM index + pattern: "*{.crai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/coverage/meta.yml b/modules/nf-core/samtools/coverage/meta.yml index e74082d9342..fb9ba6f3a1d 100644 --- a/modules/nf-core/samtools/coverage/meta.yml +++ b/modules/nf-core/samtools/coverage/meta.yml @@ -14,47 +14,56 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Reference genome index file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference genome index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - coverage: - type: file - description: Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram). - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tabulated text containing the coverage at each position or region + or an ASCII-art histogram (with --histogram). + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/samtools/cramsize/meta.yml b/modules/nf-core/samtools/cramsize/meta.yml index cab8ea44167..0383716dc3f 100644 --- a/modules/nf-core/samtools/cramsize/meta.yml +++ b/modules/nf-core/samtools/cramsize/meta.yml @@ -14,29 +14,32 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cram: - type: file - description: CRAM file - pattern: "*.cram" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: CRAM file + pattern: "*.cram" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - size: - type: file - description: Size information file - pattern: "*.size" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.size": + type: file + description: Size information file + pattern: "*.size" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@limrp" diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index 2bcd47ee161..b98cbb99092 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/depth/meta.yml b/modules/nf-core/samtools/depth/meta.yml index bc51f264861..2acd645d791 100644 --- a/modules/nf-core/samtools/depth/meta.yml +++ b/modules/nf-core/samtools/depth/meta.yml @@ -7,45 +7,51 @@ keywords: - coverage tools: - samtools: - description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region + description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – + computes the read depth at each position or region homepage: http://www.htslib.org documentation: http://www.htslib.org/doc/samtools-depth.html tool_dev_url: https://github.com/samtools/samtools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: - - meta1: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - intervals: - type: file - description: list of positions or regions in specified bed file - pattern: "*.{bed}" + - - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - intervals: + type: file + description: list of positions or regions in specified bed file + pattern: "*.{bed}" output: - - meta1: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position - pattern: "*.{tsv}" + - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The output of samtools depth has three columns - the name of the + contig or chromosome, the position and the number of reads aligned at that + position + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" - "@nevinwu" diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/dict/environment.yml +++ b/modules/nf-core/samtools/dict/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/dict/meta.yml b/modules/nf-core/samtools/dict/meta.yml index 61a5d835563..a84b1cf760a 100644 --- a/modules/nf-core/samtools/dict/meta.yml +++ b/modules/nf-core/samtools/dict/meta.yml @@ -14,30 +14,33 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - dict: - type: file - description: FASTA dictionary file - pattern: "*.{dict}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dict": + type: file + description: FASTA dictionary file + pattern: "*.{dict}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" maintainers: diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index f3c25de20f4..6721b2cb847 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -14,47 +14,62 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fa: - type: file - description: FASTA file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fasta}": + type: file + description: FASTA file + pattern: "*.{fa}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/fasta/environment.yml b/modules/nf-core/samtools/fasta/environment.yml index 2bcd47ee161..b98cbb99092 100644 --- a/modules/nf-core/samtools/fasta/environment.yml +++ b/modules/nf-core/samtools/fasta/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/fasta/meta.yml b/modules/nf-core/samtools/fasta/meta.yml index eae26f01014..6ea77632d86 100644 --- a/modules/nf-core/samtools/fasta/meta.yml +++ b/modules/nf-core/samtools/fasta/meta.yml @@ -13,47 +13,71 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - interleave: - type: boolean - description: Set true for interleaved fasta files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - interleave: + type: boolean + description: Set true for interleaved fasta files output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files. - pattern: "*_{1,2}.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_{1,2}.fasta.gz": + type: file + description: Compressed FASTA file(s) with reads with either the READ1 or READ2 + flag set in separate files. + pattern: "*_{1,2}.fasta.gz" - interleaved: - type: file - description: Compressed FASTA file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file. - pattern: "*_interleaved.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_interleaved.fasta.gz": + type: file + description: Compressed FASTA file with reads with either the READ1 or READ2 + flag set in a combined file. Needs collated input file. + pattern: "*_interleaved.fasta.gz" - singleton: - type: file - description: Compressed FASTA file with singleton reads - pattern: "*_singleton.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_singleton.fasta.gz": + type: file + description: Compressed FASTA file with singleton reads + pattern: "*_singleton.fasta.gz" - other: - type: file - description: Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset - pattern: "*_other.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_other.fasta.gz": + type: file + description: Compressed FASTA file with reads with either both READ1 and READ2 + flags set or unset + pattern: "*_other.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/fastq/meta.yml b/modules/nf-core/samtools/fastq/meta.yml index c4002a45de1..c15a0b6f84f 100644 --- a/modules/nf-core/samtools/fastq/meta.yml +++ b/modules/nf-core/samtools/fastq/meta.yml @@ -15,45 +15,69 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - interleave: - type: boolean - description: Set true for interleaved fastq file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - interleave: + type: boolean + description: Set true for interleaved fastq file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files. - pattern: "*_{1,2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_{1,2}.fastq.gz": + type: file + description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 + flag set in separate files. + pattern: "*_{1,2}.fastq.gz" - interleaved: - type: file - description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file. - pattern: "*_interleaved.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_interleaved.fastq": + type: file + description: Compressed FASTQ file with reads with either the READ1 or READ2 + flag set in a combined file. Needs collated input file. + pattern: "*_interleaved.fastq.gz" - singleton: - type: file - description: Compressed FASTQ file with singleton reads - pattern: "*_singleton.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_singleton.fastq.gz": + type: file + description: Compressed FASTQ file with singleton reads + pattern: "*_singleton.fastq.gz" - other: - type: file - description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset - pattern: "*_other.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_other.fastq.gz": + type: file + description: Compressed FASTQ file with reads with either both READ1 and READ2 + flags set or unset + pattern: "*_other.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" - "@suzannejin" diff --git a/modules/nf-core/samtools/fixmate/environment.yml b/modules/nf-core/samtools/fixmate/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/fixmate/environment.yml +++ b/modules/nf-core/samtools/fixmate/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/fixmate/meta.yml b/modules/nf-core/samtools/fixmate/meta.yml index f949ce4de3b..8d4238d4adb 100644 --- a/modules/nf-core/samtools/fixmate/meta.yml +++ b/modules/nf-core/samtools/fixmate/meta.yml @@ -1,5 +1,8 @@ name: samtools_fixmate -description: Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs. +description: Samtools fixmate is a tool that can fill in information (insert size, + cigar, mapq) about paired end reads onto the corresponding other read. Also has + options to remove secondary/unmapped alignments and recalculate whether reads are + proper pairs. keywords: - fixmate - samtools @@ -19,30 +22,34 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file, must be sorted by name, not coordinate - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file, must be sorted by name, not coordinate + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: A BAM/CRAM/SAM file with mate information added and/or proper pairs recalled - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: A BAM/CRAM/SAM file with mate information added and/or proper pairs + recalled + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 97991358e61..cdc4c2544c7 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,5 +1,6 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG + type keywords: - stats - mapping @@ -17,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flagstat": + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/getrg/environment.yml b/modules/nf-core/samtools/getrg/environment.yml index 2bcd47ee161..b98cbb99092 100644 --- a/modules/nf-core/samtools/getrg/environment.yml +++ b/modules/nf-core/samtools/getrg/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/getrg/meta.yml b/modules/nf-core/samtools/getrg/meta.yml index 770960e71a5..31e9cfb981b 100644 --- a/modules/nf-core/samtools/getrg/meta.yml +++ b/modules/nf-core/samtools/getrg/meta.yml @@ -16,29 +16,29 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - readgroup: - type: file - description: File containing readgroup string(s) + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 344e92a3f8b..f0a6bcb2a07 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -18,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idxstats": + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index 2bcd47ee161..b98cbb99092 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/import/meta.yml b/modules/nf-core/samtools/import/meta.yml index 9002e092716..5c98b8be957 100644 --- a/modules/nf-core/samtools/import/meta.yml +++ b/modules/nf-core/samtools/import/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "samtools_import" description: converts FASTQ files to unmapped SAM/BAM/CRAM @@ -18,38 +17,53 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq data to be converted to SAM/BAM/CRAM - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: fastq data to be converted to SAM/BAM/CRAM + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sam: - type: file - description: SAM file - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.sam": + type: file + description: SAM file + pattern: "*.sam" - bam: - type: file - description: Unaligned BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Unaligned BAM file + pattern: "*.bam" - cram: - type: file - description: Unaligned CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.cram": + type: file + description: Unaligned CRAM file + pattern: "*.cram" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03eb9..db8df0d5055 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,38 +15,52 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/markdup/environment.yml b/modules/nf-core/samtools/markdup/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/markdup/environment.yml +++ b/modules/nf-core/samtools/markdup/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/markdup/meta.yml b/modules/nf-core/samtools/markdup/meta.yml index 7b3d06124c6..31cb0c632f2 100644 --- a/modules/nf-core/samtools/markdup/meta.yml +++ b/modules/nf-core/samtools/markdup/meta.yml @@ -13,39 +13,62 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: A reference genome in FASTA format - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A reference genome in FASTA format + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*{.bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: CRAM file + pattern: "*{.cram}" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: SAM file + pattern: "*{.sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 2e8f3dbbb5b..235aa219457 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -15,60 +15,81 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_files: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of the reference file the CRAM was created with (optional) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_files: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of the reference file the CRAM was created with (optional) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file + pattern: "*.{bam}" - cram: - type: file - description: CRAM file - pattern: "*.{cram}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: CRAM file + pattern: "*.{cram}" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa " diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/mpileup/meta.yml b/modules/nf-core/samtools/mpileup/meta.yml index 13038fbc9bd..0655e087277 100644 --- a/modules/nf-core/samtools/mpileup/meta.yml +++ b/modules/nf-core/samtools/mpileup/meta.yml @@ -15,38 +15,41 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - intervals: - type: file - description: Interval FILE - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - intervals: + type: file + description: Interval FILE + pattern: "*.bed" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mpileup: - type: file - description: mpileup file - pattern: "*.{mpileup}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup.gz": + type: file + description: mpileup file + pattern: "*.{mpileup}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/reheader/meta.yml b/modules/nf-core/samtools/reheader/meta.yml index a5e1591452b..e9699f5637b 100644 --- a/modules/nf-core/samtools/reheader/meta.yml +++ b/modules/nf-core/samtools/reheader/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "samtools_reheader" @@ -20,30 +19,33 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: BAM/CRAM file to be reheaded - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: BAM/CRAM file to be reheaded + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Reheaded BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Reheaded BAM/CRAM file + pattern: "*.{bam,cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/sormadup/meta.yml b/modules/nf-core/samtools/sormadup/meta.yml index c37ce759583..bec58e87cc5 100644 --- a/modules/nf-core/samtools/sormadup/meta.yml +++ b/modules/nf-core/samtools/sormadup/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "samtools_sormadup" description: Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file @@ -23,6 +22,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args" + identifier: biotools:samtools - samtools_collate: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -33,6 +33,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args2" + identifier: biotools:samtools - samtools_fixmate: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -43,6 +44,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args3" + identifier: biotools:samtools - samtools_sort: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -53,6 +55,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args4" + identifier: biotools:samtools - samtools_markdup: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -63,56 +66,82 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args5" + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM files - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM files + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted and duplicate marked BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted and duplicate marked BAM file + pattern: "*.bam" - cram: - type: file - description: Sorted and duplicate marked CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted and duplicate marked CRAM file + pattern: "*.cram" - csi: - type: file - description: Sorted and duplicate marked BAM index file - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Sorted and duplicate marked BAM index file + pattern: "*.csi" - crai: - type: file - description: Sorted and duplicate marked CRAM index file - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Sorted and duplicate marked CRAM index file + pattern: "*.crai" - metrics: - type: file - description: Duplicate metrics file - pattern: "*.metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Duplicate metrics file + pattern: "*.metrics" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0ebf4..a9dbec5a8bf 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,52 +15,73 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file(s) - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta,fna}" - optional: true + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 735ff8122ae..77b020f76ed 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -16,43 +16,46 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing samtools stats output + pattern: "*.{stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 09ad4c10750..b98cbb99092 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 27be60d08cd..caa7b0150d4 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -15,77 +15,120 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) - pattern: "*.{.bai,.csi,.crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" - - qname: - type: file - description: Optional file with read names to output only select alignments - pattern: "*.{txt,list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) + pattern: "*.{.bai,.csi,.crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: optional filtered/converted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: optional filtered/converted BAM file + pattern: "*.{bam}" - cram: - type: file - description: optional filtered/converted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: optional filtered/converted CRAM file + pattern: "*.{cram}" - sam: - type: file - description: optional filtered/converted SAM file - pattern: "*.{sam}" - # bai, csi, and crai are created with `--write-index` + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sam: + type: file + description: optional filtered/converted SAM file + pattern: "*.{sam}" - bai: - type: file - description: optional BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.bai: + type: file + description: optional BAM file index + pattern: "*.{bai}" - csi: - type: file - description: optional tabix BAM file index - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.csi: + type: file + description: optional tabix BAM file index + pattern: "*.{csi}" - crai: - type: file - description: optional CRAM file index - pattern: "*.{crai}" - # unselected and unselected_index are created when passing a qname + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.crai: + type: file + description: optional CRAM file index + pattern: "*.{crai}" - unselected: - type: file - description: optional file with unselected alignments - pattern: "*.unselected.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}: + type: file + description: optional file with unselected alignments + pattern: "*.unselected.{bam,cram,sam}" - unselected_index: - type: file - description: index for the "unselected" file - pattern: "*.unselected.{bai,csi,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}.{bai,csi,crsi}: + type: file + description: index for the "unselected" file + pattern: "*.unselected.{bai,csi,crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 29e7aeb08eb..63849b037b7 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -365,6 +365,26 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_versions": { "content": [ [ diff --git a/modules/nf-core/scimap/mcmicro/meta.yml b/modules/nf-core/scimap/mcmicro/meta.yml index 4a76e3629c9..55be2f51e5c 100644 --- a/modules/nf-core/scimap/mcmicro/meta.yml +++ b/modules/nf-core/scimap/mcmicro/meta.yml @@ -11,36 +11,45 @@ tools: documentation: "https://scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap/" tool_dev_url: "https://github.com/labsyspharm/scimap" licence: ["MIT License"] + identifier: biotools:SCIMAP input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cellbyfeature: - type: file - description: CSV file with cell by feature table - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cellbyfeature: + type: file + description: CSV file with cell by feature table + pattern: "*.{csv}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Sorted CSV file - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Sorted CSV file + pattern: "*.{csv}" - h5ad: - type: file - description: Sorted H5AD file - pattern: "*.{h5ad}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.h5ad": + type: file + description: Sorted H5AD file + pattern: "*.{h5ad}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luiskuhn" maintainers: diff --git a/modules/nf-core/scimap/spatiallda/meta.yml b/modules/nf-core/scimap/spatiallda/meta.yml index b26932f2bc4..724b5cc9707 100644 --- a/modules/nf-core/scimap/spatiallda/meta.yml +++ b/modules/nf-core/scimap/spatiallda/meta.yml @@ -1,49 +1,73 @@ name: "scimap_spatiallda" -description: SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities. +description: SpatialLDA uses an LDA based approach for the identification of cellular + neighborhoods, using cell type identities. keywords: - spatial_neighborhoods - scimap - spatial_omics tools: - "scimap": - description: "Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of cells." + description: "Scimap is a scalable toolkit for analyzing spatial molecular data. + The underlying framework is generalizable to spatial datasets mapped to XY coordinates. + The package uses the anndata framework making it easy to integrate with other + popular single-cell analysis toolkits. It includes preprocessing, phenotyping, + visualization, clustering, spatial analysis and differential spatial testing. + The Python-based implementation efficiently deals with large datasets of millions + of cells." homepage: "https://scimap.xyz/" documentation: "https://scimap.xyz/tutorials/1-scimap-tutorial-getting-started/" tool_dev_url: "https://github.com/labsyspharm/scimap" doi: "10.5281/zenodo.7854095" licence: ["MIT licence"] + identifier: biotools:SCIMAP input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - phenotyped: - type: file - description: Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype. - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - phenotyped: + type: file + description: Phenotyped CSV file, it must contain the columns, sampleID, X, + Y and Phenotype. + pattern: "*.{csv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spatial_lda_output: - type: file - description: File with the motifs detected from SpatialLDA - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.csv": + type: file + description: File with the motifs detected from SpatialLDA + pattern: "*.{csv}" - composition_plot: - type: file - description: Plot with the motif composition and the cell type composition of motifs. - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.png": + type: file + description: Plot with the motif composition and the cell type composition of + motifs. + pattern: "*.{png}" - motif_location_plot: - type: file - description: Plot with the locations of the motifs. - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.html": + type: file + description: Plot with the locations of the motifs. + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" - "@chiarasch" diff --git a/modules/nf-core/scoary/meta.yml b/modules/nf-core/scoary/meta.yml index 842fe3652dc..507bd22efcd 100644 --- a/modules/nf-core/scoary/meta.yml +++ b/modules/nf-core/scoary/meta.yml @@ -12,38 +12,41 @@ tools: tool_dev_url: https://github.com/AdmiralenOla/Scoary doi: "10.1186/s13059-016-1108-8" licence: ["GPL v3"] + identifier: biotools:scoary input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genes: - type: file - description: A presence/absence matrix of genes in the pan-genome - pattern: "*.csv" - - traits: - type: file - description: A CSV file containing trait information per-sample - pattern: "*.csv" - - tree: - type: file - description: A Newick formtted tree for phylogenetic analyses - pattern: "*.{dnd,nwk,treefile}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genes: + type: file + description: A presence/absence matrix of genes in the pan-genome + pattern: "*.csv" + - traits: + type: file + description: A CSV file containing trait information per-sample + pattern: "*.csv" + - - tree: + type: file + description: A Newick formtted tree for phylogenetic analyses + pattern: "*.{dnd,nwk,treefile}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Gene associations in a CSV file per trait - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Gene associations in a CSV file per trait + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/scramble/clusteranalysis/meta.yml b/modules/nf-core/scramble/clusteranalysis/meta.yml index 4e5200fcc71..14be2cb42e1 100644 --- a/modules/nf-core/scramble/clusteranalysis/meta.yml +++ b/modules/nf-core/scramble/clusteranalysis/meta.yml @@ -1,5 +1,6 @@ name: "scramble_clusteranalysis" -description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by `cluster_identifier` +description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped + clusters found by `cluster_identifier` keywords: - soft-clipped clusters - scramble @@ -12,46 +13,65 @@ tools: documentation: "https://github.com/GeneDx/scramble" tool_dev_url: "https://github.com/GeneDx/scramble" licence: ["CC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - clusters: - type: file - description: Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier - pattern: "*clusters.txt" - - fasta: - type: file - description: Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions. - pattern: "*.{fasta,fa}" - - mei_ref: - type: file - description: Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - clusters: + type: file + description: Tab-delimited text file containing soft-clipped clusters. Has to + be generated using scramble/clusteridentifier + pattern: "*clusters.txt" + - - fasta: + type: file + description: Optional fasta reference file. This file is needed to create a + VCF file and to evaluate predicted deletions. + pattern: "*.{fasta,fa}" + - - mei_ref: + type: file + description: Optional fasta file containing the MEI reference. This file should + only be supplied in special occasions where the default isn't correct + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - meis_tab: - type: file - description: Tab-delimited text file containing MEI calls - pattern: "*_MEIs.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_MEIs.txt": + type: file + description: Tab-delimited text file containing MEI calls + pattern: "*_MEIs.txt" - dels_tab: - type: file - description: Tab-delimited text file containing predicted deletions - pattern: "*_PredictedDeletions.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PredictedDeletions.txt": + type: file + description: Tab-delimited text file containing predicted deletions + pattern: "*_PredictedDeletions.txt" - vcf: - type: file - description: A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: A VCF file containing the MEI calls and/or the predicted deletions + (depending on the given arguments) + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/scramble/clusteridentifier/meta.yml b/modules/nf-core/scramble/clusteridentifier/meta.yml index 17aab2c08a8..c8973fc8eef 100644 --- a/modules/nf-core/scramble/clusteridentifier/meta.yml +++ b/modules/nf-core/scramble/clusteridentifier/meta.yml @@ -11,38 +11,41 @@ tools: documentation: "https://github.com/GeneDx/scramble" tool_dev_url: "https://github.com/GeneDx/scramble" licence: ["CC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: The reference FASTA file (mandatory when using CRAM files) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: The reference FASTA file (mandatory when using CRAM files) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - clusters: - type: file - description: Tab-delimited file containing the soft-clipped clusters - pattern: "*.clusters.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clusters.txt": + type: file + description: Tab-delimited file containing the soft-clipped clusters + pattern: "*.clusters.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/seacr/callpeak/meta.yml b/modules/nf-core/seacr/callpeak/meta.yml index 9326b02a6c5..2ff21c18170 100644 --- a/modules/nf-core/seacr/callpeak/meta.yml +++ b/modules/nf-core/seacr/callpeak/meta.yml @@ -17,38 +17,41 @@ tools: homepage: https://github.com/FredHutch/SEACR documentation: https://github.com/FredHutch/SEACR licence: ["GPL-2.0-only"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: | - The target bedgraph file from which the peaks will be calculated. - - ctrlbedgraph: - type: file - description: | - Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. - - threshold: - type: integer - description: | - Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: | + The target bedgraph file from which the peaks will be calculated. + - ctrlbedgraph: + type: file + description: | + Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. + - - threshold: + type: integer + description: | + Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file containing the calculated peaks. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file containing the calculated peaks. + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@chris-cheshire" maintainers: diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml index fc8e43bab5b..46b0084b667 100644 --- a/modules/nf-core/segemehl/align/meta.yml +++ b/modules/nf-core/segemehl/align/meta.yml @@ -1,5 +1,6 @@ name: "segemehl_align" -description: A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection +description: A multi-split mapping algorithm for circular RNA, splicing, trans-splicing + and fusion detection keywords: - alignment - circrna @@ -7,65 +8,87 @@ keywords: - fusions tools: - "segemehl": - description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection" + description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing + and fusion detection" homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" doi: "10.1186/gb-2014-15-2-r34" licence: ["GPL v3"] + identifier: biotools:segemehl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTA or FASTQ files - pattern: "*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}" - - fasta: - type: file - description: Reference genome FASTA file used to construct Segemehl - pattern: "*.{fa,fasta}" - - index: - type: file - description: Segemehl Index file from SEGEMEHL_INDEX - pattern: "*.idx" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTA or FASTQ files + pattern: "*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}" + - - fasta: + type: file + description: Reference genome FASTA file used to construct Segemehl + pattern: "*.{fa,fasta}" + - - index: + type: file + description: Segemehl Index file from SEGEMEHL_INDEX + pattern: "*.idx" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - alignment: - type: file - description: | - File containing genomic alignments in SAM format - (please add "-b" flag to task.ext.args for BAM) - pattern: "*.{sam,bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.${suffix}: + type: file + description: | + File containing genomic alignments in SAM format + (please add "-b" flag to task.ext.args for BAM) + pattern: "*.{sam,bam}" - trans_alignments: - type: file - description: | - Custom text file containing all single split alignments predicted to be in trans - (optional, only if -S flag is set in task.ext.args) - pattern: "*.trns.txt" - - single_bed: - type: file - description: | - Bed file containing all single splice events predicted - in the split read alignments. - (optional, only if -S flag is set in task.ext.args) - pattern: "*.sngl.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.trns.txt: + type: file + description: | + Custom text file containing all single split alignments predicted to be in trans + (optional, only if -S flag is set in task.ext.args) + pattern: "*.trns.txt" - multi_bed: - type: file - description: | - Bed file containing all splice events predicted - in the split read alignments. - (optional, only if -S flag is set in task.ext.args) - pattern: "*.mult.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.mult.bed: + type: file + description: | + Bed file containing all splice events predicted + in the split read alignments. + (optional, only if -S flag is set in task.ext.args) + pattern: "*.mult.bed" + - single_bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.sngl.bed: + type: file + description: | + Bed file containing all single splice events predicted + in the split read alignments. + (optional, only if -S flag is set in task.ext.args) + pattern: "*.sngl.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" - "@nictru" diff --git a/modules/nf-core/segemehl/index/meta.yml b/modules/nf-core/segemehl/index/meta.yml index a036602da95..d6c1d983f7b 100644 --- a/modules/nf-core/segemehl/index/meta.yml +++ b/modules/nf-core/segemehl/index/meta.yml @@ -7,25 +7,29 @@ keywords: - fusions tools: - "segemehl": - description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection" + description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing + and fusion detection" homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" doi: "10.1186/gb-2014-15-2-r34" licence: ["GPL v3"] + identifier: biotools:segemehl input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta}" + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - index: - type: file - description: Segemehl index file - pattern: "*.{idx}" + - "*.idx": + type: file + description: Segemehl index file + pattern: "*.{idx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/semibin/singleeasybin/meta.yml b/modules/nf-core/semibin/singleeasybin/meta.yml index 9e7c491a461..e1f36adbfc0 100644 --- a/modules/nf-core/semibin/singleeasybin/meta.yml +++ b/modules/nf-core/semibin/singleeasybin/meta.yml @@ -12,50 +12,77 @@ tools: tool_dev_url: "https://github.com/BigDataBiology/SemiBin" doi: "10.1038/s41467-022-29843-y" licence: ["MIT"] + identifier: biotools:semibin input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram}" - - fasta: - type: file - description: Fasta file of the assembled contigs - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the assembled contigs + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: generated files - pattern: "*.csv" - - h5: - type: file - description: trained model - pattern: "*.h5" - - output_prerecluster_bins: - type: file - description: output_prerecluster_bins - pattern: "output_prerecluster_bins/*.fa" - - output_recluster_bins: - type: file - description: output_recluster_bins - pattern: "output_recluster_bins/*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: generated files + pattern: "*.csv" + - model: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.h5": + type: file + description: model file + pattern: "*.h5" + - output_fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output_prerecluster_bins/*.fa: + type: file + description: precluster fasta files + pattern: "*.fa" + - recluster_fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output_recluster_bins/*.fa: + type: file + description: recluster fasta files + pattern: "*.fa" - tsv: - type: file - description: information of bins - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: information of bins + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BigDataBiology" maintainers: diff --git a/modules/nf-core/sentieon/applyvarcal/meta.yml b/modules/nf-core/sentieon/applyvarcal/meta.yml index da92ce34366..e8505a2ae5b 100644 --- a/modules/nf-core/sentieon/applyvarcal/meta.yml +++ b/modules/nf-core/sentieon/applyvarcal/meta.yml @@ -17,68 +17,80 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: file - description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator. - pattern: "*.vcf" - - vcf_tbi: - type: file - description: tabix index for the input vcf file. - pattern: "*.vcf.tbi" - - recal: - type: file - description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: "*.recal" - - recal_index: - type: file - description: Index file for the recalibration file. - pattern: ".recal.idx" - - tranches: - type: file - description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: ".tranches" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to be recalibrated, this should be the same file as used + for the first stage VariantRecalibrator. + pattern: "*.vcf" + - vcf_tbi: + type: file + description: tabix index for the input vcf file. + pattern: "*.vcf.tbi" + - recal: + type: file + description: Recalibration file produced when the input vcf was run through + VariantRecalibrator in stage 1. + pattern: "*.recal" + - recal_index: + type: file + description: Index file for the recalibration file. + pattern: ".recal.idx" + - tranches: + type: file + description: Tranches file produced when the input vcf was run through VariantRecalibrator + in stage 1. + pattern: ".tranches" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - vcf: - type: file - description: compressed vcf file containing the recalibrated variants. - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.vcf.gz": + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of recalibrated vcf file. - pattern: "*vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.tbi": + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@assp8200" maintainers: diff --git a/modules/nf-core/sentieon/bwaindex/meta.yml b/modules/nf-core/sentieon/bwaindex/meta.yml index 0af45ad885c..acbd14d51af 100644 --- a/modules/nf-core/sentieon/bwaindex/meta.yml +++ b/modules/nf-core/sentieon/bwaindex/meta.yml @@ -13,29 +13,32 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bwa: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@maxulysse" diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml index 9dad7e68ee0..b27dd4877f2 100644 --- a/modules/nf-core/sentieon/bwamem/meta.yml +++ b/modules/nf-core/sentieon/bwamem/meta.yml @@ -15,56 +15,63 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Genome fastq files (single-end or paired-end) - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Genome fastq files (single-end or paired-end) + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - bam_and_bai: - type: file - description: BAM file with corresponding index. - pattern: "*.{bam,bai}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: BAM file with corresponding index. + pattern: "*.{bam,bai}" + - ${prefix}.{bai,crai}: + type: file + description: BAM file with corresponding index. + pattern: "*.{bam,bai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/collectvcmetrics/meta.yml b/modules/nf-core/sentieon/collectvcmetrics/meta.yml index e81e47bcfce..9a1867e444b 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/meta.yml +++ b/modules/nf-core/sentieon/collectvcmetrics/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "sentieon_collectvcmetrics" -description: Accelerated implementation of the Picard CollectVariantCallingMetrics tool. +description: Accelerated implementation of the Picard CollectVariantCallingMetrics + tool. keywords: - vcf - sentieon @@ -14,83 +14,90 @@ tools: homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ licence: ["Commercial (requires license for use; redistribution allowed)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: Sorted VCF file [required] - pattern: "*.vcf" - - tbi: - type: file - description: VCF index file [required] - pattern: "*.vcf{,.gz}.tbi" - - dbsnp: - type: file - description: dbsnp VCF file [required] - pattern: "*.vcf{,.gz}" - - dbsnp_tbi: - type: file - description: dbsnp VCF index file [required] - pattern: "*.vcf{,.gz}.tbi" - - interval: - type: file - description: BED file of genome regions to draw coverage from - pattern: "*.bed" - - fasta: - type: file - description: Genome fasta file [required] - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file [required] - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: Sorted VCF file [required] + pattern: "*.vcf" + - tbi: + type: file + description: VCF index file [required] + pattern: "*.vcf{,.gz}.tbi" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - dbsnp: + type: file + description: dbsnp VCF file [required] + pattern: "*.vcf{,.gz}" + - dbsnp_tbi: + type: file + description: dbsnp VCF index file [required] + pattern: "*.vcf{,.gz}.tbi" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file [required] + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Index of the genome fasta file [required] + pattern: "*.fai" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - interval: + type: file + description: BED file of genome regions to draw coverage from + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - metrics: - type: file - description: | - Metrics file from VCF - pattern: "*.variant_calling_detail_metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.variant_calling_detail_metrics": + type: file + description: | + Metrics file from VCF + pattern: "*.variant_calling_detail_metrics" - summary: - type: file - description: | - Summary of VCF metrics - pattern: "*.collectvcmetrics.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.variant_calling_summary_metrics": + type: file + description: | + Summary of VCF metrics + pattern: "*.collectvcmetrics.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/sentieon/coveragemetrics/meta.yml b/modules/nf-core/sentieon/coveragemetrics/meta.yml index 9f6c590cc4a..e024658ff55 100644 --- a/modules/nf-core/sentieon/coveragemetrics/meta.yml +++ b/modules/nf-core/sentieon/coveragemetrics/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "sentieon_coveragemetrics" description: Accelerated implementation of the GATK DepthOfCoverage tool. @@ -14,89 +13,129 @@ tools: homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ licence: ["Commercial (requires license for use; redistribution allowed)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM/CRAM/SAM file index - pattern: "*.{bai,crai}" - - interval: - type: file - description: BED file of genome regions to draw coverage from - pattern: "*.bed" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - gene_list: - type: file - description: RefSeq file used to aggregate the results - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM file index + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - interval: + type: file + description: BED file of genome regions to draw coverage from + pattern: "*.bed" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gene_list: + type: file + description: RefSeq file used to aggregate the results + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - per_locus: - type: file - description: The per locus coverage with no partition. - pattern: "${sample_id}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $prefix: + type: file + description: The per locus coverage with no partition. + pattern: "${sample_id}" - sample_summary: - type: file - description: The summary for PARTITION_GROUP sample, aggregated over all bases. - pattern: "${sample_id}.sample_summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_summary: + type: file + description: The summary for PARTITION_GROUP sample, aggregated over all bases. + pattern: "${sample_id}.sample_summary" - statistics: - type: file - description: The statistics for PARTITION_GROUP library, aggregated by interval. - pattern: "${sample_id}.interval_statistics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_interval_statistics: + type: file + description: The statistics for PARTITION_GROUP library, aggregated by interval. + pattern: "${sample_id}.interval_statistics" - coverage_counts: - type: file - description: Contains the histogram of loci with depth larger than x. - pattern: "${sample_id}.interval_statistics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_cumulative_coverage_counts: + type: file + description: Contains the histogram of loci with depth larger than x. + pattern: "${sample_id}.interval_statistics" - coverage_proportions: - type: file - description: Contains the normalized histogram of loci with depth larger than x. - pattern: "${sample_id}.interval_statistics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_cumulative_coverage_proportions: + type: file + description: Contains the normalized histogram of loci with depth larger than + x. + pattern: "${sample_id}.interval_statistics" - interval_summary: - type: file - description: The summary for PARTITION_GROUP library, aggregated by interval. - pattern: "${sample_id}.interval_summary" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_interval_summary: + type: file + description: The summary for PARTITION_GROUP library, aggregated by interval. + pattern: "${sample_id}.interval_summary" + - _summary: + type: file + description: The summary for PARTITION_GROUP library, aggregated by interval. + pattern: "${sample_id}.interval_summary" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/sentieon/datametrics/meta.yml b/modules/nf-core/sentieon/datametrics/meta.yml index d2d1450a692..a72ff866b46 100644 --- a/modules/nf-core/sentieon/datametrics/meta.yml +++ b/modules/nf-core/sentieon/datametrics/meta.yml @@ -11,72 +11,110 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index of th sorted BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index of th sorted BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mq_metrics: - type: file - description: File containing the information about mean base quality score for each sequencing cycle - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*mq_metrics.txt": + type: file + description: File containing the information about mean base quality score for + each sequencing cycle + pattern: "*.txt" - qd_metrics: - type: file - description: File containing the information about number of bases with a specific base quality score - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*qd_metrics.txt": + type: file + description: File containing the information about number of bases with a specific + base quality score + pattern: "*.txt" - gc_summary: - type: file - description: File containing the information about GC bias in the reference and the sample - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*gc_summary.txt": + type: file + description: File containing the information about GC bias in the reference + and the sample + pattern: "*.txt" - gc_metrics: - type: file - description: File containing the information about GC bias in the reference and the sample - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*gc_metrics.txt": + type: file + description: File containing the information about GC bias in the reference + and the sample + pattern: "*.txt" - aln_metrics: - type: file - description: File containing the statistics about the alignment of the reads - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*aln_metrics.txt": + type: file + description: File containing the statistics about the alignment of the reads + pattern: "*.txt" - is_metrics: - type: file - description: File containing the information about statistical distribution of insert sizes - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*is_metrics.txt": + type: file + description: File containing the information about statistical distribution + of insert sizes + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/dedup/meta.yml b/modules/nf-core/sentieon/dedup/meta.yml index 0efbb96c229..003d74befe7 100644 --- a/modules/nf-core/sentieon/dedup/meta.yml +++ b/modules/nf-core/sentieon/dedup/meta.yml @@ -1,5 +1,7 @@ name: sentieon_dedup -description: Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads. +description: Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector + collects read information that is used by Dedup which in turn marks or removes duplicate + reads. keywords: - mem - dedup @@ -14,76 +16,116 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file. - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - cram: - type: file - description: CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: CRAM file + pattern: "*.cram" - crai: - type: file - description: CRAM index file - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file + pattern: "*.crai" - bam: - type: file - description: BAM file. - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file. + pattern: "*.bam" - bai: - type: file - description: BAI file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAI file + pattern: "*.bai" - score: - type: file - description: The score file indicates which reads LocusCollector finds are likely duplicates. - pattern: "*.score" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.score": + type: file + description: The score file indicates which reads LocusCollector finds are likely + duplicates. + pattern: "*.score" - metrics: - type: file - description: Output file containing Dedup metrics incl. histogram data. - pattern: "*.metrics" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Output file containing Dedup metrics incl. histogram data. + pattern: "*.metrics" - metrics_multiqc_tsv: - type: file - description: Output tsv-file containing Dedup metrics excl. histogram data. - pattern: "*.metrics.multiqc.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.metrics.multiqc.tsv": + type: file + description: Output tsv-file containing Dedup metrics excl. histogram data. + pattern: "*.metrics.multiqc.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml index 25076545770..2505aff74e9 100644 --- a/modules/nf-core/sentieon/dnamodelapply/meta.yml +++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml @@ -12,65 +12,74 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - vcf: - type: file - description: INPUT VCF file - pattern: "*.{vcf,vcf.gz}" - - idx: - type: file - description: Index of the input VCF file - pattern: "*.{tbi}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - ml_model: - type: file - description: machine learning model file - pattern: "*.model" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: INPUT VCF file + pattern: "*.{vcf,vcf.gz}" + - idx: + type: file + description: Index of the input VCF file + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - ml_model: + type: file + description: machine learning model file + pattern: "*.model" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: INPUT VCF file - pattern: "*.{vcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: INPUT VCF file + pattern: "*.{vcf,vcf.gz}" - index: - type: file - description: Index of the input VCF file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz.tbi": + type: file + description: Index of the input VCF file + pattern: "*.{tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/dnascope/meta.yml b/modules/nf-core/sentieon/dnascope/meta.yml index 6b61cee828f..e3e0eba8c8e 100644 --- a/modules/nf-core/sentieon/dnascope/meta.yml +++ b/modules/nf-core/sentieon/dnascope/meta.yml @@ -1,5 +1,6 @@ name: sentieon_dnascope -description: DNAscope algorithm performs an improved version of Haplotype variant calling. +description: DNAscope algorithm performs an improved version of Haplotype variant + calling. keywords: - dnascope - sentieon @@ -11,109 +12,127 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file. - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - intervals: - type: file - description: bed or interval_list file containing interval in the reference that will be used in the analysis - pattern: "*.{bed,interval_list}" - - meta2: - type: map - description: | - Groovy Map containing meta information for fasta. - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing meta information for fasta index. - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing meta information for dbsnp. - - dbsnp: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - meta5: - type: map - description: | - Groovy Map containing meta information for dbsnp_tbi. - - dbsnp_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - meta6: - type: map - description: | - Groovy Map containing meta information for machine learning model for Dnascope. - - ml_model: - type: file - description: machine learning model file - pattern: "*.model" - - ml_model: - type: file - description: machine learning model file - pattern: "*.model" - - pcr_indel_model: - type: string - description: | - Controls the option pcr_indel_model for Dnascope. - The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". - See Sentieons documentation for further explanation. - - emit_vcf: - type: string - description: | - Controls the vcf output from Dnascope. - Possible options are "all", "confident" and "variant". - See Sentieons documentation for further explanation. - - emit_gvcf: - type: boolean - description: If true, the haplotyper will output a gvcf + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - intervals: + type: file + description: bed or interval_list file containing interval in the reference + that will be used in the analysis + pattern: "*.{bed,interval_list}" + - - meta2: + type: map + description: | + Groovy Map containing meta information for fasta. + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing meta information for fasta index. + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing meta information for dbsnp. + - dbsnp: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - - meta5: + type: map + description: | + Groovy Map containing meta information for dbsnp_tbi. + - dbsnp_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta6: + type: map + description: | + Groovy Map containing meta information for machine learning model for Dnascope. + - ml_model: + type: file + description: machine learning model file + pattern: "*.model" + - - pcr_indel_model: + type: string + description: | + Controls the option pcr_indel_model for Dnascope. + The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". + See Sentieons documentation for further explanation. + - - emit_vcf: + type: string + description: | + Controls the vcf output from Dnascope. + Possible options are "all", "confident" and "variant". + See Sentieons documentation for further explanation. + - - emit_gvcf: + type: boolean + description: If true, the haplotyper will output a gvcf output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.unfiltered.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.unfiltered.vcf.gz" - vcf_tbi: - type: file - description: Index of VCF file - pattern: "*.unfiltered.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz.tbi": + type: file + description: Index of VCF file + pattern: "*.unfiltered.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz": + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" - gvcf_tbi: - type: file - description: Index of GVCF file - pattern: "*.g.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz.tbi": + type: file + description: Index of GVCF file + pattern: "*.g.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/gvcftyper/meta.yml b/modules/nf-core/sentieon/gvcftyper/meta.yml index 5a83eb03082..f022553711c 100644 --- a/modules/nf-core/sentieon/gvcftyper/meta.yml +++ b/modules/nf-core/sentieon/gvcftyper/meta.yml @@ -12,59 +12,89 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gvcfs: - type: file - description: | - gVCF(.gz) file - pattern: "*.{vcf,vcf.gz}" - - tbis: - type: file - description: | - index of gvcf file - pattern: "*.tbi" - - intervals: - type: file - description: Interval file with the genomic regions included in the library (optional) - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Reference fasta index file - pattern: "*.fai" - - dbsnp: - type: file - description: dbSNP VCF file - pattern: "*.vcf.gz" - - dbsnp_tbi: - type: file - description: dbSNP VCF index file - pattern: "*.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gvcfs: + type: file + description: | + gVCF(.gz) file + pattern: "*.{vcf,vcf.gz}" + - tbis: + type: file + description: | + index of gvcf file + pattern: "*.tbi" + - intervals: + type: file + description: Interval file with the genomic regions included in the library + (optional) + - - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp: + type: file + description: dbSNP VCF file + pattern: "*.vcf.gz" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp_tbi: + type: file + description: dbSNP VCF index file + pattern: "*.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Genotyped VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Tbi index for VCF file - pattern: "*.vcf.gz" + - vcf_gz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.vcf.gz" + - vcf_gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/haplotyper/meta.yml b/modules/nf-core/sentieon/haplotyper/meta.yml index e5b3f34a069..ee0e6152f04 100644 --- a/modules/nf-core/sentieon/haplotyper/meta.yml +++ b/modules/nf-core/sentieon/haplotyper/meta.yml @@ -11,76 +11,117 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - recal_table: - type: file - description: Recalibration table from sentieon/qualcal (optional) - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) - - emit_vcf: - type: string - description: | - Controls the vcf output from the haplotyper. - If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all". - If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident". - If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident". - - emit_gvcf: - type: boolean - description: If true, the haplotyper will output a gvcf + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - recal_table: + type: file + description: Recalibration table from sentieon/qualcal (optional) + - - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) + - - emit_vcf: + type: string + description: | + Controls the vcf output from the haplotyper. + If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all". + If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident". + If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident". + - - emit_gvcf: + type: boolean + description: If true, the haplotyper will output a gvcf output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.unfiltered.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.unfiltered.vcf.gz" - vcf_tbi: - type: file - description: Index of VCF file - pattern: "*.unfiltered.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz.tbi": + type: file + description: Index of VCF file + pattern: "*.unfiltered.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz": + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" - gvcf_tbi: - type: file - description: Index of GVCF file - pattern: "*.g.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz.tbi": + type: file + description: Index of GVCF file + pattern: "*.g.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/qualcal/meta.yml b/modules/nf-core/sentieon/qualcal/meta.yml index 76c124b0d87..7be3b9e77e6 100644 --- a/modules/nf-core/sentieon/qualcal/meta.yml +++ b/modules/nf-core/sentieon/qualcal/meta.yml @@ -1,4 +1,3 @@ ---- name: "sentieon_qualcal" description: Generate recalibration table and optionally perform base quality recalibration keywords: @@ -12,74 +11,125 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" - - recalibration_table: - type: file - description: File containing recalibration values (optional) - pattern: "*.table" - - generate_recalibrated_bams: - type: boolean - description: If truem, writes recalibrated bams to disc - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - recalibration_table: + type: file + description: File containing recalibration values (optional) + pattern: "*.table" + - - generate_recalibrated_bams: + type: boolean + description: If truem, writes recalibrated bams to disc output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Pre Recalibration table (optional) - pattern: "*.table" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Pre Recalibration table (optional) + pattern: "*.table" - table_post: - type: file - description: Post recalibration table (optional) - pattern: "*.table.post" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table.post": + type: file + description: Post recalibration table (optional) + pattern: "*.table.post" - recal_alignment: - type: file - description: Recalibrated input files (optional) - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{cram,bam}": + type: file + description: Recalibrated input files (optional) + pattern: "*.{bam,cram}" - csv: - type: file - description: Recalibration results output file used for plotting. (optional) - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Recalibration results output file used for plotting. (optional) + pattern: "*.csv" - pdf: - type: file - description: PDF file containing graphs (optional) - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: PDF file containing graphs (optional) + pattern: "*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/sentieon/readwriter/meta.yml b/modules/nf-core/sentieon/readwriter/meta.yml index 9f107663d62..6e79ea190b0 100644 --- a/modules/nf-core/sentieon/readwriter/meta.yml +++ b/modules/nf-core/sentieon/readwriter/meta.yml @@ -1,5 +1,6 @@ name: sentieon_readwriter -description: Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file. +description: Merges BAM files, and/or convert them into cram files. Also, outputs + the result of applying the Base Quality Score Recalibration to a file. keywords: - merge - convert @@ -12,59 +13,78 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM file. - pattern: "*.{bam,cram}" - - index: - type: file - description: BAI/CRAI file. - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file. + pattern: "*.{bam,cram}" + - index: + type: file + description: BAI/CRAI file. + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - output: - type: file - description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix = .bam", CRAM "ext.prefix = .cram". Defaults to cram - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix + = .bam", CRAM "ext.prefix = .cram". Defaults to cram + pattern: "*.{bam,cram}" - index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}.${index}: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" - output_index: - type: file - description: BAM/CRAM alignment and the corresponding index file + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: BAM/CRAM alignment and the corresponding index file + - ${prefix}.${index}: + type: file + description: BAM/CRAM alignment and the corresponding index file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/tnfilter/meta.yml b/modules/nf-core/sentieon/tnfilter/meta.yml index d184dd6b7b2..41dfa94fb6d 100644 --- a/modules/nf-core/sentieon/tnfilter/meta.yml +++ b/modules/nf-core/sentieon/tnfilter/meta.yml @@ -14,72 +14,90 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - vcf: - type: file - description: compressed vcf file from tnhaplotyper2 - pattern: "*.vcf.gz" - - vcf_tbi: - type: file - description: Tabix index of vcf file - pattern: "*vcf.gz.tbi" - - stats: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" - - contamination: - type: file - description: the location and file name of the file containing the contamination information produced by ContaminationModel. - pattern: "*.contamination_data.tsv" - - segments: - type: file - description: the location and file name of the file containing the tumor segments information produced by ContaminationModel. - pattern: "*.segments" - - orientation_priors: - type: file - description: the location and file name of the file containing the orientation bias information produced by OrientationBias. - pattern: "*.orientation_data.tsv" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: compressed vcf file from tnhaplotyper2 + pattern: "*.vcf.gz" + - vcf_tbi: + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" + - stats: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - contamination: + type: file + description: the location and file name of the file containing the contamination + information produced by ContaminationModel. + pattern: "*.contamination_data.tsv" + - segments: + type: file + description: the location and file name of the file containing the tumor segments + information produced by ContaminationModel. + pattern: "*.segments" + - orientation_priors: + type: file + description: the location and file name of the file containing the orientation + bias information produced by OrientationBias. + pattern: "*.orientation_data.tsv" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" output: - vcf: - type: file - description: file containing filtered tnhaplotyper2 calls. - pattern: "*.vcf.gz" + - meta: + type: file + description: file containing filtered tnhaplotyper2 calls. + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: file containing filtered tnhaplotyper2 calls. + pattern: "*.vcf.gz" - vcf_tbi: - type: file - description: tbi file that pairs with vcf. - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" + - "*.vcf.gz.tbi": + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" - stats: - type: file - description: file containing statistics of the tnfilter run. - pattern: "*.stats" + - meta: + type: file + description: file containing statistics of the tnfilter run. + pattern: "*.stats" + - "*.vcf.gz.stats": + type: file + description: file containing statistics of the tnfilter run. + pattern: "*.stats" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" diff --git a/modules/nf-core/sentieon/tnhaplotyper2/meta.yml b/modules/nf-core/sentieon/tnhaplotyper2/meta.yml index 9a0cafd81f7..8e1f481d7b5 100644 --- a/modules/nf-core/sentieon/tnhaplotyper2/meta.yml +++ b/modules/nf-core/sentieon/tnhaplotyper2/meta.yml @@ -1,5 +1,6 @@ name: sentieon_tnhaplotyper2 -description: Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs. +description: Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched + pairs. keywords: - tnseq - tnhaplotyper2 @@ -12,122 +13,161 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta5: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta6: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta7: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta8: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - germline_resource: - type: file - description: Population vcf of germline sequencing, containing allele fractions. - pattern: "*.vcf.gz" - - germline_resource_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" - - panel_of_normals: - type: file - description: vcf file to be used as a panel of normals. - pattern: "*.vcf.gz" - - panel_of_normals_tbi: - type: file - description: Index for the panel of normals. - pattern: "*.vcf.gz.tbi" - - emit_orientation_data: - type: boolean - description: If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias. - - emit_contamination_data: - type: boolean - description: If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel. + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - germline_resource: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + pattern: "*.vcf.gz" + - - meta6: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - germline_resource_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" + - - meta7: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - panel_of_normals: + type: file + description: vcf file to be used as a panel of normals. + pattern: "*.vcf.gz" + - - meta8: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - panel_of_normals_tbi: + type: file + description: Index for the panel of normals. + pattern: "*.vcf.gz.tbi" + - - emit_orientation_data: + type: boolean + description: If true, the module will run the sentieon algorithm TNhaplotyper2 + followed by the sentieon algorithm OrientationBias. + - - emit_contamination_data: + type: boolean + description: If true, the module will run the sentieon algorithm TNhaplotyper2 + followed by the sentieon algorithm ContaminationModel. output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - orientation_data: - type: file - description: TSV file from Sentieon's algorithm OrientationBias - pattern: "*.orientation_data.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.orientation_data.tsv": + type: file + description: TSV file from Sentieon's algorithm OrientationBias + pattern: "*.orientation_data.tsv" - contamination_data: - type: file - description: TSV file from Sentieon's algorithm ContaminationModel - pattern: "*.contamination_data.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.contamination_data.tsv": + type: file + description: TSV file from Sentieon's algorithm ContaminationModel + pattern: "*.contamination_data.tsv" - contamination_segments: - type: file - description: Tumour segments file from Sentieon's algorithm ContaminationModel - pattern: "*.segments" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.segments": + type: file + description: Tumour segments file from Sentieon's algorithm ContaminationModel + pattern: "*.segments" + - stats: + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: Stats file from Sentieon's algorithm + pattern: "*.stats" - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.{vcf.gz}" - index: - type: file - description: Index of the VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of the VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/tnscope/meta.yml b/modules/nf-core/sentieon/tnscope/meta.yml index 8299888b3bd..36dcd8d8e68 100644 --- a/modules/nf-core/sentieon/tnscope/meta.yml +++ b/modules/nf-core/sentieon/tnscope/meta.yml @@ -1,5 +1,6 @@ name: sentieon_tnscope -description: TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm. +description: TNscope algorithm performs somatic variant calling on the tumor-normal + matched pair or the tumor only data, using a Haplotyper algorithm. keywords: - tnscope - sentieon @@ -11,104 +12,114 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta5: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta6: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta7: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - bam: - type: file - description: BAM file. - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - cosmic: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - cosmic_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - pon: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - pon_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - dbsnp: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - dbsnp_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - interval: - type: file - description: bed or interval_list file containing interval in the reference that will be used in the analysis - pattern: "*.{bed,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - cosmic: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - cosmic_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - pon: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - pon_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta6: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - dbsnp: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - dbsnp_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta7: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - interval: + type: file + description: bed or interval_list file containing interval in the reference + that will be used in the analysis + pattern: "*.{bed,interval_list}" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.{vcf.gz}" - index: - type: file - description: Index of the VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of the VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/varcal/meta.yml b/modules/nf-core/sentieon/varcal/meta.yml index cad7ee106f7..4661dc92d8f 100644 --- a/modules/nf-core/sentieon/varcal/meta.yml +++ b/modules/nf-core/sentieon/varcal/meta.yml @@ -14,60 +14,87 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: input vcf file containing the variants to be recalibrated - pattern: "*.vcf.gz" - - tbi: - type: file - description: tbi file matching with -vcf - pattern: "*.vcf.gz.tbi" - - resource_vcf: - type: file - description: all resource vcf files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz" - - resource_tbi: - type: file - description: all resource tbi files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz.tbi" - - labels: - type: string - description: necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: input vcf file containing the variants to be recalibrated + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - - resource_vcf: + type: file + description: all resource vcf files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz" + - - resource_tbi: + type: file + description: all resource tbi files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz.tbi" + - - labels: + type: string + description: necessary arguments for Sentieon's VarCal. Specified to directly + match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" output: - recal: - type: file - description: Output recal file used by ApplyVQSR - pattern: "*.recal" + - meta: + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" + - "*.recal": + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" - idx: - type: file - description: Index file for the recal output file - pattern: "*.idx" + - meta: + type: file + description: Index file for the recal output file + pattern: "*.idx" + - "*.idx": + type: file + description: Index file for the recal output file + pattern: "*.idx" - tranches: - type: file - description: Output tranches file used by ApplyVQSR - pattern: "*.tranches" + - meta: + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" + - "*.tranches": + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" - plots: - type: file - description: Optional output rscript file to aid in visualization of the input data and learned model. - pattern: "*plots.R" - - version: - type: file - description: File containing software versions - pattern: "*.versions.yml" + - meta: + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - "*plots.R": + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml index 86431e1c6e3..a8b64727713 100644 --- a/modules/nf-core/sentieon/wgsmetrics/meta.yml +++ b/modules/nf-core/sentieon/wgsmetrics/meta.yml @@ -11,61 +11,64 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index of th sorted BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - interval_list: - type: file - description: bed or interval_list file containing interval in the reference that will be used in the analysis - pattern: "*.{bed,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index of th sorted BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - intervals_list: + type: file + description: intervals output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wgs_metrics: - type: file - description: File containing the information about mean base quality score for each sequencing cycle - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: File containing the information about mean base quality score for + each sequencing cycle + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/seqcluster/collapse/meta.yml b/modules/nf-core/seqcluster/collapse/meta.yml index 03e9dc6330b..e3a6f7e3270 100644 --- a/modules/nf-core/seqcluster/collapse/meta.yml +++ b/modules/nf-core/seqcluster/collapse/meta.yml @@ -1,45 +1,48 @@ name: "seqcluster_collapse" -description: Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file. +description: Seqcluster collapse reduces computational complexity by collapsing identical + sequences in a FASTQ file. keywords: - smrnaseq - cluster - mirna tools: - "seqcluster": - description: "Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project." + description: "Small RNA analysis from NGS data. Seqcluster generates a list of + clusters of small RNA sequences, their genome location, their annotation and + the abundance in all the sample of the project." homepage: "https://github.com/lpantano/seqcluster" documentation: "https://github.com/lpantano/seqcluster" tool_dev_url: "https://github.com/lpantano/seqcluster" doi: "10.1093/bioinformatics/btr527" licence: ["MIT"] + identifier: biotools:seqcluster input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastq: - type: file - description: FASTQ file - pattern: "*.{fastq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: FASTQ file + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: FASTQ file - pattern: "*.{fastq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq.gz": + type: file + description: FASTQ file + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/seqfu/derep/meta.yml b/modules/nf-core/seqfu/derep/meta.yml index c3ae374a6d3..8c7741a5e0e 100644 --- a/modules/nf-core/seqfu/derep/meta.yml +++ b/modules/nf-core/seqfu/derep/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqfu_derep" -description: Dereplicate FASTX sequences, removing duplicate sequences and printing the number of identical sequences in the sequence header. Can dereplicate already dereplicated FASTA files, summing the numbers found in the headers. +description: Dereplicate FASTX sequences, removing duplicate sequences and printing + the number of identical sequences in the sequence header. Can dereplicate already + dereplicated FASTA files, summing the numbers found in the headers. keywords: - dereplicate - fasta @@ -14,30 +15,33 @@ tools: tool_dev_url: "https://telatin.github.io/seqfu2/tools/derep.html" doi: "10.3390/bioengineering8050059" licence: ["GPL v3"] + identifier: biotools:seqfu input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastas: - type: file - description: Input files (mainly FASTA, FASTQ supported) - pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastas: + type: file + description: Input files (mainly FASTA, FASTQ supported) + pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: dereplicated file (FASTA format) - pattern: "*.{fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_derep.fasta.gz": + type: file + description: dereplicated file (FASTA format) + pattern: "*.{fasta.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@telatin" maintainers: diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml index df6093c5120..f534a3f50fc 100644 --- a/modules/nf-core/seqfu/stats/meta.yml +++ b/modules/nf-core/seqfu/stats/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqfu_stats" description: Statistics for FASTA or FASTQ files @@ -8,49 +7,53 @@ keywords: - n50 tools: - "seqfu": - description: "Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files" + description: "Cross-platform compiled suite of tools to manipulate and inspect + FASTA and FASTQ files" homepage: "https://telatin.github.io/seqfu2/" documentation: "https://telatin.github.io/seqfu2/" tool_dev_url: "https://github.com/telatin/seqfu2" doi: "10.3390/bioengineering8050059" licence: ["GPL v3"] + identifier: biotools:seqfu input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - files: - type: file - description: One or more FASTA or FASTQ files - pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - files: + type: file + description: One or more FASTA or FASTQ files + pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - stats: - type: file - description: Tab-separated output file with basic sequence statistics. - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Tab-separated output file with basic sequence statistics. + pattern: "*.{tsv}" - multiqc: - type: file - description: MultiQC ready table - pattern: "*.{_mqc.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_mqc.txt": + type: file + description: MultiQC ready table + pattern: "*.{_mqc.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@telatin" maintainers: diff --git a/modules/nf-core/seqkit/concat/meta.yml b/modules/nf-core/seqkit/concat/meta.yml index c4511ce0d04..c5315f25514 100644 --- a/modules/nf-core/seqkit/concat/meta.yml +++ b/modules/nf-core/seqkit/concat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_concat" description: Concatenating multiple uncompressed sequence files together @@ -16,37 +15,35 @@ tools: tool_dev_url: https://github.com/shenwei356/seqkit doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: Sequence file in fasta/q format - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: Sequence file in fasta/q format + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: A concatenated sequence file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{fasta,fastq,fa,fq,fas,fna,faa}": + type: file + description: A concatenated sequence file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/seqkit/fq2fa/meta.yml b/modules/nf-core/seqkit/fq2fa/meta.yml index d0c55b3c190..2241fda93a7 100644 --- a/modules/nf-core/seqkit/fq2fa/meta.yml +++ b/modules/nf-core/seqkit/fq2fa/meta.yml @@ -6,39 +6,39 @@ keywords: - convert tools: - "seqkit": - description: "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen." + description: "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen." homepage: "https://github.com/shenwei356/seqkit" documentation: "https://bioinf.shenwei.me/seqkit/" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - fastq: - type: file - description: Sequence file in fastq format - pattern: "*.{fastq,fq}.gz" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fastq: + type: file + description: Sequence file in fastq format + pattern: "*.{fastq,fq}.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Sequence file in fasta format - pattern: "*.{fasta,fa}.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fa.gz": + type: file + description: Sequence file in fasta format + pattern: "*.{fasta,fa}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d-jch" diff --git a/modules/nf-core/seqkit/fx2tab/meta.yml b/modules/nf-core/seqkit/fx2tab/meta.yml index e403392ce58..4fb450dca22 100644 --- a/modules/nf-core/seqkit/fx2tab/meta.yml +++ b/modules/nf-core/seqkit/fx2tab/meta.yml @@ -1,5 +1,6 @@ name: seqkit_fx2tab -description: Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew. +description: Convert FASTA/Q to tabular format, and provide various information, like + sequence length, GC content/GC skew. keywords: - fasta - fastq @@ -14,30 +15,33 @@ tools: documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastx: - type: file - description: Sequence file in fasta/q format - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastx: + type: file + description: Sequence file in fasta/q format + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - text: - type: file - description: Text file in tabular format - pattern: "*.txt[.gz,.zstd,.zst]" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt*": + type: file + description: Text file in tabular format + pattern: "*.txt[.gz,.zstd,.zst]" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/seqkit/grep/meta.yml b/modules/nf-core/seqkit/grep/meta.yml index d74dc503c5a..309f8197486 100644 --- a/modules/nf-core/seqkit/grep/meta.yml +++ b/modules/nf-core/seqkit/grep/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "seqkit_grep" description: Select sequences from a large file based on name/ID @@ -9,46 +8,48 @@ keywords: - grep tools: - "seqkit": - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - sequence: - type: file - description: > - Fasta or fastq file containing sequences to be filtered - - pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" - - pattern: - type: file - description: > - pattern file (one record per line). If no pattern is given, a string can be specificied within the args using '-p pattern_string' - - pattern: "*.{txt,tsv}" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - sequence: + type: file + description: > + Fasta or fastq file containing sequences to be filtered + pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + - - pattern: + type: file + description: > + pattern file (one record per line). If no pattern is given, a string can be + specificied within the args using '-p pattern_string' + pattern: "*.{txt,tsv}" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filter: - type: file - description: > - Fasta or fastq file containing the filtered sequences - - pattern: "*.{fa,fq}[.gz]" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.{fa,fq}.gz": + type: file + description: > + Fasta or fastq file containing the filtered sequences + pattern: "*.{fa,fq}[.gz]" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/seqkit/pair/meta.yml b/modules/nf-core/seqkit/pair/meta.yml index 4a49926ae92..0bc01bbe595 100644 --- a/modules/nf-core/seqkit/pair/meta.yml +++ b/modules/nf-core/seqkit/pair/meta.yml @@ -6,40 +6,50 @@ keywords: - fastq tools: - seqkit: - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input paired-end FastQ files. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input paired-end FastQ files. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Paired fastq reads - pattern: "*.paired.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paired.fastq.gz": + type: file + description: Paired fastq reads + pattern: "*.paired.fastq.gz" - unpaired_reads: - type: file - description: Unpaired reads (optional) - pattern: "*.unpaired.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unpaired.fastq.gz": + type: file + description: Unpaired reads (optional) + pattern: "*.unpaired.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml index 1763521a0a4..1be01079510 100644 --- a/modules/nf-core/seqkit/replace/meta.yml +++ b/modules/nf-core/seqkit/replace/meta.yml @@ -8,35 +8,39 @@ keywords: - fasta tools: - seqkit: - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.016396" + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastx: - type: file - description: fasta/q file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastx: + type: file + description: fasta/q file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastx: - type: file - description: fasta/q file with replaced values - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fast*": + type: file + description: fasta/q file with replaced values + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" maintainers: diff --git a/modules/nf-core/seqkit/rmdup/meta.yml b/modules/nf-core/seqkit/rmdup/meta.yml index d0addd4551a..22e29c117be 100644 --- a/modules/nf-core/seqkit/rmdup/meta.yml +++ b/modules/nf-core/seqkit/rmdup/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_rmdup" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -16,34 +16,43 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.${extension}: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - log: - type: file - description: Log containing information regarding removed duplicates - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Log containing information regarding removed duplicates + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/seq/meta.yml b/modules/nf-core/seqkit/seq/meta.yml index 8d4e2b160e4..7d32aba5870 100644 --- a/modules/nf-core/seqkit/seq/meta.yml +++ b/modules/nf-core/seqkit/seq/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_seq" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/sliding/meta.yml b/modules/nf-core/seqkit/sliding/meta.yml index dbfa49c458a..e012ef06950 100644 --- a/modules/nf-core/seqkit/sliding/meta.yml +++ b/modules/nf-core/seqkit/sliding/meta.yml @@ -6,35 +6,39 @@ keywords: - windows tools: - seqkit: - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.016396" + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastx: - type: file - description: fasta/q file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastx: + type: file + description: fasta/q file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastx: - type: file - description: fasta/q window file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fast*": + type: file + description: fasta/q window file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/seqkit/sort/meta.yml b/modules/nf-core/seqkit/sort/meta.yml index 2e61ce1566f..157ff85ca5b 100644 --- a/modules/nf-core/seqkit/sort/meta.yml +++ b/modules/nf-core/seqkit/sort/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_sort" description: Sorts sequences by id/name/sequence/length @@ -15,30 +14,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta.gz,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta.gz,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml index 14babd448b6..c1e6e3def2e 100644 --- a/modules/nf-core/seqkit/split2/meta.yml +++ b/modules/nf-core/seqkit/split2/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FastQ files - pattern: "*.{fq.gz/fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FastQ files + pattern: "*.{fq.gz/fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Split fastq files - pattern: "*.{fq.gz/fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "**/*.gz": + type: file + description: Split fastq files + pattern: "*.{fq.gz/fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml index 717ba43c33f..797712b5bb9 100644 --- a/modules/nf-core/seqkit/stats/meta.yml +++ b/modules/nf-core/seqkit/stats/meta.yml @@ -6,40 +6,42 @@ keywords: - stats tools: - "seqkit": - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - reads: - type: file - description: > - Either FASTA or FASTQ files. - - pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - reads: + type: file + description: > + Either FASTA or FASTQ files. + pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: > - Tab-separated output file with basic sequence statistics. - - pattern: "*.tsv" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.tsv": + type: file + description: > + Tab-separated output file with basic sequence statistics. + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/seqkit/tab2fx/meta.yml b/modules/nf-core/seqkit/tab2fx/meta.yml index 04537148edc..7c93beb1004 100644 --- a/modules/nf-core/seqkit/tab2fx/meta.yml +++ b/modules/nf-core/seqkit/tab2fx/meta.yml @@ -14,30 +14,33 @@ tools: documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - text: - type: file - description: Text file in tabular format - pattern: "*.txt[.gz,.zst]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - text: + type: file + description: Text file in tabular format + pattern: "*.txt[.gz,.zst]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastx: - type: file - description: Sequence file in fasta/q format - pattern: "*.{fa,fq}[.gz,.zst]" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.f*": + type: file + description: Sequence file in fasta/q format + pattern: "*.{fa,fq}[.gz,.zst]" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/seqsero2/meta.yml b/modules/nf-core/seqsero2/meta.yml index 36e98bed954..9761dd7b651 100644 --- a/modules/nf-core/seqsero2/meta.yml +++ b/modules/nf-core/seqsero2/meta.yml @@ -13,38 +13,53 @@ tools: tool_dev_url: https://github.com/denglab/SeqSero2 doi: "10.1128/AEM.01746-19" licence: ["GPL v2"] + identifier: biotools:SeqSero2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTQ or FASTA formated sequences - pattern: "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTQ or FASTA formated sequences + pattern: "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: A log of serotype antigen results - pattern: "*_log.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*_log.txt: + type: file + description: A log of serotype antigen results + pattern: "*_log.txt" - tsv: - type: file - description: Tab-delimited summary of the SeqSero2 results - pattern: "*_result.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*_result.tsv: + type: file + description: Tab-delimited summary of the SeqSero2 results + pattern: "*_result.tsv" - txt: - type: file - description: Detailed summary of the SeqSero2 results - pattern: "*_result.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*_result.txt: + type: file + description: Detailed summary of the SeqSero2 results + pattern: "*_result.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/seqtk/cutn/meta.yml b/modules/nf-core/seqtk/cutn/meta.yml index 1082867938c..2e39a477595 100644 --- a/modules/nf-core/seqtk/cutn/meta.yml +++ b/modules/nf-core/seqtk/cutn/meta.yml @@ -6,35 +6,40 @@ keywords: - seqtk tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into + one interleaved file. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A single fasta file to be split. - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A single fasta file to be split. + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: The output bed which summarised locations of cuts - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: The output bed which summarised locations of cuts + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/seqtk/mergepe/meta.yml b/modules/nf-core/seqtk/mergepe/meta.yml index bfe96a12fa5..b318250ae81 100644 --- a/modules/nf-core/seqtk/mergepe/meta.yml +++ b/modules/nf-core/seqtk/mergepe/meta.yml @@ -6,35 +6,43 @@ keywords: - fastx tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into + one interleaved file. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data,respectively. - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data,respectively. + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: If single-end reads, the output is the same as the input, 1 FastQ + file for each read. If pair-end reads, the read pairs will be interleaved + and output as 1 FastQ file for each read pair. + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@emnilsson" maintainers: diff --git a/modules/nf-core/seqtk/rename/meta.yml b/modules/nf-core/seqtk/rename/meta.yml index 7696ef114a9..5b4682fa65f 100644 --- a/modules/nf-core/seqtk/rename/meta.yml +++ b/modules/nf-core/seqtk/rename/meta.yml @@ -6,35 +6,40 @@ keywords: - header tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. The seqtk rename command renames sequence names. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - sequences: - type: file - description: A FASTQ or FASTA file - pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - sequences: + type: file + description: A FASTQ or FASTA file + pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, + fna, fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sequences: - type: file - description: FASTQ/FASTA file containing renamed sequences - pattern: "*.{fastq.gz, fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gz": + type: file + description: FASTQ/FASTA file containing renamed sequences + pattern: "*.{fastq.gz, fasta.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@hseabolt" - "@mjcipriano" diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml index 54a5c2bbe13..42f67d8fe0b 100644 --- a/modules/nf-core/seqtk/sample/meta.yml +++ b/modules/nf-core/seqtk/sample/meta.yml @@ -6,38 +6,42 @@ keywords: - reads tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk sample command subsamples sequences. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files - pattern: "*.{fastq.gz}" - - sample_size: - type: integer - description: Number of reads to sample. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files + pattern: "*.{fastq.gz}" + - sample_size: + type: integer + description: Number of reads to sample. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Subsampled FastQ files - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Subsampled FastQ files + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" - "@sidorov-si" diff --git a/modules/nf-core/seqtk/seq/meta.yml b/modules/nf-core/seqtk/seq/meta.yml index adb03a0b61d..703b1dd1cb1 100644 --- a/modules/nf-core/seqtk/seq/meta.yml +++ b/modules/nf-core/seqtk/seq/meta.yml @@ -6,35 +6,41 @@ keywords: - transformation tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. The seqtk seq command enables common transformation + operations on FASTA or FASTQ files. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fastx: - type: file - description: A FASTQ or FASTA file - pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fastx: + type: file + description: A FASTQ or FASTA file + pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, + fna, fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastx: - type: file - description: FASTQ/FASTA file containing renamed sequences - pattern: "*.{fastq.gz, fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gz": + type: file + description: FASTQ/FASTA file containing renamed sequences + pattern: "*.{fastq.gz, fasta.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@hseabolt" - "@mjcipriano" diff --git a/modules/nf-core/seqtk/subseq/meta.yml b/modules/nf-core/seqtk/subseq/meta.yml index de4a8413369..2667f40d680 100644 --- a/modules/nf-core/seqtk/subseq/meta.yml +++ b/modules/nf-core/seqtk/subseq/meta.yml @@ -6,34 +6,42 @@ keywords: - fastx tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - sequences: - type: file - description: FASTQ/FASTA file - pattern: "*.{fq,fq.gz,fa,fa.gz}" - - filter_list: - type: file - description: BED file or a text file with a list of sequence names - pattern: "*.{bed,lst}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - sequences: + type: file + description: FASTQ/FASTA file + pattern: "*.{fq,fq.gz,fa,fa.gz}" + - - filter_list: + type: file + description: BED file or a text file with a list of sequence names + pattern: "*.{bed,lst}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sequences: - type: file - description: FASTQ/FASTA file - pattern: "*.{fq.gz,fa.gz}" + - meta: + type: file + description: FASTQ/FASTA file + pattern: "*.{fq.gz,fa.gz}" + - "*.gz": + type: file + description: FASTQ/FASTA file + pattern: "*.{fq.gz,fa.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sidorov-si" maintainers: diff --git a/modules/nf-core/seqtk/trim/meta.yml b/modules/nf-core/seqtk/trim/meta.yml index 11770572e16..3a0198ac0ab 100644 --- a/modules/nf-core/seqtk/trim/meta.yml +++ b/modules/nf-core/seqtk/trim/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: seqtk_trim description: Trim low quality bases from FastQ files @@ -8,37 +7,39 @@ keywords: - seqtk tools: - "seqtk": - description: "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format" + description: "Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format" homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files - pattern: "*.{fastq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Filtered FastQ files - pattern: "*.{fastq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Filtered FastQ files + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@laramiellindsey" diff --git a/modules/nf-core/sequencetools/pileupcaller/meta.yml b/modules/nf-core/sequencetools/pileupcaller/meta.yml index c33142844c0..5c42b3316c1 100644 --- a/modules/nf-core/sequencetools/pileupcaller/meta.yml +++ b/modules/nf-core/sequencetools/pileupcaller/meta.yml @@ -1,5 +1,6 @@ name: "sequencetools_pileupcaller" -description: PileupCaller is a tool to create genotype calls from bam files using read-sampling methods +description: PileupCaller is a tool to create genotype calls from bam files using + read-sampling methods keywords: - genotyping - mpileup @@ -17,50 +18,84 @@ tools: documentation: "https://github.com/stschiff/sequenceTools#readme" tool_dev_url: "https://github.com/stschiff/sequenceTools" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mpileup: - type: file - description: samtools mpileup output. - - snpfile: - type: file - description: | - Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. - Only alleles matching the Ref and Alt alleles of the provided snp file will be called. - - calling_method: - type: string - description: The desired calling method for pileupcaller. One of 'randomHaploid', 'randomDiploid', or 'majorityCall'. - - output_format: - type: string - description: The desired output format. One of 'PLINK', 'EIGENSTRAT', or 'FREQSUM'. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mpileup: + type: file + description: samtools mpileup output. + - - snpfile: + type: file + description: | + Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. + Only alleles matching the Ref and Alt alleles of the provided snp file will be called. + - - sample_names_fn: + type: file + description: File containing the sample names output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - eigenstrat: - type: file - description: A tuple containing the output Eigenstrat-formatted geno, snp and ind files. - pattern: "*.{geno,snp,ind}.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.geno": + type: file + description: A tuple containing the output Eigenstrat-formatted geno, snp and + ind files. + pattern: "*.{geno,snp,ind}.txt" + - "*.snp": + type: file + description: A tuple containing the output Eigenstrat-formatted geno, snp and + ind files. + pattern: "*.{geno,snp,ind}.txt" + - "*.ind": + type: file + description: A tuple containing the output Eigenstrat-formatted geno, snp and + ind files. + pattern: "*.{geno,snp,ind}.txt" - plink: - type: file - description: A tuple containing the output Plink-formatted bed, bim and fam files. - pattern: "*.{bed,bim,fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: A tuple containing the output Plink-formatted bed, bim and fam + files. + pattern: "*.{bed,bim,fam}" + - "*.bim": + type: file + description: A tuple containing the output Plink-formatted bed, bim and fam + files. + pattern: "*.{bed,bim,fam}" + - "*.fam": + type: file + description: A tuple containing the output Plink-formatted bed, bim and fam + files. + pattern: "*.{bed,bim,fam}" - freqsum: - type: file - description: The output freqsum-formatted file. - pattern: "*.freqsum.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.freqsum.gz": + type: file + description: The output freqsum-formatted file. + pattern: "*.freqsum.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@TCLamnidis" maintainers: diff --git a/modules/nf-core/sequenzautils/bam2seqz/meta.yml b/modules/nf-core/sequenzautils/bam2seqz/meta.yml index 45a1fdf419a..eef27d1ca5d 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/meta.yml +++ b/modules/nf-core/sequenzautils/bam2seqz/meta.yml @@ -1,52 +1,60 @@ name: sequenzautils_bam2seqz -description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file +description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz + file keywords: - sequenzautils - copy number - bam2seqz tools: - sequenzautils: - description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies. + description: Sequenza-utils provides 3 main command line programs to transform + common NGS file format - such as FASTA, BAM - to input files for the Sequenza + R package. The program - bam2seqz - process a paired set of BAM/pileup files + (tumour and matching normal), and GC-content genome-wide information, to extract + the common positions with A and B alleles frequencies. homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normalbam: - type: file - description: BAM file from the reference/normal sample - pattern: "*.{bam}" - - tumourbam: - type: file - description: BAM file from the tumour sample - pattern: "*.{bam}" - - fasta: - type: file - description: Reference FASTA file - pattern: "*.{fasta}" - - wigfile: - type: file - description: GC content wiggle file - pattern: "*.{wig.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normalbam: + type: file + description: BAM file from the reference/normal sample + pattern: "*.{bam}" + - tumourbam: + type: file + description: BAM file from the tumour sample + pattern: "*.{bam}" + - - fasta: + type: file + description: Reference FASTA file + pattern: "*.{fasta}" + - - wigfile: + type: file + description: GC content wiggle file + pattern: "*.{wig.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - seqz: - type: file - description: Seqz file - pattern: "*.{seqz.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Seqz file + pattern: "*.{seqz.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" maintainers: diff --git a/modules/nf-core/sequenzautils/gcwiggle/meta.yml b/modules/nf-core/sequenzautils/gcwiggle/meta.yml index 3ca9afcd405..e9ee3fdb8e4 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/meta.yml +++ b/modules/nf-core/sequenzautils/gcwiggle/meta.yml @@ -1,40 +1,47 @@ name: sequenzautils_gcwiggle -description: Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size. +description: Sequenza-utils gc_wiggle computes the GC percentage across the sequences, + and returns a file in the UCSC wiggle format, given a fasta file and a window size. keywords: - sequenzautils - copy number - gc_wiggle tools: - sequenzautils: - description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program -gc_wiggle- takes fasta file as an input, computes GC percentage across the sequences and returns a file in the UCSC wiggle format. + description: Sequenza-utils provides 3 main command line programs to transform + common NGS file format - such as FASTA, BAM - to input files for the Sequenza + R package. The program -gc_wiggle- takes fasta file as an input, computes GC + percentage across the sequences and returns a file in the UCSC wiggle format. homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: GC Wiggle track file - pattern: "*.{wig.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig.gz": + type: file + description: GC Wiggle track file + pattern: "*.{wig.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" maintainers: diff --git a/modules/nf-core/seqwish/induce/meta.yml b/modules/nf-core/seqwish/induce/meta.yml index 562f4014aa3..92d06b938e1 100644 --- a/modules/nf-core/seqwish/induce/meta.yml +++ b/modules/nf-core/seqwish/induce/meta.yml @@ -14,34 +14,37 @@ tools: homepage: https://github.com/ekg/seqwish documentation: https://github.com/ekg/seqwish licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf: - type: list - description: comma-separated PAF file(s) of alignments, single entry allowed - pattern: "[*.{paf,paf.gz},*.{paf,paf.gz},...]" - - fasta: - type: file - description: FASTA file used to generate alignments - pattern: "*.{fa,fa.gz,fasta,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - paf: + type: list + description: comma-separated PAF file(s) of alignments, single entry allowed + pattern: "[*.{paf,paf.gz},*.{paf,paf.gz},...]" + - fasta: + type: file + description: FASTA file used to generate alignments + pattern: "*.{fa,fa.gz,fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gfa: - type: file - description: Variation graph in GFA 1.0 format - pattern: "*.{gfa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa": + type: file + description: Variation graph in GFA 1.0 format + pattern: "*.{gfa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/seroba/run/meta.yml b/modules/nf-core/seroba/run/meta.yml index e0a704ccc22..d78f13e0e5b 100644 --- a/modules/nf-core/seroba/run/meta.yml +++ b/modules/nf-core/seroba/run/meta.yml @@ -1,45 +1,56 @@ name: "seroba_run" -description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads +description: Determine Streptococcus pneumoniae serotype from Illumina paired-end + reads keywords: - fastq - serotype - Streptococcus pneumoniae tools: - "seroba": - description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references." + description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina + NGS reads for given references." homepage: "https://sanger-pathogens.github.io/seroba/" documentation: "https://sanger-pathogens.github.io/seroba/" tool_dev_url: "https://github.com/sanger-pathogens/seroba" doi: "10.1099/mgen.0.000186" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input Illunina paired-end FASTQ files - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input Illunina paired-end FASTQ files + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: The predicted serotype in tab-delimited format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.tsv: + type: file + description: The predicted serotype in tab-delimited format + pattern: "*.tsv" - txt: - type: file - description: A detailed description of the predicted serotype - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/detailed_serogroup_info.txt: + type: file + description: A detailed description of the predicted serotype + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/severus/meta.yml b/modules/nf-core/severus/meta.yml index 844eee442a5..8ada35489ea 100644 --- a/modules/nf-core/severus/meta.yml +++ b/modules/nf-core/severus/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "severus" -description: Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT) +description: Severus is a somatic structural variation (SV) caller for long reads + (both PacBio and ONT) keywords: - structural - variation @@ -16,112 +16,201 @@ tools: tool_dev_url: "https://github.com/KolmogorovLab/Severus" doi: "10.1101/2024.03.22.24304756" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - target_input: - type: file - description: path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed) - pattern: "*.{bam,cram}" - - target_index: - type: file - description: path to one or multiple target BAM/CRAM index files - pattern: "*.{bai,crai,csi}" - - control_input: - type: file - description: path to the control BAM/CRAM file (e.g. normal, must be indexed) - pattern: "*.{bam,cram}" - - control_index: - type: file - description: path to the control BAM/CRAM file index - pattern: "*.{bai,crai,csi}" - - vcf: - type: file - description: path to vcf file used for phasing (if using haplotype specific SV calling - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing tandem repeat regions information - e.g. `[ id:'hg38']` - - bed: - type: file - description: path to bed file for tandem repeat regions (must be ordered) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - target_input: + type: file + description: path to one or multiple target BAM/CRAM files (e.g. tumor, must + be indexed) + pattern: "*.{bam,cram}" + - target_index: + type: file + description: path to one or multiple target BAM/CRAM index files + pattern: "*.{bai,crai,csi}" + - control_input: + type: file + description: path to the control BAM/CRAM file (e.g. normal, must be indexed) + pattern: "*.{bam,cram}" + - control_index: + type: file + description: path to the control BAM/CRAM file index + pattern: "*.{bai,crai,csi}" + - vcf: + type: file + description: path to vcf file used for phasing (if using haplotype specific + SV calling + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing tandem repeat regions information + e.g. `[ id:'hg38']` + - bed: + type: file + description: path to bed file for tandem repeat regions (must be ordered) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: Severus log file - pattern: "${prefix}/severus.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus.log: + type: file + description: Severus log file + pattern: "${prefix}/severus.log" - read_qual: - type: file - description: Severus read_qual file - pattern: "${prefix}/read_qual.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_qual.txt: + type: file + description: Severus read_qual file + pattern: "${prefix}/read_qual.txt" - breakpoints_double: - type: file - description: Severus breakpoints_double file - pattern: "${prefix}/breakpoints_double.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/breakpoints_double.csv: + type: file + description: Severus breakpoints_double file + pattern: "${prefix}/breakpoints_double.csv" - read_alignments: - type: file - description: read alignments file - pattern: "${prefix}/read_alignments" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_alignments: + type: file + description: read alignments file + pattern: "${prefix}/read_alignments" - read_ids: - type: file - description: read IDs for support reads - pattern: "${prefix}/read_ids" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_ids.csv: + type: file + description: read IDs for support reads + pattern: "${prefix}/read_ids" - collapsed_dup: - type: file - description: a bed file with identified collapsed duplication regions - pattern: "${prefix}/severus_collaped_dup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus_collaped_dup.bed: + type: file + description: a bed file with identified collapsed duplication regions + pattern: "${prefix}/severus_collaped_dup" - loh: - type: file - description: a bed file with predicted LOH regions - pattern: "${prefix}/severus_LOH.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus_LOH.bed: + type: file + description: a bed file with predicted LOH regions + pattern: "${prefix}/severus_LOH.bed" - all_vcf: - type: file - description: VCF file with all SVs (somatic + germline) - pattern: "${prefix}/all_SVs/severus_all.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/severus_all.vcf: + type: file + description: VCF file with all SVs (somatic + germline) + pattern: "${prefix}/all_SVs/severus_all.vcf" - all_breakpoints_clusters_list: - type: file - description: Severus breakpoints clusters list file - pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/breakpoints_clusters_list.tsv: + type: file + description: Severus breakpoints clusters list file + pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv" - all_breakpoints_clusters: - type: file - description: Severus breakpoints clusters file - pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/breakpoints_clusters.tsv: + type: file + description: Severus breakpoints clusters file + pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv" - all_plots: - type: file - description: Severus plots - pattern: "${prefix}/all_SVs/plots/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/plots/severus_*.html: + type: file + description: Severus plots + pattern: "${prefix}/all_SVs/plots/*.html" - somatic_vcf: - type: file - description: VCF file with somatic SVs - pattern: "${prefix}/somatic_SVs/severus_all.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/severus_all.vcf: + type: file + description: VCF file with somatic SVs + pattern: "${prefix}/somatic_SVs/severus_all.vcf" - somatic_breakpoints_clusters_list: - type: file - description: Severus somatic breakpoints clusters list file - pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/breakpoints_clusters_list.tsv: + type: file + description: Severus somatic breakpoints clusters list file + pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" - somatic_breakpoints_clusters: - type: file - description: Severus somatic breakpoints clusters file - pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/breakpoints_clusters.tsv: + type: file + description: Severus somatic breakpoints clusters file + pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv" - somatic_plots: - type: file - description: Severus somatic plots - pattern: "${prefix}/somatic_SVs/plots/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/plots/severus_*.html: + type: file + description: Severus somatic plots + pattern: "${prefix}/somatic_SVs/plots/*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/sexdeterrmine/meta.yml b/modules/nf-core/sexdeterrmine/meta.yml index f1b57a8f3ec..6a268477678 100644 --- a/modules/nf-core/sexdeterrmine/meta.yml +++ b/modules/nf-core/sexdeterrmine/meta.yml @@ -1,5 +1,6 @@ name: "sexdeterrmine" -description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars. +description: Calculate the relative coverage on the Gonosomes vs Autosomes from the + output of samtools depth, with error bars. keywords: - sex determination - genetic sex @@ -7,40 +8,55 @@ keywords: - ancient dna tools: - "sexdeterrmine": - description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data." + description: "A python script carry out calculate the relative coverage of X and + Y chromosomes, and their associated error bars, out of capture data." homepage: "https://github.com/TCLamnidis/Sex.DetERRmine" documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md" tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine" doi: "10.1038/s41467-018-07483-5" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - depth: - type: file - description: Output from samtools depth (with header) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - depth: + type: file + description: Output from samtools depth (with header) + pattern: "*" + - - sample_list_file: + type: file + description: File containing the list of samples to be processed. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON formatted table of relative coverages on the X and Y, with associated error bars. - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON formatted table of relative coverages on the X and Y, with + associated error bars. + pattern: "*.json" - tsv: - type: file - description: TSV table of relative coverages on the X and Y, with associated error bars. - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV table of relative coverages on the X and Y, with associated + error bars. + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@TCLamnidis" maintainers: diff --git a/modules/nf-core/sgdemux/meta.yml b/modules/nf-core/sgdemux/meta.yml index 1949348ad8f..3dd52d75aaa 100644 --- a/modules/nf-core/sgdemux/meta.yml +++ b/modules/nf-core/sgdemux/meta.yml @@ -6,61 +6,96 @@ keywords: - bgzip tools: - "sgdemux": - description: "Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments." + description: "Tool for demultiplexing sequencing data generated on Singular Genomics' + sequencing instruments." homepage: "https://github.com/Singular-Genomics/singular-demux" documentation: "https://github.com/Singular-Genomics/singular-demux#sgdemux" licence: ["For Singular G4™ Sequencing Platform only"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sample_sheet: - type: file - description: sample_sheet file (either a Singular Genomics sample sheet, or a two column csv wih Sample_Barcode and Sample_ID) - pattern: "*.{csv}" - - fastqs_dir: - type: directory - description: "Input directory containing bgzipped (not gzip) FASTQ files" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sample_sheet: + type: file + description: sample_sheet file (either a Singular Genomics sample sheet, or + a two column csv wih Sample_Barcode and Sample_ID) + pattern: "*.{csv}" + - fastqs_dir: + type: directory + description: "Input directory containing bgzipped (not gzip) FASTQ files" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_fastq: - type: file - description: Demultiplexed per-sample FASTQ files - pattern: "output/*_R*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/*_R*.fastq.gz: + type: file + description: Demultiplexed per-sample FASTQ files + pattern: "output/*_R*.fastq.gz" - metrics: - type: file - description: | - Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates - pattern: "output/metrics.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/metrics.tsv: + type: file + description: | + Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates + pattern: "output/metrics.tsv" - most_frequent_unmatched: - type: file - description: | - File containing approx. counts of barcodes that did not match the expected barcodes - pattern: "output/most_frequence_unmatched.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/most_frequent_unmatched.tsv: + type: file + description: | + File containing approx. counts of barcodes that did not match the expected barcodes + pattern: "output/most_frequence_unmatched.tsv" - per_project_metrics: - type: file - description: Summary metrics for samples in the same project - pattern: "output/per_project_metrics.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/per_project_metrics.tsv: + type: file + description: Summary metrics for samples in the same project + pattern: "output/per_project_metrics.tsv" - per_sample_metrics: - type: file - description: Summary metrics for each sample - pattern: "output/per_sample_metrics.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/per_sample_metrics.tsv: + type: file + description: Summary metrics for each sample + pattern: "output/per_sample_metrics.tsv" - sample_barcode_hop_metrics: - type: file - description: | - File output for dual-indexed runs with barcodes which are unexpected combinations of - expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT - pattern: "output/sample_barcode_hop_metrics/tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/sample_barcode_hop_metrics.tsv: + type: file + description: | + File output for dual-indexed runs with barcodes which are unexpected combinations of + expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT + pattern: "output/sample_barcode_hop_metrics/tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nh13" - "@sam-white04" diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml index ed1e5e9efed..a8d6db14534 100644 --- a/modules/nf-core/shapeit5/ligate/meta.yml +++ b/modules/nf-core/shapeit5/ligate/meta.yml @@ -14,38 +14,41 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867" licence: ["MIT"] + identifier: biotools:shapeit5 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_list: - type: file - description: | - VCF/BCF files containing genotype probabilities (GP field). - The files should be ordered by genomic position. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_list_index: - type: file - description: VCF/BCF files index. - pattern: "*.csi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_list: + type: file + description: | + VCF/BCF files containing genotype probabilities (GP field). + The files should be ordered by genomic position. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_list_index: + type: file + description: VCF/BCF files index. + pattern: "*.csi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_variants: - type: file - description: | - Output VCF/BCF file for the merged regions. - Phased information (HS field) is updated accordingly for the full region. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: | + Output VCF/BCF file for the merged regions. + Phased information (HS field) is updated accordingly for the full region. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/shapeit5/phasecommon/meta.yml b/modules/nf-core/shapeit5/phasecommon/meta.yml index 47197291ea9..5aa05232098 100644 --- a/modules/nf-core/shapeit5/phasecommon/meta.yml +++ b/modules/nf-core/shapeit5/phasecommon/meta.yml @@ -1,5 +1,6 @@ name: "shapeit5_phasecommon" -description: Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data. +description: Tool to phase common sites, typically SNP array data, or the first step + of WES/WGS data. keywords: - phasing - haplotype @@ -12,67 +13,85 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " licence: ["MIT"] + identifier: biotools:shapeit5 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - Target dataset in VCF/BCF format defined at all variable positions. - The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - pedigree: - type: file - description: | - Pedigree information in the following format: offspring father mother. - pattern: "*.{txt, tsv}" - - region: - type: string - description: | - Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - scaffold: - type: file - description: Scaffold of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - scaffold_index: - type: file - description: Index file of the scaffold file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + Target dataset in VCF/BCF format defined at all variable positions. + The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - pedigree: + type: file + description: | + Pedigree information in the following format: offspring father mother. + pattern: "*.{txt, tsv}" + - region: + type: string + description: | + Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: Scaffold of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - scaffold_index: + type: file + description: Index file of the scaffold file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - phased_variants: - type: file - description: Phased haplotypes in VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - phased_variant: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Phased variant dataset in VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/shapeit5/phaserare/meta.yml b/modules/nf-core/shapeit5/phaserare/meta.yml index dbc0aa13d03..aaf379c87bd 100644 --- a/modules/nf-core/shapeit5/phaserare/meta.yml +++ b/modules/nf-core/shapeit5/phaserare/meta.yml @@ -15,64 +15,78 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " licence: ["MIT"] + identifier: biotools:shapeit5 requirement: AVX2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_plain: - type: file - description: | - Genotypes to be phased in plain VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_plain_index: - type: file - description: Index file of the input_plain VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - input_region: - type: string - description: | - Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - pedigree: - type: file - description: | - Pedigree information in the following format: offspring father mother. - pattern: "*.{txt, tsv}" - - scaffold: - type: file - description: Scaffold of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - scaffold_index: - type: file - description: Index file of the scaffold file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - scaffold_region: - type: string - description: | - Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_plain: + type: file + description: | + Genotypes to be phased in plain VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_plain_index: + type: file + description: Index file of the input_plain VCF/BCF file containing genotype + likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - pedigree: + type: file + description: | + Pedigree information in the following format: offspring father mother. + pattern: "*.{txt, tsv}" + - input_region: + type: string + description: | + Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: Scaffold of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - scaffold_index: + type: file + description: Index file of the scaffold file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - scaffold_region: + type: string + description: | + Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - phased_variants: - type: file - description: Phased haplotypes in VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - phased_variant: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Phased variants in VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/shapeit5/switch/meta.yml b/modules/nf-core/shapeit5/switch/meta.yml index 73dd86e49d4..25352305d30 100644 --- a/modules/nf-core/shapeit5/switch/meta.yml +++ b/modules/nf-core/shapeit5/switch/meta.yml @@ -1,5 +1,6 @@ name: "shapeit5_switch" -description: Program to compute switch error rate and genotyping error rate given simulated or trio data. +description: Program to compute switch error rate and genotyping error rate given + simulated or trio data. keywords: - error - phasing @@ -13,59 +14,74 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " licence: ["MIT"] + identifier: biotools:shapeit5 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - estimate: - type: file - description: Imputed data. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - estimate_index: - type: file - description: Index file of the freq VCF/BCF file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - pedigree: - type: file - description: | - Pedigree information in the following format: offspring father mother. - pattern: "*.{txt, tsv}" - - truth: - type: file - description: Validation dataset called at the same positions as the imputed file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - truth_index: - type: file - description: Index file of the truth VCF/BCF file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - freq: - type: file - description: File containing allele frequencies at each site. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - freq_index: - type: file - description: Index file of the freq VCF/BCF file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - estimate: + type: file + description: Imputed data. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - estimate_index: + type: file + description: Index file of the freq VCF/BCF file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - pedigree: + type: file + description: | + Pedigree information in the following format: offspring father mother. + pattern: "*.{txt, tsv}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - truth: + type: file + description: Validation dataset called at the same positions as the imputed + file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - truth_index: + type: file + description: Index file of the truth VCF/BCF file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - freq: + type: file + description: File containing allele frequencies at each site. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - freq_index: + type: file + description: Index file of the freq VCF/BCF file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - errors: - type: file - description: Estimates errors from the phased file. - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Estimates errors from the phased file. + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/shasta/meta.yml b/modules/nf-core/shasta/meta.yml index e517e196068..3bb24cd9921 100644 --- a/modules/nf-core/shasta/meta.yml +++ b/modules/nf-core/shasta/meta.yml @@ -1,5 +1,8 @@ name: shasta -description: The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296. +description: The goal of the Shasta long read assembler is to rapidly produce accurate + assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. + Please note Assembler is design to focus on speed, so assembly may be considered + somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296. keywords: - nanopore - de-novo @@ -7,44 +10,60 @@ keywords: - longread tools: - shasta: - description: Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. + description: Rapidly produce accurate assembled sequence using as input DNA reads + generated by Oxford Nanopore flow cells. homepage: https://chanzuckerberg.github.io/shasta/index.html documentation: https://chanzuckerberg.github.io/shasta/index.html tool_dev_url: https://github.com/chanzuckerberg/shasta doi: "10.1038/s41587-020-0503-6" licence: ["MIT"] + identifier: biotools:shasta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input file in FASTQ format. - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input file in FASTQ format. + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly: - type: file - description: Assembled FASTA file - pattern: "${prefix}_Assembly.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_Assembly.fasta.gz": + type: file + description: Assembled FASTA file + pattern: "${prefix}_Assembly.fasta.gz" - gfa: - type: file - description: Repeat graph - pattern: "${prefix}_Assembly.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_Assembly.gfa.gz": + type: file + description: Repeat graph + pattern: "${prefix}_Assembly.gfa.gz" - results: - type: directory - description: Resulting assembly directory - pattern: "ShastaRun" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ShastaRun/: + type: directory + description: Resulting assembly directory + pattern: "ShastaRun" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" maintainers: diff --git a/modules/nf-core/shasum/meta.yml b/modules/nf-core/shasum/meta.yml index 2694db9868a..f89eb3aa612 100644 --- a/modules/nf-core/shasum/meta.yml +++ b/modules/nf-core/shasum/meta.yml @@ -10,30 +10,33 @@ tools: homepage: "https://www.gnu.org" documentation: "https://linux.die.net/man/1/shasum" licence: ["GPLv3+"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: Any file - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: Any file + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checksum: - type: file - description: File containing checksum - pattern: "*.sha256" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sha256": + type: file + description: File containing checksum + pattern: "*.sha256" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/shigatyper/meta.yml b/modules/nf-core/shigatyper/meta.yml index 65e1de01890..04e07906f13 100644 --- a/modules/nf-core/shigatyper/meta.yml +++ b/modules/nf-core/shigatyper/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: "https://github.com/CFSAN-Biostatistics/shigatyper" doi: "10.1128/AEM.00165-19" licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, is_ont:false ] - - reads: - type: file - description: Illumina or Nanopore FASTQ file - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, is_ont:false ] + - reads: + type: file + description: Illumina or Nanopore FASTQ file + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV formatted file with ShigaTyper results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: A TSV formatted file with ShigaTyper results + pattern: "*.tsv" - hits: - type: file - description: A TSV formatted file with individual gene hits - pattern: "*-hits.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-hits.tsv: + type: file + description: A TSV formatted file with individual gene hits + pattern: "*-hits.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/shigeifinder/meta.yml b/modules/nf-core/shigeifinder/meta.yml index 8951b5299b6..b2bbb0e9a1e 100644 --- a/modules/nf-core/shigeifinder/meta.yml +++ b/modules/nf-core/shigeifinder/meta.yml @@ -7,36 +7,40 @@ keywords: - serotype tools: - "shigeifinder": - description: "Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies" + description: "Cluster informed Shigella and EIEC serotyping tool from Illumina + reads and assemblies" homepage: "https://mgtdb.unsw.edu.au/ShigEiFinder/" documentation: "https://github.com/LanLab/ShigEiFinder" tool_dev_url: "https://github.com/LanLab/ShigEiFinder" doi: "10.1099/mgen.0.000704" licence: ["GPL v3"] + identifier: biotools:shigeifinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: Assembly or paired-end Illumina reads - pattern: "*.{fasta,fasta.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: Assembly or paired-end Illumina reads + pattern: "*.{fasta,fasta.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV formatted file with ShigEiFinder results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV formatted file with ShigEiFinder results + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/shinyngs/app/meta.yml b/modules/nf-core/shinyngs/app/meta.yml index 8ff58e9598c..62a82639460 100644 --- a/modules/nf-core/shinyngs/app/meta.yml +++ b/modules/nf-core/shinyngs/app/meta.yml @@ -1,5 +1,6 @@ name: "shinyngs_app" -description: build and deploy Shiny apps for interactively mining differential abundance data +description: build and deploy Shiny apps for interactively mining differential abundance + data keywords: - differential - expression @@ -7,63 +8,69 @@ keywords: - deseq2 tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. To match meta. - e.g. [ id:'test' ] - - sample: - type: file - description: | - CSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - TSV-format feature (e.g. gene) metadata - - assay_files: - type: file - description: | - List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). - - contrasts: - type: file - description: | - CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. - - differential_results: - type: file - description: | - List of TSV-format differential analysis outputs, one per row of the contrasts file + - - meta: + type: map + description: | + Groovy Map containing information on experiment, at a minimum an id. + e.g. [ id:'test' ] + - sample: + type: file + description: | + CSV-format sample sheet with sample metadata + - feature_meta: + type: file + description: | + TSV-format feature (e.g. gene) metadata + - assay_files: + type: file + description: | + List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). + - - meta2: + type: map + description: | + Groovy Map containing information on experiment, at a minimum an id. To match meta. + e.g. [ id:'test' ] + - contrasts: + type: file + description: | + CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. + - differential_results: + type: file + description: | + List of TSV-format differential analysis outputs, one per row of the contrasts file + - - contrast_stats_assay: + type: file + description: contrast statistics output: - - meta: - type: map - description: | - Groovy Map containing information on experiment. - e.g. [ id:'test' ] - - data: - type: file - description: | - A shinyngs ExploratorySummarizedExperiment - object serialized with saveRDS(). - pattern: "app/data.rds" - app: - type: file - description: | - The mini R script required build an application from data.rds. - pattern: "app/app.R" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/data.rds": + type: file + description: | + The mini R script required build an application from data.rds. + pattern: "app/app.R" + - "*/app.R": + type: file + description: | + The mini R script required build an application from data.rds. + pattern: "app/app.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shinyngs/staticdifferential/meta.yml b/modules/nf-core/shinyngs/staticdifferential/meta.yml index f49ff70b78d..f8039ca4329 100644 --- a/modules/nf-core/shinyngs/staticdifferential/meta.yml +++ b/modules/nf-core/shinyngs/staticdifferential/meta.yml @@ -7,62 +7,71 @@ keywords: - shinyngs tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing contrast information, to be passed as reference - and target levels, like '--reference_level $meta.reference - --treatment_level $meta.target' - e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - meta2: - type: map - description: | - Groovy Map containing information on experiment represented by max, - features and samples, at a minimum an id. - e.g. [ id:'test' ] - - differential_results: - type: file - description: | - CSV or TSV-format tabular file with differential analysis outputs - - sample: - type: file - description: | - CSV or TSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - CSV or TSV-format feature (e.g. gene) metadata - - assay_file: - type: file - description: | - CSV or TSV matrix file to use alongside differential statistics in - interpretation. Usually a normalised form. + - - meta: + type: map + description: | + Groovy Map containing contrast information, to be passed as reference + and target levels, like '--reference_level $meta.reference + --treatment_level $meta.target' + e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - differential_result: + type: file + description: statistic differential results + - - meta2: + type: map + description: | + Groovy Map containing information on experiment represented by max, + features and samples, at a minimum an id. + e.g. [ id:'test' ] + - sample: + type: file + description: | + CSV or TSV-format sample sheet with sample metadata + - feature_meta: + type: file + description: | + CSV or TSV-format feature (e.g. gene) metadata + - assay_file: + type: file + description: | + CSV or TSV matrix file to use alongside differential statistics in + interpretation. Usually a normalised form. output: - - meta: - type: map - description: | - Groovy Map containing contrast information - e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - volcanos_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for a volcano plot built from - the differential result table. + - meta: + type: map + description: | + Groovy Map containing contrast information + e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*/png/volcano.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for a volcano plot built from + the differential result table. - volcanos_html: - type: file - description: | - Meta-keyed tuple containing an HTML output for a volcano plot built - from the differential result table. + - meta: + type: map + description: | + Groovy Map containing contrast information + e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*/html/volcano.html": + type: file + description: | + Meta-keyed tuple containing an HTML output for a volcano plot built + from the differential result table. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shinyngs/staticexploratory/meta.yml b/modules/nf-core/shinyngs/staticexploratory/meta.yml index 5a1b49b2f2c..180ef25bfad 100644 --- a/modules/nf-core/shinyngs/staticexploratory/meta.yml +++ b/modules/nf-core/shinyngs/staticexploratory/meta.yml @@ -1,5 +1,6 @@ name: "shinyngs_staticexploratory" -description: Make exploratory plots for analysis of matrix data, including PCA, Boxplots and density plots +description: Make exploratory plots for analysis of matrix data, including PCA, Boxplots + and density plots keywords: - exploratory - plot @@ -8,93 +9,162 @@ keywords: - PCA tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on variables for use in plots, - probably experimental information, but at a minimum an id. - e.g. [ id:'treatment' ] - - sample: - type: file - description: | - CSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - TSV-format feature (e.g. gene) metadata - - assay_files: - type: file - description: | - List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). + - - meta: + type: map + description: | + Groovy Map containing information on variables for use in plots, + probably experimental information, but at a minimum an id. + e.g. [ id:'treatment' ] + - sample: + type: file + description: | + CSV-format sample sheet with sample metadata + - feature_meta: + type: file + description: | + TSV-format feature (e.g. gene) metadata + - assay_files: + type: file + description: | + List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). output: - boxplots_png: - type: file - description: | - Meta-keyed tuple containing PNG output for box plots covering input - matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing PNG output for box plots covering input + matrices. + - "*/png/boxplot.png": + type: file + description: | + Meta-keyed tuple containing PNG output for box plots covering input + matrices. - boxplots_html: - type: file - description: | - Meta-keyed tuple containing HTML output for box plots covering input - matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing HTML output for box plots covering input + matrices. + - "*/html/boxplot.html": + type: file + description: | + Meta-keyed tuple containing HTML output for box plots covering input + matrices. - densities_png: - type: file - description: | - Meta-keyed tuple containing PNG output for density plots - covering input matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing PNG output for density plots + covering input matrices. + - "*/png/density.png": + type: file + description: | + Meta-keyed tuple containing PNG output for density plots + covering input matrices. - densities_html: - type: file - description: | - Meta-keyed tuple containing HTML output for density plots - covering input matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing HTML output for density plots + covering input matrices. + - "*/html/density.html": + type: file + description: | + Meta-keyed tuple containing HTML output for density plots + covering input matrices. - pca2d_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for 2D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/png/pca2d.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. - pca2d_html: - type: file - description: | - Meta-keyed tuple containing an HTML output for 2D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing an HTML output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/html/pca2d.html": + type: file + description: | + Meta-keyed tuple containing an HTML output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. - pca3d_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for 3D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/png/pca3d.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. - pca3d_html: - type: file - description: | - Meta-keyed tuple containing an HTML output for 3D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing an HTML output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/html/pca3d.html": + type: file + description: | + Meta-keyed tuple containing an HTML output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. - mad_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for MAD correlation plots - covering specified input matrix (by default the last one in the input - list. - - mad_dendro: - type: file - description: | - Meta-keyed tuple containing an HTML output for MAD correlation plots - covering specified input matrix (by default the last one in the input - list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG output for MAD correlation plots + covering specified input matrix (by default the last one in the input + list. + - "*/png/mad_correlation.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for MAD correlation plots + covering specified input matrix (by default the last one in the input + list. + - mad_html: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/html/mad_correlation.html": + type: file + description: HTML output for MAD correlation plots + pattern: "*{.html}" - dendro: - type: file - description: | - Meta-keyed tuple containing a PNG, for a sample clustering - dendrogramcovering specified input matrix (by default the last one in - the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG, for a sample clustering + dendrogramcovering specified input matrix (by default the last one in + the input list. + - "*/png/sample_dendrogram.png": + type: file + description: | + Meta-keyed tuple containing a PNG, for a sample clustering + dendrogramcovering specified input matrix (by default the last one in + the input list. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml index 9066ada41b4..f65391dcc3b 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml @@ -1,5 +1,6 @@ name: "shinyngs_validatefomcomponents" -description: validate consistency of feature and sample annotations with matrices and contrasts +description: validate consistency of feature and sample annotations with matrices + and contrasts keywords: - expression - features @@ -7,75 +8,92 @@ keywords: - validation tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing information on features. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing information on contrasts. - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. To match meta. - e.g. [ id:'test' ] - - sample: - type: file - description: | - CSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - TSV-format feature (e.g. gene) metadata - - assay_files: - type: file - description: | - List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). - - contrasts: - type: file - description: | - CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. + - - meta: + type: map + description: | + Groovy Map containing information on experiment, at a minimum an id. + e.g. [ id:'test' ] + - sample: + type: file + description: | + CSV-format sample sheet with sample metadata + - assay_files: + type: file + description: | + List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). + - - meta2: + type: map + description: | + Groovy Map containing information on features. + e.g. [ id:'test' ] + - feature_meta: + type: file + description: | + TSV-format feature (e.g. gene) metadata + - - meta3: + type: map + description: | + Groovy Map containing information on contrasts. + e.g. [ id:'test' ] + - contrasts: + type: file + description: | + CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. output: - - meta: - type: map - description: | - Groovy Map containing information on experiment. - e.g. [ id:'test' ] - sample_meta: - type: file - description: File containing validated sample metadata - pattern: "/*.sample_metadata.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.sample_metadata.tsv": + type: file + description: File containing validated sample metadata + pattern: "/*.sample_metadata.tsv" - feature_meta: - type: file - description: File containing validated feature metadata - pattern: "/*.feature_metadata.tsv" - optional: true + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.feature_metadata.tsv": + type: file + description: File containing validated feature metadata + pattern: "/*.feature_metadata.tsv" + optional: true - assays: - type: file - description: Files containing validated matrices - pattern: "/*.assay.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.assay.tsv": + type: file + description: Files containing validated matrices + pattern: "/*.assay.tsv" - contrasts: - type: file - description: Files containing validated matrices - pattern: "/*.contrasts_file.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.contrasts_file.tsv": + type: file + description: Files containing validated matrices + pattern: "/*.contrasts_file.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shovill/meta.yml b/modules/nf-core/shovill/meta.yml index cdeb0152b5b..7f5f33962df 100644 --- a/modules/nf-core/shovill/meta.yml +++ b/modules/nf-core/shovill/meta.yml @@ -10,45 +10,73 @@ tools: homepage: https://github.com/tseemann/shovill documentation: https://github.com/tseemann/shovill/blob/master/README.md licence: ["GPL v2"] + identifier: biotools:shovill input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input paired-end FastQ files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input paired-end FastQ files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - contigs: - type: file - description: The final assembly produced by Shovill - pattern: "contigs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs.fa: + type: file + description: The final assembly produced by Shovill + pattern: "contigs.fa" - corrections: - type: file - description: List of post-assembly corrections made by Shovill - pattern: "shovill.corrections" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shovill.corrections: + type: file + description: List of post-assembly corrections made by Shovill + pattern: "shovill.corrections" - log: - type: file - description: Full log file for bug reporting - pattern: "shovill.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shovill.log: + type: file + description: Full log file for bug reporting + pattern: "shovill.log" - raw_contigs: - type: file - description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet) - pattern: "{skesa,spades,megahit,velvet}.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "{skesa,spades,megahit,velvet}.fasta": + type: file + description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, + or Velvet) + pattern: "{skesa,spades,megahit,velvet}.fasta" - gfa: - type: file - description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet - pattern: "contigs.{fastg,gfa,LastGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs.{fastg,gfa,LastGraph}: + type: file + description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet + pattern: "contigs.{fastg,gfa,LastGraph}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/sickle/meta.yml b/modules/nf-core/sickle/meta.yml index da94c23d6f6..03c49e8854a 100644 --- a/modules/nf-core/sickle/meta.yml +++ b/modules/nf-core/sickle/meta.yml @@ -6,50 +6,75 @@ keywords: - trimming tools: - "sickle": - description: "a tool that determines clipping of reads on 3' end and 5'end based on base quality " + description: "a tool that determines clipping of reads on 3' end and 5'end based + on base quality " homepage: "https://github.com/najoshi/sickle" tool_dev_url: "https://github.com/najoshi/sickle" licence: ["MIT License"] + identifier: biotools:sickle input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false] - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. File of forward reads must be supplied first and reverse reads as the second e.g. ["read.1.fastq.gz","read.2.fastq.gz"] - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - qual_type: - type: string - description: sickle needs a base quality values, which could be either illumina, solexa or sanger - pattern: "illumina or solexa or sanger" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false] + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. File of forward reads must be supplied first and reverse + reads as the second e.g. ["read.1.fastq.gz","read.2.fastq.gz"] + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - qual_type: + type: string + description: sickle needs a base quality values, which could be either illumina, + solexa or sanger + pattern: "illumina or solexa or sanger" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, qual:'Illumina' ] - single_trimmed: - type: file - description: 5' or 3' trimmed (based on base quality) single-end fastq file - pattern: "*.se.trimmed.fastq.gz" - - paired1_trimmed: - type: file - description: 5' or 3' trimmed (based on base quality) R1 fastq file - pattern: "*.pe1.trimmed.fastq.gz" - - paired2_trimmed: - type: file - description: 5' or 3' trimmed (based on base quality) R2 fastq file - pattern: "*.pe2.trimmed.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - ${prefix}.se.trimmed.fastq.gz: + type: file + description: 5' or 3' trimmed (based on base quality) single-end fastq file + pattern: "*.se.trimmed.fastq.gz" + - paired_trimmed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - ${prefix}.pe{1,2}.trimmed.fastq.gz: + type: file + description: 5' or 3' trimmed (based on base quality) paired-end fastq files + pattern: "*.pe{1,2}.trimmed.fastq.gz" + - singleton_trimmed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - ${prefix}.singleton.trimmed.fastq.gz: + type: file + description: 5' or 3' trimmed (based on base quality) singleton fastq file + pattern: "*.singleton.trimmed.fastq.gz" - log: - type: file - description: log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - "*.log": + type: file + description: log file + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BioInf2305" maintainers: diff --git a/modules/nf-core/simpleaf/index/meta.yml b/modules/nf-core/simpleaf/index/meta.yml index 5a23fb8686e..f90674af1c2 100644 --- a/modules/nf-core/simpleaf/index/meta.yml +++ b/modules/nf-core/simpleaf/index/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: simpleaf_index description: Indexing of transcriptome for gene expression quantification using SimpleAF @@ -13,56 +12,69 @@ tools: SimpleAF is a tool for quantification of gene expression from RNA-seq data homepage: https://github.com/COMBINE-lab/simpleaf licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on genome_fasta - - genome_fasta: - type: file - description: | - FASTA file containing the genome sequence - - meta2: - type: map - description: | - Groovy Map containing information on genome_gtf - - genome_gtf: - type: file - description: | - GTF file containing transcript annotations. Optional if transcript FASTA file is provided. - - meta3: - type: map - description: | - Groovy Map containing information on transcript_fasta - - transcript_fasta: - type: file - description: | - FASTA file containing the transcript sequences. Optional if transcript GTF file is provided. + - - meta: + type: map + description: | + Groovy Map containing information on genome_fasta + - genome_fasta: + type: file + description: | + FASTA file containing the genome sequence + - - meta2: + type: map + description: | + Groovy Map containing information on genome_gtf + - genome_gtf: + type: file + description: | + GTF file containing transcript annotations. Optional if transcript FASTA file is provided. + - - meta3: + type: map + description: | + Groovy Map containing information on transcript_fasta + - transcript_fasta: + type: file + description: | + FASTA file containing the transcript sequences. Optional if transcript GTF file is provided. output: - - meta: - type: map - description: | - Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) - index: - type: directory - description: | - Folder containing the Salmon index files - pattern: "salmon/index" + - meta: + type: map + description: | + Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) + - ${prefix}/index: + type: directory + description: | + Folder containing the Salmon index files + pattern: "salmon/index" - transcript_tsv: - type: file - description: | - Transcript-to-gene mapping file in 3-column TSV format - pattern: "salmon/ref/*_t2g_3col.tsv" + - meta: + type: map + description: | + Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) + - ${prefix}/ref/t2g_3col.tsv: + type: file + description: | + Transcript-to-gene mapping file in 3-column TSV format + pattern: "salmon/ref/*_t2g_3col.tsv" - salmon: - type: directory - description: | - Folder containing the Salmon files - pattern: "salmon" + - meta: + type: map + description: | + Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) + - ${prefix}: + type: directory + description: | + Folder containing the Salmon files + pattern: "salmon" - versions: - type: file - description: | - File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: | + File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" - "@maxulysse" diff --git a/modules/nf-core/simpleaf/quant/meta.yml b/modules/nf-core/simpleaf/quant/meta.yml index 545c7d0a3c0..79d7b158e2b 100644 --- a/modules/nf-core/simpleaf/quant/meta.yml +++ b/modules/nf-core/simpleaf/quant/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: simpleaf_quant -description: simpleaf is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry. +description: simpleaf is a program to simplify and customize the running and configuration + of single-cell processing with alevin-fry. keywords: - quantification - gene expression @@ -12,66 +12,71 @@ tools: SimpleAF is a tool for quantification of gene expression from RNA-seq data homepage: https://github.com/COMBINE-lab/simpleaf licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files for paired-end data. - Reads should be grouped by pairs. - - meta2: - type: map - description: | - Groovy Map containing index information - - index: - type: directory - description: Folder containing the index files - - meta3: - type: map - description: | - Groovy Map containing txp2gene information - - txp2gene: - type: file - description: | - File mapping transcripts to genes. - - chemistry: - type: string - description: | - Chemistry used for library preparation. It can be a string describing - the specific chemistry or the geometry of the barcode, UMI, and - mappable read. For example, "10xv2" and "10xv3" will apply the - appropriate settings for 10x Chromium v2 and v3 protocols, - respectively. Alternatively, you can provide a general geometry string - if your chemistry is not pre-registered. For example, instead of - "10xv2", you could use "1{b[16]u[10]x:}2{r:}", or instead of "10xv3", - you could use "1{b[16]u[12]x:}2{r:}". - - meta4: - type: map - description: | - Groovy Map containing whitelist information - - whitelist: - type: file - description: | - Whitelist file containing valid cell barcodes. Optional. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - chemistry: + type: string + description: | + Chemistry used for library preparation. It can be a string describing + the specific chemistry or the geometry of the barcode, UMI, and + mappable read. For example, "10xv2" and "10xv3" will apply the + appropriate settings for 10x Chromium v2 and v3 protocols, + respectively. Alternatively, you can provide a general geometry string + if your chemistry is not pre-registered. For example, instead of + "10xv2", you could use "1{b[16]u[10]x:}2{r:}", or instead of "10xv3", + you could use "1{b[16]u[12]x:}2{r:}". + - reads: + type: file + description: | + List of input FastQ files for paired-end data. + Reads should be grouped by pairs. + - - meta2: + type: map + description: | + Groovy Map containing index information + - index: + type: directory + description: Folder containing the index files + - - meta3: + type: map + description: | + Groovy Map containing txp2gene information + - txp2gene: + type: file + description: | + File mapping transcripts to genes. + - - resolution: + type: string + description: | + Resolution for the clustering. + - - meta4: + type: map + description: | + Groovy Map containing whitelist information + - whitelist: + type: file + description: | + Whitelist file containing valid cell barcodes. Optional. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alevin_results: - type: directory - description: | - Folder containing the Alevin results for a specific sample - pattern: "*" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Folder containing the quantification results - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" - "@maxulysse" diff --git a/modules/nf-core/sistr/meta.yml b/modules/nf-core/sistr/meta.yml index 77017684636..4cb907055d0 100644 --- a/modules/nf-core/sistr/meta.yml +++ b/modules/nf-core/sistr/meta.yml @@ -6,48 +6,70 @@ keywords: - salmonella tools: - sistr: - description: Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction + description: Salmonella In Silico Typing Resource (SISTR) commandline tool for + serovar prediction homepage: https://github.com/phac-nml/sistr_cmd documentation: https://github.com/phac-nml/sistr_cmd tool_dev_url: https://github.com/phac-nml/sistr_cmd doi: "10.1371/journal.pone.0147101" licence: ["Apache-2.0"] + identifier: biotools:SISTR input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide or protein sequences in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide or protein sequences in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: SISTR serovar prediction - pattern: "*.{tsv}" - - allele_json: - type: file - description: Allele sequences and info to JSON - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: SISTR serovar prediction + pattern: "*.{tsv}" - allele_fasta: - type: file - description: FASTA file destination of novel cgMLST alleles - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-allele.fasta": + type: file + description: FASTA file destination of novel cgMLST alleles + pattern: "*.{fasta}" + - allele_json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-allele.json": + type: file + description: Allele sequences and info to JSON + pattern: "*.{json}" - cgmlst_csv: - type: file - description: CSV file destination for cgMLST allelic profiles - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cgmlst.csv": + type: file + description: CSV file destination for cgMLST allelic profiles + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/slimfastq/meta.yml b/modules/nf-core/slimfastq/meta.yml index 72036d89829..617312ce283 100644 --- a/modules/nf-core/slimfastq/meta.yml +++ b/modules/nf-core/slimfastq/meta.yml @@ -10,30 +10,33 @@ tools: homepage: "https://github.com/Infinidat/slimfastq" tool_dev_url: "https://github.com/Infinidat/slimfastq" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: Either a single-end FASTQ file or paired-end files. - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: Either a single-end FASTQ file or paired-end files. + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sfq: - type: file - description: Either one or two sequence files in slimfastq compressed format. - pattern: "*.{sfq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sfq": + type: file + description: Either one or two sequence files in slimfastq compressed format. + pattern: "*.{sfq}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/smncopynumbercaller/meta.yml b/modules/nf-core/smncopynumbercaller/meta.yml index f318a2b7a34..9d91fc09682 100644 --- a/modules/nf-core/smncopynumbercaller/meta.yml +++ b/modules/nf-core/smncopynumbercaller/meta.yml @@ -1,5 +1,7 @@ name: "smncopynumbercaller" -description: tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file. +description: tool to call the copy number of full-length SMN1, full-length SMN2, as + well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing + (WGS) BAM file. keywords: - copy number - BAM @@ -14,38 +16,47 @@ tools: tool_dev_url: "https://github.com/Illumina/SMNCopyNumberCaller" doi: "10.1038/s41436-020-0754-0" licence: ["Apache License Version 2.0"] + identifier: "" input: - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - run_metrics: - type: file - description: File containing run parameters of SMNCopyNumberCaller - pattern: "*.{json}" - smncopynumber: - type: file - description: File containing the output of SMNCopyNumberCaller - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - out/*.tsv: + type: file + description: File containing the output of SMNCopyNumberCaller + pattern: "*.{tsv}" + - run_metrics: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - out/*.json: + type: file + description: File containing run parameters of SMNCopyNumberCaller + pattern: "*.{json}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@peterpru" maintainers: diff --git a/modules/nf-core/smoothxg/meta.yml b/modules/nf-core/smoothxg/meta.yml index 2ba721f8974..3c5de7fea09 100644 --- a/modules/nf-core/smoothxg/meta.yml +++ b/modules/nf-core/smoothxg/meta.yml @@ -1,5 +1,6 @@ name: smoothxg -description: Linearize and simplify variation graph in GFA format using blocked partial order alignment +description: Linearize and simplify variation graph in GFA format using blocked partial + order alignment keywords: - gfa - graph @@ -14,34 +15,39 @@ tools: homepage: https://github.com/pangenome/smoothxg documentation: https://github.com/pangenome/smoothxg licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA 1.0 format - pattern: "*.{gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA 1.0 format + pattern: "*.{gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gfa: - type: file - description: Linearized and simplified graph in GFA 1.0 format - pattern: "*.smoothxg.{gfa}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*smoothxg.gfa": + type: file + description: Linearized and simplified graph in GFA 1.0 format + pattern: "*.smoothxg.{gfa}" - maf: - type: file - description: write the multiple sequence alignments (MSAs) in MAF format in this file (optional) - pattern: "*.{maf}" + - "*.maf": + type: file + description: write the multiple sequence alignments (MSAs) in MAF format in + this file (optional) + pattern: "*.{maf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh, @subwaystation" maintainers: diff --git a/modules/nf-core/smoove/call/meta.yml b/modules/nf-core/smoove/call/meta.yml index bff9916b96f..379ae6e2dae 100644 --- a/modules/nf-core/smoove/call/meta.yml +++ b/modules/nf-core/smoove/call/meta.yml @@ -1,5 +1,8 @@ name: "smoove_call" -description: smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developped by Brent Pedersen. +description: smoove simplifies and speeds calling and genotyping SVs for short reads. + It also improves specificity by removing many spurious alignment signals that are + indicative of low-level noise and often contribute to spurious calls. Developped + by Brent Pedersen. keywords: - structural variants - SV @@ -7,51 +10,65 @@ keywords: - wgs tools: - "smoove": - description: "structural variant calling and genotyping with existing tools, but, smoothly" + description: "structural variant calling and genotyping with existing tools, but, + smoothly" homepage: https://github.com/brentp/smoove documentation: https://brentp.github.io/post/smoove/ tool_dev_url: https://github.com/brentp/smoove licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.{bai,crai}" - - exclude_beds: - type: file - description: A BED file containing the regions to exclude from the SV calling - pattern: "*.bed" - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.{bai,crai}" + - exclude_beds: + type: file + description: A BED file containing the regions to exclude from the SV calling + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" - "@nvnieuwk" diff --git a/modules/nf-core/snakemake/meta.yml b/modules/nf-core/snakemake/meta.yml index 3da2765988e..b82abe37f14 100644 --- a/modules/nf-core/snakemake/meta.yml +++ b/modules/nf-core/snakemake/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "snakemake" -description: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. This module runs a simple Snakemake pipeline based on input snakefile. Expect many limitations." +description: The Snakemake workflow management system is a tool to create reproducible + and scalable data analyses. This module runs a simple Snakemake pipeline based on + input snakefile. Expect many limitations." keywords: - snakemake - workflow @@ -14,45 +15,54 @@ tools: tool_dev_url: "https://github.com/snakemake/snakemake" doi: "10.1093/bioinformatics/bty350" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputs: - type: file - description: Any input file required by Snakemake - pattern: "*" - - meta2: - type: map - description: | - Meta information for Snakefile - e.g. [ id: 'snakefile' ] - - snakefile: - type: file - description: | - Snakefile to use with Snakemake. This is required for proper execution of Snakemake. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputs: + type: file + description: Any input file required by Snakemake + pattern: "*" + - - meta2: + type: map + description: | + Meta information for Snakefile + e.g. [ id: 'snakefile' ] + - snakefile: + type: file + description: | + Snakefile to use with Snakemake. This is required for proper execution of Snakemake. output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - outputs: - type: file - description: | - Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "[!.snakemake|versions.yml]**": + type: file + description: | + Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated. - snakemake_dir: - type: directory - description: | - Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '.snakemake", type: ''dir'', hidden: true': + type: directory + description: | + Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/snapaligner/align/meta.yml b/modules/nf-core/snapaligner/align/meta.yml index 137b67e18ab..37d9078eb1b 100644 --- a/modules/nf-core/snapaligner/align/meta.yml +++ b/modules/nf-core/snapaligner/align/meta.yml @@ -8,49 +8,60 @@ keywords: - sam tools: - "snapaligner": - description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data" + description: "Scalable Nucleotide Alignment Program -- a fast and accurate read + aligner for high-throughput sequencing data" homepage: "http://snap.cs.berkeley.edu" documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug" tool_dev_url: "https://github.com/amplab/snap" doi: "10.1101/2021.11.23.469039" licence: ["Apache v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq - pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: List of SNAP genome index files - pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input fastq files of size 2 for paired fastq or 1 for bam + or single fastq + pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: List of SNAP genome index files + pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Aligned BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Aligned BAM file + pattern: "*.{bam}" - bai: - type: file - description: Optional aligned BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: Optional aligned BAM file index + pattern: "*.{bai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/snapaligner/index/meta.yml b/modules/nf-core/snapaligner/index/meta.yml index bf84a6b78ff..a0d7367daf3 100644 --- a/modules/nf-core/snapaligner/index/meta.yml +++ b/modules/nf-core/snapaligner/index/meta.yml @@ -7,39 +7,49 @@ keywords: - reference tools: - "snapaligner": - description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data" + description: "Scalable Nucleotide Alignment Program -- a fast and accurate read + aligner for high-throughput sequencing data" homepage: "http://snap.cs.berkeley.edu" documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug" tool_dev_url: "https://github.com/amplab/snap" doi: "10.1101/2021.11.23.469039" licence: ["Apache v2"] + identifier: "" input: - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - - altcontigfile: - type: file - description: Optional file with a list of alt contig names, one per line. - - nonaltcontigfile: - type: file - description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size. - - altliftoverfile: - type: file - description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + - altcontigfile: + type: file + description: Optional file with a list of alt contig names, one per line. + - nonaltcontigfile: + type: file + description: Optional file that contains a list of contigs (one per line) that + will not be marked ALT regardless of size. + - altliftoverfile: + type: file + description: Optional file containing ALT-to-REF mappings (SAM format). e.g., + hs38DH.fa.alt from bwa-kit. output: - index: - type: file - description: SNAP genome index files - pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + - meta: + type: file + description: SNAP genome index files + pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + - snap/*: + type: file + description: SNAP genome index files + pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml index b747de35ea9..b52d45a304e 100644 --- a/modules/nf-core/sniffles/meta.yml +++ b/modules/nf-core/sniffles/meta.yml @@ -11,60 +11,84 @@ tools: documentation: https://github.com/fritzsedlazeck/Sniffles#readme tool_dev_url: https://github.com/fritzsedlazeck/Sniffles licence: ["MIT"] + identifier: biotools:sniffles input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: file - description: A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input - pattern: "*.{bam,cram,snf,tsv}" - - index: - type: file - description: Index of BAM/CAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: | - Reference database in FASTA format - - meta3: - type: map - description: | - Groovy Map containing tandem repeat information - e.g. [ id:'hg38' ] - - tandem_file: - type: file - description: Tandem repeat file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input: + type: file + description: A single .bam/.cram file - OR - one or more .snf files - OR - a + single .tsv file containing a list of .snf files and optional sample ids as + input + pattern: "*.{bam,cram,snf,tsv}" + - index: + type: file + description: Index of BAM/CAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: | + Reference database in FASTA format + - - meta3: + type: map + description: | + Groovy Map containing tandem repeat information + e.g. [ id:'hg38' ] + - tandem_file: + type: file + description: Tandem repeat file + pattern: "*.bed" + - - vcf_output: + type: file + description: VCF output file + pattern: "*.vcf.gz" + - - snf_output: + type: file + description: SNF output file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Compressed VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz.tbi": + type: file + description: Compressed VCF file index + pattern: "*.tbi" - snf: - type: file - description: SNF file - pattern: "*.snf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.snf": + type: file + description: SNF file + pattern: "*.snf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-hakkaart" - "@yuukiiwa" diff --git a/modules/nf-core/snippy/core/meta.yml b/modules/nf-core/snippy/core/meta.yml index cd548b67ed4..7d1c39056a7 100644 --- a/modules/nf-core/snippy/core/meta.yml +++ b/modules/nf-core/snippy/core/meta.yml @@ -12,54 +12,84 @@ tools: documentation: "https://github.com/tseemann/snippy" tool_dev_url: "https://github.com/tseemann/snippy" licence: ["GPL v2"] + identifier: biotools:snippy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Annotated variants in VCF format - pattern: "*.vcf.gz" - - aligned_fa: - type: file - description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants) - pattern: "*.aligned.fa.gz" - - reference: - type: file - description: Reference genome in GenBank (preferred) or FASTA format - pattern: "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Annotated variants in VCF format + pattern: "*.vcf.gz" + - aligned_fa: + type: file + description: A version of the reference but with - at position with depth=0 + and N for 0 < depth < --mincov (does not have variants) + pattern: "*.aligned.fa.gz" + - - reference: + type: file + description: Reference genome in GenBank (preferred) or FASTA format + pattern: "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - aln: - type: file - description: A core SNP alignment in FASTA format - pattern: "*.aln" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.aln: + type: file + description: A core SNP alignment in FASTA format + pattern: "*.aln" - full_aln: - type: file - description: A whole genome SNP alignment (includes invariant sites) - pattern: "*.full.aln" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.full.aln: + type: file + description: A whole genome SNP alignment (includes invariant sites) + pattern: "*.full.aln" - tab: - type: file - description: Tab-separated columnar list of core SNP sites with alleles but NO annotations - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tab: + type: file + description: Tab-separated columnar list of core SNP sites with alleles but + NO annotations + pattern: "*.tab" - vcf: - type: file - description: Multi-sample VCF file with genotype GT tags for all discovered alleles - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf: + type: file + description: Multi-sample VCF file with genotype GT tags for all discovered + alleles + pattern: "*.vcf" - txt: - type: file - description: Tab-separated columnar list of alignment/core-size statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: Tab-separated columnar list of alignment/core-size statistics + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/snippy/run/meta.yml b/modules/nf-core/snippy/run/meta.yml index e5fafb2f461..5b3c907d77b 100644 --- a/modules/nf-core/snippy/run/meta.yml +++ b/modules/nf-core/snippy/run/meta.yml @@ -11,100 +11,202 @@ tools: documentation: "https://github.com/tseemann/snippy" tool_dev_url: "https://github.com/tseemann/snippy" licence: ["GPL v2"] + identifier: biotools:snippy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - index: - type: file - description: Reference genome in GenBank (preferred) or FASTA format - pattern: "*.{gbk,gbk.gz,fa,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - - reference: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tab: - type: file - description: A simple tab-separated summary of all the variants - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.tab: + type: file + description: A simple tab-separated summary of all the variants + pattern: "*.tab" - csv: - type: file - description: A comma-separated version of the .tab file - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.csv: + type: file + description: A comma-separated version of the .tab file + pattern: "*.csv" - html: - type: file - description: A HTML version of the .tab file - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.html: + type: file + description: A HTML version of the .tab file + pattern: "*.html" - vcf: - type: file - description: The final annotated variants in VCF format - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.vcf: + type: file + description: The final annotated variants in VCF format + pattern: "*.vcf" - bed: - type: file - description: The variants in BED format - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.bed: + type: file + description: The variants in BED format + pattern: "*.bed" - gff: - type: file - description: The variants in GFF3 format - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.gff: + type: file + description: The variants in GFF3 format + pattern: "*.gff" - bam: - type: file - description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates. - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.bam: + type: file + description: The alignments in BAM format. Includes unmapped, multimapping reads. + Excludes duplicates. + pattern: "*.bam" - bai: - type: file - description: Index for the .bam file - pattern: "*.bam.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.bam.bai: + type: file + description: Index for the .bam file + pattern: "*.bam.bai" - log: - type: file - description: A log file with the commands run and their outputs - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.log: + type: file + description: A log file with the commands run and their outputs + pattern: "*.log" - aligned_fa: - type: file - description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants) - pattern: "*.aligned.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.aligned.fa: + type: file + description: A version of the reference but with - at position with depth=0 + and N for 0 < depth < --mincov (does not have variants) + pattern: "*.aligned.fa" - consensus_fa: - type: file - description: A version of the reference genome with all variants instantiated - pattern: "*.consensus.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.consensus.fa: + type: file + description: A version of the reference genome with all variants instantiated + pattern: "*.consensus.fa" - consensus_subs_fa: - type: file - description: A version of the reference genome with only substitution variants instantiated - pattern: "*.consensus.subs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.consensus.subs.fa: + type: file + description: A version of the reference genome with only substitution variants + instantiated + pattern: "*.consensus.subs.fa" - raw_vcf: - type: file - description: The unfiltered variant calls from Freebayes - pattern: "*.raw.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.raw.vcf: + type: file + description: The unfiltered variant calls from Freebayes + pattern: "*.raw.vcf" - filt_vcf: - type: file - description: The filtered variant calls from Freebayes - pattern: "*.filt.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.filt.vcf: + type: file + description: The filtered variant calls from Freebayes + pattern: "*.filt.vcf" - vcf_gz: - type: file - description: Compressed .vcf file via BGZIP - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.vcf.gz: + type: file + description: Compressed .vcf file via BGZIP + pattern: "*.vcf.gz" - vcf_csi: - type: file - description: Index for the .vcf.gz via bcftools index - pattern: "*.vcf.gz.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.vcf.gz.csi: + type: file + description: Index for the .vcf.gz via bcftools index + pattern: "*.vcf.gz.csi" - txt: - type: file - description: Tab-separated columnar list of statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.txt: + type: file + description: Tab-separated columnar list of statistics + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/snpdists/meta.yml b/modules/nf-core/snpdists/meta.yml index 4991f6e86c4..612638f9ffa 100644 --- a/modules/nf-core/snpdists/meta.yml +++ b/modules/nf-core/snpdists/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://github.com/tseemann/snp-dists tool_dev_url: https://github.com/tseemann/snp-dists licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment: - type: file - description: The input FASTA sequence alignment file - pattern: "*.{fasta,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: The input FASTA sequence alignment file + pattern: "*.{fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tsv: - type: file - description: The output TSV file containing SNP distance matrix - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The output TSV file containing SNP distance matrix + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index f367c696648..a3211fc7c93 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -14,29 +14,35 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] + identifier: biotools:snpeff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - db: - type: string - description: | - which db to annotate with + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fna,fa}" + - cache_version: + type: string + description: Version of the snpEff cache to download output: - cache: - type: file - description: | - snpEff cache + - meta: + type: file + description: | + snpEff cache + - snpeff_cache: + type: file + description: | + snpEff cache - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 7559c3de082..ef3d495ae74 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -14,46 +14,76 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] + identifier: biotools:snpeff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - db: - type: string - description: | - which db to annotate with - - cache: - type: file - description: | - path to snpEff cache (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - - db: + type: string + description: | + which db to annotate with + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cache: + type: file + description: | + path to snpEff cache (optional) output: - vcf: - type: file - description: | - annotated vcf - pattern: "*.ann.vcf" + - meta: + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" + - "*.ann.vcf": + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" - report: - type: file - description: snpEff report csv file - pattern: "*.csv" + - meta: + type: file + description: snpEff report csv file + pattern: "*.csv" + - "*.csv": + type: file + description: snpEff report csv file + pattern: "*.csv" - summary_html: - type: file - description: snpEff summary statistics in html file - pattern: "*.html" + - meta: + type: file + description: snpEff summary statistics in html file + pattern: "*.html" + - "*.html": + type: file + description: snpEff summary statistics in html file + pattern: "*.html" - genes_txt: - type: file - description: txt (tab separated) file having counts of the number of variants affecting each transcript and gene - pattern: "*.genes.txt" + - meta: + type: file + description: txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + pattern: "*.genes.txt" + - "*.genes.txt": + type: file + description: txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + pattern: "*.genes.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/snpsift/annotate/meta.yml b/modules/nf-core/snpsift/annotate/meta.yml index da0409e54f4..75970f662f1 100644 --- a/modules/nf-core/snpsift/annotate/meta.yml +++ b/modules/nf-core/snpsift/annotate/meta.yml @@ -7,53 +7,56 @@ keywords: - cancer genomics tools: - snpsift: - description: SnpSift is a toolbox that allows you to filter and manipulate annotated files + description: SnpSift is a toolbox that allows you to filter and manipulate annotated + files homepage: https://pcingola.github.io/SnpEff/ss_introduction/ documentation: https://pcingola.github.io/SnpEff/ss_introduction/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" licence: ["MIT"] + identifier: biotools:snpsift input: - - meta: - type: map - description: | - Groovy Map containing sample information regarding vcf file provided - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf, vcf.gz}" - - vcf_tbi: - type: file - description: Tabix file for compressed vcf provided - pattern: "*.{tbi}" - - meta2: - type: map - description: | - Groovy map containing sample information regarding database provided - - database: - type: file - description: Database for use to annotate - pattern: "*.{vcf/vcf.gz}" - - dbs_tbi: - type: file - description: Tabix file for compressed database provided - pattern: "*.{tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information regarding vcf file provided + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf, vcf.gz}" + - vcf_tbi: + type: file + description: Tabix file for compressed vcf provided + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy map containing sample information regarding database provided + - database: + type: file + description: Database for use to annotate + pattern: "*.{vcf/vcf.gz}" + - dbs_tbi: + type: file + description: Tabix file for compressed database provided + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Variant Calling File annotated - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variant Calling File annotated + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LlaneroHiboreo" maintainers: diff --git a/modules/nf-core/snpsift/dbnsfp/meta.yml b/modules/nf-core/snpsift/dbnsfp/meta.yml index 7b9d6f1d5e4..49ad72d88d8 100644 --- a/modules/nf-core/snpsift/dbnsfp/meta.yml +++ b/modules/nf-core/snpsift/dbnsfp/meta.yml @@ -1,5 +1,6 @@ name: "snpsift_dbnsfp" -description: "The dbNSFP is an integrated database of functional predictions from multiple algorithms" +description: "The dbNSFP is an integrated database of functional predictions from + multiple algorithms" keywords: - variant calling - dbnsfp @@ -8,53 +9,56 @@ keywords: - predictions tools: - snpsift: - description: SnpSift is a toolbox that allows you to filter and manipulate annotated files + description: SnpSift is a toolbox that allows you to filter and manipulate annotated + files homepage: https://pcingola.github.io/SnpEff/ss_introduction/ documentation: https://pcingola.github.io/SnpEff/ss_dbnsfp/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" licence: ["MIT"] + identifier: biotools:snpsift input: - - meta: - type: map - description: | - Groovy Map containing sample information regarding vcf file provided - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf, vcf.gz}" - - vcf_tbi: - type: file - description: Tabix file for compressed vcf provided - pattern: "*.{tbi}" - - meta2: - type: map - description: | - Groovy map containing sample information regarding database provided - - database: - type: file - description: Database for use to annotate - pattern: "*.{vcf/vcf.gz}" - - dbs_tbi: - type: file - description: Tabix file for compressed database provided - pattern: "*.{tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information regarding vcf file provided + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf, vcf.gz}" + - vcf_tbi: + type: file + description: Tabix file for compressed vcf provided + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy map containing sample information regarding database provided + - database: + type: file + description: Database for use to annotate + pattern: "*.{vcf/vcf.gz}" + - dbs_tbi: + type: file + description: Tabix file for compressed database provided + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Variant Calling File annotated - pattern: "*.{vcf}" - # + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variant Calling File annotated + pattern: "*.{vcf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LlaneroHiboreo" maintainers: diff --git a/modules/nf-core/snpsift/split/meta.yml b/modules/nf-core/snpsift/split/meta.yml index 8530461e3e0..bf1f7236103 100644 --- a/modules/nf-core/snpsift/split/meta.yml +++ b/modules/nf-core/snpsift/split/meta.yml @@ -6,36 +6,40 @@ keywords: - vcf tools: - snpsift: - description: SnpSift is a toolbox that allows you to filter and manipulate annotated files + description: SnpSift is a toolbox that allows you to filter and manipulate annotated + files homepage: https://pcingola.github.io/SnpEff/ss_introduction/ documentation: https://pcingola.github.io/SnpEff/ss_introduction/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" licence: ["MIT"] + identifier: biotools:snpsift input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file(s) - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file(s) + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out_vcfs: - type: file - description: Split/Joined VCF file(s) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Split/Joined VCF file(s) + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@SusiJo" - "@jonasscheid" diff --git a/modules/nf-core/snpsites/meta.yml b/modules/nf-core/snpsites/meta.yml index 067294829b1..eafac8e8ff8 100644 --- a/modules/nf-core/snpsites/meta.yml +++ b/modules/nf-core/snpsites/meta.yml @@ -10,28 +10,33 @@ tools: homepage: https://www.sanger.ac.uk/tool/snp-sites/ documentation: https://github.com/sanger-pathogens/snp-sites licence: ["GPL-3.0-or-later"] + identifier: "" input: - - alignment: - type: file - description: fasta alignment file - pattern: "*.{fasta,fas,fa,aln}" + - - alignment: + type: file + description: fasta alignment file + pattern: "*.{fasta,fas,fa,aln}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Variant fasta file - pattern: "*.{fas}" + - "*.fas": + type: file + description: Variant fasta file + pattern: "*.{fas}" - constant_sites: - type: file - description: Text file containing counts of constant sites - pattern: "*.{sites.txt}" + - "*.sites.txt": + type: file + description: Text file containing counts of constant sites + pattern: "*.{sites.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - constant_sites_string: - type: integer - description: Value with the number of constant sites - pattern: "*.{sites.txt}" + - CONSTANT_SITES: + type: integer + description: Value with the number of constant sites + pattern: "*.{sites.txt}" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/somalier/ancestry/meta.yml b/modules/nf-core/somalier/ancestry/meta.yml index 6cc67ba6d6e..7b7dde8d897 100644 --- a/modules/nf-core/somalier/ancestry/meta.yml +++ b/modules/nf-core/somalier/ancestry/meta.yml @@ -1,5 +1,6 @@ name: "somalier_ancestry" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,53 +15,66 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query_somalier_files: - type: file - description: Set of somalier files for query samples. Obtained via somalier extract. - pattern: "*.{somalier}" - - meta2: - type: map - description: | - Groovy Map containing labelled samples information - e.g. [ id:'test', single_end:false ] - - labelled_somalier_files: - type: file - description: Set of somalier files for labelled samples. e.g. Somalier files for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1 - pattern: "*.{somalier}" - - labels_tsv: - type: file - description: TSV for labelled samples. e.g. Somalier labels for 1kg https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_somalier_files: + type: file + description: Set of somalier files for query samples. Obtained via somalier + extract. + pattern: "*.{somalier}" + - - meta2: + type: map + description: | + Groovy Map containing labelled samples information + e.g. [ id:'test', single_end:false ] + - labels_tsv: + type: file + description: TSV for labelled samples. e.g. Somalier labels for 1kg + https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv + pattern: "*.{tsv}" + - labelled_somalier_files: + type: file + description: Set of somalier files for labelled samples. e.g. Somalier files + for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1 + pattern: "*.{somalier}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV with ancestry information for query and labelled samples. - pattern: "*.{-ancestry.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-ancestry.tsv": + type: file + description: TSV with ancestry information for query and labelled samples. + pattern: "*.{-ancestry.tsv}" - html: - type: file - description: html file with ancestry information for query and labelled samples. - pattern: "*.{-ancestry.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-ancestry.html": + type: file + description: html file with ancestry information for query and labelled samples. + pattern: "*.{-ancestry.html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml index aabaf5d6f72..256216679f7 100644 --- a/modules/nf-core/somalier/extract/meta.yml +++ b/modules/nf-core/somalier/extract/meta.yml @@ -1,5 +1,6 @@ name: "somalier_extract" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,65 +15,69 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file - - input_index: - type: file - description: index file of the input data, e.g., bam.bai, cram.crai - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'hg38' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fna,fas,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'hg38' ] - - fai: - type: file - description: FASTA index file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing sites information - e.g. [ id:'hg38' ] - - sites: - type: file - description: sites file in VCF format which can be taken from https://github.com/brentp/somalier - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file + - input_index: + type: file + description: index file of the input data, e.g., bam.bai, cram.crai + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fna,fas,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] + - fai: + type: file + description: FASTA index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing sites information + e.g. [ id:'hg38' ] + - sites: + type: file + description: sites file in VCF format which can be taken from https://github.com/brentp/somalier + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - extract: - type: file - description: binary output file based on extracted sites - pattern: "*.{somalier}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somalier": + type: file + description: binary output file based on extracted sites + pattern: "*.{somalier}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" - "@nvnieuwk" diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml index 42638f4f587..0da728218b5 100644 --- a/modules/nf-core/somalier/relate/meta.yml +++ b/modules/nf-core/somalier/relate/meta.yml @@ -1,5 +1,6 @@ name: "somalier_relate" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,47 +15,67 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - extract: - type: file - description: extract file(s) from Somalier extract - pattern: "*.somalier" - - ped: - type: file - description: optional path to a ped or fam file indicating the expected relationships among samples - pattern: "*.{ped,fam}" - - sample_groups: - type: file - description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line - pattern: "*.{txt,csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - extract: + type: file + description: extract file(s) from Somalier extract + pattern: "*.somalier" + - ped: + type: file + description: optional path to a ped or fam file indicating the expected relationships + among samples + pattern: "*.{ped,fam}" + - - sample_groups: + type: file + description: optional path to expected groups of samples such as tumor normal + pairs specified as comma-separated groups per line + pattern: "*.{txt,csv}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: html file - pattern: "*.html" + - meta: + type: file + description: html file + pattern: "*.html" + - "*.html": + type: file + description: html file + pattern: "*.html" - pairs_tsv: - type: file - description: tsv file with output stats for pairs of samples - pattern: "*.pairs.tsv" + - meta: + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" + - "*.pairs.tsv": + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" - samples_tsv: - type: file - description: tsv file with sample-level information - pattern: "*.samples.tsv" + - meta: + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" + - "*.samples.tsv": + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" - "@nvnieuwk" diff --git a/modules/nf-core/sortmerna/meta.yml b/modules/nf-core/sortmerna/meta.yml index c0a2a581fa3..3b43d006d68 100644 --- a/modules/nf-core/sortmerna/meta.yml +++ b/modules/nf-core/sortmerna/meta.yml @@ -8,67 +8,84 @@ keywords: - ribosomal RNA tools: - SortMeRNA: - description: The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. + description: The core algorithm is based on approximate seeds and allows for sensitive + analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from + metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, + fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart + aligned and rejected reads into two files. Additional applications include clustering + and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with + Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. homepage: https://hpc.nih.gov/apps/sortmeRNA.html documentation: https://github.com/biocore/sortmerna/wiki/ licence: ["GPL-3.0-or-later"] + identifier: biotools:sortmerna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fastas: - type: file - description: | - Path to reference file(s) - - meta3: - type: map - description: | - Groovy Map containing index information - e.g. [ id:'test' ] - - index: - type: directory - description: | - Path to index directory of a previous sortmerna run + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fastas: + type: file + description: | + Path to reference file(s) + - - meta3: + type: map + description: | + Groovy Map containing index information + e.g. [ id:'test' ] + - index: + type: directory + description: | + Path to index directory of a previous sortmerna run output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ], or reference information from an - indexing-only run - reads: - type: file - description: The filtered fastq reads - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*non_rRNA.fastq.gz": + type: file + description: The filtered fastq reads + pattern: "*fastq.gz" - log: - type: file - description: SortMeRNA log file - pattern: "*sortmerna.log" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*.log": + type: file + description: SortMeRNA log file + pattern: "*sortmerna.log" - index: - type: directory - description: | - Path to index directory generated by sortmern + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - idx: + type: directory + description: | + Path to index directory generated by sortmern - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@mashehu" diff --git a/modules/nf-core/sourmash/compare/meta.yml b/modules/nf-core/sourmash/compare/meta.yml index e9a3eabc29c..cfd40dbee26 100644 --- a/modules/nf-core/sourmash/compare/meta.yml +++ b/modules/nf-core/sourmash/compare/meta.yml @@ -10,58 +10,74 @@ keywords: - kmer tools: - "sourmash": - description: "Compute and compare FracMinHash signatures for DNA and protein data sets." + description: "Compute and compare FracMinHash signatures for DNA and protein data + sets." homepage: "https://sourmash.readthedocs.io/" documentation: "https://sourmash.readthedocs.io/" tool_dev_url: "https://github.com/sourmash-bio/sourmash" doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - signatures: - type: file - description: Files containing signatures (hash sketches) of samples - pattern: "*.{sig}" - - file_list: - type: file - description: | - An optional file specifying a list of file paths that should be appended to the input signatures. - - save_numpy_matrix: - type: boolean - description: | - If true, output will contain a (dis)similarity matrix numpy binary format. - At least one of save_numpy_matrix or save_csv is required. - - save_csv: - type: boolean - description: | - If true, output will contain a (dis)similarity matrix in CSV format - At least one of save_numpy_matrix or save_csv is required. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - signatures: + type: file + description: Files containing signatures (hash sketches) of samples + pattern: "*.{sig}" + - - file_list: + type: file + description: | + An optional file specifying a list of file paths that should be appended to the input signatures. + - - save_numpy_matrix: + type: boolean + description: | + If true, output will contain a (dis)similarity matrix numpy binary format. + At least one of save_numpy_matrix or save_csv is required. + - - save_csv: + type: boolean + description: | + If true, output will contain a (dis)similarity matrix in CSV format + At least one of save_numpy_matrix or save_csv is required. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - matrix: - type: file - description: An optional (dis)similarity matrix numpy binary format - pattern: "*.comp" - - csv: - type: file - description: An optional (dis)similarity matrix in CSV format - pattern: "*.comp.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*comp.npy": + type: file + description: An optional (dis)similarity matrix numpy binary format + pattern: "*.comp" - labels: - type: file - description: A text file that specifies the labels in the output numpy_matrix - pattern: "*.comp.labels.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*comp.npy.labels.txt": + type: file + description: A text file that specifies the labels in the output numpy_matrix + pattern: "*.comp.labels.txt" + - csv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*comp.csv": + type: file + description: An optional (dis)similarity matrix in CSV format + pattern: "*.comp.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@taylorreiter" maintainers: diff --git a/modules/nf-core/sourmash/gather/meta.yml b/modules/nf-core/sourmash/gather/meta.yml index 72265fa25b1..f4dd13d89bd 100644 --- a/modules/nf-core/sourmash/gather/meta.yml +++ b/modules/nf-core/sourmash/gather/meta.yml @@ -1,5 +1,6 @@ name: "sourmash_gather" -description: Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome. +description: Search a metagenome sourmash signature against one or many reference + databases and return the minimum set of genomes that contain the k-mers in the metagenome. keywords: - FracMinHash sketch - signature @@ -18,73 +19,100 @@ tools: tool_dev_url: https://github.com/sourmash-bio/sourmash doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - signature: - type: file - description: File containing signatures (hash sketches) of a sample - pattern: "*.{sig}" - - db: - type: file - description: Sourmash database (a list of signatures, SBTs, or signature zip files) - - save_unassigned: - type: boolean - description: | - If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query - - save_matches_sig: - type: boolean - description: | - If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query - - save_prefetch: - type: boolean - description: | - If true, output will contain a file with all prefetch-matched signatures from the database - - save_prefetch_csv: - type: boolean - description: | - If true, output will contain a csv file with the names of all prefetch-matched signatures + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - signature: + type: file + description: File containing signatures (hash sketches) of a sample + pattern: "*.{sig}" + - - database: + type: file + description: database + - - save_unassigned: + type: boolean + description: | + If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query + - - save_matches_sig: + type: boolean + description: | + If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query + - - save_prefetch: + type: boolean + description: | + If true, output will contain a file with all prefetch-matched signatures from the database + - - save_prefetch_csv: + type: boolean + description: | + If true, output will contain a csv file with the names of all prefetch-matched signatures output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - result: - type: file - description: | - Table with signatures classified as belonging to any of the genomes - in the sourmash database(s). - pattern: "*{csv.gz}" - - matches: - type: file - description: | - A signature containing FracMinHash sketches of genomes - in the sourmash database. - pattern: "*{sig.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv.gz": + type: file + description: | + Table with signatures classified as belonging to any of the genomes + in the sourmash database(s). + pattern: "*{csv.gz}" - unassigned: - type: file - description: | - A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes - in the sourmash database(s). - pattern: "*{sig.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_unassigned.sig.zip": + type: file + description: | + A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes + in the sourmash database(s). + pattern: "*{sig.zip}" + - matches: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_matches.sig.zip": + type: file + description: | + A signature containing FracMinHash sketches of genomes + in the sourmash database. + pattern: "*{sig.zip}" - prefetch: - type: file - description: | - All prefetch-matched signatures from the database. - pattern: "*{sig.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_prefetch.sig.zip": + type: file + description: | + All prefetch-matched signatures from the database. + pattern: "*{sig.zip}" - prefetchcsv: - type: file - description: | - The names of all prefetch-matched signatures from the database in CSV format. - pattern: "*{csv.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_prefetch.csv.gz": + type: file + description: | + The names of all prefetch-matched signatures from the database in CSV format. + pattern: "*{csv.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vmikk" - "@taylorreiter" diff --git a/modules/nf-core/sourmash/index/meta.yml b/modules/nf-core/sourmash/index/meta.yml index 8639a458962..dfdffeee128 100644 --- a/modules/nf-core/sourmash/index/meta.yml +++ b/modules/nf-core/sourmash/index/meta.yml @@ -1,5 +1,6 @@ name: sourmash_index -description: Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references. +description: Create a database of sourmash signatures (a group of FracMinHash sketches) + to be used as references. keywords: - signatures - sourmash @@ -15,33 +16,36 @@ tools: tool_dev_url: "https://github.com/sourmash-bio/sourmash" doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - signatures: - type: file - description: Files containing signature (hash sketches) of reference genomes - pattern: "*.{sig}" - - ksize: - type: integer - description: ksize value + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - signatures: + type: file + description: Files containing signature (hash sketches) of reference genomes + pattern: "*.{sig}" + - - ksize: + type: integer + description: ksize value output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - signature_index: - type: file - description: Database of signatures - pattern: "*.{sbt.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sbt.zip": + type: file + description: Database of signatures + pattern: "*.{sbt.zip}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@emnilsson" maintainers: diff --git a/modules/nf-core/sourmash/sketch/meta.yml b/modules/nf-core/sourmash/sketch/meta.yml index b0f8145a883..c759b669573 100644 --- a/modules/nf-core/sourmash/sketch/meta.yml +++ b/modules/nf-core/sourmash/sketch/meta.yml @@ -1,5 +1,6 @@ name: sourmash_sketch -description: Create a signature (a group of FracMinHash sketches) of a sequence using sourmash +description: Create a signature (a group of FracMinHash sketches) of a sequence using + sourmash keywords: - hash sketch - sourmash @@ -10,36 +11,41 @@ keywords: - kmer tools: - sourmash: - description: Compute and compare FracMinHash signatures for DNA and protein data sets. + description: Compute and compare FracMinHash signatures for DNA and protein data + sets. homepage: https://sourmash.readthedocs.io/ documentation: https://sourmash.readthedocs.io/ tool_dev_url: https://github.com/sourmash-bio/sourmash doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequence: - type: file - description: FASTA or FASTQ file containing (genomic, transcriptomic, or proteomic) sequence data - pattern: "*.{fna,fa,fasta,fastq,fq,faa}.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence: + type: file + description: FASTA or FASTQ file containing (genomic, transcriptomic, or proteomic) + sequence data + pattern: "*.{fna,fa,fasta,fastq,fq,faa}.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - signatures: - type: file - description: FracMinHash signature of the given sequence - pattern: "*.{sig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sig": + type: file + description: FracMinHash signature of the given sequence + pattern: "*.{sig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/sourmash/taxannotate/meta.yml b/modules/nf-core/sourmash/taxannotate/meta.yml index 764bdb8a502..7fa10cf6a81 100644 --- a/modules/nf-core/sourmash/taxannotate/meta.yml +++ b/modules/nf-core/sourmash/taxannotate/meta.yml @@ -1,5 +1,6 @@ name: "sourmash_taxannotate" -description: Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information. +description: Annotate list of metagenome members (based on sourmash signature matches) + with taxonomic information. keywords: - fracminhash sketch - signature @@ -18,39 +19,41 @@ tools: tool_dev_url: https://github.com/sourmash-bio/sourmash doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash ## Description of all of the variables used as input input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gather_results: - type: file - description: | - Mandatory table with signatures classified as belonging to any of the genomes - in the sourmash database(s), result of `sourmash gather` command. - - taxonomy: - type: file - description: One or more databases with lineages (in CSV format, Mandatory) -## Description of all of the variables used as output + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gather_results: + type: file + description: | + Mandatory table with signatures classified as belonging to any of the genomes + in the sourmash database(s), result of `sourmash gather` command. + - - taxonomy: + type: file + description: One or more databases with lineages (in CSV format, Mandatory) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - result: - type: file - description: | - Table with signatures classified as belonging to any of the genomes - in the sourmash database(s) with an additional 'lineage' column - containing the taxonomic information for each database match. - pattern: "*{csv.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.with-lineages.csv.gz": + type: file + description: | + Table with signatures classified as belonging to any of the genomes + in the sourmash database(s) with an additional 'lineage' column + containing the taxonomic information for each database match. + pattern: "*{csv.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vmikk" - "@taylorreiter" diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml index 167ac8c8851..e1ffcefc9da 100644 --- a/modules/nf-core/spaceranger/count/meta.yml +++ b/modules/nf-core/spaceranger/count/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_count" -description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data +description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics + data keywords: - align - count @@ -22,73 +22,77 @@ tools: tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger" licence: - "10x Genomics EULA" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', slide:'10L13-020', area: 'B1'] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', slide:'10L13-020', area: 'B1'] - `id`, `slide` and `area` are mandatory information! - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - - image: - type: file - description: Brightfield tissue H&E image in JPEG or TIFF format. - pattern: "*.{tif,tiff,jpg,jpeg}" - - cytaimage: - type: file - description: | - CytAssist instrument captured eosin stained Brightfield tissue image with fiducial - frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should - not be modified any way before passing it as input to either Space Ranger or Loupe Browser. - pattern: "*.{tif,tiff}" - - darkimage: - type: file - description: | - Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence - image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files. - pattern: "*.{tif,tiff,jpg,jpeg}" - - colorizedimage: - type: file - description: | - Required for color composite fluorescence microscope image input. - A color composite of one or more fluorescence image channels saved as a single-page, - single-file color TIFF or JPEG. - pattern: "*.{tif,tiff,jpg,jpeg}" - - alignment: - type: file - description: OPTIONAL - Path to manual image alignment. - pattern: "*.json" - - slidefile: - type: file - description: OPTIONAL - Path to slide specifications. - pattern: "*.json" - - reference: - type: directory - description: Folder containing all the reference indices needed by Space Ranger - - probeset: - type: file - description: OPTIONAL - Probe set specification. - pattern: "*.csv" + `id`, `slide` and `area` are mandatory information! + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + - image: + type: file + description: Brightfield tissue H&E image in JPEG or TIFF format. + pattern: "*.{tif,tiff,jpg,jpeg}" + - cytaimage: + type: file + description: | + CytAssist instrument captured eosin stained Brightfield tissue image with fiducial + frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should + not be modified any way before passing it as input to either Space Ranger or Loupe Browser. + pattern: "*.{tif,tiff}" + - darkimage: + type: file + description: | + Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence + image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files. + pattern: "*.{tif,tiff,jpg,jpeg}" + - colorizedimage: + type: file + description: | + Required for color composite fluorescence microscope image input. + A color composite of one or more fluorescence image channels saved as a single-page, + single-file color TIFF or JPEG. + pattern: "*.{tif,tiff,jpg,jpeg}" + - alignment: + type: file + description: OPTIONAL - Path to manual image alignment. + pattern: "*.json" + - slidefile: + type: file + description: OPTIONAL - Path to slide specifications. + pattern: "*.json" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Space Ranger + - - probeset: + type: file + description: OPTIONAL - Probe set specification. + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - outs: - type: file - description: Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list - pattern: "outs/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - outs/**: + type: file + description: Files containing the outputs of Space Ranger, see official 10X + Genomics documentation for a complete list + pattern: "outs/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/spaceranger/mkgtf/meta.yml b/modules/nf-core/spaceranger/mkgtf/meta.yml index 125b12622ba..1294b0c9b16 100644 --- a/modules/nf-core/spaceranger/mkgtf/meta.yml +++ b/modules/nf-core/spaceranger/mkgtf/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_mkgtf" -description: Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command. +description: Module to build a filtered GTF needed by the 10x Genomics Space Ranger + tool. Uses the spaceranger mkgtf command. keywords: - reference - mkref @@ -21,20 +21,23 @@ tools: tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger" licence: - "10x Genomics EULA" + identifier: "" input: - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" + - - gtf: + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" output: - gtf: - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" + - "*.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/spaceranger/mkref/meta.yml b/modules/nf-core/spaceranger/mkref/meta.yml index 453a3e56cc6..8360e2f3c10 100644 --- a/modules/nf-core/spaceranger/mkref/meta.yml +++ b/modules/nf-core/spaceranger/mkref/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_mkref" -description: Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command. +description: Module to build the reference needed by the 10x Genomics Space Ranger + tool. Uses the spaceranger mkref command. keywords: - reference - mkref @@ -21,27 +21,30 @@ tools: tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger" licence: - "10x Genomics EULA" + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder containing all the reference indices needed by Space Ranger + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Space Ranger - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/spades/meta.yml b/modules/nf-core/spades/meta.yml index 986871be75f..ec0df43481b 100644 --- a/modules/nf-core/spades/meta.yml +++ b/modules/nf-core/spades/meta.yml @@ -8,87 +8,139 @@ keywords: - de novo assembler tools: - spades: - description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. + description: SPAdes (St. Petersburg genome assembler) is intended for both standard + isolates and single-cell MDA bacteria assemblies. homepage: http://cab.spbu.ru/files/release3.15.0/manual.html documentation: http://cab.spbu.ru/files/release3.15.0/manual.html tool_dev_url: https://github.com/ablab/spades doi: 10.1089/cmb.2012.0021 licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - illumina: - type: file - description: | - List of input FastQ (Illumina or PacBio CCS reads) files - of size 1 and 2 for single-end and paired-end data, - respectively. This input data type is required. - - pacbio: - type: file - description: | - List of input PacBio CLR FastQ files of size 1. - - nanopore: - type: file - description: | - List of input FastQ files of size 1, originating from Oxford Nanopore technology. - - yml: - type: file - description: | - Path to yml file containing read information. - The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML. - File entries in this yml must contain only the file name and no paths. - pattern: "*.{yml,yaml}" - - hmm: - type: file - description: File or directory with amino acid HMMs for Spades HMM-guided mode. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - illumina: + type: file + description: | + List of input FastQ (Illumina or PacBio CCS reads) files + of size 1 and 2 for single-end and paired-end data, + respectively. This input data type is required. + - pacbio: + type: file + description: | + List of input PacBio CLR FastQ files of size 1. + - nanopore: + type: file + description: | + List of input FastQ files of size 1, originating from Oxford Nanopore technology. + - - yml: + type: file + description: | + Path to yml file containing read information. + The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML. + File entries in this yml must contain only the file name and no paths. + pattern: "*.{yml,yaml}" + - - hmm: + type: file + description: File or directory with amino acid HMMs for Spades HMM-guided mode. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - scaffolds: - type: file - description: | - Fasta file containing scaffolds - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.scaffolds.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - contigs: - type: file - description: | - Fasta file containing contigs - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.contigs.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - transcripts: - type: file - description: | - Fasta file containing transcripts - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.transcripts.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - gene_clusters: - type: file - description: | - Fasta file containing gene_clusters - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.gene_clusters.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - gfa: - type: file - description: | - gfa file containing assembly - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.gfa.gz" + - "*.assembly.gfa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.gfa.gz" + - warnings: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.warnings.log": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - log: - type: file - description: | - Spades log file - pattern: "*.spades.log" - - log: - type: file - description: | - Spades warning log file - pattern: "*.warning.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.spades.log" + - "*.spades.log": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.spades.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@drpatelh" diff --git a/modules/nf-core/spatyper/meta.yml b/modules/nf-core/spatyper/meta.yml index 2af1abca8a5..4efc3f75ca6 100644 --- a/modules/nf-core/spatyper/meta.yml +++ b/modules/nf-core/spatyper/meta.yml @@ -12,38 +12,41 @@ tools: tool_dev_url: https://github.com/HCGB-IGTP/spaTyper doi: 10.5281/zenodo.4063625 licence: ["LGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - repeats: - type: file - description: spa repeat sequences in FASTA format (Optional) - pattern: "*.{fasta}" - - repeat_order: - type: file - description: spa types and order of repeats (Optional) - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - repeats: + type: file + description: spa repeat sequences in FASTA format (Optional) + pattern: "*.{fasta}" + - - repeat_order: + type: file + description: spa types and order of repeats (Optional) + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited results + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/splitubam/meta.yml b/modules/nf-core/splitubam/meta.yml index 3d11eaaebc7..6469135712d 100644 --- a/modules/nf-core/splitubam/meta.yml +++ b/modules/nf-core/splitubam/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "splitubam" description: split one ubam into multiple, per line, fast @@ -13,33 +12,34 @@ tools: documentation: "https://github.com/fellen31/splitubam" tool_dev_url: "https://github.com/fellen31/splitubam" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - bam: - type: file - description: (u)BAM file - pattern: "*.{bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - bam: + type: file + description: (u)BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Split (u)BAM file - pattern: "*.{bam}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Split (u)BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/spotiflow/meta.yml b/modules/nf-core/spotiflow/meta.yml index fe521caa8a1..96d3d001614 100644 --- a/modules/nf-core/spotiflow/meta.yml +++ b/modules/nf-core/spotiflow/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "spotiflow" description: Spotiflow, accurate and efficient spot detection with stereographic flow. @@ -9,43 +8,42 @@ keywords: - detection tools: - "spotiflow": - description: "Spotiflow allows for accurate and efficient spot detection with stereographic flow" + description: "Spotiflow allows for accurate and efficient spot detection with + stereographic flow" homepage: "https://weigertlab.github.io/spotiflow/" documentation: "https://weigertlab.github.io/spotiflow/" tool_dev_url: "https://github.com/weigertlab/spotiflow" doi: "10.1101/2024.02.01.578426" licence: ["BSD-3"] + identifier: "" ## Spotiflow requires only an input image file input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - image_2d: - type: file - description: 2D TIF Image file with the spots to be detected - pattern: "*.{tif,tiff,png,jpg,jpeg}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - image_2d: + type: file + description: 2D TIF Image file with the spots to be detected + pattern: "*.{tif,tiff,png,jpg,jpeg}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - spots: - type: file - description: CSV file with the X, Y positions of the detected spots. - pattern: "*.{csv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.csv": + type: file + description: CSV file with the X, Y positions of the detected spots. + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" maintainers: diff --git a/modules/nf-core/spring/compress/meta.yml b/modules/nf-core/spring/compress/meta.yml index 8b52160940c..1235f6d8348 100644 --- a/modules/nf-core/spring/compress/meta.yml +++ b/modules/nf-core/spring/compress/meta.yml @@ -6,40 +6,44 @@ keywords: - lossless tools: - "spring": - description: "SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)" + description: "SPRING is a compression tool for Fastq files (containing up to 4.29 + Billion reads)" homepage: "https://github.com/shubhamchandak94/Spring" documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md" tool_dev_url: "https://github.com/shubhamchandak94/Spring" doi: "10.1093/bioinformatics/bty1015" licence: ["Free for non-commercial use"] + identifier: biotools:spring input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq1: - type: file - description: FASTQ file to compress. - pattern: "*.{fq.gz,fastq.gz}" - - fastq2: - type: file - description: Parired FASTQ file fon non single-end experiments. - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq1: + type: file + description: FASTQ file to compress. + pattern: "*.{fq.gz,fastq.gz}" + - fastq2: + type: file + description: Parired FASTQ file fon non single-end experiments. + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spring: - type: file - description: One sequence file in spring compressed format. - pattern: "*.{spring}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spring": + type: file + description: One sequence file in spring compressed format. + pattern: "*.{spring}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@xec-cm" maintainers: diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml index a3449b4fb3d..72b72b75da7 100644 --- a/modules/nf-core/spring/decompress/meta.yml +++ b/modules/nf-core/spring/decompress/meta.yml @@ -6,41 +6,45 @@ keywords: - lossless tools: - "spring": - description: "SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)" + description: "SPRING is a compression tool for Fastq files (containing up to 4.29 + Billion reads)" homepage: "https://github.com/shubhamchandak94/Spring" documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md" tool_dev_url: "https://github.com/shubhamchandak94/Spring" doi: "10.1093/bioinformatics/bty1015" licence: ["Free for non-commercial use"] + identifier: biotools:spring input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - spring: - type: file - description: Spring file to decompress. - pattern: "*.{spring}" - - write_one_fastq_gz: - type: boolean - description: | - Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - spring: + type: file + description: Spring file to decompress. + pattern: "*.{spring}" + - - write_one_fastq_gz: + type: boolean + description: | + Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions + pattern: "true or false" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Decompressed FASTQ file(s). - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Decompressed FASTQ file(s). + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@xec-cm" maintainers: diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml index 6a2151a87a2..42e2c07ccff 100644 --- a/modules/nf-core/sratools/fasterqdump/meta.yml +++ b/modules/nf-core/sratools/fasterqdump/meta.yml @@ -1,5 +1,6 @@ name: sratools_fasterqdump -description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA). +description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read + Archive (SRA). keywords: - sequencing - FASTQ @@ -11,42 +12,44 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - sra: - type: directory - description: Directory containing ETL data for the given SRA. - pattern: "*/*.sra" - - ncbi_settings: - type: file - description: > - An NCBI user settings file. - - pattern: "*.mkfg" - - certificate: - type: file - description: > - Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit - - pattern: "*.cart" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - sra: + type: directory + description: Directory containing ETL data for the given SRA. + pattern: "*/*.sra" + - - ncbi_settings: + type: file + description: > + An NCBI user settings file. + pattern: "*.mkfg" + - - certificate: + type: file + description: > + Path to a JWT cart file used to access protected dbGAP data on SRA using the + sra-toolkit + pattern: "*.cart" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Extracted FASTQ file or files if the sequencing reads are paired-end. - pattern: "*.fastq.gz" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.fastq.gz": + type: file + description: Extracted FASTQ file or files if the sequencing reads are paired-end. + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml index 7ed42d49983..3a537bfeacc 100644 --- a/modules/nf-core/sratools/prefetch/meta.yml +++ b/modules/nf-core/sratools/prefetch/meta.yml @@ -11,45 +11,47 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - id: - type: string - description: > - A string denoting an SRA id. - - - ncbi_settings: - type: file - description: > - An NCBI user settings file. - - pattern: "*.mkfg" - - certificate: - type: file - description: > - Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit - - pattern: "*.cart" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - id: + type: string + description: > + A string denoting an SRA id. + - - ncbi_settings: + type: file + description: > + An NCBI user settings file. + pattern: "*.mkfg" + - - certificate: + type: file + description: > + Path to a JWT cart file used to access protected dbGAP data on SRA using the + sra-toolkit + pattern: "*.cart" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - sra: - type: directory - description: > - Directory containing the ETL data for the given SRA id. - - pattern: "*/*.sra" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + pattern: "*/*.sra" + - "id, type: 'dir": + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + pattern: "*/*.sra" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/srst2/srst2/meta.yml b/modules/nf-core/srst2/srst2/meta.yml index 5d5a6876a6e..f7f51ba4468 100644 --- a/modules/nf-core/srst2/srst2/meta.yml +++ b/modules/nf-core/srst2/srst2/meta.yml @@ -15,56 +15,80 @@ tools: tool_dev_url: "https://github.com/katholt/srst2" doi: "10.1186/s13073-014-0090-6" licence: ["BSD"] + identifier: biotools:srst2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: should be the identification number or sample name - single_end: should be true for single end data and false for paired in data - db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option - e.g. [ id:'sample', single_end:false , db:'gene'] - - fasta: - type: file - description: | - gzipped fasta file. If files are NOT in - MiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise - default is _1, i.e. expect forward reads as sample_1.fastq.gz). - pattern: "*.fastq.gz" - - db: - type: file - description: Database in FASTA format - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + id: should be the identification number or sample name + single_end: should be true for single end data and false for paired in data + db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option + e.g. [ id:'sample', single_end:false , db:'gene'] + - fastq_s: + type: file + description: input FastQ files + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - db: + type: file + description: Database in FASTA format + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing - pattern: "*_fullgenes_*_results.txt" - - txt: - type: file - description: A tabulated summary report of samples x genes. - pattern: "*_genes_*_results.txt" - - txt: - type: file - description: A tabulated summary report of mlst subtyping. - pattern: "*_mlst_*_results.txt" - - bam: - type: file - description: Sorted BAM file - pattern: "*.sorted.bam" + - gene_results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*_genes_*_results.txt": + type: file + description: SRST2 gene results + pattern: "*_genes_*_results.txt" + - fullgene_results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*_fullgenes_*_results.txt": + type: file + description: SRST2 full gene results + pattern: "*_fullgenes_*_results.txt" + - mlst_results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*_mlst_*_results.txt": + type: file + description: SRST2 MLST results + pattern: "*_mlst_*_results.txt" - pileup: - type: file - description: SAMtools pileup file - pattern: "*.pileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*.pileup": + type: file + description: SAMtools pileup file + pattern: "*.pileup" + - sorted_bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*.sorted.bam": + type: file + description: Sorted BAM file + pattern: "*.sorted.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvhagey" maintainers: diff --git a/modules/nf-core/ssuissero/meta.yml b/modules/nf-core/ssuissero/meta.yml index d10881867ae..36f0c8d5020 100644 --- a/modules/nf-core/ssuissero/meta.yml +++ b/modules/nf-core/ssuissero/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/jimmyliu1326/SsuisSero tool_dev_url: https://github.com/jimmyliu1326/SsuisSero licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited serotype prediction - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited serotype prediction + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/stadeniolib/scramble/meta.yml b/modules/nf-core/stadeniolib/scramble/meta.yml index 8e3d6f270d8..610f859f28b 100644 --- a/modules/nf-core/stadeniolib/scramble/meta.yml +++ b/modules/nf-core/stadeniolib/scramble/meta.yml @@ -7,51 +7,57 @@ keywords: - compression tools: - "scramble": - description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats." + description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read + by distributions). This contains code for reading and writing a variety of Bioinformatics + / DNA Sequence formats." homepage: "https://github.com/jkbonfield/io_lib" documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md" tool_dev_url: "https://github.com/jkbonfield/io_lib" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fa,fasta}" - - fai: - type: file - description: FASTA index file from samtools faidx - pattern: "*.{fai}" - - gzi: - type: file - description: Optional gzip index file for BAM inputs - pattern: "*.gzi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: FASTA index file from samtools faidx + pattern: "*.{fai}" + - - gzi: + type: file + description: Optional gzip index file for BAM inputs + pattern: "*.gzi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - reads: - type: file - description: Converted reads - pattern: "*.{sam, bam, cram}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{cram,bam}": + type: file + description: Compressed BAM/CRAM file + pattern: "*.{cram,bam}" - gzi: - type: file - description: gzip index file for BAM outputs - pattern: ".{bam.gzi}" + - "*.gzi": + type: file + description: gzip index file for BAM outputs + pattern: ".{bam.gzi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/staphopiasccmec/meta.yml b/modules/nf-core/staphopiasccmec/meta.yml index e67b78fd218..584554194c0 100644 --- a/modules/nf-core/staphopiasccmec/meta.yml +++ b/modules/nf-core/staphopiasccmec/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: https://github.com/staphopia/staphopia-sccmec doi: 10.7717/peerj.5261 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited results + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index e3d1c714d30..1debc4c9b94 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - bioconda::htslib=1.18 + - bioconda::samtools=1.18 + - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index e80dbb7dd3e..d30556b515a 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -14,97 +14,189 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: - type: directory - description: STAR genome index - pattern: "star" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - star_ignore_sjdbgtf: - type: boolean - description: Ignore annotation GTF file - - seq_platform: - type: string - description: Sequencing platform - - seq_center: - type: string - description: Sequencing center + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - index: + type: directory + description: STAR genome index + pattern: "star" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - - seq_platform: + type: string + description: Sequencing platform + - - seq_center: + type: string + description: Sequencing center output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: file + description: STAR final log file + pattern: "*Log.final.out" + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: file + description: STAR lot out file + pattern: "*Log.out" + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: file + description: STAR log progress file + pattern: "*Log.progress.out" + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*d.out.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bam_sorted: - type: file - description: Sorted BAM file of read alignments (optional) - pattern: "*sortedByCoord.out.bam" + - meta: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" + - "*sortedByCoord.out.bam": + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" - bam_transcript: - type: file - description: Output BAM file of transcriptome alignment (optional) - pattern: "*toTranscriptome.out.bam" + - meta: + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" + - "*toTranscriptome.out.bam": + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" - bam_unsorted: - type: file - description: Unsorted BAM file of read alignments (optional) - pattern: "*Aligned.unsort.out.bam" + - meta: + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" + - "*Aligned.unsort.out.bam": + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" - fastq: - type: file - description: Unmapped FastQ files (optional) - pattern: "*fastq.gz" + - meta: + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" + - "*fastq.gz": + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" - tab: - type: file - description: STAR output tab file(s) (optional) - pattern: "*.tab" + - meta: + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - "*.tab": + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - spl_junc_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.SJ.out.tab": + type: file + description: STAR output splice junction tab file + pattern: "*.SJ.out.tab" + - read_per_gene_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ReadsPerGene.out.tab": + type: file + description: STAR output read per gene tab file + pattern: "*.ReadsPerGene.out.tab" - junction: - type: file - description: STAR chimeric junction output file (optional) - pattern: "*.out.junction" + - meta: + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - "*.out.junction": + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out.sam": + type: file + description: STAR output SAM file + pattern: "*.out.sam" - wig: - type: file - description: STAR output wiggle format file(s) (optional) - pattern: "*.wig" + - meta: + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" + - "*.wig": + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" - bedgraph: - type: file - description: STAR output bedGraph format file(s) (optional) - pattern: "*.bg" + - meta: + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" + - "*.bg": + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 38611dfa26e..1debc4c9b94 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.18 - bioconda::htslib=1.18 + - bioconda::samtools=1.18 - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 1061e1b8dc0..33c1f65f3d4 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -14,37 +14,40 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the reference genome - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the reference genome + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: directory - description: Folder containing the star index files - pattern: "star" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - star: + type: directory + description: Folder containing the star index files + pattern: "star" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/starsolo/meta.yml b/modules/nf-core/star/starsolo/meta.yml index c3e7c42cfc7..d9297f012a4 100644 --- a/modules/nf-core/star/starsolo/meta.yml +++ b/modules/nf-core/star/starsolo/meta.yml @@ -1,5 +1,6 @@ name: "starsolo" -description: Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information. +description: Create a counts matrix for single-cell data using STARSolo, handling + cell barcodes and UMI information. keywords: - align - count @@ -12,60 +13,102 @@ tools: documentation: "https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md" doi: "10.1101/2021.05.05.442755" licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information. - Here, you should add all the specific barcode/umi - information for each sample. - e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` - - solotype: - type: string - description: | - Type of single-cell library. - It can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3, - CB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq. - - meta2: - type: map - description: Groovy Map containing the STAR index information. - - index: - type: directory - description: STAR genome index - pattern: "star" - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - solotype: + type: string + description: | + Type of single-cell library. + It can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3, + CB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq. + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - opt_whitelist: + type: file + description: Optional whitelist file + - - meta2: + type: map + description: Groovy Map containing the STAR index information. + - index: + type: directory + description: STAR genome index + pattern: "star" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - Here, you should add all the specific barcode/umi - information for each sample. - e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - counts: + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*.Solo.out": + type: file + description: STARSolo counts matrix + pattern: "*.Solo.out" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - summary: - type: file - description: STARSolo metrics summary CSV file. - pattern: "*/Gene/Summary.csv" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*/Gene/Summary.csv": + type: file + description: STARSolo metrics summary CSV file. + pattern: "*/Gene/Summary.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ggabernet" diff --git a/modules/nf-core/staramr/search/meta.yml b/modules/nf-core/staramr/search/meta.yml index 909dd070c64..be0e60a3724 100644 --- a/modules/nf-core/staramr/search/meta.yml +++ b/modules/nf-core/staramr/search/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "staramr_search" -description: "Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases." +description: "Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder + databases." keywords: - amr - plasmid @@ -16,65 +16,123 @@ tools: tool_dev_url: "https://github.com/phac-nml/staramr" doi: "10.3390/microorganisms10020292" licence: ["Apache Software License"] + identifier: biotools:staramr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - genome_fasta: - type: file - description: | - Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids. - pattern: "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - genome_fasta: + type: file + description: | + Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids. + pattern: "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}" output: - results_xlsx: - type: file - description: Excel spreadsheet containing summary of StarAMR results. - pattern: "*_results/results.xlsx" + - meta: + type: file + description: Excel spreadsheet containing summary of StarAMR results. + pattern: "*_results/results.xlsx" + - "*_results/results.xlsx": + type: file + description: Excel spreadsheet containing summary of StarAMR results. + pattern: "*_results/results.xlsx" - summary_tsv: - type: file - description: | - A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. - A series of descriptive statistics is also provided for each genome, - as well as feedback for whether or not the genome passes several quality metrics and if not, - feedback on why the genome fails. - pattern: "*_results/summary.tsv" + - meta: + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/summary.tsv" + - "*_results/summary.tsv": + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/summary.tsv" - detailed_summary_tsv: - type: file - description: | - A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. - A series of descriptive statistics is also provided for each genome, - as well as feedback for whether or not the genome passes several quality metrics and if not, - feedback on why the genome fails. - pattern: "*_results/detailed_summary.tsv" + - meta: + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/detailed_summary.tsv" + - "*_results/detailed_summary.tsv": + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/detailed_summary.tsv" - resfinder_tsv: - type: file - description: A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line. - pattern: "*_results/resfinder.tsv" + - meta: + type: file + description: A tabular file of each AMR gene and additional BLAST information + from the ResFinder database, one gene per line. + pattern: "*_results/resfinder.tsv" + - "*_results/resfinder.tsv": + type: file + description: A tabular file of each AMR gene and additional BLAST information + from the ResFinder database, one gene per line. + pattern: "*_results/resfinder.tsv" - plasmidfinder_tsv: - type: file - description: A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line. - pattern: "*_results/plasmidfinder.tsv" + - meta: + type: file + description: A tabular file of each AMR plasmid type and additional BLAST information + from the PlasmidFinder database, one plasmid type per line. + pattern: "*_results/plasmidfinder.tsv" + - "*_results/plasmidfinder.tsv": + type: file + description: A tabular file of each AMR plasmid type and additional BLAST information + from the PlasmidFinder database, one plasmid type per line. + pattern: "*_results/plasmidfinder.tsv" - mlst_tsv: - type: file - description: A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. - pattern: "*_results/mlst.tsv" + - meta: + type: file + description: A tabular file of each multi-locus sequence type (MLST) and it's + corresponding locus/alleles, one genome per line. + pattern: "*_results/mlst.tsv" + - "*_results/mlst.tsv": + type: file + description: A tabular file of each multi-locus sequence type (MLST) and it's + corresponding locus/alleles, one genome per line. + pattern: "*_results/mlst.tsv" - settings_txt: - type: file - description: The command-line, database versions, and other settings used to run staramr. - pattern: "*_results/settings.txt" + - meta: + type: file + description: The command-line, database versions, and other settings used to + run staramr. + pattern: "*_results/settings.txt" + - "*_results/settings.txt": + type: file + description: The command-line, database versions, and other settings used to + run staramr. + pattern: "*_results/settings.txt" - pointfinder_tsv: - type: file - description: An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line. - pattern: "*_results/pointfinder.tsv" + - meta: + type: file + description: An optional tabular file of each AMR point mutation and additional + BLAST information from the PointFinder database, one gene per line. + pattern: "*_results/pointfinder.tsv" + - "*_results/pointfinder.tsv": + type: file + description: An optional tabular file of each AMR point mutation and additional + BLAST information from the PointFinder database, one gene per line. + pattern: "*_results/pointfinder.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apetkau" maintainers: diff --git a/modules/nf-core/stardist/meta.yml b/modules/nf-core/stardist/meta.yml index a6514d2febd..70e60b75db0 100644 --- a/modules/nf-core/stardist/meta.yml +++ b/modules/nf-core/stardist/meta.yml @@ -6,42 +6,41 @@ keywords: - image tools: - "stardist": - description: "Stardist is an cell segmentation tool developed in Python by Martin Weigert and Uwe Schmidt" + description: "Stardist is an cell segmentation tool developed in Python by Martin + Weigert and Uwe Schmidt" homepage: "https://stardist.net/" documentation: "https://stardist.net/faq/" tool_dev_url: "https://github.com/stardist/stardist" doi: "10.1109/ISBIC56247.2022.9854534" licence: ["BSD 3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - image: - type: file - description: Single channel nuclear image - pattern: "*.{tiff,tif}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - image: + type: file + description: Single channel nuclear image + pattern: "*.{tiff,tif}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - mask: - type: file - description: labelled mask output from stardist in tif format. - pattern: "*.{tiff,tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.stardist.tif": + type: file + description: labelled mask output from stardist in tif format. + pattern: "*.{tiff,tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" maintainers: diff --git a/modules/nf-core/stecfinder/meta.yml b/modules/nf-core/stecfinder/meta.yml index a4efed3190d..1d8452129e1 100644 --- a/modules/nf-core/stecfinder/meta.yml +++ b/modules/nf-core/stecfinder/meta.yml @@ -7,36 +7,40 @@ keywords: - fasta tools: - "stecfinder": - description: "Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies" + description: "Cluster informed Shigatoxin producing E. coli (STEC) serotyping + tool from Illumina reads and assemblies" homepage: "https://github.com/LanLab/STECFinder" documentation: "https://github.com/LanLab/STECFinder" tool_dev_url: "https://github.com/LanLab/STECFinder" doi: "10.3389/fcimb.2021.772574" licence: ["GPL v3"] + identifier: biotools:stecfinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: Illumina paired-end reads or an assembly - pattern: "*.{fastq.gz,fasta.gz,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: Illumina paired-end reads or an assembly + pattern: "*.{fastq.gz,fasta.gz,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited report of results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A tab-delimited report of results + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/stitch/meta.yml b/modules/nf-core/stitch/meta.yml index 2596fa37928..48a21c4996f 100644 --- a/modules/nf-core/stitch/meta.yml +++ b/modules/nf-core/stitch/meta.yml @@ -1,7 +1,9 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "stitch" -description: "STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format." +description: "STITCH is an R program for reference panel free, read aware, low coverage + sequencing genotype imputation. STITCH runs on a set of samples with sequencing + reads in BAM format, as well as a list of positions to genotype, and outputs imputed + genotypes in VCF format." keywords: - imputation - genomics @@ -18,102 +20,136 @@ tools: tool_dev_url: "https://github.com/rwdavies/stitch" doi: "10.1038/ng.3594" licence: ["GPL v3"] + identifier: biotools:stitch-snijderlab input: - - meta: - type: map - description: | - Groovy Map containing information about the set of positions to run the imputation over - e.g. `[ id:'test' ]` - - posfile: - type: file - description: | - Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information. - pattern: "*.tsv" - - input: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "input" - - rdata: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "RData" - - chromosome_name: - type: string - description: Name of the chromosome to impute. Should match a chromosome name in the reference genome. - - K: - type: integer - description: Number of ancestral haplotypes to use for imputation. Refer to the documentation for the `--K` argument of STITCH for more information. - - nGen: - type: integer - description: Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information. - - meta2: - type: map - description: | - Groovy Map containing information about the set of samples - e.g. `[ id:'test' ]` - - collected_crams: - type: file - description: List of sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - collected_crais: - type: file - description: List of BAM/CRAM/SAM index files - pattern: "*.{bai,crai,sai}" - - cramlist: - type: file - description: | - Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path. - pattern: "*.txt" - - meta3: - type: map - description: | - Groovy Map containing information about the reference genome used - e.g. `[ id:'test' ]` - - fasta: - type: file - description: FASTA reference genome file - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing information about the set of positions to run the imputation over + e.g. `[ id:'test' ]` + - posfile: + type: file + description: | + Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information. + pattern: "*.tsv" + - input: + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "input" + - rdata: + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "RData" + - chromosome_name: + type: string + description: Name of the chromosome to impute. Should match a chromosome name + in the reference genome. + - K: + type: integer + description: Number of ancestral haplotypes to use for imputation. Refer to + the documentation for the `--K` argument of STITCH for more information. + - nGen: + type: integer + description: Number of generations since founding of the population to use for + imputation. Refer to the documentation for the `--nGen` argument of STITCH + for more information. + - - meta2: + type: map + description: | + Groovy Map containing information about the set of samples + e.g. `[ id:'test' ]` + - collected_crams: + type: file + description: List of sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - collected_crais: + type: file + description: List of BAM/CRAM/SAM index files + pattern: "*.{bai,crai,sai}" + - cramlist: + type: file + description: | + Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path. + pattern: "*.txt" + - - meta3: + type: map + description: | + Groovy Map containing information about the reference genome used + e.g. `[ id:'test' ]` + - fasta: + type: file + description: FASTA reference genome file + pattern: "*.{fa,fasta}" + - fasta_fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - - seed: + type: integer + description: Seed for random number generation output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - input: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "input" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - 'input", type: "dir': + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "input" - rdata: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "RData" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - 'RData", type: "dir': + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "RData" - plots: - type: directory - description: | - Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH. - pattern: "plots" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - 'plots", type: "dir': + type: directory + description: | + Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH. + pattern: "plots" - vcf: - type: file - description: | - Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output. - pattern: ".vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.vcf.gz": + type: file + description: | + Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output. + pattern: ".vcf.gz" - bgen: - type: file - description: | - Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified. - pattern: ".bgen" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.bgen": + type: file + description: | + Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified. + pattern: ".bgen" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@saulpierotti" maintainers: diff --git a/modules/nf-core/stranger/meta.yml b/modules/nf-core/stranger/meta.yml index 5e0bc0bb0ca..a5486dbdbfc 100644 --- a/modules/nf-core/stranger/meta.yml +++ b/modules/nf-core/stranger/meta.yml @@ -1,5 +1,6 @@ name: stranger -description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes. +description: Annotates output files from ExpansionHunter with the pathologic implications + of the repeat sizes. keywords: - STR - repeat_expansions @@ -13,39 +14,42 @@ tools: tool_dev_url: https://github.com/moonso/stranger doi: "10.5281/zenodo.4548873" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF with repeat expansions - pattern: "*.{vcf.gz,vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - variant_catalog: - type: file - description: json file with repeat expansion sites to genotype - pattern: "*.{json}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF with repeat expansions + pattern: "*.{vcf.gz,vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - variant_catalog: + type: file + description: json file with repeat expansion sites to genotype + pattern: "*.{json}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ljmesi" maintainers: diff --git a/modules/nf-core/strelka/germline/meta.yml b/modules/nf-core/strelka/germline/meta.yml index 9a597ef01fd..5536dd8a566 100644 --- a/modules/nf-core/strelka/germline/meta.yml +++ b/modules/nf-core/strelka/germline/meta.yml @@ -1,5 +1,6 @@ name: strelka_germline -description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation +description: Strelka2 is a fast and accurate small variant caller optimized for analysis + of germline variation keywords: - variantcalling - germline @@ -8,68 +9,90 @@ keywords: - variants tools: - strelka: - description: Strelka calls somatic and germline small variants from mapped sequencing reads + description: Strelka calls somatic and germline small variants from mapped sequencing + reads homepage: https://github.com/Illumina/strelka documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x licence: ["GPL v3"] + identifier: biotools:strelka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAI index file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_index: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAI index file + pattern: "*.{bai,crai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_index: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - vcf: - type: file - description: gzipped germline variant file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*variants.vcf.gz": + type: file + description: gzipped germline variant file + pattern: "*.{vcf.gz}" - vcf_tbi: - type: file - description: index file for the vcf file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*variants.vcf.gz.tbi": + type: file + description: index file for the vcf file + pattern: "*.vcf.gz.tbi" - genome_vcf: - type: file - description: variant records and compressed non-variant blocks - pattern: "*_genome.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*genome.vcf.gz": + type: file + description: variant records and compressed non-variant blocks + pattern: "*_genome.vcf.gz" - genome_vcf_tbi: - type: file - description: index file for the genome_vcf file - pattern: "*_genome.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*genome.vcf.gz.tbi": + type: file + description: index file for the genome_vcf file + pattern: "*_genome.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@arontommi" maintainers: diff --git a/modules/nf-core/strelka/somatic/meta.yml b/modules/nf-core/strelka/somatic/meta.yml index 428bcb3f843..6f2caaa3e7f 100644 --- a/modules/nf-core/strelka/somatic/meta.yml +++ b/modules/nf-core/strelka/somatic/meta.yml @@ -1,5 +1,7 @@ name: strelka_somatic -description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs +description: Strelka2 is a fast and accurate small variant caller optimized for analysis + of germline variation in small cohorts and somatic variation in tumor/normal sample + pairs keywords: - variant calling - germline @@ -8,84 +10,106 @@ keywords: - variants tools: - strelka: - description: Strelka calls somatic and germline small variants from mapped sequencing reads + description: Strelka calls somatic and germline small variants from mapped sequencing + reads homepage: https://github.com/Illumina/strelka documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x licence: ["GPL v3"] + identifier: biotools:strelka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_normal: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_normal: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - input_tumor: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_tumor: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - manta_candidate_small_indels: - type: file - description: VCF.gz file - pattern: "*.{vcf.gz}" - - manta_candidate_small_indels_tbi: - type: file - description: VCF.gz index file - pattern: "*.tbi" - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_index: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_normal: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - input_tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_tumor: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - manta_candidate_small_indels: + type: file + description: VCF.gz file + pattern: "*.{vcf.gz}" + - manta_candidate_small_indels_tbi: + type: file + description: VCF.gz index file + pattern: "*.tbi" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_index: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf_indels: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - vcf_indels_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - vcf_snvs: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_snvs.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - vcf_snvs_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_snvs.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/stringtie/merge/meta.yml b/modules/nf-core/stringtie/merge/meta.yml index 5d02d678617..cf6902b321d 100644 --- a/modules/nf-core/stringtie/merge/meta.yml +++ b/modules/nf-core/stringtie/merge/meta.yml @@ -11,27 +11,29 @@ tools: homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual licence: ["MIT"] + identifier: biotools:stringtie input: - - stringtie_gtf: - type: file - description: | - Stringtie transcript gtf output(s). - pattern: "*.gtf" - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). - pattern: "*.gtf" + - - stringtie_gtf: + type: file + description: | + Stringtie transcript gtf output(s). + pattern: "*.gtf" + - - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). + pattern: "*.gtf" output: - - merged_gtf: - type: map - description: | - Merged gtf from annotation and stringtie output gtfs. - pattern: "*.gtf" + - gtf: + - stringtie.merged.gtf: + type: file + description: Merged gtf file + pattern: "stringtie.merged.gtf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" maintainers: diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml index d8ebdd88aa0..e55b2abfcb1 100644 --- a/modules/nf-core/stringtie/stringtie/meta.yml +++ b/modules/nf-core/stringtie/stringtie/meta.yml @@ -12,46 +12,67 @@ tools: homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual licence: ["MIT"] + identifier: biotools:stringtie input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Stringtie transcript gtf output(s). - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Stringtie transcript gtf output(s). + - - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - transcript_gtf: - type: file - description: transcript gtf - pattern: "*.{transcripts.gtf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.gtf": + type: file + description: transcript gtf + pattern: "*.{transcripts.gtf}" + - abundance: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abundance.txt": + type: file + description: abundance + pattern: "*.{abundance.txt}" - coverage_gtf: - type: file - description: coverage gtf - pattern: "*.{coverage.gtf}" - - abudance: - type: file - description: abudance - pattern: "*.{abudance.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coverage.gtf": + type: file + description: coverage gtf + pattern: "*.{coverage.gtf}" - ballgown: - type: file - description: for running ballgown - pattern: "*.{ballgown}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ballgown": + type: file + description: for running ballgown + pattern: "*.{ballgown}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/subread/featurecounts/meta.yml b/modules/nf-core/subread/featurecounts/meta.yml index 38a37945631..a9b045b7dce 100644 --- a/modules/nf-core/subread/featurecounts/meta.yml +++ b/modules/nf-core/subread/featurecounts/meta.yml @@ -7,43 +7,55 @@ keywords: - reference tools: - featurecounts: - description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads. + description: featureCounts is a highly efficient general-purpose read summarization + program that counts mapped reads for genomic features such as genes, exons, + promoter, gene bodies, genomic bins and chromosomal locations. It can be used + to count both RNA-seq and genomic DNA-seq reads. homepage: http://bioinf.wehi.edu.au/featureCounts/ documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf doi: "10.1093/bioinformatics/btt656" licence: ["GPL v3"] + identifier: biotools:subread input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - annotation: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf,saf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: BAM files containing mapped reads + pattern: "*.bam" + - annotation: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf,saf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - counts: - type: file - description: Counts of reads mapping to features - pattern: "*featureCounts.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt": + type: file + description: Counts of reads mapping to features + pattern: "*featureCounts.txt" - summary: - type: file - description: Summary log file - pattern: "*.featureCounts.txt.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt.summary": + type: file + description: Summary log file + pattern: "*.featureCounts.txt.summary" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml index e5118d28948..820d4f163ca 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "summarizedexperiment_summarizedexperiment" description: | @@ -11,68 +10,77 @@ keywords: - assay tools: - "summarizedexperiment": - description: "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples." + description: "The SummarizedExperiment container contains one or more assays, + each represented by a matrix-like object of numeric or other mode. The rows + typically represent genomic ranges of interest and the columns represent samples." homepage: "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html" tool_dev_url: "https://github.com/Bioconductor/SummarizedExperiment" doi: "10.18129/B9.bioc.SummarizedExperiment" licence: ["Artistic-2.0"] + identifier: biotools:summarizedexperiment input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - matrix_files: - type: directory - description: | - One or more paths to CSV or TSV matrix files. All files must have the - same rows and columns. - pattern: "*.{csv,tsv}" - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference from which matrix rows are derived e.g. `[ id:'yeast' ]` - - rowdata: - type: file - description: | - Metadata on matrix features. One column must contain all matrix row - IDs. - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole, - as represented by the matrix columns and the sample sheet e.g. - `[id:'SRP123456' ]` - - coldata: - type: file - description: | - Metadata on matrix columns. One column must contain all matrix column - IDs. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - matrix_files: + type: directory + description: | + One or more paths to CSV or TSV matrix files. All files must have the + same rows and columns. + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference from which matrix rows are derived e.g. `[ id:'yeast' ]` + - rowdata: + type: file + description: | + Metadata on matrix features. One column must contain all matrix row + IDs. + pattern: "*.{csv,tsv}" + - - meta3: + type: map + description: | + Groovy Map containing information related to the experiment as a whole, + as represented by the matrix columns and the sample sheet e.g. + `[id:'SRP123456' ]` + - coldata: + type: file + description: | + Metadata on matrix columns. One column must contain all matrix column + IDs. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - rds: - type: file - description: Serialised SummarizedExperiment object - pattern: "*.SummarizedExperiment.rds" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.rds": + type: file + description: Serialised SummarizedExperiment object + pattern: "*.SummarizedExperiment.rds" - log: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/survivor/bedpetovcf/meta.yml b/modules/nf-core/survivor/bedpetovcf/meta.yml index 6045d4fbc1a..8a1b4f941f1 100644 --- a/modules/nf-core/survivor/bedpetovcf/meta.yml +++ b/modules/nf-core/survivor/bedpetovcf/meta.yml @@ -13,29 +13,32 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedpe: - type: file - description: BEDPE file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedpe: + type: file + description: BEDPE file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/survivor/filter/meta.yml b/modules/nf-core/survivor/filter/meta.yml index 64565408d30..cc6c8d61ad6 100644 --- a/modules/nf-core/survivor/filter/meta.yml +++ b/modules/nf-core/survivor/filter/meta.yml @@ -13,45 +13,47 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file to filter - pattern: "*.{vcf}" - - bed: - type: file - description: BED file with regions to ignore (NA to disable) - - minsv: - type: integer - description: Min SV size (-1 to disable) - - maxsv: - type: integer - description: Max SV size (-1 to disable) - - minallelefreq: - type: float - description: Min allele frequency (0-1) - - minnumreads: - type: integer - description: Min number of reads support [RE flag (-1 to disable)] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf_file: + type: file + description: VCF file to filter + - bed: + type: file + description: BED file with regions to ignore (NA to disable) + - - minsv: + type: integer + description: Min SV size (-1 to disable) + - - maxsv: + type: integer + description: Max SV size (-1 to disable) + - - minallelefreq: + type: float + description: Min allele frequency (0-1) + - - minnumreads: + type: integer + description: Min number of reads support [RE flag (-1 to disable)] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Filtered VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Filtered VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LlaneroHiboreo" maintainers: diff --git a/modules/nf-core/survivor/merge/meta.yml b/modules/nf-core/survivor/merge/meta.yml index 529e9175dde..f60f68bc767 100644 --- a/modules/nf-core/survivor/merge/meta.yml +++ b/modules/nf-core/survivor/merge/meta.yml @@ -1,5 +1,6 @@ name: "survivor_merge" -description: Compare or merge VCF files to generate a consensus or multi sample VCF files. +description: Compare or merge VCF files to generate a consensus or multi sample VCF + files. keywords: - survivor - merge @@ -13,50 +14,54 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - The VCF files to be merged - Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158 - pattern: "*.vcf" - - max_distance_breakpoints: - type: integer - description: Max distance between breakpoints (0-1 percent of length, 1- number of bp) - - min_supporting_callers: - type: integer - description: Minimum number of supporting caller - - account_for_type: - type: integer - description: Take the type into account (1==yes, else no) - - account_for_sv_strands: - type: integer - description: Take the strands of SVs into account (1==yes, else no) - - estimate_distanced_by_sv_size: - type: integer - description: Estimate distance based on the size of SV (1==yes, else no) - - min_sv_size: - type: integer - description: Minimum size of SVs to be taken into account + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + The VCF files to be merged + Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158 + pattern: "*.vcf" + - - max_distance_breakpoints: + type: integer + description: Max distance between breakpoints (0-1 percent of length, 1- number + of bp) + - - min_supporting_callers: + type: integer + description: Minimum number of supporting caller + - - account_for_type: + type: integer + description: Take the type into account (1==yes, else no) + - - account_for_sv_strands: + type: integer + description: Take the strands of SVs into account (1==yes, else no) + - - estimate_distanced_by_sv_size: + type: integer + description: Estimate distance based on the size of SV (1==yes, else no) + - - min_sv_size: + type: integer + description: Minimum size of SVs to be taken into account output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The merged VCF file - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: The merged VCF file + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/survivor/simsv/meta.yml b/modules/nf-core/survivor/simsv/meta.yml index 80b6d1c918a..504b6ae2a35 100644 --- a/modules/nf-core/survivor/simsv/meta.yml +++ b/modules/nf-core/survivor/simsv/meta.yml @@ -1,4 +1,3 @@ ---- name: "survivor_simsv" description: Simulate an SV VCF file based on a reference genome keywords: @@ -14,70 +13,98 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing fasta information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: The reference genome - pattern: "*.{fasta,fna,fa}" - - meta2: - type: map - description: | - Groovy Map containing fasta index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: The index of the reference genome - pattern: "*.fai" - - meta3: - type: map - description: | - Groovy Map containing parameters information - e.g. `[ id:'test', single_end:false ]` - - parameters: - type: file - description: A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied - pattern: "*.txt" - - snp_mutation_frequency: - type: float - description: The SNP mutation frequency in the output VCF (0-1) - - sim_reads: - type: integer - description: Whether or not to simulate reads (1==yes, else no) + - - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: The reference genome + pattern: "*.{fasta,fna,fa}" + - - meta2: + type: map + description: | + Groovy Map containing fasta index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: The index of the reference genome + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing parameters information + e.g. `[ id:'test', single_end:false ]` + - parameters: + type: file + description: A text file containing the parameters to be used for the simulation. + Gets automatically generated using defaults when this is not supplied + pattern: "*.txt" + - - snp_mutation_frequency: + type: float + description: The SNP mutation frequency in the output VCF (0-1) + - - sim_reads: + type: integer + description: Whether or not to simulate reads (1==yes, else no) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - parameters: - type: file - description: The created parameters file - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: The created parameters file + pattern: "*.txt" - vcf: - type: file - description: A VCF containing the simulated variants - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf": + type: file + description: A VCF containing the simulated variants + pattern: "*.vcf" - bed: - type: file - description: A BED file of the simulated structural variants - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: A BED file of the simulated structural variants + pattern: "*.bed" - fasta: - type: file - description: A Fasta file file containing the variants from the output VCF - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta": + type: file + description: A Fasta file file containing the variants from the output VCF + pattern: "*.fasta" - insertions: - type: file - description: A Fasta file file containing insertion sequences - pattern: "*.insertions.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.insertions.fa": + type: file + description: A Fasta file file containing insertion sequences + pattern: "*.insertions.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/survivor/stats/meta.yml b/modules/nf-core/survivor/stats/meta.yml index ba450a72727..cc89f0aead6 100644 --- a/modules/nf-core/survivor/stats/meta.yml +++ b/modules/nf-core/survivor/stats/meta.yml @@ -13,39 +13,42 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file to filter - pattern: "*.{vcf}" - - minsv: - type: integer - description: Min SV size (-1 to disable) - - maxsv: - type: integer - description: Max SV size (-1 to disable) - - minnumreads: - type: integer - description: Min number of reads support [RE flag (-1 to disable)] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file to filter + pattern: "*.{vcf}" + - - minsv: + type: integer + description: Min SV size (-1 to disable) + - - maxsv: + type: integer + description: Max SV size (-1 to disable) + - - minnumreads: + type: integer + description: Min number of reads support [RE flag (-1 to disable)] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: File containing statistics given input VCF file - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing statistics given input VCF file + pattern: "*.{stats}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/svaba/meta.yml b/modules/nf-core/svaba/meta.yml index d78ea0e8c99..24753c6a56a 100644 --- a/modules/nf-core/svaba/meta.yml +++ b/modules/nf-core/svaba/meta.yml @@ -1,5 +1,6 @@ name: "svaba" -description: SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements +description: SvABA is an efficient and accurate method for detecting SVs from short-read + sequencing data using genome-wide local assembly with low memory and computing requirements keywords: - sv - structural variants @@ -13,147 +14,248 @@ tools: tool_dev_url: "https://github.com/walaj/svaba" doi: "10.1101/gr.221028.117" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: should be the identification number or sample name. If there is normal file meta should be common - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing FASTA information - id: should be the identification number for alignment file and should be the same used to create BWA index files - e.g. [ id:'fasta' ] - - meta3: - type: map - description: | - Groovy Map containing BWA information - id: should be the identification number same as fasta file - e.g. [ id:'bwa' ] - - meta4: - type: map - description: | - Groovy Map containing dbSNP information - id: should be the identification number for dbSNP files - e.g. [ id:'test' ] - - meta5: - type: map - description: | - Groovy Map containing regions information - id: should be the identification number for regions - e.g. [ id:'test' ] - - tumorbam: - type: file - description: Tumor or metastatic sample, BAM, SAM or CRAM file - pattern: "*.{bam,cram,sam}" - - tummorbai: - type: file - description: Index - pattern: "*.{bai,crai,sai}" - - normalbam: - type: file - description: Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file - pattern: "*.{bam,cram,sam}" - - normalbai: - type: file - description: Index - pattern: "*.{bai,crai,sai}" - - bwa_index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta|fa}" - - fasta_fai: - type: file - description: Index of FASTA file - pattern: "*.{fai}" - - dbsnp: - type: file - description: VCF file including dbSNP variants - pattern: "*.vcf.gz" - - dbsnp_tbi: - type: file - description: Index of VCF file including dbSNP variants - pattern: "*.vcf.gz.tbi" - - regions: - type: file - description: Targeted intervals. Accepts BED file or Samtools-style string - pattern: "*.bed|*.txt|*.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + id: should be the identification number or sample name. If there is normal file meta should be common + e.g. [ id:'test' ] + - tumorbam: + type: file + description: Tumor or metastatic sample, BAM, SAM or CRAM file + pattern: "*.{bam,cram,sam}" + - tumorbai: + type: file + description: Index of the tumor or metastatic sample + pattern: "*.{bai,crai,sai}" + - normalbam: + type: file + description: Control (or normal) of matching tumor/metastatic sample, BAM, SAM + or CRAM file + pattern: "*.{bam,cram,sam}" + - normalbai: + type: file + description: Index + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing FASTA information + id: should be the identification number for alignment file and should be the same used to create BWA index files + e.g. [ id:'fasta' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta|fa}" + - - meta2: + type: map + description: | + Groovy Map containing FASTA information + id: should be the identification number for alignment file and should be the same used to create BWA index files + e.g. [ id:'fasta' ] + - fasta_fai: + type: file + description: Index of FASTA file + pattern: "*.{fai}" + - - meta3: + type: map + description: | + Groovy Map containing BWA information + id: should be the identification number same as fasta file + e.g. [ id:'bwa' ] + - bwa_index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta4: + type: map + description: | + Groovy Map containing dbSNP information + id: should be the identification number for dbSNP files + e.g. [ id:'test' ] + - dbsnp: + type: file + description: VCF file including dbSNP variants + pattern: "*.vcf.gz" + - - meta4: + type: map + description: | + Groovy Map containing dbSNP information + id: should be the identification number for dbSNP files + e.g. [ id:'test' ] + - dbsnp_tbi: + type: file + description: Index of VCF file including dbSNP variants + pattern: "*.vcf.gz.tbi" + - - meta5: + type: map + description: | + Groovy Map containing regions information + id: should be the identification number for regions + e.g. [ id:'test' ] + - regions: + type: file + description: Targeted intervals. Accepts BED file or Samtools-style string + pattern: "*.bed|*.txt|*.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sv: - type: file - description: Filtered SVs for tumor only cases - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.sv.vcf.gz": + type: file + description: Filtered SVs for tumor only cases + pattern: "*.vcf.gz" - indel: - type: file - description: Filtered Indels for tumor only cases - pattern: "*.vcf.gz" - - som_sv: - type: file - description: Somatic filtered SVs for tumor/normal paired samples - pattern: "*.vcf.gz" - - som_indel: - type: file - description: Somatic filtered Indels for tumor/normal paired samples - pattern: "*.vcf.gz" - - germ_sv: - type: file - description: Germline filtered SVs for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.indel.vcf.gz": + type: file + description: Filtered Indels for tumor only cases + pattern: "*.vcf.gz" - germ_indel: - type: file - description: Germline filtered Indels for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.germline.indel.vcf.gz": + type: file + description: Germline filtered Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - germ_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.germline.sv.vcf.gz": + type: file + description: Germline filtered SVs for tumor/normal paired samples + pattern: "*.vcf.gz" + - som_indel: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.somatic.indel.vcf.gz": + type: file + description: Somatic filtered Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - som_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.somatic.sv.vcf.gz": + type: file + description: Somatic filtered SVs for tumor/normal paired samples + pattern: "*.vcf.gz" - unfiltered_sv: - type: file - description: Unfiltered SVs for tumor only cases - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.sv.vcf.gz": + type: file + description: Unfiltered SVs for tumor only cases + pattern: "*.vcf.gz" - unfiltered_indel: - type: file - description: Unfiltered Indels for tumor only cases - pattern: "*.vcf.gz" - - unfiltered_som_sv: - type: file - description: Unfiltered somatic SVs for tumor/normal paired samples - pattern: "*.vcf.gz" - - unfiltered_som_indel: - type: file - description: Unfiltered somatic Indels for tumor/normal paired samples - pattern: "*.vcf.gz" - - unfiltered_germ_sv: - type: file - description: Unfiltered germline SVs for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.indel.vcf.gz": + type: file + description: Unfiltered Indels for tumor only cases + pattern: "*.vcf.gz" - unfiltered_germ_indel: - type: file - description: Unfiltered germline Indels for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.germline.indel.vcf.gz": + type: file + description: Unfiltered germline Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - unfiltered_germ_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.germline.sv.vcf.gz": + type: file + description: Unfiltered germline SVs for tumor/normal paired samples + pattern: "*.vcf.gz" + - unfiltered_som_indel: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.somatic.indel.vcf.gz": + type: file + description: Unfiltered somatic Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - unfiltered_som_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.somatic.sv.vcf.gz": + type: file + description: Unfiltered somatic SVs for tumor/normal paired samples + pattern: "*.vcf.gz" - raw_calls: - type: file - description: Raw, unfiltered variants - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bps.txt.gz": + type: file + description: Raw, unfiltered variants + pattern: "*.txt.gz" - discordants: - type: file - description: Information on all clusters of discordant reads identified with 2+ reads - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.discordants.txt.gz": + type: file + description: Information on all clusters of discordant reads identified with + 2+ reads + pattern: "*.txt.gz" - log: - type: file - description: Log file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: Log file + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/svanalyzer/svbenchmark/meta.yml b/modules/nf-core/svanalyzer/svbenchmark/meta.yml index c8a76ac1996..8f5d652bbdf 100644 --- a/modules/nf-core/svanalyzer/svbenchmark/meta.yml +++ b/modules/nf-core/svanalyzer/svbenchmark/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "svanalyzer_svbenchmark" -description: "SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity." +description: "SVbenchmark compares a set of “test” structural variants in VCF format + to a known truth set (also in VCF format) and outputs estimates of sensitivity and + specificity." keywords: - structural variant - sv @@ -14,75 +15,110 @@ tools: tool_dev_url: "https://github.com/nhansen/SVanalyzer" license: "['CC0']" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing test sample information - e.g. `[ id:'test' ]` - - meta2: - type: map - description: | - Groovy Map containing reference genome information for fasta - e.g. `[ id:'test2' ]` - - meta3: - type: map - description: | - Groovy Map containing reference genome information for fai - e.g. `[ id:'test3' ]` - - test: - type: file - description: A VCF-formatted file of structural variants to test (required) - pattern: "*.{vcf,vcf.gz}" - - test_tbi: - type: file - description: A VCF-formatted file index of structural variants to test only for zipped files - pattern: "*.{vcf.gz.tbi}" - - truth: - type: file - description: A VCF-formatted file of variants to compare against (required) - pattern: "*.{vcf,vcf.gz}" - - truth_tbi: - type: file - description: A VCF-formatted file of variants to compare against only for zipped files - pattern: "*.{vcf.gz.tbi}" - - fasta: - type: file - description: The reference FASTA file for the supplied VCF file or files (required) - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - bed: - type: file - description: BED File of regions from which to include variants. Used to filter both test and truth variants. - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing test sample information + e.g. `[ id:'test' ]` + - test: + type: file + description: A VCF-formatted file of structural variants to test (required) + pattern: "*.{vcf,vcf.gz}" + - test_tbi: + type: file + description: A VCF-formatted file index of structural variants to test only + for zipped files + pattern: "*.{vcf.gz.tbi}" + - truth: + type: file + description: A VCF-formatted file of variants to compare against (required) + pattern: "*.{vcf,vcf.gz}" + - truth_tbi: + type: file + description: A VCF-formatted file of variants to compare against only for zipped + files + pattern: "*.{vcf.gz.tbi}" + - bed: + type: file + description: BED File of regions from which to include variants. Used to filter + both test and truth variants. + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing reference genome information for fasta + e.g. `[ id:'test2' ]` + - fasta: + type: file + description: The reference FASTA file for the supplied VCF file or files (required) + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta3: + type: map + description: | + Groovy Map containing reference genome information for fai + e.g. `[ id:'test3' ]` + - fai: + type: file + description: The reference FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information inherited from test vcf - e.g. `[ id:'test']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fns: - type: file - description: VCF file with False Negatives - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.falsenegatives.vcf.gz": + type: file + description: VCF file with False Negatives + pattern: "*.{vcf.gz}" - fps: - type: file - description: VCF file with False Positives - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.falsepositives.vcf.gz": + type: file + description: VCF file with False Positives + pattern: "*.{vcf.gz}" - distances: - type: file - description: TSV file with genomic distances and size differences between structural variants compared - pattern: "*.{distances}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.distances": + type: file + description: TSV file with genomic distances and size differences between structural + variants compared + pattern: "*.{distances}" - log: - type: file - description: LOG file of the run - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.log": + type: file + description: LOG file of the run + pattern: "*.{log}" - report: - type: file - description: Text file reporting RECALL, PRECISION and F1. - pattern: "*.{report}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.report": + type: file + description: Text file reporting RECALL, PRECISION and F1. + pattern: "*.{report}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/svdb/build/meta.yml b/modules/nf-core/svdb/build/meta.yml index c5c5a99265d..dd3789d43f4 100644 --- a/modules/nf-core/svdb/build/meta.yml +++ b/modules/nf-core/svdb/build/meta.yml @@ -10,29 +10,35 @@ tools: homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input VCF file(s) or folder - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input VCF file(s) or folder + pattern: "*" + - - input_type: + type: string + description: input type output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: SVDB database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.db": + type: file + description: SVDB database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index bf44cd967b3..f725b65248d 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - - svdb=2.8.1 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.19.2 - htslib=1.19.1 + - samtools=1.19.2 + - svdb=2.8.1 diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml index e53e61fe743..7dc7c67588a 100644 --- a/modules/nf-core/svdb/merge/meta.yml +++ b/modules/nf-core/svdb/merge/meta.yml @@ -10,33 +10,37 @@ tools: homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - priority: - type: list - description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator'] - - vcfs: - type: list - description: Two or more VCF files. Order of files should correspond to the order of tags used for priority. - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcfs: + type: list + description: Two or more VCF files. Order of files should correspond to the + order of tags used for priority. + pattern: "*.{vcf,vcf.gz}" + - - priority: + type: list + description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator'] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: merged VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: merged VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/svdb/query/meta.yml b/modules/nf-core/svdb/query/meta.yml index d11c51e6412..f8cd33c8d80 100644 --- a/modules/nf-core/svdb/query/meta.yml +++ b/modules/nf-core/svdb/query/meta.yml @@ -10,52 +10,54 @@ tools: homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - in_occs: - type: list - description: A list of allele count tags - - in_frqs: - type: list - description: A list of allele frequency tags - - vcf: - type: file - description: query vcf file - pattern: "*.{vcf,vcf.gz}" - - vcf_dbs: - type: file - description: path to a database vcf, or a comma separated list of vcfs - pattern: "*.{vcf,vcf.gz}" - - bedpe_dbs: - type: file - description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files - pattern: "*.{bedpe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: query vcf file + pattern: "*.{vcf,vcf.gz}" + - - in_occs: + type: list + description: A list of allele count tags + - - in_frqs: + type: list + description: A list of allele frequency tags + - - out_occs: + type: list + description: A list of allele count tags + - - out_frqs: + type: list + description: A list of allele frequency tags + - - vcf_dbs: + type: file + description: path to a database vcf, or a comma separated list of vcfs + pattern: "*.{vcf,vcf.gz}" + - - bedpe_dbs: + type: file + description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, + or a comma separated list of files + pattern: "*.{bedpe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - out_occs: - type: list - description: A list of allele count tags - - out_frqs: - type: list - description: A list of allele frequency tags - vcf: - type: file - description: Annotated output VCF file - pattern: "*_query.vcf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_query.vcf": + type: file + description: Annotated output VCF file + pattern: "*_query.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" diff --git a/modules/nf-core/svtk/baftest/meta.yml b/modules/nf-core/svtk/baftest/meta.yml index fcae45bd8dd..1d1519317b9 100644 --- a/modules/nf-core/svtk/baftest/meta.yml +++ b/modules/nf-core/svtk/baftest/meta.yml @@ -9,47 +9,51 @@ keywords: - structural variants tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: A BED file created with `svtk vcf2bed` - pattern: "*.bed" - - baf: - type: file - description: A BAF file created with `gatk PrintSVEvidence` - pattern: "*.baf.txt.gz" - - baf_index: - type: file - description: The index of the BAF file - pattern: "*.baf.txt.gz.tbi" - - batch: - type: file - description: A text file containing information about the sample(s) - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: A BED file created with `svtk vcf2bed` + pattern: "*.bed" + - baf: + type: file + description: A BAF file created with `gatk PrintSVEvidence` + pattern: "*.baf.txt.gz" + - baf_index: + type: file + description: The index of the BAF file + pattern: "*.baf.txt.gz.tbi" + - batch: + type: file + description: A text file containing information about the sample(s) + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - metrics: - type: file - description: The results file from the BAF test - pattern: "*.metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: The results file from the BAF test + pattern: "*.metrics" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/countsvtypes/meta.yml b/modules/nf-core/svtk/countsvtypes/meta.yml index bc398ec1e72..70b333899f8 100644 --- a/modules/nf-core/svtk/countsvtypes/meta.yml +++ b/modules/nf-core/svtk/countsvtypes/meta.yml @@ -7,36 +7,40 @@ keywords: - structural variants tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" doi: "10.1038/s41586-020-2287-8" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF file containing structural variants - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF file containing structural variants + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - counts: - type: file - description: A tab-delimited file containing the counts of the SV types - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A tab-delimited file containing the counts of the SV types + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/rdtest2vcf/meta.yml b/modules/nf-core/svtk/rdtest2vcf/meta.yml index c1851f5738d..8a702f9f82f 100644 --- a/modules/nf-core/svtk/rdtest2vcf/meta.yml +++ b/modules/nf-core/svtk/rdtest2vcf/meta.yml @@ -8,48 +8,59 @@ keywords: - vcf tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" doi: "10.1038/s41586-020-2287-8" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: An RdTest-formatted bed - pattern: "*.bed" - - samples: - type: file - description: A text file containing the names of all samples that need to be added to the VCF - pattern: "*.txt" - - fasta_fai: - type: file - description: The reference file of a FASTA file containing the contigs - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: An RdTest-formatted bed + pattern: "*.bed" + - samples: + type: file + description: A text file containing the names of all samples that need to be + added to the VCF + pattern: "*.txt" + - - fasta_fai: + type: file + description: The reference file of a FASTA file containing the contigs + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The converted VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The converted VCF + pattern: "*.vcf.gz" - tbi: - type: file - description: The index of the converted VCF - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: The index of the converted VCF + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/standardize/meta.yml b/modules/nf-core/svtk/standardize/meta.yml index e0d35cf4dde..84090cbacdd 100644 --- a/modules/nf-core/svtk/standardize/meta.yml +++ b/modules/nf-core/svtk/standardize/meta.yml @@ -8,51 +8,44 @@ keywords: - standardization tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" licence: ["MIT"] + identifier: "" input: - - args: - type: map - description: | - Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. - ``` - { - [ - "args": "", - "caller": "delly" // Should be either delly, lumpy, manta, wham or melt - ] - } - ``` - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A gzipped VCF file to be standardized - pattern: "*.vcf.gz" - - fasta_fai: - type: file - description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: A gzipped VCF file to be standardized + pattern: "*.vcf.gz" + - - fasta_fai: + type: file + description: Optional fasta index file that specifies the contigs to be used + in the VCF header (defaults to all contigs of GRCh37) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - standardized_vcf: - type: file - description: A gzipped version of the standardized VCF file - pattern: "*.std.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.std.vcf.gz": + type: file + description: A gzipped version of the standardized VCF file + pattern: "*.std.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/vcf2bed/meta.yml b/modules/nf-core/svtk/vcf2bed/meta.yml index 4b1d2e63e13..7cc6d23362b 100644 --- a/modules/nf-core/svtk/vcf2bed/meta.yml +++ b/modules/nf-core/svtk/vcf2bed/meta.yml @@ -8,39 +8,43 @@ keywords: - structural variants tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A VCF file created with a structural variant caller - pattern: "*.vcf.gz" - - tbi: - type: file - description: The index for the VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: A VCF file created with a structural variant caller + pattern: "*.vcf.gz" + - tbi: + type: file + description: The index for the VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: The created BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: The created BED file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtyper/svtyper/meta.yml b/modules/nf-core/svtyper/svtyper/meta.yml index 2184620d36b..6846e2ec722 100644 --- a/modules/nf-core/svtyper/svtyper/meta.yml +++ b/modules/nf-core/svtyper/svtyper/meta.yml @@ -1,5 +1,6 @@ name: "svtyper_svtyper" -description: SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data +description: SVTyper performs breakpoint genotyping of structural variants (SVs) using + whole genome sequencing data keywords: - sv - structural variants @@ -12,55 +13,79 @@ tools: tool_dev_url: "https://github.com/hall-lab/svtyper" doi: "10.1038/nmeth.3505" licence: ["MIT"] + identifier: biotools:svtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing sample information for FASTA file - e.g. [ id:'fasta'] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - vcf: - type: file - description: Matching VCF of alignments - pattern: "*.vcf" - - fasta: - type: file - description: FASTA file used to generate alignments - pattern: "*.{fa,fasta}" - - fai: - type: file - description: FAI file used to generate alignments - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bam_index: + type: file + description: Index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - vcf: + type: file + description: Matching VCF of alignments + pattern: "*.vcf" + - - meta2: + type: map + description: | + Groovy Map containing sample information for FASTA file + e.g. [ id:'fasta'] + - fasta: + type: file + description: FASTA file used to generate alignments + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information for FASTA file + e.g. [ id:'fasta'] + - fai: + type: file + description: FAI file used to generate alignments + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON file including Library information - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: JSON file including Library information + pattern: "*.json" - gt_vcf: - type: file - description: Genotyped SVs - pattern: "*.vcf" - - relevant_bam: - type: file - description: Relevant alignments - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: Genotyped SVs + pattern: "*.vcf" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: BAM file with + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/svtyper/svtypersso/meta.yml b/modules/nf-core/svtyper/svtypersso/meta.yml index edbf8e3ce5c..d89b1035fa3 100644 --- a/modules/nf-core/svtyper/svtypersso/meta.yml +++ b/modules/nf-core/svtyper/svtypersso/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "svtyper_svtypersso" -description: SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample +description: SVTyper-sso computes structural variant (SV) genotypes based on breakpoint + depth on a SINGLE sample keywords: - sv - structural variants @@ -15,53 +15,61 @@ tools: tool_dev_url: "https://github.com/hall-lab/svtyper" doi: "10.1038/nmeth.3505" licence: ["MIT"] + identifier: biotools:svtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing sample information for reference FASTA file - e.g. [ id:'fasta'] - - bam: - type: file - description: BAM or CRAM file with alignments - pattern: "*.{bam,cram}" - - bam_index: - type: file - description: BAI file matching the BAM file - pattern: "*.{bai}" - - vcf: - type: file - description: Matching VCF of alignments - pattern: "*.vcf" - - fasta: - type: file - description: indexed reference FASTA file (recommended for reading CRAM files) - pattern: "*.{fa,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: BAM or CRAM file with alignments + pattern: "*.{bam,cram}" + - bam_index: + type: file + description: BAI file matching the BAM file + pattern: "*.{bai}" + - vcf: + type: file + description: Matching VCF of alignments + pattern: "*.vcf" + - - meta2: + type: map + description: | + Groovy Map containing sample information for reference FASTA file + e.g. [ id:'fasta'] + - fasta: + type: file + description: indexed reference FASTA file (recommended for reading CRAM files) + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - json: - type: file - description: JSON file including library information - pattern: "*.json" - gt_vcf: - type: file - description: Genotyped SVs - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: Genotyped SVs + pattern: "*.vcf" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: JSON file including library information + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tstoeriko" maintainers: diff --git a/modules/nf-core/svync/meta.yml b/modules/nf-core/svync/meta.yml index dacc5738ba5..cad35715cdd 100644 --- a/modules/nf-core/svync/meta.yml +++ b/modules/nf-core/svync/meta.yml @@ -1,4 +1,3 @@ ---- name: "svync" description: A tool to standardize VCF files from structural variant callers keywords: @@ -14,41 +13,42 @@ tools: documentation: "https://github.com/nvnieuwk/svync" tool_dev_url: "https://github.com/nvnieuwk/svync" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: The input VCF file containing structural variants - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: The index of the input VCF file containing structural variants - pattern: "*.tbi" - - config: - type: file - description: The config stating how the standardization should happen - pattern: "*.{yml,yaml}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: The input VCF file containing structural variants + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: The index of the input VCF file containing structural variants + pattern: "*.tbi" + - config: + type: file + description: The config stating how the standardization should happen + pattern: "*.{yml,yaml}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The standardized VCF file - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: The standardized VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index c863e9207c0..017c259da1c 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml index 621d49ea0ea..131e92cfdbd 100644 --- a/modules/nf-core/tabix/bgzip/meta.yml +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -13,33 +13,42 @@ tools: documentation: http://www.htslib.org/doc/bgzip.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: file to compress or to decompress + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: file to compress or to decompress output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Output compressed/decompressed file - pattern: "*." + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: Output compressed/decompressed file + pattern: "*." - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}.gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index c863e9207c0..017c259da1c 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 438aba4d18d..806fbc121fc 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -13,38 +13,50 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file - pattern: "*.{bed,gff,sam,vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Sorted tab-delimited genome file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gz: - type: file - description: Output compressed file - pattern: "*.{gz}" - - tbi: - type: file - description: tabix index file - pattern: "*.{gz.tbi}" - - csi: - type: file - description: tabix alternate index file - pattern: "*.{gz.csi}" + - gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.tbi": + type: file + description: tabix index file + pattern: "*.tbi" + - gz_csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.csi": + type: file + description: csi index file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@DLBPointon" diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index ae5b4f439f1..7864832d93c 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -11,34 +11,43 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file compressed with bgzip - pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tab: + type: file + description: TAB-delimited genome position file compressed with bgzip + pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: tabix index file + pattern: "*.{tbi}" - csi: - type: file - description: coordinate sorted index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: coordinate sorted index file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tailfindr/meta.yml b/modules/nf-core/tailfindr/meta.yml index 47cc2a37020..f221e0fc4e7 100644 --- a/modules/nf-core/tailfindr/meta.yml +++ b/modules/nf-core/tailfindr/meta.yml @@ -1,41 +1,46 @@ name: "tailfindr" -description: Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA +description: Estimating poly(A)-tail lengths from basecalled fast5 files produced + by Nanopore sequencing of RNA and DNA keywords: - polya tail - fast5 - nanopore tools: - "tailfindr": - description: "An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads." + description: "An R package for estimating poly(A)-tail lengths in Oxford Nanopore + RNA and DNA reads." homepage: "https://github.com/adnaniazi/tailfindr" documentation: "https://github.com/adnaniazi/tailfindr/blob/master/README.md" tool_dev_url: "https://github.com/adnaniazi/tailfindr" doi: "10.1261/rna.071332.119" licence: ["AGPL v3"] + identifier: biotools:tailfindr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fast5: - type: file - description: fast5 file - pattern: "*.fast5" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fast5: + type: file + description: fast5 file + pattern: "*.fast5" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv_gz: - type: file - description: Compressed csv file - pattern: "*.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.csv.gz": + type: file + description: Compressed csv file + pattern: "*.csv.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucacozzuto" maintainers: diff --git a/modules/nf-core/taxonkit/name2taxid/meta.yml b/modules/nf-core/taxonkit/name2taxid/meta.yml index e96c8993ac7..7a8d16e801e 100644 --- a/modules/nf-core/taxonkit/name2taxid/meta.yml +++ b/modules/nf-core/taxonkit/name2taxid/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "taxonkit_name2taxid" description: Convert taxon names to TaxIds @@ -15,38 +14,40 @@ tools: tool_dev_url: "https://github.com/shenwei356/taxonkit" doi: "10.1016/j.jgg.2021.03.006" licence: ["MIT"] + identifier: biotools:taxonkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - name: - type: string - description: Taxon name to look up (provide either this or names.txt, not both) - - names_txt: - type: file - description: File with taxon names to look up, each on their own line (provide either this or name, not both) - - taxdb: - type: file - description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - name: + type: string + description: Taxon name to look up (provide either this or names.txt, not both) + - names_txt: + type: file + description: File with taxon names to look up, each on their own line (provide + either this or name, not both) + - - taxdb: + type: file + description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file of Taxon names and their taxon ID - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: TSV file of Taxon names and their taxon ID + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/taxpasta/merge/meta.yml b/modules/nf-core/taxpasta/merge/meta.yml index a4cbed946c1..5e2d7ab0d15 100644 --- a/modules/nf-core/taxpasta/merge/meta.yml +++ b/modules/nf-core/taxpasta/merge/meta.yml @@ -15,46 +15,55 @@ tools: documentation: "https://taxpasta.readthedocs.io/" tool_dev_url: "https://github.com/taxprofiler/taxpasta" licence: ["Apache-2.0"] + identifier: biotools:taxpasta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profiles: - type: file - description: A list of taxonomic profiler output files (typically in text format, mandatory) - pattern: "*.{tsv,csv,arrow,parquet,biom}" - - profiler: - type: string - description: Name of the profiler used to generate the profile (mandatory) - pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" - - format: - type: string - description: Type of output file to be generated - pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" - - taxonomy: - type: directory - description: Directory containing at a minimum nodes.dmp and names.dmp files (optional) - pattern: "*/" - - samplesheet: - type: file - description: A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the Nextflow work directory of the executed process. The profiles must be provided even if you give a samplesheet as argument (optional) - pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profiles: + type: file + description: A list of taxonomic profiler output files (typically in text format, + mandatory) + pattern: "*.{tsv,csv,arrow,parquet,biom}" + - - profiler: + type: string + description: Name of the profiler used to generate the profile (mandatory) + pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + - - format: + type: string + description: Type of output file to be generated + pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" + - - taxonomy: + type: directory + description: Directory containing at a minimum nodes.dmp and names.dmp files + (optional) + pattern: "*/" + - - samplesheet: + type: file + description: A samplesheet describing the sample name and a filepath to a taxonomic + abundance profile that needs to be relative from the Nextflow work directory + of the executed process. The profiles must be provided even if you give a + samplesheet as argument (optional) + pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_profiles: - type: file - description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table. - pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tsv,csv,arrow,parquet,biom}": + type: file + description: Output file with standardised multiple profiles in one go and have + all profiles combined into a single table. + pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@jfy133" diff --git a/modules/nf-core/taxpasta/standardise/meta.yml b/modules/nf-core/taxpasta/standardise/meta.yml index b855905a7ce..ca7a28ecad8 100644 --- a/modules/nf-core/taxpasta/standardise/meta.yml +++ b/modules/nf-core/taxpasta/standardise/meta.yml @@ -15,42 +15,46 @@ tools: documentation: "https://taxpasta.readthedocs.io/" tool_dev_url: "https://github.com/taxprofiler/taxpasta" licence: ["Apache-2.0"] + identifier: biotools:taxpasta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profile: - type: file - description: profiler output file (mandatory) - pattern: "*" - - profiler: - type: string - description: Name of the profiler used to generate the profile (mandatory) - pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" - - format: - type: string - description: Type of output file to be generated - pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" - - taxonomy: - type: directory - description: Directory containing at a minimum nodes.dmp and names.dmp files (optional) - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profile: + type: file + description: profiler output file (mandatory) + pattern: "*" + - - profiler: + type: string + description: Name of the profiler used to generate the profile (mandatory) + pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + - - format: + type: string + description: Type of output file to be generated + pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" + - - taxonomy: + type: directory + description: Directory containing at a minimum nodes.dmp and names.dmp files + (optional) + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - standardised_profile: - type: file - description: Standardised taxonomic profile - pattern: "*.{tsv,csv,arrow,parquet,biom}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tsv,csv,arrow,parquet,biom}": + type: file + description: Standardised taxonomic profile + pattern: "*.{tsv,csv,arrow,parquet,biom}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/tbprofiler/profile/meta.yml b/modules/nf-core/tbprofiler/profile/meta.yml index a53aa3e3bc7..98989dda107 100644 --- a/modules/nf-core/tbprofiler/profile/meta.yml +++ b/modules/nf-core/tbprofiler/profile/meta.yml @@ -6,52 +6,80 @@ keywords: - serotype tools: - tbprofiler: - description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data + description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance + and lineage from WGS data homepage: https://github.com/jodyphelan/TBProfiler documentation: https://jodyphelan.gitbook.io/tb-profiler/ tool_dev_url: https://github.com/jodyphelan/TBProfiler doi: "10.1186/s13073-019-0650-x" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file - pattern: "*.{fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file + pattern: "*.{fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with alignment details - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam/*.bam: + type: file + description: BAM file with alignment details + pattern: "*.bam" - csv: - type: file - description: Optional CSV formated result file of resistance and strain type - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.csv: + type: file + description: Optional CSV formated result file of resistance and strain type + pattern: "*.csv" - json: - type: file - description: JSON formated result file of resistance and strain type - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.json: + type: file + description: JSON formated result file of resistance and strain type + pattern: "*.json" - txt: - type: file - description: Optional text file of resistance and strain type - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.txt: + type: file + description: Optional text file of resistance and strain type + pattern: "*.txt" - vcf: - type: file - description: VCF with variant info again refernce genomes - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf/*.vcf.gz: + type: file + description: VCF with variant info again refernce genomes + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/tcoffee/align/meta.yml b/modules/nf-core/tcoffee/align/meta.yml index 4125d1ed2c2..518be2b39d5 100644 --- a/modules/nf-core/tcoffee/align/meta.yml +++ b/modules/nf-core/tcoffee/align/meta.yml @@ -6,69 +6,84 @@ keywords: - genomics tools: - "tcoffee": - description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - meta3: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_infos']` - - template: - type: file - description: T_coffee template file that maps sequences to the accessory information files to be used. - pattern: "*" - - accessory_informations: - type: file - description: Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures. - pattern: "*" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - meta3: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_infos']` + - template: + type: file + description: T_coffee template file that maps sequences to the accessory information + files to be used. + pattern: "*" + - accessory_informations: + type: file + description: Accessory files to be used in the alignment. For example, it could + be protein structures or secondary structures. + pattern: "*" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file in FASTA format. May be gzipped. - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file in FASTA format. May be gzipped. + pattern: "*.aln{.gz,}" - lib: - type: file - description: optional output, the library generated from the MSA file. - pattern: "*.*lib" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.*lib": + type: file + description: optional output, the library generated from the MSA file. + pattern: "*.*lib" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/tcoffee/alncompare/meta.yml b/modules/nf-core/tcoffee/alncompare/meta.yml index 31502555d9e..0dd0c9ee97a 100644 --- a/modules/nf-core/tcoffee/alncompare/meta.yml +++ b/modules/nf-core/tcoffee/alncompare/meta.yml @@ -6,47 +6,52 @@ keywords: - evaluation tools: - "tcoffee": - description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence" + description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein + Sequence" homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', ... ] - - msa: - type: file - description: fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - - ref_msa: - type: file - description: fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', ... ] + - msa: + type: file + description: fasta file containing the alignment to be evaluated. Can be gzipped + or uncompressed + pattern: "*.{aln,fa,fasta,fas}{.gz,}" + - ref_msa: + type: file + description: fasta file containing the reference alignment used for the evaluation. + Can be gzipped or uncompressed + pattern: "*.{aln,fa,fasta,fas}{.gz,}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scores: - type: file - description: a file containing the score of the alignment - pattern: "*.scores" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.scores": + type: file + description: a file containing the score of the alignment + pattern: "*.scores" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@l-mansouri" - "@luisas" diff --git a/modules/nf-core/tcoffee/consensus/meta.yml b/modules/nf-core/tcoffee/consensus/meta.yml index 54d608300a0..c485e06a41d 100644 --- a/modules/nf-core/tcoffee/consensus/meta.yml +++ b/modules/nf-core/tcoffee/consensus/meta.yml @@ -6,57 +6,61 @@ keywords: - genomics tools: - tcoffee: - description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - pigz: description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - aln: - type: file - description: List of multiple sequence alignments in FASTA format to be used to compute the consensus - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - aln: + type: file + description: List of multiple sequence alignments in FASTA format to be used + to compute the consensus + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - alignment: - type: file - description: Consensus alignment in FASTA format - pattern: "*.{fa,fasta,aln}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.{aln,aln.gz}": + type: file + description: Consensus alignment in FASTA format + pattern: "*.{fa,fasta,aln}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/tcoffee/irmsd/meta.yml b/modules/nf-core/tcoffee/irmsd/meta.yml index e13e7ddadf3..cf930ea038b 100644 --- a/modules/nf-core/tcoffee/irmsd/meta.yml +++ b/modules/nf-core/tcoffee/irmsd/meta.yml @@ -6,58 +6,46 @@ keywords: - evaluation tools: - "tcoffee": - description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence" + description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein + Sequence" homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', ... ] - - msa: - type: file - description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - - - meta2: - type: map - description: | - Groovy Map containing information about the structures - e.g. [ id:'test', ... ] - - - template: - type: file - description: Template file matching the structures to the sequences in the alignment. - pattern: "*" - - - structures: - type: directory - description: Directory containing the structures file matching the sequences in the alignment in PDB format - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', ... ] + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - irmsd: - type: file - description: File containing the irmsd of the alignment - pattern: "*" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.irmsd: + type: file + description: File containing the irmsd of the alignment + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" diff --git a/modules/nf-core/tcoffee/seqreformat/meta.yml b/modules/nf-core/tcoffee/seqreformat/meta.yml index 0571c7d875d..17111df376d 100644 --- a/modules/nf-core/tcoffee/seqreformat/meta.yml +++ b/modules/nf-core/tcoffee/seqreformat/meta.yml @@ -6,41 +6,39 @@ keywords: - genomics tools: - "tcoffee": - description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - - infile: - type: file - description: Input file to be reformatted - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - infile: + type: file + description: Input file to be reformatted output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - formatted_file: - type: file - description: Formatted file - pattern: "*" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.txt: + type: file + description: Formatted file + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml index 26a17e70983..615d140e6bb 100644 --- a/modules/nf-core/tcoffee/tcs/environment.yml +++ b/modules/nf-core/tcoffee/tcs/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::t-coffee=13.46.0.919e8c6b + - "bioconda::t-coffee=13.46.0.919e8c6b" - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/tcs/meta.yml b/modules/nf-core/tcoffee/tcs/meta.yml index 7a13e79a8b6..2846d4ba188 100644 --- a/modules/nf-core/tcoffee/tcs/meta.yml +++ b/modules/nf-core/tcoffee/tcs/meta.yml @@ -1,62 +1,72 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tcoffee_tcs" -description: Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score. +description: Compute the TCS score for a MSA or for a MSA plus a library file. Outputs + the tcs as it is and a csv with just the total TCS score. keywords: - alignment - MSA - evaluation tools: - "tcoffee": - description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence" + description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein + Sequence" homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', ... ] - - msa: - type: file - description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - - meta2: - type: map - description: | - Groovy Map containing library information - e.g. [ id:'test', ... ] - - lib: - type: file - description: lib file containing the alignment library of the given msa. - pattern: "*{.tc_lib,*_lib}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', ... ] + - msa: + type: file + description: fasta file containing the alignment to be evaluated. May be gzipped + or uncompressed. + pattern: "*.{aln,fa,fasta,fas}{.gz,}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - lib: + type: file + description: lib file containing the alignment library of the given msa. + pattern: "*{.tc_lib,*_lib}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tcs: - type: file - description: The msa represented in tcs format, prepended with TCS scores - pattern: "*.tcs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tcs": + type: file + description: The msa represented in tcs format, prepended with TCS scores + pattern: "*.tcs" - scores: - type: file - description: a file containing the score of the alignment in csv format - pattern: "*.scores" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.scores": + type: file + description: a file containing the score of the alignment in csv format + pattern: "*.scores" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alessiovignoli" diff --git a/modules/nf-core/thermorawfileparser/meta.yml b/modules/nf-core/thermorawfileparser/meta.yml index 5c604c63cf2..7235bc31ac5 100644 --- a/modules/nf-core/thermorawfileparser/meta.yml +++ b/modules/nf-core/thermorawfileparser/meta.yml @@ -9,39 +9,41 @@ keywords: - proteomics tools: - thermorawfileparser: - description: "Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono" + description: "Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library + for running on Linux with mono" homepage: "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md" documentation: "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md" tool_dev_url: "https://github.com/compomics/ThermoRawFileParser" doi: "10.1021/acs.jproteome.9b00328" licence: ["Apache Software"] + identifier: biotools:ThermoRawFileParser input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - raw: - type: file - description: Thermo RAW file - pattern: "*.{raw,RAW}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - raw: + type: file + description: Thermo RAW file + pattern: "*.{raw,RAW}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spectra: - type: file - description: Mass spectra in open format - pattern: "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}": + type: file + description: Mass spectra in open format + pattern: "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/tiara/tiara/meta.yml b/modules/nf-core/tiara/tiara/meta.yml index e9d6b0553d7..8d86ae9fde5 100644 --- a/modules/nf-core/tiara/tiara/meta.yml +++ b/modules/nf-core/tiara/tiara/meta.yml @@ -1,50 +1,69 @@ name: "tiara_tiara" -description: Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle +description: Domain-level classification of contigs to bacterial, archaeal, eukaryotic, + or organelle keywords: - contigs - metagenomics - classify tools: - "tiara": - description: "Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch." + description: "Deep-learning-based approach for identification of eukaryotic sequences + in the metagenomic data powered by PyTorch." homepage: "https://ibe-uw.github.io/tiara/" documentation: https://ibe-uw.github.io/tiara/" tool_dev_url: "https://github.com/ibe-uw/tiara" doi: "10.1093/bioinformatics/btab672" licence: ["MIT"] + identifier: biotools:tiara-metagenomics input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file of assembled contigs. - pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file of assembled contigs. + pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classifications: - type: file - description: TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag --gz is set. - pattern: "*.{txt,txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.{txt,txt.gz}: + type: file + description: TSV file containing per-contig classification probabilities and + overall classifications. Gzipped if flag --gz is set. + pattern: "*.{txt,txt.gz}" - log: - type: file - description: Log file containing tiara model parameters. Gzipped if flag --gz is set. - pattern: "log_*.{txt,txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - log_*.{txt,txt.gz}: + type: file + description: Log file containing tiara model parameters. Gzipped if flag --gz + is set. + pattern: "log_*.{txt,txt.gz}" - fasta: - type: file - description: | - (optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs - pattern: "*.{fasta,fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fasta,fasta.gz}": + type: file + description: | + (optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs + pattern: "*.{fasta,fasta.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml index c28546cc824..88b72641dbd 100644 --- a/modules/nf-core/tiddit/cov/meta.yml +++ b/modules/nf-core/tiddit/cov/meta.yml @@ -12,45 +12,54 @@ tools: documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: "10.12688/f1000research.11168.1" licence: ["GPL v3"] + identifier: biotools:tiddit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: | - Reference genome file. Only needed when passing in CRAM instead of BAM. - If not using CRAM, please pass an empty file instead. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: | + Reference genome file. Only needed when passing in CRAM instead of BAM. + If not using CRAM, please pass an empty file instead. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - cov: - type: file - description: The coverage of different regions in bed format. Optional. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: The coverage of different regions in bed format. Optional. + pattern: "*.bed" - wig: - type: file - description: The coverage of different regions in WIG format. Optional. - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: The coverage of different regions in WIG format. Optional. + pattern: "*.wig" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml index bfcbc4e3fd8..21527baf13d 100644 --- a/modules/nf-core/tiddit/sv/meta.yml +++ b/modules/nf-core/tiddit/sv/meta.yml @@ -11,56 +11,65 @@ tools: documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: 10.12688/f1000research.11168.1 licence: ["GPL-3.0-or-later"] + identifier: biotools:tiddit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test_fasta']` - - fasta: - type: file - description: Input FASTA file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing sample information from bwa index - e.g. `[ id:'test_bwa-index' ]` - - bwa_index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test_fasta']` + - fasta: + type: file + description: Input FASTA file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information from bwa index + e.g. `[ id:'test_bwa-index' ]` + - bwa_index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: vcf - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: vcf + pattern: "*.{vcf}" - ploidy: - type: file - description: tab - pattern: "*.{ploidies.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ploidies.tab": + type: file + description: tab + pattern: "*.{ploidies.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/tidk/explore/meta.yml b/modules/nf-core/tidk/explore/meta.yml index 582aaf56cda..72d15954b98 100644 --- a/modules/nf-core/tidk/explore/meta.yml +++ b/modules/nf-core/tidk/explore/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_explore" description: | @@ -10,42 +9,52 @@ keywords: - search tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The input fasta file - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The input fasta file + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - explore_tsv: - type: file - description: Telomeres and their frequencies in TSV format - pattern: "*.tidk.explore.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tidk.explore.tsv": + type: file + description: Telomeres and their frequencies in TSV format + pattern: "*.tidk.explore.tsv" - top_sequence: - type: file - description: | - The most frequent telomere sequence if one or more - sequences are identified by the toolkit - pattern: "*.top.sequence.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.top.sequence.txt": + type: file + description: | + The most frequent telomere sequence if one or more + sequences are identified by the toolkit + pattern: "*.top.sequence.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tidk/plot/meta.yml b/modules/nf-core/tidk/plot/meta.yml index 451195c8547..75289b28434 100644 --- a/modules/nf-core/tidk/plot/meta.yml +++ b/modules/nf-core/tidk/plot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_plot" description: | @@ -11,36 +10,40 @@ keywords: - plot tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - tsv: - type: file - description: Search results in TSV format from `tidk search` - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tsv: + type: file + description: Search results in TSV format from `tidk search` + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - svg: - type: file - description: Telomere search plot - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.svg": + type: file + description: Telomere search plot + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tidk/search/meta.yml b/modules/nf-core/tidk/search/meta.yml index 8ba07350158..9a30ff1545d 100644 --- a/modules/nf-core/tidk/search/meta.yml +++ b/modules/nf-core/tidk/search/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_search" description: Searches a genome for a telomere string such as TTAGGG @@ -8,43 +7,53 @@ keywords: - search tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The input fasta file - pattern: "*.{fsa,fa,fasta}" - - string: - type: string - description: Search string such as TTAGGG + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The input fasta file + pattern: "*.{fsa,fa,fasta}" + - - string: + type: string + description: Search string such as TTAGGG output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - tsv: - type: file - description: Search results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: Search results in TSV format + pattern: "*.tsv" - bedgraph: - type: file - description: Search results in BEDGRAPH format - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.bedgraph": + type: file + description: Search results in BEDGRAPH format + pattern: "*.bedgraph" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/topas/gencons/meta.yml b/modules/nf-core/topas/gencons/meta.yml index 4bef8632826..c6ec267664c 100644 --- a/modules/nf-core/topas/gencons/meta.yml +++ b/modules/nf-core/topas/gencons/meta.yml @@ -1,68 +1,114 @@ name: "topas_gencons" -description: Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA +description: Create fasta consensus with TOPAS toolkit with options to penalize substitutions + for typical DNA damage present in ancient DNA keywords: - consensus - fasta - ancient DNA tools: - "topas": - description: "This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules." + description: "This toolkit allows the efficient manipulation of sequence data + in various ways. It is organized into modules: The FASTA processing modules, + the FASTQ processing modules, the GFF processing modules and the VCF processing + modules." homepage: "https://github.com/subwaystation/TOPAS" documentation: "https://github.com/subwaystation/TOPAS/wiki/Overview-Modules" tool_dev_url: "https://github.com/subwaystation/TOPAS" doi: "10.1038/s41598-017-17723-1" licence: ["CC-BY"] + identifier: biotools:TOPAS input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps - pattern: "*.vcf.gz" - - vcf_indels: - type: file - description: Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels - pattern: "*.vcf.gz" - - reference: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - fai: - type: file - description: Optional index for the fasta file of reference genome - pattern: "*.fai" - - vcf_output: - type: boolean - description: Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Gzipped compressed vcf file generated with GATK UnifiedGenotyper + containing the called snps + pattern: "*.vcf.gz" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf_indels: + type: file + description: Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper + containing the called indels + pattern: "*.vcf.gz" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Optional index for the fasta file of reference genome + pattern: "*.fai" + - - vcf_output: + type: boolean + description: Boolean value to indicate if a compressed vcf file with the consensus + calls included as SNPs should be produced output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Gzipped consensus fasta file with bases under threshold replaced with Ns - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta.gz": + type: file + description: Gzipped consensus fasta file with bases under threshold replaced + with Ns + pattern: "*.fasta.gz" - vcf: - type: file - description: Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Gzipped vcf file with updated calls for the SNPs used in the consensus + generation and for bases under threshold replaced with Ns + pattern: "*.vcf.gz" - ccf: - type: file - description: Statistics file containing information about the consensus calls in the fasta file - pattern: "*.ccf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ccf": + type: file + description: Statistics file containing information about the consensus calls + in the fasta file + pattern: "*.ccf" - log: - type: file - description: Log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aidaanva" maintainers: diff --git a/modules/nf-core/toulligqc/meta.yml b/modules/nf-core/toulligqc/meta.yml index 61c69794c29..b269eccf801 100644 --- a/modules/nf-core/toulligqc/meta.yml +++ b/modules/nf-core/toulligqc/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "toulligqc" description: "A post sequencing QC tool for Oxford Nanopore sequencers" @@ -13,45 +12,64 @@ tools: documentation: https://github.com/GenomiqueENS/toulligQC tool_dev_url: https://github.com/GenomiqueENS/toulligQC licence: ["CECILL-2.1"] + identifier: biotools:ToulligQC input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ontfile: - type: file - description: Input ONT file - pattern: "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ontfile: + type: file + description: Input ONT file + pattern: "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report_data: - type: file - description: Report data emitted from toulligqc - pattern: "*.data" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.data": + type: file + description: Report data emitted from toulligqc + pattern: "*.data" - report_html: - type: file - description: Report data in html format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.html": + type: file + description: Report data in html format + pattern: "*.html" - plots_html: - type: file - description: Plots emitted in html format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/images/*.html": + type: file + description: Plots emitted in html format + pattern: "*.html" - plotly_js: - type: file - description: Plots emitted from toulligqc - pattern: "plotly.min.js" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/images/plotly.min.js": + type: file + description: Plots emitted from toulligqc + pattern: "plotly.min.js" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Salome-Brunon" maintainers: diff --git a/modules/nf-core/transdecoder/longorf/meta.yml b/modules/nf-core/transdecoder/longorf/meta.yml index 49f0baeb149..05225e812c9 100644 --- a/modules/nf-core/transdecoder/longorf/meta.yml +++ b/modules/nf-core/transdecoder/longorf/meta.yml @@ -1,5 +1,6 @@ name: transdecoder_longorf -description: TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file. +description: TransDecoder identifies candidate coding regions within transcript sequences. + it is used to build gff file. keywords: - eucaryotes - gff @@ -7,50 +8,76 @@ keywords: - coding tools: - transdecoder: - description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + description: TransDecoder identifies candidate coding regions within transcript + sequences, such as those generated by de novo RNA-Seq transcript assembly using + Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat + and Cufflinks. homepage: https://github.com/TransDecoder documentation: https://github.com/TransDecoder/TransDecoder/wiki tool_dev_url: https://github.com/TransDecoder/TransDecoder licence: ["Broad Institute"] + identifier: biotools:TransDecoder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pep: - type: file - description: all ORFs meeting the minimum length criteria, regardless of coding potential. file - pattern: "*.{pep}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.pep: + type: file + description: all ORFs meeting the minimum length criteria, regardless of coding + potential. file + pattern: "*.{pep}" - gff3: - type: file - description: positions of all ORFs as found in the target transcripts. file - pattern: "*.{gff3}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.gff3: + type: file + description: positions of all ORFs as found in the target transcripts. file + pattern: "*.{gff3}" - cds: - type: file - description: the nucleotide coding sequence for all detected ORFs. file - pattern: "*{cds}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.cds: + type: file + description: the nucleotide coding sequence for all detected ORFs. file + pattern: "*{cds}" - dat: - type: file - description: nucleotide frequencies - pattern: "*{dat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.dat: + type: file + description: nucleotide frequencies + pattern: "*{dat}" - folder: - type: directory - description: contains all the files from the run + - ${output_dir_name}: + type: directory + description: contains all the files from the run + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Danilo2771" maintainers: diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml index b3bd9da1e99..b6ba5174a64 100644 --- a/modules/nf-core/transdecoder/predict/meta.yml +++ b/modules/nf-core/transdecoder/predict/meta.yml @@ -1,5 +1,6 @@ name: transdecoder_predict -description: TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf +description: TransDecoder identifies candidate coding regions within transcript sequences. + It is used to build gff file. You can use this module after transdecoder_longorf keywords: - eukaryotes - gff @@ -7,51 +8,76 @@ keywords: - transcroder tools: - transdecoder: - description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + description: TransDecoder identifies candidate coding regions within transcript + sequences, such as those generated by de novo RNA-Seq transcript assembly using + Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat + and Cufflinks. homepage: https://github.com/TransDecoder documentation: https://github.com/TransDecoder/TransDecoder/wiki tool_dev_url: https://github.com/TransDecoder/TransDecoder licence: ["Broad Institute"] + identifier: biotools:TransDecoder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta}" - - fold: - type: directory - description: Output from the module transdecoder_longorf - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file + pattern: "*.{fasta}" + - - fold: + type: directory + description: Output from the module transdecoder_longorf + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pep: - type: file - description: All ORFs meeting the minimum length criteria, regardless of coding potential - pattern: "*.{pep}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.pep": + type: file + description: All ORFs meeting the minimum length criteria, regardless of coding + potential + pattern: "*.{pep}" - gff3: - type: file - description: Positions of all ORFs as found in the target transcripts - pattern: "*.{gff3}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.gff3": + type: file + description: Positions of all ORFs as found in the target transcripts + pattern: "*.{gff3}" - cds: - type: file - description: the nucleotide coding sequence for all detected ORFs - pattern: "*{cds}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.cds": + type: file + description: the nucleotide coding sequence for all detected ORFs + pattern: "*{cds}" - bed: - type: file - description: bed file - pattern: "*{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.bed": + type: file + description: bed file + pattern: "*{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Danilo2771" maintainers: diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e649088cee0..576cb4c5963 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -14,50 +14,77 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: | - List of input adapter trimmed FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. - pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{3prime,5prime,trimmed,val}*.fq.gz": + type: file + description: | + List of input adapter trimmed FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. + pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Trim Galore! trimming report + pattern: "*_{report.txt}" - unpaired: - type: file - description: | - FastQ files containing unpaired reads from read 1 or read 2 - pattern: "*unpaired*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*unpaired*.fq.gz": + type: file + description: | + FastQ files containing unpaired reads from read 1 or read 2 + pattern: "*unpaired*.fq.gz" - html: - type: file - description: FastQC report (optional) - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report (optional) + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive (optional) - pattern: "*_{fastqc.zip}" - - log: - type: file - description: Trim Galore! trimming report - pattern: "*_{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive (optional) + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/trimmomatic/meta.yml b/modules/nf-core/trimmomatic/meta.yml index 2d38bf50f39..e74014d5d97 100644 --- a/modules/nf-core/trimmomatic/meta.yml +++ b/modules/nf-core/trimmomatic/meta.yml @@ -11,47 +11,74 @@ tools: documentation: "https://github.com/usadellab/Trimmomatic" doi: "10.1093/bioinformatics/btu170" licence: ["GPL v3"] + identifier: biotools:trimmomatic input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively. - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively. + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - trimmed_reads: - type: file - description: The trimmed/modified paired end fastq reads - pattern: "*.paired.trim*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paired.trim*.fastq.gz": + type: file + description: The trimmed/modified paired end fastq reads + pattern: "*.paired.trim*.fastq.gz" - unpaired_reads: - type: file - description: The trimmed/modified unpaired end fastq reads - pattern: "*.unpaired.trim_*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unpaired.trim_*.fastq.gz": + type: file + description: The trimmed/modified unpaired end fastq reads + pattern: "*.unpaired.trim_*.fastq.gz" - trim_log: - type: file - description: trimmomatic log file, from the trim_log parameter - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_trim.log": + type: file + description: trimmomatic log file, from the trim_log parameter + pattern: "*.log" - out_log: - type: file - description: log of output from the standard out - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_out.log": + type: file + description: log of output from the standard out + pattern: "*.log" - summary: - type: file - description: trimmomatic summary file of surviving and dropped reads - pattern: "*.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary": + type: file + description: trimmomatic summary file of surviving and dropped reads + pattern: "*.summary" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alyssa-ab" maintainers: diff --git a/modules/nf-core/trinity/meta.yml b/modules/nf-core/trinity/meta.yml index 963043240d5..564ed65d353 100644 --- a/modules/nf-core/trinity/meta.yml +++ b/modules/nf-core/trinity/meta.yml @@ -13,35 +13,44 @@ tools: tool_dev_url: "https://github.com/trinityrnaseq/trinityrnaseq/" doi: "10.1038/nbt.1883" licence: ["BSD-3-clause"] + identifier: biotools:trinity input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fasta/fastq reads to be assembled into a transcriptome. - pattern: "*.{fa|fasta|fq|fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fasta/fastq reads to be assembled into a transcriptome. + pattern: "*.{fa|fasta|fq|fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - transcript_fasta: - type: file - description: de novo assembled transcripts fasta file compressed - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa.gz": + type: file + description: de novo assembled transcripts fasta file compressed + pattern: "*.fa.gz" - log: - type: file - description: Log from trinity - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log from trinity + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@timslittle" - "@gallvp" diff --git a/modules/nf-core/trust4/meta.yml b/modules/nf-core/trust4/meta.yml index 89bc4d29679..da2a5ff43fc 100644 --- a/modules/nf-core/trust4/meta.yml +++ b/modules/nf-core/trust4/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "trust4" description: Run TRUST4 on RNA-seq data @@ -13,62 +12,139 @@ tools: documentation: "https://github.com/liulab-dfci/TRUST4" tool_dev_url: "https://github.com/liulab-dfci/TRUST4" licence: ["GPL v3"] + identifier: biotools:trust4 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: BAM file from bulk or single-cell RNA-seq data - pattern: "*.bam" - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively - - fasta: - type: file - description: Path to the fasta file coordinate and sequence of V/D/J/C genes - - ref: - type: file - description: Path to detailed V/D/J/C gene reference file, such as from IMGT database. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: BAM file from bulk or single-cell RNA-seq data + pattern: "*.bam" + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Path to the fasta file coordinate and sequence of V/D/J/C genes + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vdj_reference: + type: file + description: reference file of V/D/J genes + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - barcode_read: + type: file + description: barcode read file + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - umi_read: + type: file + description: umi read file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - tsv: - type: file - description: tsv files created by TRUST4 - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: tsv files created by TRUST4 + pattern: "*.tsv" + - airr_files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_airr.tsv": + type: file + description: TRUST4 results in AIRR format + pattern: "*_airr.tsv" - airr_tsv: - type: file - description: TRUST4 results in AIRR format - pattern: "*_airr.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}_airr.tsv: + type: file + description: TRUST4 results in AIRR format + pattern: "*_airr.tsv" - report_tsv: - type: file - description: TRUST4 report in tsv format - pattern: "*_report.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_report.tsv": + type: file + description: TRUST4 report in tsv format + pattern: "*_report.tsv" - fasta: - type: file - description: Fasta files created by TRUST4 - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fa": + type: file + description: Fasta files created by TRUST4 + pattern: "*.fa" - out: - type: file - description: Further report files - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.out": + type: file + description: Further report files + pattern: "*.out" - fq: - type: file - description: Fastq files created by TRUST4 - pattern: "*.fq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fq": + type: file + description: Fastq files created by TRUST4 + pattern: "*.fq" + - outs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "**": + type: file + description: outputt files - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mapo9, @Joaodemeirelles" maintainers: diff --git a/modules/nf-core/truvari/bench/meta.yml b/modules/nf-core/truvari/bench/meta.yml index 1d8cf5bb237..85f2f97fbc0 100644 --- a/modules/nf-core/truvari/bench/meta.yml +++ b/modules/nf-core/truvari/bench/meta.yml @@ -1,4 +1,3 @@ ---- name: "truvari_bench" description: Given baseline and comparison sets of variants, calculate the recall/precision/f-measure keywords: @@ -15,96 +14,147 @@ tools: tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: Input SV VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Input SV VCF index file - pattern: "*.vcf.gz.tbi" - - truth_vcf: - type: file - description: Input VCF file with truth SVs - pattern: "*.vcf.gz" - - tbi: - type: file - description: Input VCF index file with truth SVs - pattern: "*.vcf.gz.tbi" - - bed: - type: file - description: BED file containing regions to compare - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Reference FASTA file - pattern: "*.{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing fasta index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: Reference FASTA index file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: Input SV VCF file + pattern: "*.vcf.gz" + - tbi: + type: file + description: Input SV VCF index file + pattern: "*.vcf.gz.tbi" + - truth_vcf: + type: file + description: Input VCF file with truth SVs + pattern: "*.vcf.gz" + - truth_tbi: + type: file + description: Input VCF index file with truth SVs + pattern: "*.vcf.gz.tbi" + - bed: + type: file + description: BED file containing regions to compare + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Reference FASTA file + pattern: "*.{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing fasta index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Reference FASTA index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fn_vcf: - type: file - description: VCF file with false negatives - pattern: "*.fn.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fn.vcf.gz": + type: file + description: VCF file with false negatives + pattern: "*.fn.vcf.gz" - fn_tbi: - type: file - description: VCF index file with false negatives - pattern: "*.fn.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fn.vcf.gz.tbi": + type: file + description: VCF index file with false negatives + pattern: "*.fn.vcf.gz.tbi" - fp_vcf: - type: file - description: VCF file with false positives - pattern: "*.fp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fp.vcf.gz": + type: file + description: VCF file with false positives + pattern: "*.fp.vcf.gz" - fp_tbi: - type: file - description: VCF index file with false positives - pattern: "*.fp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fp.vcf.gz.tbi": + type: file + description: VCF index file with false positives + pattern: "*.fp.vcf.gz.tbi" - tp_base_vcf: - type: file - description: VCF file with base true positives - pattern: "*.tp-base.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-base.vcf.gz": + type: file + description: VCF file with base true positives + pattern: "*.tp-base.vcf.gz" - tp_base_tbi: - type: file - description: VCF index file with base true positives - pattern: "*.tp-base.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-base.vcf.gz.tbi": + type: file + description: VCF index file with base true positives + pattern: "*.tp-base.vcf.gz.tbi" - tp_comp_vcf: - type: file - description: VCF file with compared true positives - pattern: "*.tp-comp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-comp.vcf.gz": + type: file + description: VCF file with compared true positives + pattern: "*.tp-comp.vcf.gz" - tp_comp_tbi: - type: file - description: VCF index file with compared true positives - pattern: "*.tp-comp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-comp.vcf.gz.tbi": + type: file + description: VCF index file with compared true positives + pattern: "*.tp-comp.vcf.gz.tbi" - summary: - type: file - description: Summary JSON file with results from the benchmark - pattern: "*.summary.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.summary.json": + type: file + description: Summary JSON file with results from the benchmark + pattern: "*.summary.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/truvari/consistency/meta.yml b/modules/nf-core/truvari/consistency/meta.yml index 6e3baf863fa..9a7c6fe1c48 100644 --- a/modules/nf-core/truvari/consistency/meta.yml +++ b/modules/nf-core/truvari/consistency/meta.yml @@ -14,30 +14,33 @@ tools: tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - vcfs: - type: file - description: two or more VCF files to compare - pattern: "*.{vcf,gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - vcfs: + type: file + description: two or more VCF files to compare + pattern: "*.{vcf,gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - consistency: - type: file - description: Output report in txt or json format - pattern: "*.{txt,json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.{txt,json}": + type: file + description: Output report in txt or json format + pattern: "*.{txt,json}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/truvari/segment/meta.yml b/modules/nf-core/truvari/segment/meta.yml index eb554706856..cf5ab12552d 100644 --- a/modules/nf-core/truvari/segment/meta.yml +++ b/modules/nf-core/truvari/segment/meta.yml @@ -14,30 +14,33 @@ tools: tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - vcf: - type: file - description: Input VCF file - pattern: "*.{vcf,gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - vcf: + type: file + description: Input VCF file + pattern: "*.{vcf,gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Segmented VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.vcf": + type: file + description: Segmented VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/trycycler/cluster/meta.yml b/modules/nf-core/trycycler/cluster/meta.yml index a17357b9341..ba5539e61e8 100644 --- a/modules/nf-core/trycycler/cluster/meta.yml +++ b/modules/nf-core/trycycler/cluster/meta.yml @@ -8,47 +8,41 @@ keywords: - genomics tools: - "trycycler": - description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes + description: Trycycler is a tool for generating consensus long-read assemblies + for bacterial genomes homepage: https://github.com/rrwick/Trycycler documentation: https://github.com/rrwick/Trycycler/wiki doi: 10.1186/s13059-021-02483-z licence: ["GPL v3"] + identifier: biotools:trycycler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: Long-read FASTQ file, optionally gzip compressed - - - assemblies: - type: file - description: Input assemblies whose contigs will be clustered - - - out_dir: - type: directory - description: Output directory for clustering results - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - contigs: + type: file + description: Contigs file + - reads: + type: file + description: Long-read FASTQ file, optionally gzip compressed output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - cluster_dir: - type: directory - description: Output directory containing clustering results - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*": + type: directory + description: Output directory containing clustering results - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@watsonar" maintainers: diff --git a/modules/nf-core/trycycler/subsample/meta.yml b/modules/nf-core/trycycler/subsample/meta.yml index 38c7f9b232f..5a0fed8ff41 100644 --- a/modules/nf-core/trycycler/subsample/meta.yml +++ b/modules/nf-core/trycycler/subsample/meta.yml @@ -6,44 +6,39 @@ keywords: - genomics tools: - "trycycler": - description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes + description: Trycycler is a tool for generating consensus long-read assemblies + for bacterial genomes homepage: https://github.com/rrwick/Trycycler documentation: https://github.com/rrwick/Trycycler/wiki doi: 10.1186/s13059-021-02483-z licence: ["GPL v3"] + identifier: biotools:trycycler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: Long-read FASTQ file, optionally gzip compressed - - - out_dir: - type: directory - description: Output directory for subsampled read sets - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Long-read FASTQ file, optionally gzip compressed output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - subreads: - type: file - description: Subsampled read sets - pattern: "*.{fastq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*/*.fastq.gz": + type: file + description: Subsampled read sets + pattern: "*.{fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@watsonar" maintainers: diff --git a/modules/nf-core/tsebra/meta.yml b/modules/nf-core/tsebra/meta.yml index 18660d49e17..b7808efe05e 100644 --- a/modules/nf-core/tsebra/meta.yml +++ b/modules/nf-core/tsebra/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tsebra" -description: Transcript Selector for BRAKER TSEBRA combines gene predictions by selecing transcripts based on their extrisic evidence support +description: Transcript Selector for BRAKER TSEBRA combines gene predictions by selecing + transcripts based on their extrisic evidence support keywords: - genomics - transcript @@ -11,55 +11,66 @@ keywords: - evidence tools: - "tsebra": - description: TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons + description: TSEBRA is a combiner tool that selects transcripts from gene predictions + based on the support by extrisic evidence in form of introns and start/stop + codons homepage: "https://github.com/Gaius-Augustus/TSEBRA" documentation: "https://github.com/Gaius-Augustus/TSEBRA" tool_dev_url: "https://github.com/Gaius-Augustus/TSEBRA" doi: "10.1186/s12859-021-04482-0" licence: ["Artistic-2.0"] + identifier: biotools:tsebra input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gtfs: - type: list - description: List of gene prediction files in gtf - pattern: "*.gtf" - - hints_files: - type: list - description: List of files containing extrinsic evidence in gff - pattern: "*.gff" - - keep_gtfs: - type: list - description: | - List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all - transcripts from these gene sets are included in the output - pattern: "*.gtf" - - config: - type: file - description: Configuration file that sets the parameter for TSEBRA - pattern: "*.cfg" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gtfs: + type: list + description: List of gene prediction files in gtf + pattern: "*.gtf" + - - hints_files: + type: list + description: List of files containing extrinsic evidence in gff + pattern: "*.gff" + - - keep_gtfs: + type: list + description: | + List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all + transcripts from these gene sets are included in the output + pattern: "*.gtf" + - - config: + type: file + description: Configuration file that sets the parameter for TSEBRA + pattern: "*.cfg" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsebra_gtf: - type: file - description: Output file for the combined gene predictions in gtf - pattern: "*.gtf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gtf": + type: file + description: Output file for the combined gene predictions in gtf + pattern: "*.gtf" - tsebra_scores: - type: file - description: Transcript scores as a table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: Transcript scores as a table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml index 9ee5fd365d8..d4c6a549255 100644 --- a/modules/nf-core/tximeta/tximport/meta.yml +++ b/modules/nf-core/tximeta/tximport/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tximeta_tximport" description: | @@ -18,102 +17,131 @@ tools: tool_dev_url: "https://github.com/thelovelab/tximeta" doi: "10.1371/journal.pcbi.1007664" licence: ["GPL-2"] + identifier: biotools:tximeta input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference e.g. `[ id:'yeast' ]` - - tx2gene: - type: file - description: A transcript to gene mapping table such as those generated - by custom/tx2gene - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - coldata: - type: file - description: | - Optional 'coldata' file equivalent to a sample sheet where the first - column corresponds to the sample names (directory names in the input - salmon/ kallisto results) - pattern: "*.{csv,tsv}" - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: directory + description: Directory containing quantification files + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference e.g. `[ id:'yeast' ]` + - tx2gene: + type: file + description: A transcript to gene mapping table such as those generated by custom/tx2gene + pattern: "*.{csv,tsv}" + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - tpm_gene: - type: file - description: | - Abundance (TPM) values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_tpm.tsv" - counts_gene: - type: file - description: | - Count values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts.tsv": + type: file + description: | + Count values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_counts.tsv" - counts_gene_length_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'lengthScaledTPM' - pattern: "*gene_counts_length_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_length_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'lengthScaledTPM' + pattern: "*gene_counts_length_scaled.tsv" - counts_gene_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'scaledTPM' - pattern: "*gene_counts_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'scaledTPM' + pattern: "*gene_counts_scaled.tsv" - lengths_gene: - type: file - description: | - Length values derived from tximport output after summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_lengths.tsv": + type: file + description: | + Length values derived from tximport output after summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - tpm_transcript: - type: file - description: | - Abundance (TPM) values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_tpm.tsv" - counts_transcript: - type: file - description: | - Count values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_counts.tsv": + type: file + description: | + Count values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_counts.tsv" - lengths_transcript: - type: file - description: | - Length values derived from tximport output without summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_lengths.tsv": + type: file + description: | + Length values derived from tximport output without summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml index 2467a28f219..9222d31d20b 100644 --- a/modules/nf-core/ucsc/bedclip/meta.yml +++ b/modules/nf-core/ucsc/bedclip/meta.yml @@ -9,30 +9,36 @@ tools: description: Remove lines from bed file that refer to off-chromosome locations. homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - - sizes: + type: file + description: Chromosome sizes file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml index a60118abe5b..5d42cbde78c 100755 --- a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml @@ -12,34 +12,37 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: https://genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedGraph}" - - sizes: - type: file - description: chromosome sizes file - pattern: "*.{sizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedGraph}" + - - sizes: + type: file + description: chromosome sizes file + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigwig: - type: file - description: bigWig file - pattern: "*.{bigWig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigWig": + type: file + description: bigWig file + pattern: "*.{bigWig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedtobigbed/meta.yml b/modules/nf-core/ucsc/bedtobigbed/meta.yml index aae1996f4fc..6afc3148ef0 100755 --- a/modules/nf-core/ucsc/bedtobigbed/meta.yml +++ b/modules/nf-core/ucsc/bedtobigbed/meta.yml @@ -12,38 +12,41 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: https://genome.ucsc.edu/goldenPath/help/bigBed.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: bed file - pattern: "*.{bed}" - - sizes: - type: file - description: chromosome sizes file - pattern: "*.{sizes}" - - autosql: - type: file - description: autoSql file to describe the columns of the BED file - pattern: "*.{as}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed file + pattern: "*.{bed}" + - - sizes: + type: file + description: chromosome sizes file + pattern: "*.{sizes}" + - - autosql: + type: file + description: autoSql file to describe the columns of the BED file + pattern: "*.{as}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigbed: - type: file - description: bigBed file - pattern: "*.{bigBed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigBed": + type: file + description: bigBed file + pattern: "*.{bigBed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml b/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml index 9b2884477d8..c215f36266c 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml @@ -10,34 +10,37 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: bed file - pattern: "*.{bed}" - - bigwig: - type: file - description: bigwig file - pattern: "*.{bigwig,bw}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed file + pattern: "*.{bed}" + - - bigwig: + type: file + description: bigwig file + pattern: "*.{bigwig,bw}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tab: - type: file - description: tab file - pattern: "*.{tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: tab file + pattern: "*.{tab}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/ucsc/gtftogenepred/meta.yml b/modules/nf-core/ucsc/gtftogenepred/meta.yml index 02122e4101e..cf04154d4a1 100644 --- a/modules/nf-core/ucsc/gtftogenepred/meta.yml +++ b/modules/nf-core/ucsc/gtftogenepred/meta.yml @@ -11,34 +11,43 @@ tools: description: Convert GTF files to GenePred format homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - genepred: - type: file - description: genepred file - pattern: "*.{genepred}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.genepred": + type: file + description: genepred file + pattern: "*.{genepred}" - refflat: - type: file - description: refflat file - pattern: "*.{refflat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.refflat": + type: file + description: refflat file + pattern: "*.{refflat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" - "@anoronh4" diff --git a/modules/nf-core/ucsc/liftover/meta.yml b/modules/nf-core/ucsc/liftover/meta.yml index c1c40d96625..9905b6870a6 100644 --- a/modules/nf-core/ucsc/liftover/meta.yml +++ b/modules/nf-core/ucsc/liftover/meta.yml @@ -9,38 +9,47 @@ tools: description: Move annotations from one assembly to another homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Browser Extensible Data (BED) file - pattern: "*.{bed}" - - chain: - type: file - description: Chain file - pattern: "*.{chain,chain.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Browser Extensible Data (BED) file + pattern: "*.{bed}" + - - chain: + type: file + description: Chain file + pattern: "*.{chain,chain.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - lifted: - type: file - description: BED file containing successfully lifted variants - pattern: "*.{lifted.bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lifted.bed": + type: file + description: BED file containing successfully lifted variants + pattern: "*.{lifted.bed}" - unlifted: - type: file - description: BED file containing variants that couldn't be lifted - pattern: "*.{unlifted.bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unlifted.bed": + type: file + description: BED file containing variants that couldn't be lifted + pattern: "*.{unlifted.bed}" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml index f747648065f..97bf98b16ad 100644 --- a/modules/nf-core/ucsc/wigtobigwig/meta.yml +++ b/modules/nf-core/ucsc/wigtobigwig/meta.yml @@ -11,28 +11,35 @@ tools: or bedGraph format) to binary big wig format homepage: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - wig: - type: file - description: wig file - pattern: "*.{wig}" - - chromsizes: - type: file - description: chromosome sizes file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - wig: + type: file + description: wig file + pattern: "*.{wig}" + - - sizes: + type: file + description: Chromosome sizes file output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bw: - type: file - description: bigwig file - pattern: "*.{bw}" + - meta: + type: file + description: bigwig file + pattern: "*.{bw}" + - "*.bw": + type: file + description: bigwig file + pattern: "*.{bw}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@projectoriented" diff --git a/modules/nf-core/ultra/align/environment.yml b/modules/nf-core/ultra/align/environment.yml index 39d65509991..23c5097c14f 100644 --- a/modules/nf-core/ultra/align/environment.yml +++ b/modules/nf-core/ultra/align/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::ultra_bioinformatics=0.1 - bioconda::samtools=1.17 + - bioconda::ultra_bioinformatics=0.1 diff --git a/modules/nf-core/ultra/align/meta.yml b/modules/nf-core/ultra/align/meta.yml index 79b9e30aadb..bb5298d1451 100644 --- a/modules/nf-core/ultra/align/meta.yml +++ b/modules/nf-core/ultra/align/meta.yml @@ -1,5 +1,6 @@ name: "ultra_align" -description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome +description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection + - Map reads on genome keywords: - uLTRA - align @@ -15,42 +16,45 @@ tools: tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" licence: ["GNU GPLV3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A fasta or fastq file of reads to align - pattern: "*.{fa,fasta,fastq}" - - genome: - type: file - description: A fasta file of reference genome - pattern: "*.{fa,fasta}" - - pickle: - type: file - description: Pickle files generated by uLTRA index - pattern: "*.pickle" - - db: - type: file - description: Database generated by uLTRA index - pattern: "*.db" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A fasta or fastq file of reads to align + pattern: "*.{fa,fasta,fastq}" + - - genome: + type: file + description: A fasta file of reference genome + pattern: "*.{fa,fasta}" + - - pickle: + type: file + description: Pickle files generated by uLTRA index + pattern: "*.pickle" + - db: + type: file + description: Database generated by uLTRA index + pattern: "*.db" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: The aligned reads in bam format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: The aligned reads in bam format + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/ultra/index/meta.yml b/modules/nf-core/ultra/index/meta.yml index 1bf59abab07..236bcc2d588 100644 --- a/modules/nf-core/ultra/index/meta.yml +++ b/modules/nf-core/ultra/index/meta.yml @@ -1,5 +1,6 @@ name: "ultra_index" -description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment +description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection + - Index gtf file for reads alignment keywords: - uLTRA - index @@ -15,28 +16,31 @@ tools: tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" licence: ["GNU GPLV3"] + identifier: "" input: - - fasta: - type: file - description: A fasta file of the genome to use as reference for mapping - pattern: "*.{fasta, fa}" - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" + - - fasta: + type: file + description: A fasta file of the genome to use as reference for mapping + pattern: "*.{fasta, fa}" + - - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" output: + - index: + - "*.pickle": + type: file + description: Index file + pattern: "*.pickle" + - "*.db": + type: file + description: Index database + pattern: "*.db" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pickle: - type: file - description: Index files generated by uLTRA index - pattern: "*.pickle" - - pickle: - type: file - description: database file generated by uLTRA index - pattern: "*.db" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/ultra/pipeline/meta.yml b/modules/nf-core/ultra/pipeline/meta.yml index 7e51a5e63a1..4c26b6d137c 100644 --- a/modules/nf-core/ultra/pipeline/meta.yml +++ b/modules/nf-core/ultra/pipeline/meta.yml @@ -15,38 +15,41 @@ tools: tool_dev_url: https://github.com/ksahlin/uLTRA doi: "10.1093/bioinformatics/btab540" licence: ["GNU GPLV3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A fasta or fastq file of reads to align - pattern: "*.{fasta,fastq}" - - genome: - type: file - description: fasta file of reference genome - pattern: "*.fasta" - - gtf: - type: file - description: A annotation of use the genome - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A fasta or fastq file of reads to align + pattern: "*.{fasta,fastq}" + - - genome: + type: file + description: fasta file of reference genome + pattern: "*.fasta" + - - gtf: + type: file + description: A annotation of use the genome + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: The aligned reads in sam format - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: The aligned reads in sam format + pattern: "*.sam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" - "@lassefolkersen" diff --git a/modules/nf-core/ultraplex/meta.yml b/modules/nf-core/ultraplex/meta.yml index 66659aac669..581c64c12d8 100644 --- a/modules/nf-core/ultraplex/meta.yml +++ b/modules/nf-core/ultraplex/meta.yml @@ -1,5 +1,6 @@ name: "ultraplex" -description: Ultraplex is an all-in-one software package for processing and demultiplexing fastq files. +description: Ultraplex is an all-in-one software package for processing and demultiplexing + fastq files. keywords: - demultiplex - fastq @@ -12,38 +13,53 @@ tools: tool_dev_url: https://github.com/ulelab/ultraplex doi: "10.5281/zenodo.465128" licence: ["MIT"] + identifier: biotools:ultraplex input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: Zipped FASTQ file - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file(s) to demultiplex + - - barcode_file: + type: file + description: FASTQ file containing barcode sequences + - - adapter_seq: + type: string + description: adapter sequence output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "*[!no_match].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*[!no_match].fastq.gz": + type: file + description: Demultiplexed sample FASTQ files + pattern: "*[!no_match].fastq.gz" - no_match_fastq: - type: file - description: FASTQ file containing reads that could not be demultiplexed - pattern: "*no_match.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*no_match.fastq.gz": + type: file + description: FASTQ file containing reads that could not be demultiplexed + pattern: "*no_match.fastq.gz" - report: - type: file - description: File containing demultiplexing log - pattern: "*.log" + - "*.log": + type: file + description: File containing demultiplexing log + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CharlotteAnne" - "@oscarwilkins" diff --git a/modules/nf-core/umicollapse/meta.yml b/modules/nf-core/umicollapse/meta.yml index c1361f9ad12..8b366c24438 100644 --- a/modules/nf-core/umicollapse/meta.yml +++ b/modules/nf-core/umicollapse/meta.yml @@ -1,58 +1,76 @@ ---- name: "umicollapse" -description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached + to the read. keywords: - umicollapse - deduplication - genomics tools: - "umicollapse": - description: "UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)." + description: "UMICollapse contains tools for dealing with Unique Molecular Identifiers + (UMIs)/Random Molecular Tags (RMTs)." homepage: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" documentation: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" tool_dev_url: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" doi: "10.7717/peerj.8275" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input. - pattern: "*.{bai}" - - mode: - type: string - description: | - Selects the mode of Umicollapse - either fastq or bam need to be provided. - pattern: "{fastq,bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input bam file + pattern: "*.bam" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input. + pattern: "*.{bai}" + - - mode: + type: string + description: | + Selects the mode of Umicollapse - either fastq or bam need to be provided. + pattern: "{fastq,bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*dedup*fastq.gz": + type: file + description: FASTQ file with deduplicated UMIs. + pattern: "*dedup*fastq.gz" - log: - type: file - description: A log file with the deduplication statistics. - pattern: "*_{UMICollapse.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_UMICollapse.log": + type: file + description: A log file with the deduplication statistics. + pattern: "*_{UMICollapse.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CharlotteAnne" - "@chris-cheshire" diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml index 38d3fd46542..6cbd84116d5 100644 --- a/modules/nf-core/umitools/dedup/meta.yml +++ b/modules/nf-core/umitools/dedup/meta.yml @@ -1,5 +1,6 @@ name: umitools_dedup -description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached + to the read. keywords: - umitools - deduplication @@ -7,60 +8,89 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" - - get_output_stats: - type: boolean - description: | - Whether or not to generate output stats. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" + - - get_output_stats: + type: boolean + description: | + Whether or not to generate output stats. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - tsv_edit_distance: - type: file - description: Reports the (binned) average edit distance between the UMIs at each position. - pattern: "*edit_distance.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*edit_distance.tsv": + type: file + description: Reports the (binned) average edit distance between the UMIs at + each position. + pattern: "*edit_distance.tsv" - tsv_per_umi: - type: file - description: UMI-level summary statistics. - pattern: "*per_umi.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_umi.tsv": + type: file + description: UMI-level summary statistics. + pattern: "*per_umi.tsv" - tsv_umi_per_position: - type: file - description: Tabulates the counts for unique combinations of UMI and position. - pattern: "*per_position.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_position.tsv": + type: file + description: Tabulates the counts for unique combinations of UMI and position. + pattern: "*per_position.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml index 7695b271762..648ffbd26f3 100644 --- a/modules/nf-core/umitools/extract/meta.yml +++ b/modules/nf-core/umitools/extract/meta.yml @@ -1,5 +1,6 @@ name: umitools_extract -description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place +description: Extracts UMI barcode from a read and add it to the read name, leaving + any sample barcode in place keywords: - UMI - barcode @@ -8,38 +9,49 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: "MIT" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: list - description: | - List of input FASTQ files whose UMIs will be extracted. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: > - Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: > + Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. + | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" - log: - type: file - description: Logfile for umi_tools - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Logfile for umi_tools + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/group/meta.yml b/modules/nf-core/umitools/group/meta.yml index c989836f7fa..e755684aa82 100644 --- a/modules/nf-core/umitools/group/meta.yml +++ b/modules/nf-core/umitools/group/meta.yml @@ -9,52 +9,73 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" - - create_bam: - type: boolean - description: | - Whether or not to create a read group tagged BAM file. - - get_group_info: - type: boolean - description: | - Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" + - - create_bam: + type: boolean + description: | + Whether or not to create a read group tagged BAM file. + - - get_group_info: + type: boolean + description: | + Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: a read group tagged BAM file. - pattern: "${prefix}.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: a read group tagged BAM file. + pattern: "${prefix}.{bam}" - tsv: - type: file - description: Flatfile describing the read groups, see docs for complete info of all columns - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Flatfile describing the read groups, see docs for complete info + of all columns + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/umitools/prepareforrsem/meta.yml b/modules/nf-core/umitools/prepareforrsem/meta.yml index 8b85366cc4a..3e8ead2576e 100644 --- a/modules/nf-core/umitools/prepareforrsem/meta.yml +++ b/modules/nf-core/umitools/prepareforrsem/meta.yml @@ -8,43 +8,53 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Prepared BAM file. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Prepared BAM file. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@pinin4fjords" diff --git a/modules/nf-core/unicycler/meta.yml b/modules/nf-core/unicycler/meta.yml index 406b14703ed..5bd8583fc18 100644 --- a/modules/nf-core/unicycler/meta.yml +++ b/modules/nf-core/unicycler/meta.yml @@ -13,47 +13,58 @@ tools: tool_dev_url: https://github.com/rrwick/Unicycler doi: 10.1371/journal.pcbi.1005595 licence: ["GPL v3"] + identifier: biotools:unicycler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - shortreads: - type: file - description: | - List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - longreads: - type: file - description: | - List of input FastQ files of size 1, PacBio or Nanopore long reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shortreads: + type: file + description: | + List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - longreads: + type: file + description: | + List of input FastQ files of size 1, PacBio or Nanopore long reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scaffolds: - type: file - description: Fasta file containing scaffolds - pattern: "*.{scaffolds.fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.scaffolds.fa.gz": + type: file + description: Fasta file containing scaffolds + pattern: "*.{scaffolds.fa.gz}" - gfa: - type: file - description: gfa file containing assembly - pattern: "*.{assembly.gfa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly.gfa.gz": + type: file + description: gfa file containing assembly + pattern: "*.{assembly.gfa.gz}" - log: - type: file - description: unicycler log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: unicycler log file + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@drpatelh" diff --git a/modules/nf-core/universc/meta.yml b/modules/nf-core/universc/meta.yml index 92a46bc6f4b..af350b380ed 100644 --- a/modules/nf-core/universc/meta.yml +++ b/modules/nf-core/universc/meta.yml @@ -1,5 +1,6 @@ name: "universc" -description: Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data +description: Module to run UniverSC an open-source pipeline to demultiplex and process + single-cell RNA-Seq data keywords: - demultiplex - align @@ -9,31 +10,42 @@ keywords: - umi tools: - "universc": - description: "UniverSC: a flexible cross-platform single-cell data processing pipeline" + description: "UniverSC: a flexible cross-platform single-cell data processing + pipeline" homepage: "https://hub.docker.com/r/tomkellygenetics/universc" documentation: "https://raw.githubusercontent.com/minoda-lab/universc/master/man/launch_universc.sh" tool_dev_url: "https://github.com/minoda-lab/universc" doi: "10.1101/2021.01.19.427209" licence: ["GPL-3.0-or-later"] + identifier: biotools:universc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - reference: + type: file + description: Reference genome file output: - outs: - type: file - description: Files containing the outputs of Cell Ranger - pattern: "sample-${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "sample-${meta.id}/outs/*" + - sample-${meta.id}/outs/*: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "sample-${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@kbattenb" - "@tomkellygenetics" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f55d..290346b3fa7 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untarfiles/meta.yml b/modules/nf-core/untarfiles/meta.yml index 3810882641b..1d23eb25721 100644 --- a/modules/nf-core/untarfiles/meta.yml +++ b/modules/nf-core/untarfiles/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - files: - type: string - description: A list containing references to individual archive files - pattern: "*/**" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/**: + type: string + description: A list containing references to individual archive files + pattern: "*/**" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml index e8e377e2af8..426fccb76b0 100644 --- a/modules/nf-core/unzip/meta.yml +++ b/modules/nf-core/unzip/meta.yml @@ -7,35 +7,39 @@ keywords: - archiving tools: - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version + of 7zip, see www.7-zip.org) for Unix. homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: ZIP file - pattern: "*.zip" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: ZIP file + pattern: "*.zip" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - unzipped_archive: - type: directory - description: Directory contents of the unzipped archive - pattern: "${archive.baseName}/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/: + type: directory + description: Directory contents of the unzipped archive + pattern: "${archive.baseName}/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/unzipfiles/meta.yml b/modules/nf-core/unzipfiles/meta.yml index 20020ad651f..7735c0cd63b 100644 --- a/modules/nf-core/unzipfiles/meta.yml +++ b/modules/nf-core/unzipfiles/meta.yml @@ -7,35 +7,39 @@ keywords: - archiving tools: - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version + of 7zip, see www.7-zip.org) for Unix. homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: ZIP file - pattern: "*.zip" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: ZIP file + pattern: "*.zip" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - files: - type: list - description: A list containing references to individual archive files - pattern: "*/**" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/**: + type: list + description: A list containing references to individual archive files + pattern: "*/**" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@pinin4fjords" diff --git a/modules/nf-core/upd/meta.yml b/modules/nf-core/upd/meta.yml index 9375d56d4c8..a0e90063289 100644 --- a/modules/nf-core/upd/meta.yml +++ b/modules/nf-core/upd/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "upd" description: Simple software to call UPD regions from germline exome/wgs trios. @@ -13,31 +12,34 @@ tools: documentation: https://github.com/bjhall/upd tool_dev_url: https://github.com/bjhall/upd licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: BED file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@hrydbeck" maintainers: diff --git a/modules/nf-core/upp/align/meta.yml b/modules/nf-core/upp/align/meta.yml index a5470c2c087..08781fa6fc3 100644 --- a/modules/nf-core/upp/align/meta.yml +++ b/modules/nf-core/upp/align/meta.yml @@ -13,44 +13,48 @@ tools: tool_dev_url: "https://github.com/smirarab/sepp/tree/master" doi: "10.1093/bioinformatics/btad007" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed, + depending on if compress is set to true or false + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml index 5c2fc921aca..801db6fa7f3 100644 --- a/modules/nf-core/vardictjava/meta.yml +++ b/modules/nf-core/vardictjava/meta.yml @@ -14,56 +14,60 @@ tools: tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava" doi: "10.1093/nar/gkw227 " licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: One or two BAM files. Supply two BAM files to run Vardict in paired mode. - pattern: "*.bam" - - bais: - type: file - description: Index/indices of the BAM file(s) - pattern: "*.bai" - - bed: - type: file - description: BED with the regions of interest - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA of the reference genome - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the FASTA of the reference genome - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: One or two BAM files. Supply two BAM files to run Vardict in paired + mode. + pattern: "*.bam" + - bais: + type: file + description: Index/indices of the BAM file(s) + pattern: "*.bai" + - bed: + type: file + description: BED with the regions of interest + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the FASTA of the reference genome + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file output - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file output + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/variantbam/meta.yml b/modules/nf-core/variantbam/meta.yml index 817dccb5c24..d470d7a4df9 100644 --- a/modules/nf-core/variantbam/meta.yml +++ b/modules/nf-core/variantbam/meta.yml @@ -9,36 +9,40 @@ keywords: - subsample bam tools: - variantbam: - description: Filtering and profiling of next-generational sequencing data using region-specific rules + description: Filtering and profiling of next-generational sequencing data using + region-specific rules homepage: https://github.com/walaj/VariantBam documentation: https://github.com/walaj/VariantBam#table-of-contents tool_dev_url: https://github.com/walaj/VariantBam doi: 10.1093/bioinformatics/btw111 licence: ["Apache-2.0"] + identifier: biotools:variantbam input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Filtered or downsampled BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Filtered or downsampled BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/varlociraptor/callvariants/meta.yml b/modules/nf-core/varlociraptor/callvariants/meta.yml index 85ef816d34f..a72d90c8c3f 100644 --- a/modules/nf-core/varlociraptor/callvariants/meta.yml +++ b/modules/nf-core/varlociraptor/callvariants/meta.yml @@ -1,65 +1,87 @@ name: "varlociraptor_callvariants" -description: Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing +description: Call variants for a given scenario specified with the varlociraptor calling + grammar, preprocessed by varlociraptor preprocessing keywords: - observations - variants - calling tools: - "varlociraptor": - description: "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control." + description: "Flexible, uncertainty-aware variant calling with parameter free + filtration via FDR control." homepage: "https://varlociraptor.github.io/docs/estimating/" documentation: "https://varlociraptor.github.io/docs/calling/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" licence: ["GPL v3"] + identifier: biotools:varlociraptor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal_vcf: - type: file - description: Sorted VCF/BCF file (list) - pattern: "*.{bcf,vcf,vcf.gz}" - - tumor_vcf: - type: file - description: Sorted VCF/BCF file (optional) - pattern: "*.{bcf,bcf.gz,vcf,vcf.gz}" - - scenario: - type: file - description: Yaml file containing scenario information (optional) - pattern: "*.{yml,yaml}" - - scenario_sample: - type: string - description: (List of) sample name(s) to be processed as named in the scenario yml (optional) - pattern: "*.{bcf,vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal_vcf: + type: file + description: Sorted VCF/BCF file (list) + pattern: "*.{bcf,vcf,vcf.gz}" + - tumor_vcf: + type: file + description: Sorted VCF/BCF file (optional) + pattern: "*.{bcf,bcf.gz,vcf,vcf.gz}" + - - scenario: + type: file + description: Yaml file containing scenario information (optional) + pattern: "*.{yml,yaml}" + - - scenario_sample_name: + type: string + description: Sample name for the scenario output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf_gz: - type: file - description: Compressed VCF file containing sample observations - pattern: "*.vcf.gz" - bcf_gz: - type: file - description: BCF file containing sample observations - pattern: "*.bcf.gz" - - vcf: - type: file - description: VCF file containing sample observations - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf.gz": + type: file + description: BCF file containing sample observations + pattern: "*.bcf.gz" + - vcf_gz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file containing sample observations + pattern: "*.vcf.gz" - bcf: - type: file - description: BCF file containing sample observations - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: BCF file containing sample observations + pattern: "*.bcf" + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: VCF file containing sample observations + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml b/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml index 624b0754fa3..1c48146ab74 100644 --- a/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml +++ b/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml @@ -1,59 +1,65 @@ name: "varlociraptor_estimatealignmentproperties" -description: In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner. +description: In order to judge about candidate indel and structural variants, Varlociraptor + needs to know about certain properties of the underlying sequencing experiment in + combination with the used read aligner. keywords: - estimation - alignment - variants tools: - "varlociraptor": - description: "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control." + description: "Flexible, uncertainty-aware variant calling with parameter free + filtration via FDR control." homepage: "https://varlociraptor.github.io/docs/estimating/" documentation: "https://varlociraptor.github.io/docs/estimating/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" licence: ["GPL v3"] + identifier: biotools:varlociraptor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference index information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index for reference fasta file (must be with samtools index) - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index for reference fasta file (must be with samtools index) + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - alignment_properties_json: - type: file - description: File containing alignment properties - pattern: "*.alignment-properties.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.alignment-properties.json": + type: file + description: File containing alignment properties + pattern: "*.alignment-properties.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/varlociraptor/preprocess/meta.yml b/modules/nf-core/varlociraptor/preprocess/meta.yml index 7fd3de5bb8f..0cd13723026 100644 --- a/modules/nf-core/varlociraptor/preprocess/meta.yml +++ b/modules/nf-core/varlociraptor/preprocess/meta.yml @@ -1,79 +1,106 @@ name: "varlociraptor_preprocess" -description: Obtains per-sample observations for the actual calling process with varlociraptor calls +description: Obtains per-sample observations for the actual calling process with varlociraptor + calls keywords: - observations - variants - preprocessing tools: - "varlociraptor": - description: "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control." + description: "Flexible, uncertainty-aware variant calling with parameter free + filtration via FDR control." homepage: "https://varlociraptor.github.io/docs/estimating/" documentation: "https://varlociraptor.github.io/docs/calling/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" licence: ["GPL v3"] + identifier: biotools:varlociraptor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - candidates: - type: file - description: Sorted BCF/VCF file - pattern: "*.{bcf,vcf,vcf.gz}" - - alignment_json: - type: file - description: File containing alignment properties obtained with varlociraptor/estimatealignmentproperties - pattern: "*.json" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference index information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index for reference fasta file (must be with samtools index) - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - candidates: + type: file + description: Sorted BCF/VCF file + pattern: "*.{bcf,vcf,vcf.gz}" + - alignment_json: + type: file + description: File containing alignment properties obtained with varlociraptor/estimatealignmentproperties + pattern: "*.json" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index for reference fasta file (must be with samtools index) + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf_gz: - type: file - description: Compressed VCF file containing sample observations - pattern: "*.vcf.gz" - bcf_gz: - type: file - description: BCF file containing sample observations - pattern: "*.bcf.gz" - - vcf: - type: file - description: VCF file containing sample observations - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf.gz": + type: file + description: BCF file containing sample observations + pattern: "*.bcf.gz" + - vcf_gz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file containing sample observations + pattern: "*.vcf.gz" - bcf: - type: file - description: BCF file containing sample observations - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: BCF file containing sample observations + pattern: "*.bcf" + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: VCF file containing sample observations + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/vcf2cytosure/meta.yml b/modules/nf-core/vcf2cytosure/meta.yml index 2430f1aee41..0c38d9c8de6 100644 --- a/modules/nf-core/vcf2cytosure/meta.yml +++ b/modules/nf-core/vcf2cytosure/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "vcf2cytosure" description: Convert VCF with structural variations to CytoSure format @@ -14,64 +13,65 @@ tools: documentation: "https://github.com/NBISweden/vcf2cytosure" tool_dev_url: "https://github.com/NBISweden/vcf2cytosure" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - sv_vcf: - type: file - description: VCF file with structural variants - pattern: "*.{vcf,vcf.gz}" - - coverage_bed: - type: file - description: Bed file with coverage data - pattern: "*.bed" - - cns: - type: file - description: CN file from CNVkit, not compatible with coverage_bed file - - snv_vcf: - type: file - description: | - VCF file with SNVs to calculate probe coverage, - not compatible with coverage_bed + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - sv_vcf: + type: file + description: VCF file with structural variants pattern: "*.{vcf,vcf.gz}" - - blacklist_bed: - type: file - description: Bed file with regions to exclude - pattern: "*.bed" - + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - coverage_bed: + type: file + description: Bed file with coverage data + pattern: "*.bed" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - cns: + type: file + description: CN file from CNVkit, not compatible with coverage_bed file + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - snv_vcf: + type: file + description: | + VCF file with SNVs to calculate probe coverage, + not compatible with coverage_bed + pattern: "*.{vcf,vcf.gz}" + - - blacklist_bed: + type: file + description: Bed file with regions to exclude + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cgh: - type: file - description: SV:s in CytoSure format - pattern: "*.cgh" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.cgh": + type: file + description: SV:s in CytoSure format + pattern: "*.cgh" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jemten" diff --git a/modules/nf-core/vcf2db/meta.yml b/modules/nf-core/vcf2db/meta.yml index b6529a6ae05..48795c21685 100644 --- a/modules/nf-core/vcf2db/meta.yml +++ b/modules/nf-core/vcf2db/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://github.com/quinlan-lab/vcf2db" tool_dev_url: "https://github.com/quinlan-lab/vcf2db" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.vcf.gz" - - ped: - type: file - description: PED file - pattern: "*.ped" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.vcf.gz" + - ped: + type: file + description: PED file + pattern: "*.ped" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: Gemini-compatible database file - pattern: "*.db" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.db": + type: file + description: Gemini-compatible database file + pattern: "*.db" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml index b091f2b1015..e5ce0838131 100644 --- a/modules/nf-core/vcf2maf/meta.yml +++ b/modules/nf-core/vcf2maf/meta.yml @@ -13,34 +13,41 @@ tools: tool_dev_url: "https://github.com/mskcc/vcf2maf" doi: "10.5281/zenodo.593251" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to convert to MAF format. Must be uncompressed. - - vep_cache: - type: file - description: | - Path to VEP cache dir. Required for correct running of VEP. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to convert to MAF format. Must be uncompressed. + - - fasta: + type: file + description: | + Path to reference genome fasta file. + - - vep_cache: + type: file + description: | + Path to VEP cache dir. Required for correct running of VEP. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - maf: - type: file - description: MAF file produced from VCF - pattern: "*.maf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.maf": + type: file + description: MAF file produced from VCF + pattern: "*.maf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/vcfanno/meta.yml b/modules/nf-core/vcfanno/meta.yml index 89c781ad166..18d27127c22 100644 --- a/modules/nf-core/vcfanno/meta.yml +++ b/modules/nf-core/vcfanno/meta.yml @@ -1,5 +1,6 @@ name: vcfanno -description: quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files +description: quickly annotate your VCF with any number of INFO fields from any number + of VCFs or BED files keywords: - vcf - bed @@ -14,48 +15,53 @@ tools: tool_dev_url: https://github.com/brentp/vcfanno doi: "10.1186/s13059-016-0973-5" license: ["MIT"] + identifier: biotools:vcfanno input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: query VCF file - pattern: "*.{vcf, vcf.gz}" - - vcf_tabix: - type: file - description: tabix index of query VCF - only needed if vcf is compressed - pattern: "*.vcf.gz.tbi" - - specific_resources: - type: map - description: A list of sample specific reference files defined in toml config, must also include indices if bgzipped. - - toml: - type: file - description: configuration file with reference file basenames - pattern: "*.toml" - - lua: - type: file - description: Lua file for custom annotations - pattern: "*.lua" - - resources: - type: map - description: List of reference files defined in toml config, must also include indices if bgzipped. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: query VCF file + pattern: "*.{vcf, vcf.gz}" + - tbi: + type: file + description: tabix index file for the query VCF + pattern: "*.tbi" + - specific_resources: + type: map + description: A list of sample specific reference files defined in toml config, + must also include indices if bgzipped. + - - toml: + type: file + description: configuration file with reference file basenames + pattern: "*.toml" + - - lua: + type: file + description: Lua file for custom annotations + pattern: "*.lua" + - - resources: + type: map + description: List of reference files defined in toml config, must also include + indices if bgzipped. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Annotated VCF file - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Annotated VCF file + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@matthdsm" diff --git a/modules/nf-core/vcflib/vcfbreakmulti/meta.yml b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml index 42a50ce4704..08dec641e37 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/meta.yml +++ b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml @@ -1,5 +1,6 @@ name: "vcflib_vcfbreakmulti" -description: If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields +description: If multiple alleles are specified in a single record, break the record + into several lines preserving allele-specific INFO fields keywords: - vcflib - vcfbreakmulti @@ -11,34 +12,37 @@ tools: documentation: https://github.com/vcflib/vcflib#USAGE doi: "10.1101/2021.05.21.445151" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.{.vcf.gz,vcf}" - - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.{.vcf.gz,vcf}" + - tbi: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/vcflib/vcffilter/meta.yml b/modules/nf-core/vcflib/vcffilter/meta.yml index f9fe81b52c0..359770651bd 100644 --- a/modules/nf-core/vcflib/vcffilter/meta.yml +++ b/modules/nf-core/vcflib/vcffilter/meta.yml @@ -13,34 +13,37 @@ tools: tool_dev_url: "https://github.com/vcflib/vcflib" doi: "10.1371/journal.pcbi.1009123" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test_sample_1' ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: Index file - pattern: "*.{tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test_sample_1' ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: Index file + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Filtered VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Filtered VCF file + pattern: "*.{vcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zachary-foster" maintainers: diff --git a/modules/nf-core/vcflib/vcffixup/meta.yml b/modules/nf-core/vcflib/vcffixup/meta.yml index be7eac6a960..4d95e4f0d4a 100644 --- a/modules/nf-core/vcflib/vcffixup/meta.yml +++ b/modules/nf-core/vcflib/vcffixup/meta.yml @@ -1,5 +1,6 @@ name: "vcflib_vcffixup" -description: Generates a VCF stream where AC and NS have been generated for each record using sample genotypes. +description: Generates a VCF stream where AC and NS have been generated for each record + using sample genotypes. keywords: - vcf - vcflib @@ -12,34 +13,37 @@ tools: documentation: https://github.com/vcflib/vcflib#USAGE doi: "10.1101/2021.05.21.445151" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.{.vcf.gz,vcf}" - - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.{.vcf.gz,vcf}" + - tbi: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/vcflib/vcfuniq/meta.yml b/modules/nf-core/vcflib/vcfuniq/meta.yml index 8adf6b62b4d..407b729f58c 100644 --- a/modules/nf-core/vcflib/vcfuniq/meta.yml +++ b/modules/nf-core/vcflib/vcfuniq/meta.yml @@ -1,5 +1,6 @@ name: vcflib_vcfuniq -description: List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record. +description: List unique genotypes. Like GNU uniq, but for VCF records. Remove records + which have the same position, ref, and alt as the previous record. keywords: - vcf - uniq @@ -11,34 +12,37 @@ tools: documentation: https://github.com/vcflib/vcflib#USAGE doi: "10.1101/2021.05.21.445151" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - tbi: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/vcftools/meta.yml b/modules/nf-core/vcftools/meta.yml index 09ad5908abc..b4c564ecaf2 100644 --- a/modules/nf-core/vcftools/meta.yml +++ b/modules/nf-core/vcftools/meta.yml @@ -6,287 +6,681 @@ keywords: - sort tools: - vcftools: - description: A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries + description: A set of tools written in Perl and C++ for working with VCF files. + This package only contains the C++ libraries whereas the package perl-vcftools-vcf + contains the perl libraries homepage: http://vcftools.sourceforge.net/ documentation: http://vcftools.sourceforge.net/man_latest.html licence: ["LGPL"] + identifier: biotools:vcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variant_file: - type: file - description: variant input file which can be vcf, vcf.gz, or bcf format. - - bed: - type: file - description: bed file which can be used with different arguments in vcftools (optional) - - diff_variant_file: - type: file - description: secondary variant file which can be used with the 'diff' suite of tools (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variant_file: + type: file + description: variant input file which can be vcf, vcf.gz, or bcf format. + - - bed: + type: file + description: bed file which can be used with different arguments in vcftools + (optional) + - - diff_variant_file: + type: file + description: secondary variant file which can be used with the 'diff' suite + of tools (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: vcf file (optional) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: vcf file (optional) + pattern: "*.vcf" - bcf: - type: file - description: bcf file (optional) - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: bcf file (optional) + pattern: "*.bcf" - frq: - type: file - description: Allele frequency for each site (optional) - pattern: "*.frq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.frq": + type: file + description: Allele frequency for each site (optional) + pattern: "*.frq" - frq_count: - type: file - description: Allele counts for each site (optional) - pattern: "*.frq.count" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.frq.count": + type: file + description: Allele counts for each site (optional) + pattern: "*.frq.count" - idepth: - type: file - description: mean depth per individual (optional) - pattern: "*.idepth" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idepth": + type: file + description: mean depth per individual (optional) + pattern: "*.idepth" - ldepth: - type: file - description: depth per site summed across individuals (optional) - pattern: "*.ildepth" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldepth": + type: file + description: depth per site summed across individuals (optional) + pattern: "*.ildepth" - ldepth_mean: - type: file - description: mean depth per site calculated across individuals (optional) - pattern: "*.ldepth.mean" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldepth.mean": + type: file + description: mean depth per site calculated across individuals (optional) + pattern: "*.ldepth.mean" - gdepth: - type: file - description: depth for each genotype in vcf file (optional) - pattern: "*.gdepth" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gdepth": + type: file + description: depth for each genotype in vcf file (optional) + pattern: "*.gdepth" - hap_ld: - type: file - description: r2, D, and D’ statistics using phased haplotypes (optional) - pattern: "*.hap.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap.ld": + type: file + description: r2, D, and D’ statistics using phased haplotypes (optional) + pattern: "*.hap.ld" - geno_ld: - type: file - description: squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional) - pattern: "*.geno.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.geno.ld": + type: file + description: squared correlation coefficient between genotypes encoded as 0, + 1 and 2 to represent the number of non-reference alleles in each individual + (optional) + pattern: "*.geno.ld" - geno_chisq: - type: file - description: test for genotype independence via the chi-squared statistic (optional) - pattern: "*.geno.chisq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.geno.chisq": + type: file + description: test for genotype independence via the chi-squared statistic (optional) + pattern: "*.geno.chisq" - list_hap_ld: - type: file - description: r2 statistics of the sites contained in the provided input file verses all other sites (optional) - pattern: "*.list.hap.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list.hap.ld": + type: file + description: r2 statistics of the sites contained in the provided input file + verses all other sites (optional) + pattern: "*.list.hap.ld" - list_geno_ld: - type: file - description: r2 statistics of the sites contained in the provided input file verses all other sites (optional) - pattern: "*.list.geno.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list.geno.ld": + type: file + description: r2 statistics of the sites contained in the provided input file + verses all other sites (optional) + pattern: "*.list.geno.ld" - interchrom_hap_ld: - type: file - description: r2 statistics for sites (haplotypes) on different chromosomes (optional) - pattern: "*.interchrom.hap.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interchrom.hap.ld": + type: file + description: r2 statistics for sites (haplotypes) on different chromosomes (optional) + pattern: "*.interchrom.hap.ld" - interchrom_geno_ld: - type: file - description: r2 statistics for sites (genotypes) on different chromosomes (optional) - pattern: "*.interchrom.geno.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interchrom.geno.ld": + type: file + description: r2 statistics for sites (genotypes) on different chromosomes (optional) + pattern: "*.interchrom.geno.ld" - tstv: - type: file - description: Transition / Transversion ratio in bins of size defined in options (optional) - pattern: "*.TsTv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv": + type: file + description: Transition / Transversion ratio in bins of size defined in options + (optional) + pattern: "*.TsTv" - tstv_summary: - type: file - description: Summary of all Transitions and Transversions (optional) - pattern: "*.TsTv.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv.summary": + type: file + description: Summary of all Transitions and Transversions (optional) + pattern: "*.TsTv.summary" - tstv_count: - type: file - description: Transition / Transversion ratio as a function of alternative allele count (optional) - pattern: "*.TsTv.count" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv.count": + type: file + description: Transition / Transversion ratio as a function of alternative allele + count (optional) + pattern: "*.TsTv.count" - tstv_qual: - type: file - description: Transition / Transversion ratio as a function of SNP quality threshold (optional) - pattern: "*.TsTv.qual" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv.qual": + type: file + description: Transition / Transversion ratio as a function of SNP quality threshold + (optional) + pattern: "*.TsTv.qual" - filter_summary: - type: file - description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional) - pattern: "*.FILTER.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.FILTER.summary": + type: file + description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category + (optional) + pattern: "*.FILTER.summary" - sites_pi: - type: file - description: Nucleotide divergency on a per-site basis (optional) - pattern: "*.sites.pi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sites.pi": + type: file + description: Nucleotide divergency on a per-site basis (optional) + pattern: "*.sites.pi" - windowed_pi: - type: file - description: Nucleotide diversity in windows, with window size determined by options (optional) - pattern: "*windowed.pi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.windowed.pi": + type: file + description: Nucleotide diversity in windows, with window size determined by + options (optional) + pattern: "*windowed.pi" - weir_fst: - type: file - description: Fst estimate from Weir and Cockerham’s 1984 paper (optional) - pattern: "*.weir.fst" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.weir.fst": + type: file + description: Fst estimate from Weir and Cockerham’s 1984 paper (optional) + pattern: "*.weir.fst" - heterozygosity: - type: file - description: Heterozygosity on a per-individual basis (optional) - pattern: "*.het" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.het": + type: file + description: Heterozygosity on a per-individual basis (optional) + pattern: "*.het" - hwe: - type: file - description: Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional) - pattern: "*.hwe" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hwe": + type: file + description: Contains the Observed numbers of Homozygotes and Heterozygotes + and the corresponding Expected numbers under HWE (optional) + pattern: "*.hwe" - tajima_d: - type: file - description: Tajima’s D statistic in bins with size of the specified number in options (optional) - pattern: "*.Tajima.D" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Tajima.D": + type: file + description: Tajima’s D statistic in bins with size of the specified number + in options (optional) + pattern: "*.Tajima.D" - freq_burden: - type: file - description: Number of variants within each individual of a specific frequency in options (optional) - pattern: "*.ifreqburden" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ifreqburden": + type: file + description: Number of variants within each individual of a specific frequency + in options (optional) + pattern: "*.ifreqburden" - lroh: - type: file - description: Long Runs of Homozygosity (optional) - pattern: "*.LROH" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.LROH": + type: file + description: Long Runs of Homozygosity (optional) + pattern: "*.LROH" - relatedness: - type: file - description: Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional) - pattern: "*.relatedness" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.relatedness": + type: file + description: Relatedness statistic based on the method of Yang et al, Nature + Genetics 2010 (doi:10.1038/ng.608) (optional) + pattern: "*.relatedness" - relatedness2: - type: file - description: Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional) - pattern: "*.relatedness2" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.relatedness2": + type: file + description: Relatedness statistic based on the method of Manichaikul et al., + BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional) + pattern: "*.relatedness2" - lqual: - type: file - description: per-site SNP quality (optional) - pattern: "*.lqual" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lqual": + type: file + description: per-site SNP quality (optional) + pattern: "*.lqual" - missing_individual: - type: file - description: Missingness on a per-individual basis (optional) - pattern: "*.imiss" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.imiss": + type: file + description: Missingness on a per-individual basis (optional) + pattern: "*.imiss" - missing_site: - type: file - description: Missingness on a per-site basis (optional) - pattern: "*.lmiss" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lmiss": + type: file + description: Missingness on a per-site basis (optional) + pattern: "*.lmiss" - snp_density: - type: file - description: Number and density of SNPs in bins of size defined by option (optional) - pattern: "*.snpden" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.snpden": + type: file + description: Number and density of SNPs in bins of size defined by option (optional) + pattern: "*.snpden" - kept_sites: - type: file - description: All sites that have been kept after filtering (optional) - pattern: "*.kept.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.kept.sites": + type: file + description: All sites that have been kept after filtering (optional) + pattern: "*.kept.sites" - removed_sites: - type: file - description: All sites that have been removed after filtering (optional) - pattern: "*.removed.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.removed.sites": + type: file + description: All sites that have been removed after filtering (optional) + pattern: "*.removed.sites" - singeltons: - type: file - description: Location of singletons, and the individual they occur in (optional) - pattern: "*.singeltons" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.singletons": + type: file + description: Location of singletons, and the individual they occur in (optional) + pattern: "*.singeltons" - indel_hist: - type: file - description: Histogram file of the length of all indels (including SNPs) (optional) - pattern: "*.indel_hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.indel.hist": + type: file + description: Histogram file of the length of all indels (including SNPs) (optional) + pattern: "*.indel_hist" - hapcount: - type: file - description: Unique haplotypes within user specified bins (optional) - pattern: "*.hapcount" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hapcount": + type: file + description: Unique haplotypes within user specified bins (optional) + pattern: "*.hapcount" - mendel: - type: file - description: Mendel errors identified in trios (optional) - pattern: "*.mendel" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mendel": + type: file + description: Mendel errors identified in trios (optional) + pattern: "*.mendel" - format: - type: file - description: Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional) - pattern: "*.FORMAT" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.FORMAT": + type: file + description: Extracted information from the genotype fields in the VCF file + relating to a specfied FORMAT identifier (optional) + pattern: "*.FORMAT" - info: - type: file - description: Extracted information from the INFO field in the VCF file (optional) - pattern: "*.INFO" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.INFO": + type: file + description: Extracted information from the INFO field in the VCF file (optional) + pattern: "*.INFO" - genotypes_matrix: - type: file - description: | - Genotypes output as large matrix. - Genotypes of each individual on a separate line. - Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles. - Missing genotypes are represented by -1 (optional) - pattern: "*.012" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.012": + type: file + description: | + Genotypes output as large matrix. + Genotypes of each individual on a separate line. + Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles. + Missing genotypes are represented by -1 (optional) + pattern: "*.012" - genotypes_matrix_individual: - type: file - description: Details the individuals included in the main genotypes_matrix file (optional) - pattern: "*.012.indv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.012.indv": + type: file + description: Details the individuals included in the main genotypes_matrix file + (optional) + pattern: "*.012.indv" - genotypes_matrix_position: - type: file - description: Details the site locations included in the main genotypes_matrix file (optional) - pattern: "*.012.pos" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.012.pos": + type: file + description: Details the site locations included in the main genotypes_matrix + file (optional) + pattern: "*.012.pos" - impute_hap: - type: file - description: Phased haplotypes in IMPUTE reference-panel format (optional) - pattern: "*.impute.hap" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.impute.hap": + type: file + description: Phased haplotypes in IMPUTE reference-panel format (optional) + pattern: "*.impute.hap" - impute_hap_legend: - type: file - description: Impute haplotype legend file (optional) - pattern: "*.impute.hap.legend" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.impute.hap.legend": + type: file + description: Impute haplotype legend file (optional) + pattern: "*.impute.hap.legend" - impute_hap_indv: - type: file - description: Impute haplotype individuals file (optional) - pattern: "*.impute.hap.indv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.impute.hap.indv": + type: file + description: Impute haplotype individuals file (optional) + pattern: "*.impute.hap.indv" - ldhat_sites: - type: file - description: Output data in LDhat format, sites (optional) - pattern: "*.ldhat.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldhat.sites": + type: file + description: Output data in LDhat format, sites (optional) + pattern: "*.ldhat.sites" - ldhat_locs: - type: file - description: output data in LDhat format, locations (optional) - pattern: "*.ldhat.locs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldhat.locs": + type: file + description: output data in LDhat format, locations (optional) + pattern: "*.ldhat.locs" - beagle_gl: - type: file - description: Genotype likelihoods for biallelic sites (optional) - pattern: "*.BEAGLE.GL" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.BEAGLE.GL": + type: file + description: Genotype likelihoods for biallelic sites (optional) + pattern: "*.BEAGLE.GL" - beagle_pl: - type: file - description: Genotype likelihoods for biallelic sites (optional) - pattern: "*.BEAGLE.PL" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.BEAGLE.PL": + type: file + description: Genotype likelihoods for biallelic sites (optional) + pattern: "*.BEAGLE.PL" - ped: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.ped" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ped": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.ped" - map_: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.map" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.map": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.map" - tped: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.tped" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tped": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.tped" - tfam: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.tfam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tfam": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.tfam" - diff_sites_in_files: - type: file - description: Sites that are common / unique to each file specified in optional inputs (optional) - pattern: "*.diff.sites.in.files" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.sites_in_files": + type: file + description: Sites that are common / unique to each file specified in optional + inputs (optional) + pattern: "*.diff.sites.in.files" - diff_indv_in_files: - type: file - description: Individuals that are common / unique to each file specified in optional inputs (optional) - pattern: "*.diff.indv.in.files" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.indv_in_files": + type: file + description: Individuals that are common / unique to each file specified in + optional inputs (optional) + pattern: "*.diff.indv.in.files" - diff_sites: - type: file - description: Discordance on a site by site basis, specified in optional inputs (optional) - pattern: "*.diff.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.sites": + type: file + description: Discordance on a site by site basis, specified in optional inputs + (optional) + pattern: "*.diff.sites" - diff_indv: - type: file - description: Discordance on a individual by individual basis, specified in optional inputs (optional) - pattern: "*.diff.indv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.indv": + type: file + description: Discordance on a individual by individual basis, specified in optional + inputs (optional) + pattern: "*.diff.indv" - diff_discd_matrix: - type: file - description: Discordance matrix between files specified in optional inputs (optional) - pattern: "*.diff.discordance.matrix" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.discordance.matrix": + type: file + description: Discordance matrix between files specified in optional inputs (optional) + pattern: "*.diff.discordance.matrix" - diff_switch_error: - type: file - description: Switch errors found between sites (optional) - pattern: "*.diff.switch" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.switch": + type: file + description: Switch errors found between sites (optional) + pattern: "*.diff.switch" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Mark-S-Hill" maintainers: diff --git a/modules/nf-core/velocyto/meta.yml b/modules/nf-core/velocyto/meta.yml index b5c0cacc625..9c4a8f77486 100644 --- a/modules/nf-core/velocyto/meta.yml +++ b/modules/nf-core/velocyto/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "velocyto" description: | @@ -36,49 +35,53 @@ tools: tool_dev_url: https://github.com/velocyto-team/velocyto.py doi: "10.1038/s41586-018-0414-6" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - barcodes: - type: file - description: Valid barcodes file, to filter the bam - pattern: "*.tsv.gz" - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - sorted_bam: - type: file - description: Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam` - pattern: "*.bam" - - gtf: - type: file - description: genome annotation file - pattern: "*.gtf" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - barcodes: + type: file + description: Valid barcodes file, to filter the bam + pattern: "*.tsv.gz" + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - sorted_bam: + type: file + description: Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t + CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam` + pattern: "*.bam" + - - gtf: + type: file + description: genome annotation file + pattern: "*.gtf" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - loom: - type: file - description: Loom file with counts divided in spliced/unspliced/ambiguous. - pattern: "*.loom" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.loom": + type: file + description: Loom file with counts divided in spliced/unspliced/ambiguous. + pattern: "*.loom" + - "*.velocyto.log": + type: file + description: Loom file with counts divided in spliced/unspliced/ambiguous. + pattern: "*.loom" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tucano" maintainers: diff --git a/modules/nf-core/verifybamid/verifybamid/meta.yml b/modules/nf-core/verifybamid/verifybamid/meta.yml index 1897edd1529..82cedad03b4 100644 --- a/modules/nf-core/verifybamid/verifybamid/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid/meta.yml @@ -1,79 +1,127 @@ name: "verifybamid_verifybamid" -description: Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. +description: Detecting and estimating inter-sample DNA contamination became a crucial + quality assessment step to ensure high quality sequence reads and reliable downstream + analysis. keywords: - qc - contamination - bam tools: - "verifybamid": - description: "verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples." + description: "verifyBamID is a software that verifies whether the reads in particular + file match previously known genotypes for an individual (or group of individuals), + and checks whether the reads are contaminated as a mixture of two samples." homepage: "https://genome.sph.umich.edu/wiki/VerifyBamID" documentation: "http://genome.sph.umich.edu/wiki/VerifyBamID" tool_dev_url: "https://github.com/statgen/verifyBamID" doi: "10.1016/j.ajhg.2012.09.004" licence: ["GPL v3"] + identifier: biotools:verifybamid input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file. - It also requires to contain "@RG" header lines to annotation different readGroups (sequencing runs and lanes). - The SM tag in the "@RG" header should match with one of the genotyped sample. - pattern: "*.bam" - - bai: - type: file - description: BAM index file BAI - pattern: "*.bai" - - refvcf: - type: file - description: | - The input VCF file contains - (1) external genotype information and/or - (2) allele frequency information as AF entry or AC/AN entries in the INFO field. - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file. + It also requires to contain "@RG" header lines to annotation different readGroups (sequencing runs and lanes). + The SM tag in the "@RG" header should match with one of the genotyped sample. + pattern: "*.bam" + - bai: + type: file + description: BAM index file BAI + pattern: "*.bai" + - - refvcf: + type: file + description: | + The input VCF file contains + (1) external genotype information and/or + (2) allele frequency information as AF entry or AC/AN entries in the INFO field. + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: Detailed summary of the verifyBamID result. - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Detailed summary of the verifyBamID result. + pattern: "*.log" - selfsm: - type: file - description: Per-sample statistics describing how well the sample matches to the annotated sample. - pattern: "*.selfSM" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selfSM": + type: file + description: Per-sample statistics describing how well the sample matches to + the annotated sample. + pattern: "*.selfSM" - depthsm: - type: file - description: The depth distribution of the sequence reads per sample - pattern: "*.depthSM" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthSM": + type: file + description: The depth distribution of the sequence reads per sample + pattern: "*.depthSM" - selfrg: - type: file - description: Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without --ignoreRG option) - pattern: "*.selfRG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selfRG": + type: file + description: Per-readGroup statistics describing how well each lane matches + to the annotated sample. (available only without --ignoreRG option) + pattern: "*.selfRG" - depthrg: - type: file - description: The depth distribution of the sequence reads per readGroup. (available only without --ignoreRG option) - pattern: "*.depthRG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthRG": + type: file + description: The depth distribution of the sequence reads per readGroup. (available + only without --ignoreRG option) + pattern: "*.depthRG" - bestsm: - type: file - description: Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with --best option) - pattern: "*.bestSM" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bestSM": + type: file + description: Per-sample best-match statistics with best-matching sample among + the genotyped sample (available only with --best option) + pattern: "*.bestSM" - bestrg: - type: file - description: Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with --best and without --ignoreRG option) - pattern: "*.bestRG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bestRG": + type: file + description: Per-readgroup best-match statistics with best-matching sample among + the genotyped sample (available only with --best and without --ignoreRG option) + pattern: "*.bestRG" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@manifestoso" maintainers: diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml index 313047deb64..b511fc3cd01 100644 --- a/modules/nf-core/verifybamid/verifybamid2/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml @@ -1,5 +1,7 @@ name: "VERIFYBAMID_VERIFYBAMID2" -description: Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. +description: Detecting and estimating inter-sample DNA contamination became a crucial + quality assessment step to ensure high quality sequence reads and reliable downstream + analysis. keywords: - contamination - bam @@ -7,80 +9,117 @@ keywords: - DNA contamination estimation tools: - "verifybamid2": - description: "A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method." + description: "A robust tool for DNA contamination estimation from sequence reads + using ancestry-agnostic method." homepage: "http://griffan.github.io/VerifyBamID" documentation: "http://griffan.github.io/VerifyBamID" tool_dev_url: "https://github.com/Griffan/VerifyBamID" doi: "10.1101/gr.246934.118" licence: ["MIT"] + identifier: biotools:verifybamid input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAI/CRAI/CSI index file - pattern: "*.{bai,crai,csi}" - - svd_ud: - type: file - description: .UD matrix file from SVD result of genotype matrix - pattern: "*.UD" - - svd_mu: - type: file - description: .mu matrix file of genotype matrix - pattern: "*.mu" - - svd_bed: - type: file - description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] - pattern: "*.bed" - - references: - type: file - description: reference file [Required] - pattern: "*.fasta" - - refvcf: - type: file - description: Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional] - pattern: "*.vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAI/CRAI/CSI index file + pattern: "*.{bai,crai,csi}" + - - svd_ud: + type: file + description: .UD matrix file from SVD result of genotype matrix + pattern: "*.UD" + - svd_mu: + type: file + description: .mu matrix file of genotype matrix + pattern: "*.mu" + - svd_bed: + type: file + description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] + pattern: "*.bed" + - - refvcf: + type: file + description: Reference panel VCF with genotype information, for generation of + .UD .mu .bed files [Optional] + pattern: "*.vcf" + - - references: + type: file + description: reference file [Required] + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mu: - type: file - description: .mu matrix file of genotype matrix from customized reference vcf input - pattern: "*.mu" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Detailed summary of the VerifyBamId2 results + pattern: "*.log" - ud: - type: file - description: .UD matrix file from customized reference vcf input - pattern: "*.UD" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.UD": + type: file + description: .UD matrix file from customized reference vcf input + pattern: "*.UD" - bed: - type: file - description: .Bed file from customized reference marker vcf input - pattern: "*.bed" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - log: - type: file - description: Detailed summary of the VerifyBamId2 results - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: .Bed file from customized reference marker vcf input + pattern: "*.bed" + - mu: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mu": + type: file + description: .mu matrix file of genotype matrix from customized reference vcf + input + pattern: "*.mu" - self_sm: - type: file - description: Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level. - pattern: "*.selfSM" - - ancenstry: - type: file - description: PC coordinates for both intended sample and contaminating sample, with each row being one PC. - pattern: "*.Ancestry" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selfSM": + type: file + description: Shares the same format as legacy VB1 and the key information FREEMIX + indicates the estimated contamination level. + pattern: "*.selfSM" + - ancestry: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Ancestry": + type: file + description: Ancestry information + pattern: "*.Ancestry" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@manifestoso" maintainers: diff --git a/modules/nf-core/vg/construct/meta.yml b/modules/nf-core/vg/construct/meta.yml index 0f1c2b84ff1..e8ef6ad962c 100644 --- a/modules/nf-core/vg/construct/meta.yml +++ b/modules/nf-core/vg/construct/meta.yml @@ -1,5 +1,6 @@ name: "vg_construct" -description: Constructs a graph from a reference and variant calls or a multiple sequence alignment file +description: Constructs a graph from a reference and variant calls or a multiple sequence + alignment file keywords: - vg - graph @@ -15,47 +16,62 @@ tools: homepage: https://github.com/vgteam/vg documentation: https://github.com/vgteam/vg/wiki licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: list - description: | - Either one or more VCF files containing different contigs or a multiple sequence alignment file - pattern: "*.{vcf.gz,fa,fasta,fna,clustal}" - - tbis: - type: list - description: The index files for the VCF files - pattern: "*.tbi" - - insertions_fasta: - type: file - description: A FASTA file containing insertion sequences (referred to in the VCF file(s)) - pattern: "*.{fa,fasta,fna}" - - fasta: - type: file - description: The reference FASTA file (cannot be used in combination with `msa`, but is required when using `vcfs`) - pattern: "*.{fa,fasta,fna}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: list + description: | + Either one or more VCF files containing different contigs or a multiple sequence alignment file + pattern: "*.{vcf.gz,fa,fasta,fna,clustal}" + - tbis: + type: list + description: The index files for the VCF files + pattern: "*.tbi" + - insertions_fasta: + type: file + description: A FASTA file containing insertion sequences (referred to in the + VCF file(s)) + pattern: "*.{fa,fasta,fna}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference FASTA file (cannot be used in combination with `msa`, + but is required when using `vcfs`) + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - graph: - type: file - description: The constructed graph - pattern: "*.vg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vg": + type: file + description: The constructed graph + pattern: "*.vg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/vg/deconstruct/meta.yml b/modules/nf-core/vg/deconstruct/meta.yml index e1275e47eab..86e8ef22905 100644 --- a/modules/nf-core/vg/deconstruct/meta.yml +++ b/modules/nf-core/vg/deconstruct/meta.yml @@ -1,5 +1,6 @@ name: vg_deconstruct -description: Deconstruct snarls present in a variation graph in GFA format to variants in VCF format +description: Deconstruct snarls present in a variation graph in GFA format to variants + in VCF format keywords: - vcf - gfa @@ -15,38 +16,43 @@ tools: homepage: https://github.com/vgteam/vg documentation: https://github.com/vgteam/vg/wiki licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA format - pattern: "*.{gfa}" - - pb: - type: file - description: Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with "pb". See "vg snarls". - pattern: "*.{pb}" - - gbwt: - type: file - description: Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE. - pattern: "*.{gbwt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA format + pattern: "*.{gfa}" + - - pb: + type: file + description: Optional snarls file (from vg snarls) to avoid recomputing. Usually + ends with "pb". See "vg snarls". + pattern: "*.{pb}" + - - gbwt: + type: file + description: Optional GBWT file (from vg gbwt) so to only consider alt traversals + that correspond to GBWT threads FILE. + pattern: "*.{gbwt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Variants in VCF format - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variants in VCF format + pattern: "*.{vcf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh, @subwaystation" maintainers: diff --git a/modules/nf-core/vg/index/meta.yml b/modules/nf-core/vg/index/meta.yml index 1761ac6aea1..c929349e813 100644 --- a/modules/nf-core/vg/index/meta.yml +++ b/modules/nf-core/vg/index/meta.yml @@ -13,34 +13,44 @@ tools: homepage: https://github.com/vgteam/vg documentation: https://github.com/vgteam/vg/wiki licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: list - description: One or more input graph files created with `vg/construct` - pattern: "*.vg" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: list + description: One or more input graph files created with `vg/construct` + pattern: "*.vg" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - xg: - type: file - description: File containing a succint, queryable version of the input graph(s) or read for GCSA or distance indexing - pattern: "*.xg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xg": + type: file + description: File containing a succint, queryable version of the input graph(s) + or read for GCSA or distance indexing + pattern: "*.xg" - vg_index: - type: file - description: An index of the graph(s) created when `--index-sorted-vg` is supplied. - pattern: "*.vgi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vgi": + type: file + description: An index of the graph(s) created when `--index-sorted-vg` is supplied. + pattern: "*.vgi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/viennarna/rnacofold/meta.yml b/modules/nf-core/viennarna/rnacofold/meta.yml index fa68573698e..61d512995f4 100644 --- a/modules/nf-core/viennarna/rnacofold/meta.yml +++ b/modules/nf-core/viennarna/rnacofold/meta.yml @@ -31,37 +31,47 @@ tools: documentation: "https://viennarna.readthedocs.io/en/latest/" doi: 10.1186/1748-7188-6-26 licence: ["custom"] + identifier: biotools:viennarna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rnacofold_fasta: - type: file - description: | - A fasta file containing RNA or transcript sequences - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rnacofold_fasta: + type: file + description: | + A fasta file containing RNA or transcript sequences + pattern: "*.{fasta,fa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - rnacofold_csv: - type: file - description: The CSV Output of RNAcofold that has the predicted structure and energies - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: The CSV Output of RNAcofold that has the predicted structure and + energies + pattern: "*.{csv}" - rnacofold_ps: - type: file - description: The text Output of RNAfold that contains the predicted secondary structure in postscript format - pattern: "*.{ps}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ps": + type: file + description: The text Output of RNAfold that contains the predicted secondary + structure in postscript format + pattern: "*.{ps}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kokul-atx" maintainers: diff --git a/modules/nf-core/viennarna/rnafold/meta.yml b/modules/nf-core/viennarna/rnafold/meta.yml index 0081b30a0b5..ef7bf479d19 100644 --- a/modules/nf-core/viennarna/rnafold/meta.yml +++ b/modules/nf-core/viennarna/rnafold/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "viennarna_rnafold" -description: Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs. +description: Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate + minimum free energy secondary structures and partition function of RNAs. keywords: - RNA - fasta @@ -21,25 +21,46 @@ tools: documentation: "https://viennarna.readthedocs.io/en/latest/" doi: 10.1186/1748-7188-6-26 licence: ["custom"] + identifier: biotools:viennarna input: - - fasta: - type: file - description: | - A fasta file containing RNA or transcript sequences - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + A fasta file containing RNA or transcript sequences + pattern: "*.{fasta,fa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rnafold_txt: - type: file - description: The text Output of RNAfold that - pattern: "*.{fold}" + - meta: + type: file + description: The text Output of RNAfold that + pattern: "*.{fold}" + - "*.fold": + type: file + description: The text Output of RNAfold that + pattern: "*.{fold}" - rnafold_ps: - type: file - description: The text Output of RNAfold that - pattern: "*.ss" + - meta: + type: file + description: The text Output of RNAfold that + pattern: "*.ss" + - "*.ps": + type: file + description: The text Output of RNAfold that + pattern: "*.ss" + - versions: + - meta: + type: file + description: File containing software versions + pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kokul-atx" maintainers: diff --git a/modules/nf-core/viennarna/rnalfold/meta.yml b/modules/nf-core/viennarna/rnalfold/meta.yml index 7c7d24a1890..b642745a698 100644 --- a/modules/nf-core/viennarna/rnalfold/meta.yml +++ b/modules/nf-core/viennarna/rnalfold/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "viennarna_rnalfold" description: calculate locally stable secondary structures of RNAs @@ -22,23 +21,25 @@ tools: documentation: "https://viennarna.readthedocs.io/en/latest/" doi: 10.1186/1748-7188-6-26 licence: ["custom"] + identifier: biotools:viennarna input: - - fasta: - type: file - description: | - A fasta file containing RNA or transcript sequences - pattern: "*.{fasta,fa}" + - - fasta: + type: file + description: | + A fasta file containing RNA or transcript sequences + pattern: "*.{fasta,fa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rnalfold_txt: - type: file - description: The text Output of RNALfold - pattern: "*.{lfold}" - + - "*.lfold": + type: file + description: The text Output of RNALfold + pattern: "*.{lfold}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kokul-atx" maintainers: diff --git a/modules/nf-core/vireo/meta.yml b/modules/nf-core/vireo/meta.yml index 43c491235a9..77e5fa42072 100644 --- a/modules/nf-core/vireo/meta.yml +++ b/modules/nf-core/vireo/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "vireo" description: Use vireo to perform donor deconvolution for multiplexed scRNA-seq data @@ -14,61 +13,75 @@ tools: tool_dev_url: "https://github.com/single-cell-genetics/vireo" doi: "10.1186/s13059-019-1865-2" licence: ["Apache-2.0"] + identifier: biotools:Vireo input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - cell_data: - type: file - description: The cell genotype file in VCF format or cellSNP folder with sparse matrices. - pattern: "*.vcf|*/" - - n_donor: - type: integer - description: Number of donors to demultiplex. - - donor_file: - type: file - description: The optional donor genotype file in VCF format. - pattern: "*.vcf" - - vartrix_data: - type: file - description: The optional cell genotype files in vartrix outputs. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - cell_data: + type: file + description: The cell genotype file in VCF format or cellSNP folder with sparse + matrices. + pattern: "*.vcf|*/" + - n_donor: + type: integer + description: Number of donors to demultiplex. + - donor_file: + type: file + description: The optional donor genotype file in VCF format. + pattern: "*.vcf" + - vartrix_data: + type: file + description: The optional cell genotype files in vartrix outputs. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - summary: - type: file - description: Summary tsv file of deconvolution result. - pattern: "*_summary.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_summary.tsv": + type: file + description: Summary tsv file of deconvolution result. + pattern: "*_summary.tsv" - donor_ids: - type: file - description: Donor assignment with detailed statistics. - pattern: "*_donor_ids.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_donor_ids.tsv": + type: file + description: Donor assignment with detailed statistics. + pattern: "*_donor_ids.tsv" - prob_singlets: - type: file - description: contains probability of classifing singlets - pattern: "*_prob_singlet.tsv.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_prob_singlet.tsv.gz": + type: file + description: contains probability of classifing singlets + pattern: "*_prob_singlet.tsv.gz" - prob_doublets: - type: file - description: contains probability of classifing doublets - pattern: "*_prob_doublet.tsv.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_prob_doublet.tsv.gz": + type: file + description: contains probability of classifing doublets + pattern: "*_prob_doublet.tsv.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/vrhyme/extractunbinned/meta.yml b/modules/nf-core/vrhyme/extractunbinned/meta.yml index ef52cf111c5..c9a9b941d59 100644 --- a/modules/nf-core/vrhyme/extractunbinned/meta.yml +++ b/modules/nf-core/vrhyme/extractunbinned/meta.yml @@ -8,40 +8,51 @@ keywords: - extractunbinned tools: - "vrhyme": - description: "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs)." + description: "vRhyme functions by utilizing coverage variance comparisons and + supervised machine learning classification of sequence features to construct + viral metagenome-assembled genomes (vMAGs)." homepage: https://github.com/AnantharamanLab/vRhyme documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 licence: ["GPL v3 license", "GPL v3"] + identifier: biotools:vrhyme input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing contigs/scaffolds input into vRhyme - pattern: "*.{fasta,fna,fa}" - - membership: - type: file - description: TSV file containing information regarding which bins input sequences were placed information - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - membership: + type: file + description: TSV file containing information regarding which bins input sequences + were placed information + pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing contigs/scaffolds input into vRhyme + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - unbinned_sequences: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_unbinned_sequences.fasta": + type: file + description: FASTA file containing unbinned sequences + pattern: "*_unbinned_sequences.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - unbinnned_sequences: - type: file - description: FASTA file containing sequences unbinned by vRhyme - pattern: "*_unbinned_sequences.fasta" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/vrhyme/linkbins/meta.yml b/modules/nf-core/vrhyme/linkbins/meta.yml index df8aea7c9bb..1302b2ea24f 100644 --- a/modules/nf-core/vrhyme/linkbins/meta.yml +++ b/modules/nf-core/vrhyme/linkbins/meta.yml @@ -8,35 +8,41 @@ keywords: - linkbins tools: - "vrhyme": - description: "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs)." + description: "vRhyme functions by utilizing coverage variance comparisons and + supervised machine learning classification of sequence features to construct + viral metagenome-assembled genomes (vMAGs)." homepage: https://github.com/AnantharamanLab/vRhyme documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 licence: ["GPL v3 license", "GPL v3"] + identifier: biotools:vrhyme input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bins: - type: directory - description: Directory file containing bin FASTA files output by vRhyme (each bin having multiple sequences) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bins: + type: directory + description: Directory file containing bin FASTA files output by vRhyme (each + bin having multiple sequences) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - linked_bins: - type: file - description: FASTA file containing all bins that have been linked by N's - pattern: "*_linked_bins.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_linked_bins.fasta": + type: file + description: FASTA file containing all bins that have been linked by N's + pattern: "*_linked_bins.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/vrhyme/vrhyme/environment.yml b/modules/nf-core/vrhyme/vrhyme/environment.yml index c343a66a165..b4f66fea212 100644 --- a/modules/nf-core/vrhyme/vrhyme/environment.yml +++ b/modules/nf-core/vrhyme/vrhyme/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - bioconda::vrhyme=1.1.0 - - conda-forge::python=3.10.8 # Locked with the container - - conda-forge::numpy=1.23.5 # Locked with the container - - conda-forge::scikit-learn=1.2.2 # Locked with the container + - conda-forge::numpy=1.23.5 + - conda-forge::python=3.10.8 + - conda-forge::scikit-learn=1.2.2 diff --git a/modules/nf-core/vrhyme/vrhyme/meta.yml b/modules/nf-core/vrhyme/vrhyme/meta.yml index 659d805b88c..e020a1acde0 100644 --- a/modules/nf-core/vrhyme/vrhyme/meta.yml +++ b/modules/nf-core/vrhyme/vrhyme/meta.yml @@ -8,48 +8,70 @@ keywords: - vrhyme tools: - "vrhyme": - description: "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs)." + description: "vRhyme functions by utilizing coverage variance comparisons and + supervised machine learning classification of sequence features to construct + viral metagenome-assembled genomes (vMAGs)." homepage: https://github.com/AnantharamanLab/vRhyme documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 licence: ["GPL v3", "GPL v3 license"] + identifier: biotools:vrhyme input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Preprocessed FASTQ file containing sample reads - pattern: "*.{fastq}" - - fasta: - type: file - description: Contigs/scaffolds identified as viral - pattern: "*.{fna,fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Preprocessed FASTQ file containing sample reads + pattern: "*.{fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Contigs/scaffolds identified as viral + pattern: "*.{fna,fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bins: - type: directory - description: Directory containing bin FASTA files - pattern: "**/vRhyme_best_bins_fasta/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vRhyme_best_bins_fasta/: + type: directory + description: Directory containing bin FASTA files + pattern: "**/vRhyme_best_bins_fasta/" - membership: - type: file - description: TSV file describing the contig/scaffold membership of each bin - pattern: "vRhyme_best_bins.*.membership.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "**/vRhyme_best_bins.*.membership.tsv": + type: file + description: TSV file describing the contig/scaffold membership of each bin + pattern: "vRhyme_best_bins.*.membership.tsv" - summary: - type: file - description: TSV file summarizing the attributes of each bin - pattern: "vRhyme_best_bins.*.summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "**/vRhyme_best_bins.*.summary.tsv": + type: file + description: TSV file summarizing the attributes of each bin + pattern: "vRhyme_best_bins.*.summary.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/vsearch/cluster/meta.yml b/modules/nf-core/vsearch/cluster/meta.yml index 60d64347c50..5013feb55e2 100644 --- a/modules/nf-core/vsearch/cluster/meta.yml +++ b/modules/nf-core/vsearch/cluster/meta.yml @@ -1,67 +1,160 @@ name: "vsearch_cluster" -description: Cluster sequences using a single-pass, greedy centroid-based clustering algorithm. +description: Cluster sequences using a single-pass, greedy centroid-based clustering + algorithm. keywords: - vsearch - clustering - microbiome tools: - vsearch: - description: VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative) + description: VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative) homepage: https://github.com/torognes/vsearch documentation: https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf tool_dev_url: https://github.com/torognes/vsearch doi: 10.7717/peerj.2584 licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - fasta: - type: file - description: Sequences to cluster in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - fasta: + type: file + description: Sequences to cluster in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - aln: - type: file - description: Results in pairwise alignment format - pattern: "*.aln.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.aln.gz": + type: file + description: Results in pairwise alignment format + pattern: "*.aln.gz" - biom: - type: file - description: Results in an OTU table in the biom version 1.0 file format - pattern: "*.biom.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.biom.gz": + type: file + description: Results in an OTU table in the biom version 1.0 file format + pattern: "*.biom.gz" - mothur: - type: file - description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format - pattern: "*.mothur.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.mothur.tsv.gz": + type: file + description: Results in an OTU table in the mothur ’shared’ tab-separated plain + text file format + pattern: "*.mothur.tsv.gz" - otu: - type: file - description: Results in an OTU table in the classic tab-separated plain text format - pattern: "*.otu.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.otu.tsv.gz": + type: file + description: Results in an OTU table in the classic tab-separated plain text + format + pattern: "*.otu.tsv.gz" - bam: - type: file - description: Results written in bam format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: Results written in bam format + pattern: "*.bam" - out: - type: file - description: Results in tab-separated output, columns defined by user - pattern: "*.out.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.out.tsv.gz": + type: file + description: Results in tab-separated output, columns defined by user + pattern: "*.out.tsv.gz" - blast: - type: file - description: Tab delimited results in blast-like tabular format - pattern: "*.blast.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.blast.tsv.gz": + type: file + description: Tab delimited results in blast-like tabular format + pattern: "*.blast.tsv.gz" - uc: - type: file - description: Tab delimited results in a uclust-like format with 10 columns - pattern: "*.uc.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.uc.tsv.gz": + type: file + description: Tab delimited results in a uclust-like format with 10 columns + pattern: "*.uc.gz" + - centroids: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.centroids.fasta.gz": + type: file + description: Centroid sequences in FASTA format + pattern: "*.centroids.fasta.gz" + - clusters: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.clusters.fasta*.gz": + type: file + description: Clustered sequences in FASTA format + pattern: "*.clusters.fasta*.gz" + - profile: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.profile.txt.gz": + type: file + description: Profile of the clustering results + pattern: "*.profile.txt.gz" + - msa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.msa.fasta.gz": + type: file + description: Multiple sequence alignment of the centroids + pattern: "*.msa.fasta.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/vsearch/dereplicate/meta.yml b/modules/nf-core/vsearch/dereplicate/meta.yml index 061f34346af..5023f81cf71 100644 --- a/modules/nf-core/vsearch/dereplicate/meta.yml +++ b/modules/nf-core/vsearch/dereplicate/meta.yml @@ -1,5 +1,7 @@ name: "vsearch_dereplicate" -description: Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same). +description: Merge strictly identical sequences contained in filename. Identical sequences + are defined as having the same length and the same string of nucleotides (case insensitive, + T and U are considered the same). keywords: - vsearch/dereplicate - vsearch @@ -16,34 +18,42 @@ tools: tool_dev_url: https://github.com/torognes/vsearch doi: 10.7717/peerj.2584 licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - fasta: - type: file - description: Sequences to be sorted in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - fasta: + type: file + description: Sequences to be sorted in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: dereplicated fasta - pattern: "*.fasta" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ]` + - "*.derep.fasta": + type: file + description: dereplicated fasta + pattern: "*.fasta" - clustering: - type: file - description: dereplicated derep.uc file - pattern: "*.uc" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ]` + - "*.derep.uc": + type: file + description: dereplicated derep.uc file + pattern: "*.uc" - log: - type: file - description: a log file of the run - pattern: "*.derep.log" + - "*.derep.log": + type: file + description: a log file of the run + pattern: "*.derep.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@chriswyatt1" maintainers: diff --git a/modules/nf-core/vsearch/fastqfilter/meta.yml b/modules/nf-core/vsearch/fastqfilter/meta.yml index 02ac685eeba..b91fc90d609 100644 --- a/modules/nf-core/vsearch/fastqfilter/meta.yml +++ b/modules/nf-core/vsearch/fastqfilter/meta.yml @@ -1,5 +1,6 @@ name: "vsearch_fastqfilter" -description: Performs quality filtering and / or conversion of a FASTQ file to FASTA format. +description: Performs quality filtering and / or conversion of a FASTQ file to FASTA + format. keywords: - vsearch/fastqfilter - vsearch @@ -10,35 +11,44 @@ keywords: - population genetics tools: - "vsearch": - description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" + description: "VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative)" homepage: "https://github.com/torognes/vsearch" tool_dev_url: "https://github.com/torognes/vsearch" doi: "10.7717/peerj.2584" licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'sample1'] - - fastq: - type: file - description: FASTQ file to filter - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'sample1'] + - fastq: + type: file + description: FASTQ file to filter + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'sample1'] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Filtered FASTA file - pattern: "*.fasta" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'sample1'] + - "*.fasta": + type: file + description: Filtered FASTA file + pattern: "*.fasta" - log: - type: file - description: Log file of the run - pattern: "*.log" + - "*.log": + type: file + description: Log file of the run + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FernandoDuarteF" maintainers: diff --git a/modules/nf-core/vsearch/sintax/meta.yml b/modules/nf-core/vsearch/sintax/meta.yml index 97cd5ebe8a7..7b387b903c1 100644 --- a/modules/nf-core/vsearch/sintax/meta.yml +++ b/modules/nf-core/vsearch/sintax/meta.yml @@ -6,32 +6,44 @@ keywords: - taxonomy tools: - "vsearch": - description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" + description: "VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative)" homepage: "https://github.com/torognes/vsearch" tool_dev_url: "https://github.com/torognes/vsearch" doi: "10.7717/peerj.2584" licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing query file information e.g. [ id:'test' ] - - queryfasta: - type: file - description: Query sequences in FASTA or FASTQ format - pattern: "*.{fasta,fa,fna,faa,fastq,fq}" - - db: - type: file - description: Reference database file in FASTA or UDB format - pattern: "*" + - - meta: + type: map + description: Groovy Map containing query file information e.g. [ id:'test' ] + - queryfasta: + type: file + description: Query sequences in FASTA or FASTQ format + pattern: "*.{fasta,fa,fna,faa,fastq,fq}" + - - db: + type: file + description: Reference database file in FASTA or UDB format + pattern: "*" output: - tsv: - type: file - description: Results written to tab-delimited file - pattern: "*.{tsv}" + - meta: + type: file + description: Results written to tab-delimited file + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Results written to tab-delimited file + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jtangrot" maintainers: diff --git a/modules/nf-core/vsearch/sort/meta.yml b/modules/nf-core/vsearch/sort/meta.yml index ddf28a30787..62a7b31619d 100644 --- a/modules/nf-core/vsearch/sort/meta.yml +++ b/modules/nf-core/vsearch/sort/meta.yml @@ -1,5 +1,6 @@ name: "vsearch_sort" -description: Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength). +description: Sort fasta entries by decreasing abundance (--sortbysize) or sequence + length (--sortbylength). keywords: - vsearch/sort - vsearch @@ -10,38 +11,47 @@ keywords: - population genetics tools: - vsearch: - description: VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative) + description: VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative) homepage: https://github.com/torognes/vsearch documentation: https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf tool_dev_url: https://github.com/torognes/vsearch doi: 10.7717/peerj.2584 licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - fasta: - type: file - description: Sequences to be sorted in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - sort_arg: - type: string - description: Argument to provide to sort algorithm. Sort by abundance with --sortbysize or by sequence length with --sortbylength. - enum: ["--sortbysize", "--sortbylength"] + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - fasta: + type: file + description: Sequences to be sorted in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - sort_arg: + type: string + description: Argument to provide to sort algorithm. Sort by abundance with --sortbysize + or by sequence length with --sortbylength. + enum: ["--sortbysize", "--sortbylength"] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Sorted FASTA file - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Sorted FASTA file + pattern: "*.{fasta}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/vsearch/usearchglobal/meta.yml b/modules/nf-core/vsearch/usearchglobal/meta.yml index ba56f1778e4..9f4b4203efa 100644 --- a/modules/nf-core/vsearch/usearchglobal/meta.yml +++ b/modules/nf-core/vsearch/usearchglobal/meta.yml @@ -1,5 +1,6 @@ name: "vsearch_usearchglobal" -description: Compare target sequences to fasta-formatted query sequences using global pairwise alignment. +description: Compare target sequences to fasta-formatted query sequences using global + pairwise alignment. keywords: - vsearch - usearch @@ -7,74 +8,136 @@ keywords: - fasta tools: - "vsearch": - description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" + description: "VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative)" homepage: "https://github.com/torognes/vsearch" tool_dev_url: "https://github.com/torognes/vsearch" doi: "10.7717/peerj.2584" licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - queryfasta: - type: file - description: Query sequences in FASTA format - pattern: "*.{fasta,fa,fna,faa}" - - db: - type: file - description: Reference database file in FASTA or UDB format - pattern: "*" - - idcutoff: - type: float - description: Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included) - - outoption: - type: string - description: Specify the type of output file to be generated by selecting one of the vsearch output file options - pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" - - user_columns: - type: string - description: If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string. + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - queryfasta: + type: file + description: Query sequences in FASTA format + pattern: "*.{fasta,fa,fna,faa}" + - - db: + type: file + description: Reference database file in FASTA or UDB format + pattern: "*" + - - idcutoff: + type: float + description: Reject the sequence match if the pairwise identity is lower than + the given id cutoff value (value ranging from 0.0 to 1.0 included) + - - outoption: + type: string + description: Specify the type of output file to be generated by selecting one + of the vsearch output file options + pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" + - - user_columns: + type: string + description: If using the `userout` option, specify which columns to include + in output, with fields separated with `+` (e.g. query+target+id). See USEARCH + manual for valid options. For other output options, use an empty string. output: - aln: - type: file - description: Results in pairwise alignment format - pattern: "*.{aln}" + - meta: + type: file + description: Results in pairwise alignment format + pattern: "*.{aln}" + - "*.aln": + type: file + description: Results in pairwise alignment format + pattern: "*.{aln}" - biom: - type: file - description: Results in an OTU table in the biom version 1.0 file format - pattern: "*.{biom}" + - meta: + type: file + description: Results in an OTU table in the biom version 1.0 file format + pattern: "*.{biom}" + - "*.biom": + type: file + description: Results in an OTU table in the biom version 1.0 file format + pattern: "*.{biom}" - lca: - type: file - description: Last common ancestor (LCA) information about the hits of each query in tab-separated format - pattern: "*.{lca}" + - meta: + type: file + description: Last common ancestor (LCA) information about the hits of each query + in tab-separated format + pattern: "*.{lca}" + - "*.lca": + type: file + description: Last common ancestor (LCA) information about the hits of each query + in tab-separated format + pattern: "*.{lca}" - mothur: - type: file - description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format - pattern: "*.{mothur}" + - meta: + type: file + description: Results in an OTU table in the mothur ’shared’ tab-separated plain + text file format + pattern: "*.{mothur}" + - "*.mothur": + type: file + description: Results in an OTU table in the mothur ’shared’ tab-separated plain + text file format + pattern: "*.{mothur}" - otu: - type: file - description: Results in an OTU table in the classic tab-separated plain text format - pattern: "*.{otu}" + - meta: + type: file + description: Results in an OTU table in the classic tab-separated plain text + format + pattern: "*.{otu}" + - "*.otu": + type: file + description: Results in an OTU table in the classic tab-separated plain text + format + pattern: "*.{otu}" - sam: - type: file - description: Results written in sam format - pattern: "*.{sam}" + - meta: + type: file + description: Results written in sam format + pattern: "*.{sam}" + - "*.sam": + type: file + description: Results written in sam format + pattern: "*.{sam}" - tsv: - type: file - description: Results in tab-separated output, columns defined by user - pattern: "*.{tsv}" + - meta: + type: file + description: Results in tab-separated output, columns defined by user + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Results in tab-separated output, columns defined by user + pattern: "*.{tsv}" - txt: - type: file - description: Tab delimited results in blast-like tabular format - pattern: "*.{txt}" + - meta: + type: file + description: Tab delimited results in blast-like tabular format + pattern: "*.{txt}" + - "*.txt": + type: file + description: Tab delimited results in blast-like tabular format + pattern: "*.{txt}" - uc: - type: file - description: Tab delimited results in a uclust-like format with 10 columns - pattern: "*.{uc}" + - meta: + type: file + description: Tab delimited results in a uclust-like format with 10 columns + pattern: "*.{uc}" + - "*.uc": + type: file + description: Tab delimited results in a uclust-like format with 10 columns + pattern: "*.{uc}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jtangrot" maintainers: diff --git a/modules/nf-core/vt/decompose/meta.yml b/modules/nf-core/vt/decompose/meta.yml index 0a08d876730..d9c75de331c 100644 --- a/modules/nf-core/vt/decompose/meta.yml +++ b/modules/nf-core/vt/decompose/meta.yml @@ -1,4 +1,3 @@ ---- name: "vt_decompose" description: decomposes multiallelic variants into biallelic in a VCF file. keywords: @@ -14,34 +13,37 @@ tools: documentation: "https://genome.sph.umich.edu/wiki/Vt" tool_dev_url: "https://github.com/atks/vt" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: The VCF file to decompose - pattern: "*.vcf(.gz)?" - - intervals: - type: file - description: The intervals of the variants of decompose - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: The VCF file to decompose + pattern: "*.vcf(.gz)?" + - intervals: + type: file + description: The intervals of the variants of decompose + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The decomposed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: The decomposed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/vt/normalize/meta.yml b/modules/nf-core/vt/normalize/meta.yml index 37e7bca1612..845baa489db 100644 --- a/modules/nf-core/vt/normalize/meta.yml +++ b/modules/nf-core/vt/normalize/meta.yml @@ -1,4 +1,3 @@ ---- name: "vt_normalize" description: normalizes variants in a VCF file keywords: @@ -13,60 +12,70 @@ tools: documentation: "https://genome.sph.umich.edu/wiki/Vt" tool_dev_url: "https://github.com/atks/vt" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: The VCF file to normalize - pattern: "*.vcf(.gz)?" - - tbi: - type: file - description: The tabix index of the VCF file when bgzipped - pattern: "*.tbi" - - intervals: - type: file - description: The intervals of the variants of normalize - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fn,fna,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: The index of the reference fasta file (OPTIONAL) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: The VCF file to normalize + pattern: "*.vcf(.gz)?" + - tbi: + type: file + description: The tabix index of the VCF file when bgzipped + pattern: "*.tbi" + - intervals: + type: file + description: The intervals of the variants of normalize + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fn,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: The index of the reference fasta file (OPTIONAL) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The normalized VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: The normalized VCF file + pattern: "*.vcf.gz" - fai: - type: file - description: The created index of the reference fasta file (only when the fai wasn't supplied) - pattern: "*.fai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${fasta}.fai: + type: file + description: The created index of the reference fasta file (only when the fai + wasn't supplied) + pattern: "*.fai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml index dc5cd5a8fd8..df9024fdb39 100644 --- a/modules/nf-core/wfmash/meta.yml +++ b/modules/nf-core/wfmash/meta.yml @@ -14,49 +14,55 @@ tools: tool_dev_url: https://github.com/waveygang/wfmash doi: 10.5281/zenodo.6949373 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta_gz: - type: file - description: BGZIPPED FASTA target file to create the mappings from. - pattern: "{fa.gz,fna.gz,fasta.gz}" - - paf: - type: file - description: Optional inpute file in PAF format to derive the precise alignments for. - pattern: "*.{paf}" - - query_self: - type: boolean - description: If set to true, the input FASTA will also be used as the query FASTA. - - gzi: - type: file - description: The GZI index of the input FASTA file. - pattern: "*.{gzi}" - - fai: - type: file - description: The FASTA index of the input FASTA file. - pattern: "*.{fai}" - - fasta_query_list: - type: file - description: Optional inpute file in FASTA format specifying the query sequences as a list. - pattern: "*.{fa,fna,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_gz: + type: file + description: BGZIPPED FASTA target file to create the mappings from. + pattern: "{fa.gz,fna.gz,fasta.gz}" + - paf: + type: file + description: Optional inpute file in PAF format to derive the precise alignments + for. + pattern: "*.{paf}" + - gzi: + type: file + description: The GZI index of the input FASTA file. + pattern: "*.{gzi}" + - fai: + type: file + description: The FASTA index of the input FASTA file. + pattern: "*.{fai}" + - - query_self: + type: boolean + description: If set to true, the input FASTA will also be used as the query + FASTA. + - - fasta_query_list: + type: file + description: Optional inpute file in FASTA format specifying the query sequences + as a list. + pattern: "*.{fa,fna,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignments in PAF format - pattern: "*.{paf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignments in PAF format + pattern: "*.{paf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/wgsim/meta.yml b/modules/nf-core/wgsim/meta.yml index b57c67b8d18..018d60fb872 100644 --- a/modules/nf-core/wgsim/meta.yml +++ b/modules/nf-core/wgsim/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://github.com/lh3/wgsim" tool_dev_url: "https://github.com/lh3/wgsim" licence: ["MIT"] + identifier: biotools:wgsim input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Simulated FASTQ read files - pattern: "*.{fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq": + type: file + description: Simulated FASTQ read files + pattern: "*.{fastq}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/whamg/meta.yml b/modules/nf-core/whamg/meta.yml index fc19fce9b89..55f6a304df0 100644 --- a/modules/nf-core/whamg/meta.yml +++ b/modules/nf-core/whamg/meta.yml @@ -1,5 +1,7 @@ name: "whamg" -description: The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery. +description: The wham suite consists of two programs, wham and whamg. wham, the original + tool, is a very sensitive method with a high false discovery rate. The second program, + whamg, is more accurate and better suited for general structural variant (SV) discovery. keywords: - whamg - wham @@ -14,46 +16,65 @@ tools: tool_dev_url: "https://github.com/zeeev/wham" doi: "10.1371/journal.pcbi.1004572" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - fasta: - type: file - description: Reference Fasta file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference Fasta - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - fasta: + type: file + description: Reference Fasta file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference Fasta + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of the VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of the VCF file + pattern: "*.vcf.gz.tbi" + - graph: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Graph file + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/windowmasker/convert/meta.yml b/modules/nf-core/windowmasker/convert/meta.yml index d9e46e79822..e163f8bd1ff 100644 --- a/modules/nf-core/windowmasker/convert/meta.yml +++ b/modules/nf-core/windowmasker/convert/meta.yml @@ -6,35 +6,38 @@ keywords: - windowmasker tools: - windowmasker: - description: "A program to mask highly repetitive and low complexity DNA sequences within a genome." + description: "A program to mask highly repetitive and low complexity DNA sequences + within a genome." homepage: "https://blast.ncbi.nlm.nih.gov/Blast.cgi" documentation: "ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/README.windowmasker" doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: biotools:windowmasker input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - counts: - type: file - description: valid unit counts file - pattern: "*.{ascii,binary,oascii,obinary,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - counts: + type: file + description: valid unit counts file + pattern: "*.{ascii,binary,oascii,obinary,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - counts: - type: file - description: valid unit counts file - pattern: "*.{ascii,binary,oascii,obinary}" + - converted: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: converted file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/windowmasker/mkcounts/meta.yml b/modules/nf-core/windowmasker/mkcounts/meta.yml index 436ed7a5052..825a0674e44 100644 --- a/modules/nf-core/windowmasker/mkcounts/meta.yml +++ b/modules/nf-core/windowmasker/mkcounts/meta.yml @@ -11,31 +11,32 @@ tools: homepage: https://github.com/ncbi/ncbi-cxx-toolkit-public documentation: https://ncbi.github.io/cxx-toolkit/ licence: ["MIT"] + identifier: biotools:windowmasker input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: An input nucleotide fasta file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: An input nucleotide fasta file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: | - An output file containing genomic locations of low - complexity and highly repetitive regions - pattern: "${prefix}.txt" + - counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: A file containing frequency counts of repetitive units. + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/windowmasker/ustat/meta.yml b/modules/nf-core/windowmasker/ustat/meta.yml index 6a07c935239..bc51a9340c1 100644 --- a/modules/nf-core/windowmasker/ustat/meta.yml +++ b/modules/nf-core/windowmasker/ustat/meta.yml @@ -1,5 +1,6 @@ name: windowmasker_ustat -description: A program to take a counts file and creates a file of genomic co-ordinates to be masked. +description: A program to take a counts file and creates a file of genomic co-ordinates + to be masked. keywords: - fasta - interval @@ -11,39 +12,39 @@ tools: homepage: https://github.com/ncbi/ncbi-cxx-toolkit-public documentation: https://ncbi.github.io/cxx-toolkit/ licence: ["MIT"] + identifier: biotools:windowmasker input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - counts: - type: file - description: Contains count data of repetitive regions. - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: An input nucleotide fasta file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - counts: + type: file + description: Contains count data of repetitive regions. + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: An input nucleotide fasta file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - wm_intervals: - type: file - description: | - An output file containing genomic locations of low - complexity and highly repetitive regions - pattern: "${output}" + - intervals: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: intervals - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/wisecondorx/convert/meta.yml b/modules/nf-core/wisecondorx/convert/meta.yml index d70d9d69ab2..07233d2953d 100644 --- a/modules/nf-core/wisecondorx/convert/meta.yml +++ b/modules/nf-core/wisecondorx/convert/meta.yml @@ -12,52 +12,56 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Reads in BAM/CRAM format - pattern: "*.{bam,cram}" - - bai: - type: file - description: index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference fasta meta information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA file (mandatory when using CRAM files) - pattern: "*.{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference fasta index meta information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the reference FASTA file (mandatory when using CRAM files) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Reads in BAM/CRAM format + pattern: "*.{bam,cram}" + - bai: + type: file + description: index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference fasta meta information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA file (mandatory when using CRAM files) + pattern: "*.{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference fasta index meta information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the reference FASTA file (mandatory when using CRAM + files) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - npz: - type: file - description: The output NPZ file - pattern: "*.npz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.npz": + type: file + description: The output NPZ file + pattern: "*.npz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wisecondorx/gender/meta.yml b/modules/nf-core/wisecondorx/gender/meta.yml index cd4da24f7bc..ccf1052ee19 100644 --- a/modules/nf-core/wisecondorx/gender/meta.yml +++ b/modules/nf-core/wisecondorx/gender/meta.yml @@ -1,5 +1,6 @@ name: "wisecondorx_gender" -description: Returns the gender of a .npz resulting from convert, based on a Gaussian mixture model trained during the newref phase +description: Returns the gender of a .npz resulting from convert, based on a Gaussian + mixture model trained during the newref phase keywords: - copy number analysis - gender determination @@ -12,34 +13,38 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - npz: - type: file - description: Single sample NPZ file (from which to determine the gender) - pattern: "*.npz" - - reference: - type: file - description: Reference NPZ file - pattern: "*.npz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - npz: + type: file + description: Single sample NPZ file (from which to determine the gender) + pattern: "*.npz" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Reference NPZ file + pattern: "*.npz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gender: - type: string - description: The gender of the input NPZ file - pattern: "(fe)?male" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wisecondorx/newref/meta.yml b/modules/nf-core/wisecondorx/newref/meta.yml index d5efefeb53f..d05b1820001 100644 --- a/modules/nf-core/wisecondorx/newref/meta.yml +++ b/modules/nf-core/wisecondorx/newref/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputs: - type: file - description: Multiple NPZ files from healthy patients - pattern: "*.{npz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputs: + type: file + description: Multiple NPZ files from healthy patients + pattern: "*.{npz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - npz: - type: file - description: The reference NPZ file - pattern: "*.{npz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.npz": + type: file + description: The reference NPZ file + pattern: "*.{npz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wisecondorx/predict/meta.yml b/modules/nf-core/wisecondorx/predict/meta.yml index 0f347ee36d4..ae17554578b 100644 --- a/modules/nf-core/wisecondorx/predict/meta.yml +++ b/modules/nf-core/wisecondorx/predict/meta.yml @@ -13,68 +13,107 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - npz: - type: file - description: An NPZ file created with WisecondorX convert - pattern: "*.npz" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - reference: - type: file - description: A reference NPZ file created with WisecondorX newref - pattern: "*.npz" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - blacklist: - type: file - description: OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - npz: + type: file + description: An NPZ file created with WisecondorX convert + pattern: "*.npz" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: A reference NPZ file created with WisecondorX newref + pattern: "*.npz" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - blacklist: + type: file + description: OPTIONAL - A BED file containing blacklist regions (used mainly + when the reference is small) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - aberrations_bed: - type: file - description: OPTIONAL - Output abberations in BED format. This gets created with the `--bed` option - pattern: "*_aberrations.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_aberrations.bed": + type: file + description: OPTIONAL - Output abberations in BED format. This gets created + with the `--bed` option + pattern: "*_aberrations.bed" - bins_bed: - type: file - description: OPTIONAL - Output bins in BED format. This gets created with the `--bed` option - pattern: "*_bins.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bins.bed": + type: file + description: OPTIONAL - Output bins in BED format. This gets created with the + `--bed` option + pattern: "*_bins.bed" - segments_bed: - type: file - description: OPTIONAL - Output segments in BED format. This gets created with the `--bed` option - pattern: "*_segments.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_segments.bed": + type: file + description: OPTIONAL - Output segments in BED format. This gets created with + the `--bed` option + pattern: "*_segments.bed" - chr_statistics: - type: file - description: OPTIONAL - Statistics per chromosome in TXT format. This gets created with the `--bed` option - pattern: "*_chr_statistics.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_chr_statistics.txt": + type: file + description: OPTIONAL - Statistics per chromosome in TXT format. This gets created + with the `--bed` option + pattern: "*_chr_statistics.txt" - chr_plots: - type: list - description: OPTIONAL - A list containing the CNV plots of each chromosome. This gets created with the `--plot` option - pattern: "[!genome_wide]*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "[!genome_wide]*.png": + type: list + description: OPTIONAL - A list containing the CNV plots of each chromosome. + This gets created with the `--plot` option + pattern: "[!genome_wide]*.png" - genome_plot: - type: file - description: OPTIONAL - A plot containing the CNV information of the whole genome - pattern: "genome_wide.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome_wide.png: + type: file + description: OPTIONAL - A plot containing the CNV information of the whole genome + pattern: "genome_wide.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wittyer/meta.yml b/modules/nf-core/wittyer/meta.yml index cda7f751b3c..40110aa2447 100644 --- a/modules/nf-core/wittyer/meta.yml +++ b/modules/nf-core/wittyer/meta.yml @@ -12,52 +12,67 @@ tools: documentation: "https://github.com/Illumina/witty.er" tool_dev_url: "https://github.com/Illumina/witty.er" licence: ["BSD-2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - query_vcf: - type: file - description: A VCF with called variants to benchmark against the standard - pattern: "*.{vcf}" - - truth_vcf: - type: file - description: A standard VCF to compare against - pattern: "*.{vcf}" - - bed: - type: file - description: A BED file specifying regions to be included in the analysis (optional) - pattern: "*.bed" - - wittyer_config: - type: file - description: | - Config file in json format used to specify per variant type settings. - Used in place of include bed arguments. (optional) - pattern: "*.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - query_vcf: + type: file + description: A VCF with called variants to benchmark against the standard + pattern: "*.{vcf}" + - truth_vcf: + type: file + description: A standard VCF to compare against + pattern: "*.{vcf}" + - bed: + type: file + description: A BED file specifying regions to be included in the analysis (optional) + pattern: "*.bed" + - wittyer_config: + type: file + description: | + Config file in json format used to specify per variant type settings. + Used in place of include bed arguments. (optional) + pattern: "*.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Detailed per-sample-pair, per-svtype, per-bin stats - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: Detailed per-sample-pair, per-svtype, per-bin stats + pattern: "*.json" - bench_vcf: - type: file - description: Updated query and truth entries merged into one file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Updated query and truth entries merged into one file + pattern: "*.vcf.gz" - bench_vcf_tbi: - type: file - description: Index of merged query and truth entries VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz.tbi": + type: file + description: Index of merged query and truth entries VCF file + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@famosab" maintainers: diff --git a/modules/nf-core/xengsort/index/meta.yml b/modules/nf-core/xengsort/index/meta.yml index 570c781d09b..145d15f075e 100644 --- a/modules/nf-core/xengsort/index/meta.yml +++ b/modules/nf-core/xengsort/index/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "xengsort_index" description: Fast lightweight accurate xenograft sorting @@ -18,43 +17,45 @@ tools: tool_dev_url: "https://gitlab.com/genomeinformatics/xengsort" doi: "10.4230/LIPIcs.WABI.2020.4" licence: ["MIT"] + identifier: "" input: - - host_fasta: - type: file - description: | - Reference genome fasta file from host, compressed or uncompressed. - - graft_fasta: - type: file - description: | - Reference genome fasta file from graft, compressed or uncompressed. - - index: - type: string - description: | - File name prefix to store index files. - - nobjects: - type: string - description: | - Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000. - - mask: - type: string - description: | - Gapped k-mer mask (quoted string like '#__##_##__#'). - + - - host_fasta: + type: file + description: | + Reference genome fasta file from host, compressed or uncompressed. + - - graft_fasta: + type: file + description: | + Reference genome fasta file from graft, compressed or uncompressed. + - - index: + type: string + description: | + File name prefix to store index files. + - - nobjects: + type: string + description: | + Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000. + - - mask: + type: string + description: | + Gapped k-mer mask (quoted string like '#__##_##__#'). output: - hash: - type: file - description: File with index hash file. - pattern: "*hash" + - ${index}.hash: + type: file + description: File with index hash file. + pattern: "*hash" - info: - type: file - description: File with index info file. - pattern: "*info" + - ${index}.info: + type: file + description: File with index info file. + pattern: "*info" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@diegomscoelho" maintainers: diff --git a/modules/nf-core/xz/compress/meta.yml b/modules/nf-core/xz/compress/meta.yml index bdc002ad4a0..27be72969cb 100644 --- a/modules/nf-core/xz/compress/meta.yml +++ b/modules/nf-core/xz/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "xz_compress" description: Compresses files with xz. @@ -8,41 +7,40 @@ keywords: - archive tools: - "xz": - description: "xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2." + description: "xz is a general-purpose data compression tool with command line + syntax similar to gzip and bzip2." homepage: "https://tukaani.org/xz/" documentation: "https://tukaani.org/xz/man/xz.1.html" tool_dev_url: "https://github.com/tukaani-project/xz" licence: ["GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - raw_file: - type: file - description: File to be compressed - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - raw_file: + type: file + description: File to be compressed + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - archive: - type: file - description: The compressed file - pattern: "*.xz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $archive: + type: file + description: The compressed file + pattern: "*.xz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/xz/decompress/meta.yml b/modules/nf-core/xz/decompress/meta.yml index 831f9f6ee63..89b87ed301c 100644 --- a/modules/nf-core/xz/decompress/meta.yml +++ b/modules/nf-core/xz/decompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "xz_decompress" description: Decompresses files with xz. @@ -8,39 +7,40 @@ keywords: - compression tools: - "xz": - description: "xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2." + description: "xz is a general-purpose data compression tool with command line + syntax similar to gzip and bzip2." homepage: "https://tukaani.org/xz/" documentation: "https://tukaani.org/xz/man/xz.1.html" tool_dev_url: "https://github.com/tukaani-project/xz" licence: ["GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - archive: - type: file - description: File to be decompressed - pattern: "*.{xz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - archive: + type: file + description: File to be decompressed + pattern: "*.{xz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - file: - type: file - description: The decompressed file - pattern: "*.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $decompressed_file: + type: file + description: The decompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/yahs/meta.yml b/modules/nf-core/yahs/meta.yml index 7ddcc7781ee..bb3112e8038 100644 --- a/modules/nf-core/yahs/meta.yml +++ b/modules/nf-core/yahs/meta.yml @@ -13,49 +13,64 @@ tools: tool_dev_url: "https://github.com/c-zhou/yahs" doi: "10.1093/bioinformatics/btac808" licence: ["MIT"] + identifier: biotools:yahs input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - # - - hic_map: - type: file - description: BED file containing coordinates of read alignments - pattern: "*.{bed,bam,bin}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: index of the reference file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - hic_map: + type: file + description: BED file containing coordinates of read alignments + pattern: "*.{bed,bam,bin}" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: index of the reference file + pattern: "*.{fai}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scaffolds_fasta: - type: file - description: FASTA file with resulting contigs - pattern: "*scaffolds_final.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*scaffolds_final.fa": + type: file + description: FASTA file with resulting contigs + pattern: "*scaffolds_final.fa" - scaffolds_agp: - type: file - description: AGP file containing contigs placing coordinates - pattern: "*scaffolds_final.agp" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*scaffolds_final.agp": + type: file + description: AGP file containing contigs placing coordinates + pattern: "*scaffolds_final.agp" - binary: - type: file - description: BIN file with alignment results of Hi-C reads to the contigs in internal YaHS binary format - pattern: "*bin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*bin": + type: file + description: BIN file with alignment results of Hi-C reads to the contigs in + internal YaHS binary format + pattern: "*bin" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ksenia-krasheninnikova" maintainers: diff --git a/modules/nf-core/yak/count/meta.yml b/modules/nf-core/yak/count/meta.yml index c5e35302eb4..b8c519e8b98 100644 --- a/modules/nf-core/yak/count/meta.yml +++ b/modules/nf-core/yak/count/meta.yml @@ -14,33 +14,34 @@ tools: documentation: "https://github.com/lh3/yak/blob/master/README.md" tool_dev_url: "https://github.com/lh3/yak" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastq: - type: file - description: reads fastq/fasta file - pattern: "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: reads fastq/fasta file + pattern: "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - yak: - type: file - description: k-mer hash table of input - pattern: "*.{yak}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.yak": + type: file + description: k-mer hash table of input + pattern: "*.{yak}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" maintainers: diff --git a/modules/nf-core/yara/index/meta.yml b/modules/nf-core/yara/index/meta.yml index c2a1a95bccf..7c4a9eb7d61 100644 --- a/modules/nf-core/yara/index/meta.yml +++ b/modules/nf-core/yara/index/meta.yml @@ -8,29 +8,37 @@ keywords: - reference tools: - yara: - description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + description: Yara is an exact tool for aligning DNA sequencing reads to reference + genomes. homepage: https://github.com/seqan/seqan documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"] + identifier: biotools:yara input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: file - description: YARA genome index files - pattern: "yara.*" + - meta: + type: file + description: YARA genome index files + pattern: "yara.*" + - ${fasta}*: + type: file + description: YARA genome index files + pattern: "yara.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" maintainers: diff --git a/modules/nf-core/yara/mapper/meta.yml b/modules/nf-core/yara/mapper/meta.yml index c6f060322fa..d4f68eebf86 100644 --- a/modules/nf-core/yara/mapper/meta.yml +++ b/modules/nf-core/yara/mapper/meta.yml @@ -6,48 +6,58 @@ keywords: - reference tools: - yara: - description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + description: Yara is an exact tool for aligning DNA sequencing reads to reference + genomes. homepage: https://github.com/seqan/seqan documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"] + identifier: biotools:yara input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing index information - e.g. [ id:'test' ] - - index: - type: file - description: YARA genome index files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing index information + e.g. [ id:'test' ] + - index: + type: file + description: YARA genome index files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapped.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - bai: - type: file - description: Sorted BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapped.bam.bai": + type: file + description: Sorted BAM file index + pattern: "*.{bai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" maintainers: diff --git a/modules/nf-core/zip/meta.yml b/modules/nf-core/zip/meta.yml index f4bfcd04389..c2b87259f65 100644 --- a/modules/nf-core/zip/meta.yml +++ b/modules/nf-core/zip/meta.yml @@ -7,34 +7,38 @@ keywords: - archiving tools: - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version + of 7zip, see www.7-zip.org) for Unix. homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files: - type: file - description: File or list of files to be zipped + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files: + type: file + description: File or list of files to be zipped output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - zipped_archive: - type: file - description: ZIP file - pattern: "*.zip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.zip: + type: file + description: ZIP file + pattern: "*.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@pinin4fjords"