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* 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 <jfy133@gmail.com> 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 <mahesh.binzer-panchal@nbis.se> * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * some changes * corrected meta * removed environment.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * 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 <fmartinez@incliva.es> * 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 <fmartinez@incliva.es> 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 <mashehu@users.noreply.github.com> --------- 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 <mashehu@users.noreply.github.com> * 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 <maxime.garcia@seqera.io> * Update modules/nf-core/sniffles/meta.yml Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> --------- Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> * 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 <max.u.garcia@gmail.com> * Added nf-test for dshbio/splitbed (#6516) * updated ensemblvep modules and added nf-tests (#6538) * updating ensemblvep modules * fix tests --------- Co-authored-by: Lucpen <lucia.penaperez@hasta-login.local> * 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 <ibarrarellano@gmail.com> Co-authored-by: Krešimir Beštak <kbestak@gmail.com> 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 <jfy133@gmail.com> * 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 <perisateesh@gmail.com> * 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 <maxime.garcia@seqera.io> --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> * 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 <usman@smme.edu.pk> * 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 <joon.klaps@kuleuven.be> * 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 <mahesh.binzer-panchal@nbis.se> * Boolean flag types --------- Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * 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 <phil.ewels@scilifelab.se> * 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 <core@nf-co.re> * 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 <uoi4@cdc.gov> 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 <chasem@wustl.edu> * 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 <max.u.garcia@gmail.com> * 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 <jfy133@gmail.com> * 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 <maxime.garcia@seqera.io> * 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 <maxime.garcia@seqera.io> 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 <usman@smme.edu.pk> 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 <jfy133@gmail.com> Co-authored-by: YSims <yy5@sanger.ac.uk> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> 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 <luisa.santus95@gmail.com> Co-authored-by: Francisco Martínez <f.martinezpico@gmail.com> Co-authored-by: fmartinez <fmartinez@incliva.es> 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 <mashehu@users.noreply.github.com> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> Co-authored-by: Ömer An <bounlu@gmail.com> Co-authored-by: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Lucía Peña-Pérez <lucia.pena.perez@scilifelab.se> Co-authored-by: Lucpen <lucia.penaperez@hasta-login.local> 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 <ibarrarellano@gmail.com> Co-authored-by: Krešimir Beštak <kbestak@gmail.com> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Eric Wei <ercweizy@gmail.com> Co-authored-by: Sateesh <perisateesh@gmail.com> Co-authored-by: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com> Co-authored-by: Nur M Shahir <nmshahir@gmail.com> Co-authored-by: shahirnm <uoi4@cdc.gov> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> Co-authored-by: Marius Bjørnstad <pmb@fa2k.net> Co-authored-by: Stephen Kelly <stevekm@users.noreply.github.com> 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 <vsmalladi@gmail.com> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> * 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 <phil.ewels@scilifelab.se> * 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 <core@nf-co.re> * 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 <mm49@sanger.ac.uk> * 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 <jfy133@gmail.com> * 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 <jfy133@gmail.com> 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 <aida.andrades@gmail.com> * 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 <maxime.garcia@seqera.io> * 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 <maxime.garcia@seqera.io> * 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 <jfy133@gmail.com> * 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 <mielczarekv@rki.de> * 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 <john.palmer@bccdc.ca> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * `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 <mahesh.binzer-panchal@nbis.se> * 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 <mahesh.binzer-panchal@nbis.se> * 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 <jonathan.manning@seqera.io> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> 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 <cortexspam-github@yahoo.fr> * Simplify versions processing --------- Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr> * 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 <max.u.garcia@gmail.com> * hack: Hard code version https://github.com/google/deepvariant/issues/830 --------- Co-authored-by: Felix Lenner <felix.lenner@igp.uu.se> Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * 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/n…
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