diff --git a/.cache.tar.xz b/.cache.tar.xz index 66ea8a7aa0..626490b642 100644 Binary files a/.cache.tar.xz and b/.cache.tar.xz differ diff --git a/public/components.json b/public/components.json index 31cda5818b..adcb10417e 100644 --- a/public/components.json +++ b/public/components.json @@ -7792,6 +7792,10 @@ "name": "rnafusion", "version": "3.0.2" }, + { + "name": "rnafusion", + "version": "3.0.2" + }, { "name": "rnafusion", "version": "3.0.2" @@ -25650,6 +25654,14 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "pathogensurveillance", + "version": "dev" + }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "pathogensurveillance", "version": "dev" @@ -107768,6 +107780,10 @@ "name": "genomeassembler", "version": "dev" }, + { + "name": "genomeassembler", + "version": "dev" + }, { "name": "genomeassembler", "version": "dev" @@ -126296,6 +126312,177 @@ ] } }, + { + "name": "parabricks_fq2bammeth", + "path": "modules/nf-core/parabricks/fq2bammeth/meta.yml", + "type": "module", + "meta": { + "name": "parabricks_fq2bammeth", + "description": "VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence", + "keywords": [ + "align", + "sort", + "bqsr", + "duplicates", + "bwameth" + ], + "tools": [ + { + "parabricks": { + "description": "NVIDIA Clara Parabricks GPU-accelerated genomics tools", + "homepage": "https://www.nvidia.com/en-us/clara/genomics/", + "documentation": "https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html#fq2bam-meth-reference", + "licence": [ + "custom" + ], + "identifier": "" + } + } + ], + "input": [ + [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "reads": { + "type": "file", + "description": "fastq.gz files", + "pattern": "*.fastq.gz" + } + } + ], + [ + { + "meta2": { + "type": "map", + "description": "Groovy Map containing fasta information\n" + } + }, + { + "fasta": { + "type": "file", + "description": "reference fasta file - must be unzipped", + "pattern": "*.fasta" + } + } + ], + [ + { + "meta3": { + "type": "map", + "description": "Groovy Map containing index information\n" + } + }, + { + "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": [ + { + "bam": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bam": { + "type": "file", + "description": "Sorted BAM file", + "pattern": "*.bam" + } + } + ] + }, + { + "bai": [ + { + "meta": { + "type": "map", + "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n" + } + }, + { + "*.bai": { + "type": "file", + "description": "index corresponding to sorted BAM file", + "pattern": "*.bai" + } + } + ] + }, + { + "qc_metrics": [ + { + "qc_metrics": { + "type": "directory", + "description": "(optional) optional directory of qc metrics", + "pattern": "qc_metrics" + } + } + ] + }, + { + "bqsr_table": [ + { + "*.table": { + "type": "file", + "description": "(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr", + "pattern": "*.table" + } + } + ] + }, + { + "duplicate_metrics": [ + { + "duplicate-metrics.txt": { + "type": "file", + "description": "(optional) metrics calculated from marking duplcates in the bam file", + "pattern": "*-duplicate-metrics.txt" + } + } + ] + }, + { + "versions": [ + { + "versions.yml": { + "type": "file", + "description": "File containing software versions", + "pattern": "versions.yml" + } + } + ] + } + ], + "authors": [ + "@sateeshperi" + ], + "maintainers": [ + "@sateeshperi" + ] + } + }, { "name": "parabricks_genotypegvcf", "path": "modules/nf-core/parabricks/genotypegvcf/meta.yml", @@ -142524,6 +142711,13 @@ "pattern": "*.{bai}" } }, + { + "bamlist": { + "type": "file", + "description": "(Optional) File with list of BAM/CRAM files to impute. One file per line.", + "pattern": "*.{txt}" + } + }, { "reference_haplotype_file": { "type": "file", @@ -199035,6 +199229,10 @@ "name": "datasync", "version": "dev" }, + { + "name": "deepmodeloptim", + "version": "dev" + }, { "name": "demo", "version": "1.0.1" @@ -199296,6 +199494,10 @@ "name": "datasync", "version": "dev" }, + { + "name": "deepmodeloptim", + "version": "dev" + }, { "name": "demo", "version": "1.0.1" @@ -199545,6 +199747,10 @@ "name": "createtaxdb", "version": "dev" }, + { + "name": "deepmodeloptim", + "version": "dev" + }, { "name": "demo", "version": "1.0.1" diff --git a/public/pipeline_names.json b/public/pipeline_names.json index 6c3e319496..0387d10388 100644 --- a/public/pipeline_names.json +++ b/public/pipeline_names.json @@ -1 +1 @@ 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\ No newline at end of file +{"pipeline":["airrflow","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","datasync","deepmodeloptim","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","drugresponseeval","dualrnaseq","eager","epitopeprediction","fastquorum","fetchngs","funcscan","genomeannotator","genomeassembler","genomeskim","gwas","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","lncpipe","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylseq","mhcquant","mnaseseq","molkart","multiplesequencealign","nanoseq","nanostring","nascent","omicsgenetraitassociation","oncoanalyser","pairgenomealign","pangenome","pathogensurveillance","pgdb","phageannotator","phaseimpute","phyloplace","pixelator","proteinfold","proteomicslfq","radseq","rangeland","raredisease","readsimulator","reportho","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","slamseq","smrnaseq","spatialvi","spinningjenny","taxprofiler","tbanalyzer","tfactivity","troughgraph","variantbenchmarking","variantcatalogue","viralintegration","viralrecon"]} 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