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Code Issues Releases Packages Activity

Update versions key in meta.yml for all modules (#787)

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Harshil Patel 2021-10-03 08:20:26 +01:00 committed by GitHub
parent cf15ece503
commit 49da864287
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GPG key ID: 4AEE18F83AFDEB23
252 changed files with 517 additions and 502 deletions
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4
modules/abacas/meta.yml
View file

@ -48,9 +48,9 @@ output:
'test.abacas.MULTIFASTA.fa' ] 'test.abacas.MULTIFASTA.fa' ]
pattern: "*.{abacas}*" pattern: "*.{abacas}*"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/adapterremoval/meta.yml
View file

@ -41,9 +41,9 @@ output:
type: file type: file
description: AdapterRemoval log file description: AdapterRemoval log file
pattern: "*.log" pattern: "*.log"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/agrvate/meta.yml
View file

@ -38,9 +38,9 @@ output:
type: directory type: directory
description: Results of the agrvate assessement description: Results of the agrvate assessement
pattern: "*-results" pattern: "*-results"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

4
modules/allelecounter/meta.yml
View file

@ -39,9 +39,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- alleleCount: - alleleCount:
type: file type: file

4
modules/amps/meta.yml
View file

@ -41,9 +41,9 @@ input:
pattern: "def_anc|default|scan|ancient|crawl" pattern: "def_anc|default|scan|ancient|crawl"
output: output:
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- json: - json:
type: file type: file

4
modules/arriba/meta.yml
View file

@ -37,9 +37,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- fusions: - fusions:
type: file type: file

4
modules/artic/guppyplex/meta.yml
View file

@ -34,9 +34,9 @@ output:
type: file type: file
description: Aggregated FastQ files description: Aggregated FastQ files
pattern: "*.{fastq.gz}" pattern: "*.{fastq.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/artic/minion/meta.yml
View file

@ -103,9 +103,9 @@ output:
type: file type: file
description: JSON file for MultiQC description: JSON file for MultiQC
pattern: "*.json" pattern: "*.json"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/bamaligncleaner/meta.yml
View file

@ -27,9 +27,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/bandage/image/meta.yml
View file

@ -35,9 +35,9 @@ output:
type: file type: file
description: Bandage image in SVG format description: Bandage image in SVG format
pattern: "*.svg" pattern: "*.svg"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

4
modules/bbmap/align/meta.yml
View file

@ -39,9 +39,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/bbmap/bbduk/meta.yml
View file

@ -39,9 +39,9 @@ output:
type: file type: file
description: The trimmed/modified fastq reads description: The trimmed/modified fastq reads
pattern: "*fastq.gz" pattern: "*fastq.gz"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- log: - log:
type: file type: file

4
modules/bbmap/bbsplit/meta.yml
View file

@ -49,9 +49,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- index: - index:
type: directory type: directory

4
modules/bbmap/index/meta.yml
View file

@ -20,9 +20,9 @@ input:
pattern: "*.{fna,fa,fasta}" pattern: "*.{fna,fa,fasta}"
output: output:
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- db: - db:
type: directory type: directory

4
modules/bcftools/concat/meta.yml
View file

@ -34,9 +34,9 @@ output:
type: file type: file
description: VCF concatenated output file description: VCF concatenated output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

4
modules/bcftools/consensus/meta.yml
View file

@ -39,9 +39,9 @@ output:
type: file type: file
description: FASTA reference consensus file description: FASTA reference consensus file
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bcftools/filter/meta.yml
View file

@ -31,9 +31,9 @@ output:
type: file type: file
description: VCF filtered output file description: VCF filtered output file
pattern: "*.{vcf}" pattern: "*.{vcf}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bcftools/isec/meta.yml
View file

@ -39,9 +39,9 @@ output:
type: directory type: directory
description: Folder containing the set operations results perform on the vcf files description: Folder containing the set operations results perform on the vcf files
pattern: "${prefix}" pattern: "${prefix}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bcftools/merge/meta.yml
View file

@ -37,9 +37,9 @@ output:
type: file type: file
description: VCF merged output file description: VCF merged output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bcftools/mpileup/meta.yml
View file

@ -43,9 +43,9 @@ output:
type: file type: file
description: Text output file containing stats description: Text output file containing stats
pattern: "*{stats.txt}" pattern: "*{stats.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bcftools/norm/meta.yml
View file

@ -37,9 +37,9 @@ output:
type: file type: file
description: VCF normalized output file description: VCF normalized output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

4
modules/bcftools/query/meta.yml
View file

@ -53,9 +53,9 @@ output:
type: file type: file
description: VCF query output file description: VCF query output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

4
modules/bcftools/reheader/meta.yml
View file

@ -38,9 +38,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- vcf: - vcf:
type: file type: file

4
modules/bcftools/stats/meta.yml
View file

@ -32,9 +32,9 @@ output:
type: file type: file
description: Text output file containing stats description: Text output file containing stats
pattern: "*_{stats.txt}" pattern: "*_{stats.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bcftools/view/meta.yml
View file

@ -54,9 +54,9 @@ output:
type: file type: file
description: VCF normalized output file description: VCF normalized output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

4
modules/bedtools/bamtobed/meta.yml
View file

@ -28,9 +28,9 @@ output:
type: file type: file
description: Bed file containing genomic intervals. description: Bed file containing genomic intervals.
pattern: "*.{bed}" pattern: "*.{bed}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@yuukiiwa" - "@yuukiiwa"

4
modules/bedtools/complement/meta.yml
View file

@ -32,9 +32,9 @@ output:
type: file type: file
description: Bed file with all genomic intervals that are not covered by at least one record from the input file. description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
pattern: "*.{bed}" pattern: "*.{bed}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"

4
modules/bedtools/genomecov/meta.yml
View file

@ -35,9 +35,9 @@ output:
type: file type: file
description: Computed genome coverage file description: Computed genome coverage file
pattern: "*.${extension}" pattern: "*.${extension}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"

4
modules/bedtools/getfasta/meta.yml
View file

@ -24,9 +24,9 @@ output:
type: file type: file
description: Output fasta file with extracted sequences description: Output fasta file with extracted sequences
pattern: "*.{fa}" pattern: "*.{fa}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bedtools/intersect/meta.yml
View file

@ -35,9 +35,9 @@ output:
type: file type: file
description: File containing the description of overlaps found between the two features description: File containing the description of overlaps found between the two features
pattern: "*.${extension}" pattern: "*.${extension}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"

4
modules/bedtools/makewindows/meta.yml
View file

@ -31,9 +31,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- tab: - tab:
type: file type: file

4
modules/bedtools/maskfasta/meta.yml
View file

@ -34,9 +34,9 @@ output:
type: file type: file
description: Output masked fasta file description: Output masked fasta file
pattern: "*.{fa}" pattern: "*.{fa}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bedtools/merge/meta.yml
View file

@ -28,9 +28,9 @@ output:
type: file type: file
description: Overlapped bed file with combined features description: Overlapped bed file with combined features
pattern: "*.{bed}" pattern: "*.{bed}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"

4
modules/bedtools/slop/meta.yml
View file

@ -28,9 +28,9 @@ output:
type: file type: file
description: Slopped BED file description: Slopped BED file
pattern: "*.{bed}" pattern: "*.{bed}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"

4
modules/bedtools/sort/meta.yml
View file

@ -28,9 +28,9 @@ output:
type: file type: file
description: Sorted BED file description: Sorted BED file
pattern: "*.{bed}" pattern: "*.{bed}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"

4
modules/bedtools/subtract/meta.yml
View file

@ -36,9 +36,9 @@ output:
type: file type: file
description: File containing the difference between the two sets of features description: File containing the difference between the two sets of features
patters: "*.bed" patters: "*.bed"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/bismark/align/meta.yml
View file

@ -50,9 +50,9 @@ output:
type: file type: file
description: Bismark alignment reports description: Bismark alignment reports
pattern: "*{report.txt}" pattern: "*{report.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/bismark/deduplicate/meta.yml
View file

@ -43,9 +43,9 @@ output:
type: file type: file
description: Bismark deduplication reports description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}" pattern: "*.{deduplication_report.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/bismark/genomepreparation/meta.yml
View file

@ -28,9 +28,9 @@ output:
type: dir type: dir
description: Bismark genome index directory description: Bismark genome index directory
pattern: "BismarkIndex" pattern: "BismarkIndex"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/bismark/methylationextractor/meta.yml
View file

@ -58,9 +58,9 @@ output:
type: file type: file
description: Text file containing methylation bias information description: Text file containing methylation bias information
pattern: "*.{M-bias.txt}" pattern: "*.{M-bias.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/bismark/report/meta.yml
View file

@ -51,9 +51,9 @@ output:
type: file type: file
description: Bismark reports description: Bismark reports
pattern: "*.{html,txt}" pattern: "*.{html,txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/bismark/summary/meta.yml
View file

@ -45,9 +45,9 @@ output:
type: file type: file
description: Bismark summary description: Bismark summary
pattern: "*.{html,txt}" pattern: "*.{html,txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/blast/blastn/meta.yml
View file

@ -31,9 +31,9 @@ output:
type: file type: file
description: File containing blastn hits description: File containing blastn hits
pattern: "*.{blastn.txt}" pattern: "*.{blastn.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/blast/makeblastdb/meta.yml
View file

@ -21,9 +21,9 @@ output:
type: directory type: directory
description: Output directory containing blast database files description: Output directory containing blast database files
pattern: "*" pattern: "*"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bowtie/align/meta.yml
View file

@ -33,9 +33,9 @@ output:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- fastq: - fastq:
type: file type: file

4
modules/bowtie/build/meta.yml
View file

@ -22,9 +22,9 @@ output:
type: file type: file
description: Bowtie genome index files description: Bowtie genome index files
pattern: "*.ebwt" pattern: "*.ebwt"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@kevinmenden" - "@kevinmenden"

4
modules/bowtie2/align/meta.yml
View file

@ -33,9 +33,9 @@ output:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- fastq: - fastq:
type: file type: file

4
modules/bowtie2/build/meta.yml
View file

@ -23,9 +23,9 @@ output:
type: file type: file
description: Bowtie2 genome index files description: Bowtie2 genome index files
pattern: "*.bt2" pattern: "*.bt2"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"

4
modules/bwa/aln/meta.yml
View file

@ -41,9 +41,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- sai: - sai:
type: file type: file

4
modules/bwa/index/meta.yml
View file

@ -22,9 +22,9 @@ output:
type: file type: file
description: BWA genome index files description: BWA genome index files
pattern: "*.{amb,ann,bwt,pac,sa}" pattern: "*.{amb,ann,bwt,pac,sa}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@drpatelh" - "@drpatelh"

4
modules/bwa/mem/meta.yml
View file

@ -36,9 +36,9 @@ output:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@drpatelh" - "@drpatelh"

4
modules/bwa/sampe/meta.yml
View file

@ -45,9 +45,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/bwa/samse/meta.yml
View file

@ -46,9 +46,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/bwamem2/index/meta.yml
View file

@ -21,9 +21,9 @@ output:
type: file type: file
description: BWA genome index files description: BWA genome index files
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}" pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxulysse" - "@maxulysse"

4
modules/bwamem2/mem/meta.yml
View file

@ -36,9 +36,9 @@ output:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxulysse" - "@maxulysse"

4
modules/bwameth/align/meta.yml
View file

@ -43,9 +43,9 @@ output:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/bwameth/index/meta.yml
View file

@ -24,9 +24,9 @@ output:
type: dir type: dir
description: Directory containing bwameth genome index description: Directory containing bwameth genome index
pattern: "index" pattern: "index"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

4
modules/cat/cat/meta.yml
View file

@ -21,9 +21,9 @@ input:
description: Full name of output file with or without .gz extension description: Full name of output file with or without .gz extension
output: output:
- version: - versions:
type: file type: file
description: File containing version of the pigz software description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- file_out: - file_out:
type: file type: file

5
modules/cat/fastq/meta.yml
View file

@ -28,6 +28,11 @@ output:
type: file type: file
description: Merged fastq file description: Merged fastq file
pattern: "*.{merged.fastq.gz}" pattern: "*.{merged.fastq.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

4
modules/chromap/chromap/meta.yml
View file

@ -63,9 +63,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bed: - bed:
type: file type: file

4
modules/chromap/index/meta.yml
View file

@ -20,9 +20,9 @@ input:
description: Fasta reference file. description: Fasta reference file.
output: output:
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- index: - index:
type: file type: file

4
modules/cnvkit/meta.yml
View file

@ -75,9 +75,9 @@ output:
type: file type: file
description: File containing copy number segment information description: File containing copy number segment information
pattern: "*.{cns}" pattern: "*.{cns}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@kaurravneet4123" - "@kaurravneet4123"

4
modules/cooler/digest/meta.yml
View file

@ -26,9 +26,9 @@ input:
documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html
output: output:
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bed: - bed:
type: file type: file

4
modules/cooler/dump/meta.yml
View file

@ -28,9 +28,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bedpe: - bedpe:
type: file type: file

4
modules/custom/dumpsoftwareversions/meta.yml
View file

@ -24,9 +24,9 @@ output:
type: file type: file
description: MultiQC custom content YML file containing software versions description: MultiQC custom content YML file containing software versions
pattern: "software_versions_mqc.yml" pattern: "software_versions_mqc.yml"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/cutadapt/meta.yml
View file

@ -36,9 +36,9 @@ output:
type: file type: file
description: cuatadapt log file description: cuatadapt log file
pattern: "*cutadapt.log" pattern: "*cutadapt.log"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@drpatelh" - "@drpatelh"

4
modules/damageprofiler/meta.yml
View file

@ -40,9 +40,9 @@ input:
pattern: "*.{fai}" pattern: "*.{fai}"
output: output:
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- results: - results:
type: dir type: dir

4
modules/deeptools/computematrix/meta.yml
View file

@ -46,9 +46,9 @@ output:
description: | description: |
tabular file containing the scores of the generated matrix tabular file containing the scores of the generated matrix
pattern: "*.{computeMatrix.vals.mat.tab}" pattern: "*.{computeMatrix.vals.mat.tab}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/deeptools/plotfingerprint/meta.yml
View file

@ -50,9 +50,9 @@ output:
description: | description: |
file containing BAM file quality metrics file containing BAM file quality metrics
pattern: "*.{qcmetrics.txt}" pattern: "*.{qcmetrics.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/deeptools/plotheatmap/meta.yml
View file

@ -44,9 +44,9 @@ output:
File containing the matrix of values File containing the matrix of values
used to generate the heatmap used to generate the heatmap
pattern: "*.{plotHeatmap.mat.tab}" pattern: "*.{plotHeatmap.mat.tab}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/deeptools/plotprofile/meta.yml
View file

@ -44,9 +44,9 @@ output:
File containing the matrix of values File containing the matrix of values
used to generate the profile used to generate the profile
pattern: "*.{plotProfile.mat.tab}" pattern: "*.{plotProfile.mat.tab}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/delly/call/meta.yml
View file

@ -38,9 +38,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bcf: - bcf:
type: file type: file

4
modules/diamond/blastp/meta.yml
View file

@ -34,9 +34,9 @@ output:
type: file type: file
description: File containing blastp hits description: File containing blastp hits
pattern: "*.{blastp.txt}" pattern: "*.{blastp.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/diamond/blastx/meta.yml
View file

@ -34,9 +34,9 @@ output:
type: file type: file
description: File containing blastx hits description: File containing blastx hits
pattern: "*.{blastx.txt}" pattern: "*.{blastx.txt}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/diamond/makedb/meta.yml
View file

@ -25,9 +25,9 @@ output:
type: file type: file
description: File of the indexed DIAMOND database description: File of the indexed DIAMOND database
pattern: "*.{dmnd}" pattern: "*.{dmnd}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/dragonflye/meta.yml
View file

@ -28,9 +28,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- contigs: - contigs:
type: file type: file

4
modules/dshbio/exportsegments/meta.yml
View file

@ -32,9 +32,9 @@ output:
type: file type: file
description: Assembly segment sequences in FASTA format description: Assembly segment sequences in FASTA format
pattern: "*.{fa}" pattern: "*.{fa}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

4
modules/dshbio/filterbed/meta.yml
View file

@ -30,9 +30,9 @@ output:
type: file type: file
description: Features in gzipped BED format description: Features in gzipped BED format
pattern: "*.{bed.gz}" pattern: "*.{bed.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

4
modules/dshbio/filtergff3/meta.yml
View file

@ -30,9 +30,9 @@ output:
type: file type: file
description: Features in gzipped GFF3 format description: Features in gzipped GFF3 format
pattern: "*.{gff3.gz}" pattern: "*.{gff3.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

4
modules/dshbio/splitbed/meta.yml
View file

@ -30,9 +30,9 @@ output:
type: file type: file
description: Features in split gzipped BED formatted files description: Features in split gzipped BED formatted files
pattern: "*.{bed.gz}" pattern: "*.{bed.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

4
modules/dshbio/splitgff3/meta.yml
View file

@ -30,9 +30,9 @@ output:
type: file type: file
description: Features in split gzipped GFF3 formatted files description: Features in split gzipped GFF3 formatted files
pattern: "*.{gff3.gz}" pattern: "*.{gff3.gz}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

4
modules/ensemblvep/meta.yml
View file

@ -56,9 +56,9 @@ output:
type: file type: file
description: VEP report file description: VEP report file
pattern: "*.html" pattern: "*.html"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxulysse" - "@maxulysse"

4
modules/expansionhunter/meta.yml
View file

@ -37,9 +37,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', gender:'female' ] e.g. [ id:'test', gender:'female' ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- vcf: - vcf:
type: file type: file

4
modules/fastani/meta.yml
View file

@ -35,9 +35,9 @@ output:
type: file type: file
description: Results of the query description: Results of the query
pattern: "*.ani.txt" pattern: "*.ani.txt"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

4
modules/fastp/meta.yml
View file

@ -44,9 +44,9 @@ output:
type: file type: file
description: fastq log file description: fastq log file
pattern: "*.log" pattern: "*.log"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- reads_fail: - reads_fail:
type: file type: file

4
modules/fastqc/meta.yml
View file

@ -40,9 +40,9 @@ output:
type: file type: file
description: FastQC report archive description: FastQC report archive
pattern: "*_{fastqc.zip}" pattern: "*_{fastqc.zip}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@drpatelh" - "@drpatelh"

4
modules/fasttree/meta.yml
View file

@ -19,9 +19,9 @@ input:
pattern: "*.{fasta,fas,fa,mfa}" pattern: "*.{fasta,fas,fa,mfa}"
output: output:
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- phylogeny: - phylogeny:
type: file type: file

4
modules/fgbio/callmolecularconsensusreads/meta.yml
View file

@ -36,9 +36,9 @@ output:
description: | description: |
Output SAM or BAM file to write consensus reads. Output SAM or BAM file to write consensus reads.
pattern: "*.{bam,sam}" pattern: "*.{bam,sam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/fgbio/sortbam/meta.yml
View file

@ -34,9 +34,9 @@ output:
description: | description: |
Output SAM or BAM file. Output SAM or BAM file.
pattern: "*.{bam,sam}" pattern: "*.{bam,sam}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/flash/meta.yml
View file

@ -35,9 +35,9 @@ output:
type: file type: file
description: The merged fastq reads description: The merged fastq reads
pattern: "*fastq.gz" pattern: "*fastq.gz"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/gatk4/applybqsr/meta.yml
View file

@ -45,9 +45,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/gatk4/baserecalibrator/meta.yml
View file

@ -45,9 +45,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- table: - table:
type: file type: file

4
modules/gatk4/bedtointervallist/meta.yml
View file

@ -31,9 +31,9 @@ output:
type: file type: file
description: gatk interval list file description: gatk interval list file
pattern: "*.interval_list" pattern: "*.interval_list"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@kevinmenden" - "@kevinmenden"

4
modules/gatk4/createsequencedictionary/meta.yml
View file

@ -22,9 +22,9 @@ output:
type: file type: file
description: gatk dictionary file description: gatk dictionary file
pattern: "*.{dict}" pattern: "*.{dict}"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxulysse" - "@maxulysse"

4
modules/gatk4/fastqtosam/meta.yml
View file

@ -34,9 +34,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/gatk4/getpileupsummaries/meta.yml
View file

@ -48,9 +48,9 @@ output:
type: file type: file
description: File containing the pileup summary table. description: File containing the pileup summary table.
pattern: "*.pileups.table" pattern: "*.pileups.table"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:

4
modules/gatk4/haplotypecaller/meta.yml
View file

@ -46,9 +46,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- vcf: - vcf:
type: file type: file

4
modules/gatk4/intervallisttools/meta.yml
View file

@ -33,9 +33,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- interval_list: - interval_list:
type: file type: file

4
modules/gatk4/markduplicates/meta.yml
View file

@ -32,9 +32,9 @@ output:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- bam: - bam:
type: file type: file

4
modules/gatk4/mergebamalignment/meta.yml
View file

@ -37,9 +37,9 @@ output:
type: file type: file
description: The merged bam file description: The merged bam file
pattern: "*.bam" pattern: "*.bam"
- version: - versions:
type: file type: file
description: File containing software version description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@kevinmenden" - "@kevinmenden"

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