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Fix formatting in yaml files, add yamllint config (#1279)

Browse Source 
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
rpetit3-patch-1
Matthias Hörtenhuber 2 years ago committed by GitHub
parent 12b0bc5aa9
commit e745e167c1
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
426 changed files with 4712 additions and 4664 deletions
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12
.github/workflows/code-linting.yml vendored
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@ -12,9 +12,7 @@ jobs:
steps: steps:
- uses: actions/checkout@v2 - uses: actions/checkout@v2
- uses: actions/setup-node@v1 - uses: actions/setup-node@v2
with:
node-version: "10"
- name: Install markdownlint - name: Install markdownlint
run: npm install -g markdownlint-cli run: npm install -g markdownlint-cli
@ -27,9 +25,7 @@ jobs:
steps: steps:
- uses: actions/checkout@v2 - uses: actions/checkout@v2
- uses: actions/setup-node@v1 - uses: actions/setup-node@v2
with:
node-version: "10"
- name: Install editorconfig-checker - name: Install editorconfig-checker
run: npm install -g editorconfig-checker run: npm install -g editorconfig-checker
@ -44,9 +40,7 @@ jobs:
uses: actions/checkout@v2 uses: actions/checkout@v2
- name: Install NodeJS - name: Install NodeJS
uses: actions/setup-node@v1 uses: actions/setup-node@v2
with:
node-version: "10"
- name: Install yaml-lint - name: Install yaml-lint
run: npm install -g yaml-lint run: npm install -g yaml-lint

6
.gitpod.yml
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@ -1,14 +1,14 @@
image: nfcore/gitpod:latest image: nfcore/gitpod:latest
vscode: vscode:
extensions: # based on nf-core.nf-core-extensionpack extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files - codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer # - cssho.vscode-svgviewer # SVG viewer
- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting # - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level - oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code - streetsidesoftware.code-spell-checker # Spelling checker for source code

2
.markdownlint.yml
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@ -8,4 +8,4 @@ header-increment: false
no-duplicate-header: no-duplicate-header:
siblings_only: true siblings_only: true
ul-indent: ul-indent:
indent: 4 indent: 4

5
.yamllint.yml
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@ -0,0 +1,5 @@
extends: default
rules:
document-start: disable
line-length: disable

2
modules/abacas/meta.yml
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@ -14,7 +14,7 @@ tools:
documentation: http://abacas.sourceforge.net/documentation.html documentation: http://abacas.sourceforge.net/documentation.html
tool_dev_url: None tool_dev_url: None
doi: "10.1093/bioinformatics/btp347" doi: "10.1093/bioinformatics/btp347"
licence: ['GPL v2-or-later'] licence: ["GPL v2-or-later"]
input: input:
- meta: - meta:

80
modules/adapterremoval/meta.yml
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@ -1,50 +1,50 @@
name: adapterremoval name: adapterremoval
description: Trim sequencing adapters and collapse overlapping reads description: Trim sequencing adapters and collapse overlapping reads
keywords: keywords:
- trimming - trimming
- adapters - adapters
- merging - merging
- fastq - fastq
tools: tools:
- adapterremoval: - adapterremoval:
description: The AdapterRemoval v2 tool for merging and clipping reads. description: The AdapterRemoval v2 tool for merging and clipping reads.
homepage: https://github.com/MikkelSchubert/adapterremoval homepage: https://github.com/MikkelSchubert/adapterremoval
documentation: https://adapterremoval.readthedocs.io documentation: https://adapterremoval.readthedocs.io
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:
type: map type: map
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false, collapse:false ] e.g. [ id:'test', single_end:false, collapse:false ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
pattern: "*.{fq,fastq,fg.gz,fastq.gz}" pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input adapter trimmed FastQ files of size 1 or 2 for List of input adapter trimmed FastQ files of size 1 or 2 for
single-end or collapsed data and paired-end data, respectively. single-end or collapsed data and paired-end data, respectively.
pattern: "*.{fastq.gz}" pattern: "*.{fastq.gz}"
- log: - log:
type: file type: file
description: AdapterRemoval log file description: AdapterRemoval log file
pattern: "*.log" pattern: "*.log"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxibor" - "@maxibor"

2
modules/agrvate/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/VishnuRaghuram94/AgrVATE documentation: https://github.com/VishnuRaghuram94/AgrVATE
tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/amps/meta.yml
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@ -24,7 +24,7 @@ tools:
documentation: "https://github.com/keyfm/amps" documentation: "https://github.com/keyfm/amps"
tool_dev_url: "https://github.com/keyfm/amps" tool_dev_url: "https://github.com/keyfm/amps"
doi: "10.1186/s13059-019-1903-0" doi: "10.1186/s13059-019-1903-0"
licence: ['GPL >=3'] licence: ["GPL >=3"]
input: input:
- maltextract_results: - maltextract_results:

2
modules/arriba/meta.yml
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@ -10,7 +10,7 @@ tools:
documentation: https://arriba.readthedocs.io/en/latest/ documentation: https://arriba.readthedocs.io/en/latest/
tool_dev_url: https://github.com/suhrig/arriba tool_dev_url: https://github.com/suhrig/arriba
doi: "10.1101/gr.257246.119" doi: "10.1101/gr.257246.119"
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/artic/guppyplex/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://artic.readthedocs.io/en/latest/ documentation: https://artic.readthedocs.io/en/latest/
tool_dev_url: https://github.com/artic-network/fieldbioinformatics tool_dev_url: https://github.com/artic-network/fieldbioinformatics
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

8
modules/artic/minion/meta.yml
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@ -1,6 +1,6 @@
name: artic_minion name: artic_minion
description: | description: |
Run the alignment/variant-call/consensus logic of the artic pipeline Run the alignment/variant-call/consensus logic of the artic pipeline
keywords: keywords:
- artic - artic
- aggregate - aggregate
@ -12,7 +12,7 @@ tools:
documentation: https://artic.readthedocs.io/en/latest/ documentation: https://artic.readthedocs.io/en/latest/
tool_dev_url: https://github.com/artic-network/fieldbioinformatics tool_dev_url: https://github.com/artic-network/fieldbioinformatics
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
@ -21,11 +21,11 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- fastq: - fastq:
type: file type: file
description: FastQ file containing reads description: FastQ file containing reads
pattern: "*.{fastq.gz}" pattern: "*.{fastq.gz}"
- fast5_dir: - fast5_dir:
type: directory type: directory
description: Directory containing MinION FAST5 files description: Directory containing MinION FAST5 files
pattern: "*" pattern: "*"
- sequencing_summary: - sequencing_summary:
type: file type: file

2
modules/assemblyscan/meta.yml
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@ -10,7 +10,7 @@ tools:
documentation: https://github.com/rpetit3/assembly-scan documentation: https://github.com/rpetit3/assembly-scan
tool_dev_url: https://github.com/rpetit3/assembly-scan tool_dev_url: https://github.com/rpetit3/assembly-scan
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/ataqv/ataqv/meta.yml
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@ -9,7 +9,7 @@ tools:
documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
tool_dev_url: https://github.com/ParkerLab/ataqv tool_dev_url: https://github.com/ParkerLab/ataqv
doi: "https://doi.org/10.1016/j.cels.2020.02.009" doi: "https://doi.org/10.1016/j.cels.2020.02.009"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

2
modules/bakta/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/oschwengers/bakta documentation: https://github.com/oschwengers/bakta
tool_dev_url: https://github.com/oschwengers/bakta tool_dev_url: https://github.com/oschwengers/bakta
doi: "10.1099/mgen.0.000685" doi: "10.1099/mgen.0.000685"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

2
modules/bamaligncleaner/meta.yml
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@ -8,7 +8,7 @@ tools:
homepage: https://github.com/maxibor/bamAlignCleaner homepage: https://github.com/maxibor/bamAlignCleaner
documentation: https://github.com/maxibor/bamAlignCleaner documentation: https://github.com/maxibor/bamAlignCleaner
tool_dev_url: https://github.com/maxibor/bamAlignCleaner tool_dev_url: https://github.com/maxibor/bamAlignCleaner
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

9
modules/bamcmp/meta.yml
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@ -10,14 +10,15 @@ keywords:
tools: tools:
- bamcmp: - bamcmp:
description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, description:
sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
reads which multimap to the contamination genome will be spuriously kept. sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
reads which multimap to the contamination genome will be spuriously kept.
homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
doi: "10.1158/1541-7786.MCR-16-0431" doi: "10.1158/1541-7786.MCR-16-0431"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

2
modules/bamtools/convert/meta.yml
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@ -19,7 +19,7 @@ tools:
documentation: https://github.com/pezmaster31/bamtools/wiki documentation: https://github.com/pezmaster31/bamtools/wiki
tool_dev_url: http://github.com/pezmaster31/bamtools tool_dev_url: http://github.com/pezmaster31/bamtools
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/bamtools/split/meta.yml
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@ -13,7 +13,7 @@ tools:
documentation: https://github.com/pezmaster31/bamtools/wiki documentation: https://github.com/pezmaster31/bamtools/wiki
tool_dev_url: http://github.com/pezmaster31/bamtools tool_dev_url: http://github.com/pezmaster31/bamtools
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/bamutil/trimbam/meta.yml
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@ -13,7 +13,7 @@ tools:
documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
tool_dev_url: https://github.com/statgen/bamUtil tool_dev_url: https://github.com/statgen/bamUtil
doi: "10.1101/gr.176552.114" doi: "10.1101/gr.176552.114"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

74
modules/bandage/image/meta.yml
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@ -1,44 +1,44 @@
name: bandage_image name: bandage_image
description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
keywords: keywords:
- gfa - gfa
- graph - graph
- assembly - assembly
- visualisation - visualisation
tools: tools:
- bandage: - bandage:
description: | description: |
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
homepage: https://github.com/rrwick/Bandage homepage: https://github.com/rrwick/Bandage
documentation: https://github.com/rrwick/Bandage documentation: https://github.com/rrwick/Bandage
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- gfa: - gfa:
type: file type: file
description: Assembly graph in GFA 1.0 format description: Assembly graph in GFA 1.0 format
pattern: "*.gfa" pattern: "*.gfa"
output: output:
- meta: - meta:
type: map type: map
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 ]
- png: - png:
type: file type: file
description: Bandage image in PNG format description: Bandage image in PNG format
pattern: "*.png" pattern: "*.png"
- svg: - svg:
type: file type: file
description: Bandage image in SVG format description: Bandage image in SVG format
pattern: "*.svg" pattern: "*.svg"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@heuermh" - "@heuermh"

12
modules/bbmap/align/meta.yml
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@ -13,7 +13,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None tool_dev_url: None
doi: "" doi: ""
licence: ['UC-LBL license (see package)'] licence: ["UC-LBL license (see package)"]
input: input:
- meta: - meta:
@ -24,14 +24,14 @@ input:
- fastq: - fastq:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- ref: - ref:
type: file type: file
description: | description: |
Either "ref" a directory containing an index, the name of another directory Either "ref" a directory containing an index, the name of another directory
with a "ref" subdirectory containing an index or the name of a fasta formatted with a "ref" subdirectory containing an index or the name of a fasta formatted
nucleotide file containg the reference to map to. nucleotide file containg the reference to map to.
output: output:
- meta: - meta:

16
modules/bbmap/bbduk/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None tool_dev_url: None
doi: "" doi: ""
licence: ['UC-LBL license (see package)'] licence: ["UC-LBL license (see package)"]
input: input:
- meta: - meta:
@ -20,14 +20,14 @@ input:
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- contaminants: - contaminants:
type: file type: file
description: | description: |
Reference files containing adapter and/or contaminant sequences for sequence kmer matching Reference files containing adapter and/or contaminant sequences for sequence kmer matching
output: output:
- meta: - meta:

2
modules/bbmap/bbsplit/meta.yml
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@ -12,7 +12,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None tool_dev_url: None
doi: "" doi: ""
licence: ['UC-LBL license (see package)'] licence: ["UC-LBL license (see package)"]
input: input:
- meta: - meta:

2
modules/bbmap/index/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None tool_dev_url: None
doi: "" doi: ""
licence: ['UC-LBL license (see package)'] licence: ["UC-LBL license (see package)"]
input: input:
- fasta: - fasta:

68
modules/bcftools/concat/meta.yml
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@ -1,43 +1,43 @@
name: bcftools_concat name: bcftools_concat
description: Concatenate VCF files description: Concatenate VCF files
keywords: keywords:
- variant calling - variant calling
- concat - concat
- bcftools - bcftools
- VCF - VCF
tools: tools:
- concat: - concat:
description: | description: |
Concatenate VCF files. Concatenate VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcfs: - vcfs:
type: files type: files
description: | description: |
List containing 2 or more vcf files List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ] e.g. [ 'file1.vcf', 'file2.vcf' ]
output: output:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF concatenated output file description: VCF concatenated output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

84
modules/bcftools/consensus/meta.yml
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@ -1,49 +1,49 @@
name: bcftools_consensus name: bcftools_consensus
description: Compresses VCF files description: Compresses VCF files
keywords: keywords:
- variant calling - variant calling
- consensus - consensus
- VCF - VCF
tools: tools:
- consensus: - consensus:
description: | description: |
Create consensus sequence by applying VCF variants to a reference fasta file. Create consensus sequence by applying VCF variants to a reference fasta file.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF file description: VCF file
pattern: "*.{vcf}" pattern: "*.{vcf}"
- tbi: - tbi:
type: file type: file
description: tabix index file description: tabix index file
pattern: "*.{tbi}" pattern: "*.{tbi}"
- fasta: - fasta:
type: file type: file
description: FASTA reference file description: FASTA reference file
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- fasta: - fasta:
type: file type: file
description: FASTA reference consensus file description: FASTA reference consensus file
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

68
modules/bcftools/filter/meta.yml
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@ -1,41 +1,41 @@
name: bcftools_filter name: bcftools_filter
description: Filters VCF files description: Filters VCF files
keywords: keywords:
- variant calling - variant calling
- filtering - filtering
- VCF - VCF
tools: tools:
- filter: - filter:
description: | description: |
Apply fixed-threshold filters to VCF files. Apply fixed-threshold filters to VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF input file description: VCF input file
pattern: "*.{vcf}" pattern: "*.{vcf}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF filtered output file description: VCF filtered output file
pattern: "*.{vcf}" pattern: "*.{vcf}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

2
modules/bcftools/index/meta.yml
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documentation: https://samtools.github.io/bcftools/howtos/index.html documentation: https://samtools.github.io/bcftools/howtos/index.html
tool_dev_url: https://github.com/samtools/bcftools tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/gigascience/giab008" doi: "10.1093/gigascience/giab008"
licence: ['MIT', 'GPL-3.0-or-later'] licence: ["MIT", "GPL-3.0-or-later"]
input: input:
- meta: - meta:

84
modules/bcftools/isec/meta.yml
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name: bcftools_isec name: bcftools_isec
description: Apply set operations to VCF files description: Apply set operations to VCF files
keywords: keywords:
- variant calling - variant calling
- intersect - intersect
- union - union
- complement - complement
- VCF - VCF
tools: tools:
- isec: - isec:
description: | description: |
Computes intersections, unions and complements of VCF files. Computes intersections, unions and complements of VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcfs: - vcfs:
type: files type: files
description: | description: |
List containing 2 or more vcf files List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ] e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis: - tbis:
type: files type: files
description: | description: |
List containing the tbi index files corresponding to the vcfs input files List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
output: output:
- meta: - meta:
type: map type: map
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 ]
- results: - results:
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}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

80
modules/bcftools/merge/meta.yml
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name: bcftools_merge name: bcftools_merge
description: Merge VCF files description: Merge VCF files
keywords: keywords:
- variant calling - variant calling
- merge - merge
- VCF - VCF
tools: tools:
- merge: - merge:
description: | description: |
Merge VCF files. Merge VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcfs: - vcfs:
type: files type: files
description: | description: |
List containing 2 or more vcf files List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ] e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis: - tbis:
type: files type: files
description: | description: |
List containing the tbi index files corresponding to the vcfs input files List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
output: output:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF merged output file description: VCF merged output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

100
modules/bcftools/mpileup/meta.yml
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name: bcftools_mpileup name: bcftools_mpileup
description: Compresses VCF files description: Compresses VCF files
keywords: keywords:
- variant calling - variant calling
- mpileup - mpileup
- VCF - VCF
tools: tools:
- mpileup: - mpileup:
description: | description: |
Generates genotype likelihoods at each genomic position with coverage. Generates genotype likelihoods at each genomic position with coverage.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: Input BAM file description: Input BAM file
pattern: "*.{bam}" pattern: "*.{bam}"
- fasta: - fasta:
type: file type: file
description: FASTA reference file description: FASTA reference file
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
- save_mpileup: - save_mpileup:
type: boolean type: boolean
description: Save mpileup file generated by bcftools mpileup description: Save mpileup file generated by bcftools mpileup
patter: "*.mpileup" patter: "*.mpileup"
output: output:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF gzipped output file description: VCF gzipped output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- tbi: - tbi:
type: file type: file
description: tabix index file description: tabix index file
pattern: "*.{tbi}" pattern: "*.{tbi}"
- stats: - stats:
type: file type: file
description: Text output file containing stats description: Text output file containing stats
pattern: "*{stats.txt}" pattern: "*{stats.txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

70
modules/bcftools/norm/meta.yml
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@ -6,41 +6,41 @@ keywords:
- variant calling - variant calling
- VCF - VCF
tools: tools:
- norm: - norm:
description: | description: |
Normalize VCF files. Normalize VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: | description: |
The vcf file to be normalized The vcf file to be normalized
e.g. 'file1.vcf' e.g. 'file1.vcf'
- fasta: - fasta:
type: file type: file
description: FASTA reference file description: FASTA reference file
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF normalized output file description: VCF normalized output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

96
modules/bcftools/query/meta.yml
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@ -6,56 +6,56 @@ keywords:
- bcftools - bcftools
- VCF - VCF
tools: tools:
- query: - query:
description: | description: |
Extracts fields from VCF or BCF files and outputs them in user-defined format. Extracts fields from VCF or BCF files and outputs them in user-defined format.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: | description: |
The vcf file to be qeuried. The vcf file to be qeuried.
pattern: "*.{vcf.gz, vcf}" pattern: "*.{vcf.gz, vcf}"
- tbi: - tbi:
type: file type: file
description: | description: |
The tab index for the VCF file to be inspected. The tab index for the VCF file to be inspected.
pattern: "*.tbi" pattern: "*.tbi"
- regions: - regions:
type: file type: file
description: | description: |
Optionally, restrict the operation to regions listed in this file. Optionally, restrict the operation to regions listed in this file.
- targets: - targets:
type: file type: file
description: | description: |
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
- samples: - samples:
type: file type: file
description: | description: |
Optional, file of sample names to be included or excluded. Optional, file of sample names to be included or excluded.
e.g. 'file.tsv' e.g. 'file.tsv'
output: output:
- meta: - meta:
type: map type: map
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 ]
- txt: - txt:
type: file type: file
description: BCFTools query output file description: BCFTools query output file
pattern: "*.txt" pattern: "*.txt"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"
- "@drpatelh" - "@drpatelh"

2
modules/bcftools/reheader/meta.yml
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@ -11,7 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://samtools.github.io/bcftools/bcftools.html#reheader documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
doi: 10.1093/gigascience/giab008 doi: 10.1093/gigascience/giab008
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/bcftools/sort/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
tool_dev_url: https://github.com/samtools/bcftools tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/bioinformatics/btp352" doi: "10.1093/bioinformatics/btp352"
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

70
modules/bcftools/stats/meta.yml
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name: bcftools_stats name: bcftools_stats
description: Generates stats from VCF files description: Generates stats from VCF files
keywords: keywords:
- variant calling - variant calling
- stats - stats
- VCF - VCF
tools: tools:
- stats: - stats:
description: | description: |
Parses VCF or BCF and produces text file stats which is suitable for Parses VCF or BCF and produces text file stats which is suitable for
machine processing and can be plotted using plot-vcfstats. machine processing and can be plotted using plot-vcfstats.
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF input file description: VCF input file
pattern: "*.{vcf}" pattern: "*.{vcf}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- stats: - stats:
type: file type: file
description: Text output file containing stats description: Text output file containing stats
pattern: "*_{stats.txt}" pattern: "*_{stats.txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

110
modules/bcftools/view/meta.yml
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name: bcftools_view name: bcftools_view
description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
keywords: keywords:
- variant calling - variant calling
- view - view
- bcftools - bcftools
- VCF - VCF
tools: tools:
- view: - view:
description: | description: |
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: | description: |
The vcf file to be inspected. The vcf file to be inspected.
e.g. 'file.vcf' e.g. 'file.vcf'
- index: - index:
type: file type: file
description: | description: |
The tab index for the VCF file to be inspected. The tab index for the VCF file to be inspected.
e.g. 'file.tbi' e.g. 'file.tbi'
- regions: - regions:
type: file type: file
description: | description: |
Optionally, restrict the operation to regions listed in this file. Optionally, restrict the operation to regions listed in this file.
e.g. 'file.vcf' e.g. 'file.vcf'
- targets: - targets:
type: file type: file
description: | description: |
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
e.g. 'file.vcf' e.g. 'file.vcf'
- samples: - samples:
type: file type: file
description: | description: |
Optional, file of sample names to be included or excluded. Optional, file of sample names to be included or excluded.
e.g. 'file.tsv' e.g. 'file.tsv'
output: output:
- meta: - meta:
type: map type: map
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 ]
- vcf: - vcf:
type: file type: file
description: VCF normalized output file description: VCF normalized output file
pattern: "*.{vcf.gz}" pattern: "*.{vcf.gz}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@abhi18av" - "@abhi18av"

62
modules/bedtools/bamtobed/meta.yml
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name: bedtools_bamtobed name: bedtools_bamtobed
description: Converts a bam file to a bed12 file. description: Converts a bam file to a bed12 file.
keywords: keywords:
- bam - bam
- bed - bed
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: Input BAM file description: Input BAM file
pattern: "*.{bam}" pattern: "*.{bam}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Bed file containing genomic intervals. description: Bed file containing genomic intervals.
pattern: "*.{bed}" pattern: "*.{bed}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@yuukiiwa" - "@yuukiiwa"
- "@drpatelh" - "@drpatelh"

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modules/bedtools/complement/meta.yml
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name: bedtools_complement name: bedtools_complement
description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
keywords: keywords:
- bed - bed
- complement - complement
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Input BED file description: Input BED file
pattern: "*.{bed}" pattern: "*.{bed}"
- sizes: - sizes:
type: file type: file
description: File which defines the chromosome lengths for a given genome description: File which defines the chromosome lengths for a given genome
pattern: "*.{sizes}" pattern: "*.{sizes}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
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}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"
- "@sruthipsuresh" - "@sruthipsuresh"
- "@drpatelh" - "@drpatelh"

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modules/bedtools/genomecov/meta.yml
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name: bedtools_genomecov name: bedtools_genomecov
description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
keywords: keywords:
- bed - bed
- bam - bam
- genomecov - genomecov
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- intervals: - intervals:
type: file type: file
description: BAM/BED/GFF/VCF description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}" pattern: "*.{bam|bed|gff|vcf}"
- scale: - scale:
type: value type: value
description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
- sizes: - sizes:
type: file type: file
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
- extension: - extension:
type: string type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output: output:
- meta: - meta:
type: map type: map
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 ]
- genomecov: - genomecov:
type: file type: file
description: Computed genome coverage file description: Computed genome coverage file
pattern: "*.${extension}" pattern: "*.${extension}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"
- "@sruthipsuresh" - "@sruthipsuresh"
- "@drpatelh" - "@drpatelh"
- "@sidorov-si" - "@sidorov-si"
- "@chris-cheshire" - "@chris-cheshire"

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modules/bedtools/getfasta/meta.yml
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name: bedtools_getfasta name: bedtools_getfasta
description: extract sequences in a FASTA file based on intervals defined in a feature file. description: extract sequences in a FASTA file based on intervals defined in a feature file.
keywords: keywords:
- bed - bed
- fasta - fasta
- getfasta - getfasta
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- bed: - bed:
type: file type: file
description: Bed feature file description: Bed feature file
pattern: "*.{bed}" pattern: "*.{bed}"
- fasta: - fasta:
type: file type: file
description: Input fasta file description: Input fasta file
pattern: "*.{fa,fasta}" pattern: "*.{fa,fasta}"
output: output:
- fasta: - fasta:
type: file type: file
description: Output fasta file with extracted sequences description: Output fasta file with extracted sequences
pattern: "*.{fa}" pattern: "*.{fa}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

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modules/bedtools/intersect/meta.yml
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name: bedtools_intersect name: bedtools_intersect
description: Allows one to screen for overlaps between two sets of genomic features. description: Allows one to screen for overlaps between two sets of genomic features.
keywords: keywords:
- bed - bed
- intersect - intersect
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- intervals1: - intervals1:
type: file type: file
description: BAM/BED/GFF/VCF description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}" pattern: "*.{bam|bed|gff|vcf}"
- intervals2: - intervals2:
type: file type: file
description: BAM/BED/GFF/VCF description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}" pattern: "*.{bam|bed|gff|vcf}"
- extension: - extension:
type: value type: value
description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.). description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
output: output:
- meta: - meta:
type: map type: map
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 ]
- intersect: - intersect:
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}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"
- "@sruthipsuresh" - "@sruthipsuresh"
- "@drpatelh" - "@drpatelh"
- "@sidorov-si" - "@sidorov-si"

2
modules/bedtools/makewindows/meta.yml
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documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
tool_dev_url: None tool_dev_url: None
doi: "10.1093/bioinformatics/btq033" doi: "10.1093/bioinformatics/btq033"
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map

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modules/bedtools/maskfasta/meta.yml
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name: bedtools_maskfasta name: bedtools_maskfasta
description: masks sequences in a FASTA file based on intervals defined in a feature file. description: masks sequences in a FASTA file based on intervals defined in a feature file.
keywords: keywords:
- bed - bed
- fasta - fasta
- maskfasta - maskfasta
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Bed feature file description: Bed feature file
pattern: "*.{bed}" pattern: "*.{bed}"
- fasta: - fasta:
type: file type: file
description: Input fasta file description: Input fasta file
pattern: "*.{fa,fasta}" pattern: "*.{fa,fasta}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- fasta: - fasta:
type: file type: file
description: Output masked fasta file description: Output masked fasta file
pattern: "*.{fa}" pattern: "*.{fa}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

64
modules/bedtools/merge/meta.yml
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name: bedtools_merge name: bedtools_merge
description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
keywords: keywords:
- bed - bed
- merge - merge
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Input BED file description: Input BED file
pattern: "*.{bed}" pattern: "*.{bed}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Overlapped bed file with combined features description: Overlapped bed file with combined features
pattern: "*.{bed}" pattern: "*.{bed}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"
- "@sruthipsuresh" - "@sruthipsuresh"
- "@drpatelh" - "@drpatelh"

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modules/bedtools/slop/meta.yml
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name: bedtools_slop name: bedtools_slop
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r) description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
keywords: keywords:
- bed - bed
- slopBed - slopBed
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Input BED file description: Input BED file
pattern: "*.{bed}" pattern: "*.{bed}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bed: - bed:
type: file type: file
description: Slopped BED file description: Slopped BED file
pattern: "*.{bed}" pattern: "*.{bed}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"
- "@sruthipsuresh" - "@sruthipsuresh"
- "@drpatelh" - "@drpatelh"

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modules/bedtools/sort/meta.yml
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name: bedtools_sort name: bedtools_sort
description: Sorts a feature file by chromosome and other criteria. description: Sorts a feature file by chromosome and other criteria.
keywords: keywords:
- bed - bed
- sort - sort
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- intervals: - intervals:
type: file type: file
description: BED/BEDGRAPH description: BED/BEDGRAPH
pattern: "*.{bed|bedGraph}" pattern: "*.{bed|bedGraph}"
- extension: - extension:
type: string type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output: output:
- meta: - meta:
type: map type: map
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 ]
- sorted: - sorted:
type: file type: file
description: Sorted output file description: Sorted output file
pattern: "*.${extension}" pattern: "*.${extension}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@Emiller88" - "@Emiller88"
- "@sruthipsuresh" - "@sruthipsuresh"
- "@drpatelh" - "@drpatelh"
- "@chris-cheshire" - "@chris-cheshire"

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modules/bedtools/subtract/meta.yml
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name: bedtools_subtract name: bedtools_subtract
description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A. description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
keywords: keywords:
- bed - bed
- gff - gff
- vcf - vcf
- subtract - subtract
tools: tools:
- bedtools: - bedtools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

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modules/biobambam/bammarkduplicates2/meta.yml
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name: biobambam_bammarkduplicates2 name: biobambam_bammarkduplicates2
description: Locate and tag duplicate reads in a BAM file description: Locate and tag duplicate reads in a BAM file
keywords: keywords:
- markduplicates - markduplicates
- bam - bam
- cram - cram
tools: tools:
- biobambam: - biobambam:
description: | description: |
biobambam is a set of tools for early stage alignment file processing. biobambam is a set of tools for early stage alignment file processing.
homepage: https://gitlab.com/german.tischler/biobambam2 homepage: https://gitlab.com/german.tischler/biobambam2
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
doi: 10.1186/1751-0473-9-13 doi: 10.1186/1751-0473-9-13
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: BAM/CRAM file description: BAM/CRAM file
pattern: "*.{bam,cram}" pattern: "*.{bam,cram}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: BAM file with duplicate reads marked/removed description: BAM file with duplicate reads marked/removed
pattern: "*.{bam}" pattern: "*.{bam}"
- metrics: - metrics:
type: file type: file
description: Duplicate metrics file generated by biobambam description: Duplicate metrics file generated by biobambam
pattern: "*.{metrics.txt}" pattern: "*.{metrics.txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@muffato" - "@muffato"

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modules/bismark/align/meta.yml
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name: bismark_align name: bismark_align
description: Performs alignment of BS-Seq reads using bismark description: Performs alignment of BS-Seq reads using bismark
keywords: keywords:
- bismark - bismark
- 3-letter genome - 3-letter genome
- map - map
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- bam - bam
tools: tools:
- bismark: - bismark:
description: | description: |
Bismark is a tool to map bisulfite treated sequencing reads Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion. and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- index: - index:
type: dir type: dir
description: Bismark genome index directory description: Bismark genome index directory
pattern: "BismarkIndex" pattern: "BismarkIndex"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- unmapped: - unmapped:
type: file type: file
description: Output FastQ file(s) containing unmapped reads description: Output FastQ file(s) containing unmapped reads
pattern: "*.{fq.gz}" pattern: "*.{fq.gz}"
- report: - report:
type: file type: file
description: Bismark alignment reports description: Bismark alignment reports
pattern: "*{report.txt}" pattern: "*{report.txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

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modules/bismark/deduplicate/meta.yml
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name: bismark_deduplicate name: bismark_deduplicate
description: | description: |
Removes alignments to the same position in the genome Removes alignments to the same position in the genome
from the Bismark mapping output. from the Bismark mapping output.
keywords: keywords:
- bismark - bismark
- 3-letter genome - 3-letter genome
- map - map
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- bam - bam
tools: tools:
- bismark: - bismark:
description: | description: |
Bismark is a tool to map bisulfite treated sequencing reads Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion. and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: BAM file containing read alignments description: BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: Deduplicated output BAM file containing read alignments description: Deduplicated output BAM file containing read alignments
pattern: "*.{deduplicated.bam}" pattern: "*.{deduplicated.bam}"
- report: - report:
type: file type: file
description: Bismark deduplication reports description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}" pattern: "*.{deduplication_report.txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

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name: bismark_genomepreparation name: bismark_genomepreparation
description: | description: |
Converts a specified reference genome into two different bisulfite Converts a specified reference genome into two different bisulfite
converted versions and indexes them for alignments. converted versions and indexes them for alignments.
keywords: keywords:
- bismark - bismark
- 3-letter genome - 3-letter genome
- index - index
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- fasta - fasta
tools: tools:
- bismark: - bismark:
description: | description: |
Bismark is a tool to map bisulfite treated sequencing reads Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion. and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- index: - index:
type: dir type: dir
description: Bismark genome index directory description: Bismark genome index directory
pattern: "BismarkIndex" pattern: "BismarkIndex"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

120
modules/bismark/methylationextractor/meta.yml
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name: bismark_methylationextractor name: bismark_methylationextractor
description: Extracts methylation information for individual cytosines from alignments. description: Extracts methylation information for individual cytosines from alignments.
keywords: keywords:
- bismark - bismark
- consensus - consensus
- map - map
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- bam - bam
- bedGraph - bedGraph
tools: tools:
- bismark: - bismark:
description: | description: |
Bismark is a tool to map bisulfite treated sequencing reads Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion. and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: BAM file containing read alignments description: BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- index: - index:
type: dir type: dir
description: Bismark genome index directory description: Bismark genome index directory
pattern: "BismarkIndex" pattern: "BismarkIndex"
output: output:
- meta: - meta:
type: map type: map
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 ]
- bedgraph: - bedgraph:
type: file type: file
description: Bismark output file containing coverage and methylation metrics description: Bismark output file containing coverage and methylation metrics
pattern: "*.{bedGraph.gz}" pattern: "*.{bedGraph.gz}"
- methylation_calls: - methylation_calls:
type: file type: file
description: Bismark output file containing strand-specific methylation calls description: Bismark output file containing strand-specific methylation calls
pattern: "*.{txt.gz}" pattern: "*.{txt.gz}"
- coverage: - coverage:
type: file type: file
description: Bismark output file containing coverage metrics description: Bismark output file containing coverage metrics
pattern: "*.{cov.gz}" pattern: "*.{cov.gz}"
- report: - report:
type: file type: file
description: Bismark splitting reports description: Bismark splitting reports
pattern: "*_{splitting_report.txt}" pattern: "*_{splitting_report.txt}"
- mbias: - mbias:
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}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

106
modules/bismark/report/meta.yml
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name: bismark_report name: bismark_report
description: Collects bismark alignment reports description: Collects bismark alignment reports
keywords: keywords:
- bismark - bismark
- qc - qc
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- report - report
tools: tools:
- bismark: - bismark:
description: | description: |
Bismark is a tool to map bisulfite treated sequencing reads Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion. and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- align_report: - align_report:
type: file type: file
description: Bismark alignment reports description: Bismark alignment reports
pattern: "*{report.txt}" pattern: "*{report.txt}"
- splitting_report: - splitting_report:
type: file type: file
description: Bismark splitting reports description: Bismark splitting reports
pattern: "*{splitting_report.txt}" pattern: "*{splitting_report.txt}"
- dedup_report: - dedup_report:
type: file type: file
description: Bismark deduplication reports description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}" pattern: "*.{deduplication_report.txt}"
- mbias: - mbias:
type: file type: file
description: Text file containing methylation bias information description: Text file containing methylation bias information
pattern: "*.{txt}" pattern: "*.{txt}"
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- meta: - meta:
type: map type: map
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 ]
- report: - report:
type: file type: file
description: Bismark reports description: Bismark reports
pattern: "*.{html,txt}" pattern: "*.{html,txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

94
modules/bismark/summary/meta.yml
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name: bismark_summary name: bismark_summary
description: | description: |
Uses Bismark report files of several samples in a run folder Uses Bismark report files of several samples in a run folder
to generate a graphical summary HTML report. to generate a graphical summary HTML report.
keywords: keywords:
- bismark - bismark
- qc - qc
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- report - report
- summary - summary
tools: tools:
- bismark: - bismark:
description: | description: |
Bismark is a tool to map bisulfite treated sequencing reads Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion. and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- bam: - bam:
type: file type: file
description: Bismark alignment description: Bismark alignment
pattern: "*.{bam}" pattern: "*.{bam}"
- align_report: - align_report:
type: file type: file
description: Bismark alignment reports description: Bismark alignment reports
pattern: "*{report.txt}" pattern: "*{report.txt}"
- dedup_report: - dedup_report:
type: file type: file
description: Bismark deduplication reports description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}" pattern: "*.{deduplication_report.txt}"
- splitting_report: - splitting_report:
type: file type: file
description: Bismark splitting reports description: Bismark splitting reports
pattern: "*{splitting_report.txt}" pattern: "*{splitting_report.txt}"
- mbias: - mbias:
type: file type: file
description: Text file containing methylation bias information description: Text file containing methylation bias information
pattern: "*.{txt}" pattern: "*.{txt}"
output: output:
- summary: - summary:
type: file type: file
description: Bismark summary description: Bismark summary
pattern: "*.{html,txt}" pattern: "*.{html,txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

68
modules/blast/blastn/meta.yml
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name: blast_blastn name: blast_blastn
description: Queries a BLAST DNA database description: Queries a BLAST DNA database
keywords: keywords:
- fasta - fasta
- blast - blast
- blastn - blastn
- DNA sequence - DNA sequence
tools: tools:
- blast: - blast:
description: | description: |
BLAST finds regions of similarity between biological sequences. BLAST finds regions of similarity between biological sequences.
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2 doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work'] licence: ["US-Government-Work"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- fasta: - fasta:
type: file type: file
description: Input fasta file containing queries sequences description: Input fasta file containing queries sequences
pattern: "*.{fa,fasta}" pattern: "*.{fa,fasta}"
- db: - db:
type: directory type: directory
description: Directory containing blast database description: Directory containing blast database
pattern: "*" pattern: "*"
output: output:
- txt: - txt:
type: file type: file
description: File containing blastn hits description: File containing blastn hits
pattern: "*.{blastn.txt}" pattern: "*.{blastn.txt}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

48
modules/blast/makeblastdb/meta.yml
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name: blast_makeblastdb name: blast_makeblastdb
description: Builds a BLAST database description: Builds a BLAST database
keywords: keywords:
- fasta - fasta
- blast - blast
- database - database
tools: tools:
- blast: - blast:
description: | description: |
BLAST finds regions of similarity between biological sequences. BLAST finds regions of similarity between biological sequences.
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2 doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work'] licence: ["US-Government-Work"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input fasta file description: Input fasta file
pattern: "*.{fa,fasta}" pattern: "*.{fa,fasta}"
output: output:
- db: - db:
type: directory type: directory
description: Output directory containing blast database files description: Output directory containing blast database files
pattern: "*" pattern: "*"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

78
modules/bowtie/align/meta.yml
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name: bowtie_align name: bowtie_align
description: Align reads to a reference genome using bowtie description: Align reads to a reference genome using bowtie
keywords: keywords:
- align - align
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- bowtie: - bowtie:
description: | description: |
bowtie is a software package for mapping DNA sequences against bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['Artistic-2.0'] licence: ["Artistic-2.0"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- index: - index:
type: file type: file
description: Bowtie genome index files description: Bowtie genome index files
pattern: "*.ebwt" pattern: "*.ebwt"
output: output:
- bam: - bam:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- fastq: - fastq:
type: file type: file
description: Unaligned FastQ files description: Unaligned FastQ files
pattern: "*.fastq.gz" pattern: "*.fastq.gz"
authors: authors:
- "@kevinmenden" - "@kevinmenden"

50
modules/bowtie/build/meta.yml
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name: bowtie_build name: bowtie_build
description: Create bowtie index for reference genome description: Create bowtie index for reference genome
keywords: keywords:
- index - index
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- bowtie: - bowtie:
description: | description: |
bowtie is a software package for mapping DNA sequences against bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['Artistic-2.0'] licence: ["Artistic-2.0"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- index: - index:
type: file type: file
description: Bowtie genome index files description: Bowtie genome index files
pattern: "*.ebwt" pattern: "*.ebwt"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@kevinmenden" - "@kevinmenden"
- "@drpatelh" - "@drpatelh"

88
modules/bowtie2/align/meta.yml
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name: bowtie2_align name: bowtie2_align
description: Align reads to a reference genome using bowtie2 description: Align reads to a reference genome using bowtie2
keywords: keywords:
- align - align
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- bowtie2: - bowtie2:
description: | description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences. sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923 doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- index: - index:
type: file type: file
description: Bowtie2 genome index files description: Bowtie2 genome index files
pattern: "*.ebwt" pattern: "*.ebwt"
output: output:
- bam: - bam:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- fastq: - fastq:
type: file type: file
description: Unaligned FastQ files description: Unaligned FastQ files
pattern: "*.fastq.gz" pattern: "*.fastq.gz"
- log: - log:
type: file type: file
description: Aligment log description: Aligment log
pattern: "*.log" pattern: "*.log"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

52
modules/bowtie2/build/meta.yml
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name: bowtie2_build name: bowtie2_build
description: Builds bowtie index for reference genome description: Builds bowtie index for reference genome
keywords: keywords:
- build - build
- index - index
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- bowtie2: - bowtie2:
description: | description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences. sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923 doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- index: - index:
type: file type: file
description: Bowtie2 genome index files description: Bowtie2 genome index files
pattern: "*.bt2" pattern: "*.bt2"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

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modules/bwa/aln/meta.yml
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- map - map
- fastq - fastq
tools: tools:
- bwa: - bwa:
description: | description: |
BWA is a software package for mapping DNA sequences against BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324" doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: | description: |
Groovy Map containing sample information List of input FastQ files of size 1 and 2 for single-end and paired-end data,
e.g. [ id:'test', single_end:false ] respectively.
- reads: - index:
type: file type: file
description: | description: BWA genome index files
List of input FastQ files of size 1 and 2 for single-end and paired-end data, pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
output: output:
- meta: - meta:

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name: bwa_index name: bwa_index
description: Create BWA index for reference genome description: Create BWA index for reference genome
keywords: keywords:
- index - index
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- bwa: - bwa:
description: | description: |
BWA is a software package for mapping DNA sequences against BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- index: - index:
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}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@drpatelh" - "@drpatelh"
- "@maxulysse" - "@maxulysse"

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name: bwa_mem name: bwa_mem
description: Performs fastq alignment to a fasta reference using BWA description: Performs fastq alignment to a fasta reference using BWA
keywords: keywords:
- mem - mem
- bwa - bwa
- alignment - alignment
- map - map
- fastq - fastq
- bam - bam
- sam - sam
tools: tools:
- bwa: - bwa:
description: | description: |
BWA is a software package for mapping DNA sequences against BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- index: - index:
type: file type: file
description: BWA genome index files description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
- sort_bam: - sort_bam:
type: boolean type: boolean
description: use samtools sort (true) or samtools view (false) description: use samtools sort (true) or samtools view (false)
pattern: "true or false" pattern: "true or false"
output: output:
- bam: - bam:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@drpatelh" - "@drpatelh"
- "@jeremy1805" - "@jeremy1805"

22
modules/bwa/sampe/meta.yml
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@ -11,14 +11,14 @@ keywords:
- sam - sam
- bam - bam
tools: tools:
- bwa: - bwa:
description: | description: |
BWA is a software package for mapping DNA sequences against BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324" doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
@ -35,9 +35,9 @@ input:
description: SAI file specified alongside meta and reads in input channel. description: SAI file specified alongside meta and reads in input channel.
pattern: "*.sai" pattern: "*.sai"
- index: - index:
type: directory type: directory
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
pattern: "bwa/" pattern: "bwa/"
output: output:
- meta: - meta:

22
modules/bwa/samse/meta.yml
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@ -12,14 +12,14 @@ keywords:
- bam - bam
tools: tools:
- bwa: - bwa:
description: | description: |
BWA is a software package for mapping DNA sequences against BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324" doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
@ -36,9 +36,9 @@ input:
description: SAI file specified alongside meta and reads in input channel. description: SAI file specified alongside meta and reads in input channel.
pattern: "*.sai" pattern: "*.sai"
- index: - index:
type: directory type: directory
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
pattern: "bwa/" pattern: "bwa/"
output: output:
- meta: - meta:

46
modules/bwamem2/index/meta.yml
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@ -1,30 +1,30 @@
name: bwamem2_index name: bwamem2_index
description: Create BWA-mem2 index for reference genome description: Create BWA-mem2 index for reference genome
keywords: keywords:
- index - index
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- bwa: - bwa:
description: | description: |
BWA-mem2 is a software package for mapping DNA sequences against BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2 homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: https://github.com/bwa-mem2/bwa-mem2#usage documentation: https://github.com/bwa-mem2/bwa-mem2#usage
licence: ['MIT'] licence: ["MIT"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- index: - index:
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}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxulysse" - "@maxulysse"

84
modules/bwamem2/mem/meta.yml
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name: bwamem2_mem name: bwamem2_mem
description: Performs fastq alignment to a fasta reference using BWA description: Performs fastq alignment to a fasta reference using BWA
keywords: keywords:
- mem - mem
- bwa - bwa
- alignment - alignment
- map - map
- fastq - fastq
- bam - bam
- sam - sam
tools: tools:
- bwa: - bwa:
description: | description: |
BWA-mem2 is a software package for mapping DNA sequences against BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2 homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- index: - index:
type: file type: file
description: BWA genome index files description: BWA genome index files
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
- sort_bam: - sort_bam:
type: boolean type: boolean
description: use samtools sort (true) or samtools view (false) description: use samtools sort (true) or samtools view (false)
pattern: "true or false" pattern: "true or false"
output: output:
- bam: - bam:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@maxulysse" - "@maxulysse"

90
modules/bwameth/align/meta.yml
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@ -1,52 +1,52 @@
name: bwameth_align name: bwameth_align
description: Performs alignment of BS-Seq reads using bwameth description: Performs alignment of BS-Seq reads using bwameth
keywords: keywords:
- bwameth - bwameth
- alignment - alignment
- 3-letter genome - 3-letter genome
- map - map
- methylation - methylation
- 5mC - 5mC
- methylseq - methylseq
- bisulphite - bisulphite
- fastq - fastq
- bam - bam
tools: tools:
- bwameth: - bwameth:
description: | description: |
Fast and accurate alignment of BS-Seq reads Fast and accurate alignment of BS-Seq reads
using bwa-mem and a 3-letter genome. using bwa-mem and a 3-letter genome.
homepage: https://github.com/brentp/bwa-meth homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129 arxiv: arXiv:1401.1129
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- index: - index:
type: dir type: dir
description: Directory containing bwameth genome index description: Directory containing bwameth genome index
output: output:
- meta: - meta:
type: map type: map
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 ]
- bam: - bam:
type: file type: file
description: Output BAM file containing read alignments description: Output BAM file containing read alignments
pattern: "*.{bam}" pattern: "*.{bam}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

52
modules/bwameth/index/meta.yml
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@ -1,33 +1,33 @@
name: bwameth_index name: bwameth_index
description: Performs indexing of c2t converted reference genome description: Performs indexing of c2t converted reference genome
keywords: keywords:
- bwameth - bwameth
- 3-letter genome - 3-letter genome
- index - index
- methylseq - methylseq
- bisulphite - bisulphite
- fasta - fasta
tools: tools:
- bwameth: - bwameth:
description: | description: |
Fast and accurate alignment of BS-Seq reads Fast and accurate alignment of BS-Seq reads
using bwa-mem and a 3-letter genome. using bwa-mem and a 3-letter genome.
homepage: https://github.com/brentp/bwa-meth homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129 arxiv: arXiv:1401.1129
licence: ['MIT'] licence: ["MIT"]
input: input:
- fasta: - fasta:
type: file type: file
description: Input genome fasta file description: Input genome fasta file
output: output:
- index: - index:
type: dir type: dir
description: Directory containing bwameth genome index description: Directory containing bwameth genome index
pattern: "index" pattern: "index"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@phue" - "@phue"

2
modules/cat/cat/meta.yml
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@ -10,7 +10,7 @@ tools:
homepage: None homepage: None
documentation: https://man7.org/linux/man-pages/man1/cat.1.html documentation: https://man7.org/linux/man-pages/man1/cat.1.html
tool_dev_url: None tool_dev_url: None
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- files_in: - files_in:
type: file type: file

62
modules/cat/fastq/meta.yml
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@ -1,39 +1,39 @@
name: cat_fastq name: cat_fastq
description: Concatenates fastq files description: Concatenates fastq files
keywords: keywords:
- fastq - fastq
- concatenate - concatenate
tools: tools:
- cat: - cat:
description: | description: |
The cat utility reads files sequentially, writing them to the standard output. The cat utility reads files sequentially, writing them to the standard output.
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
licence: ['GPL-3.0-or-later'] licence: ["GPL-3.0-or-later"]
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: list type: list
description: | description: |
List of input FastQ files to be concatenated. List of input FastQ files to be concatenated.
output: output:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: Merged fastq file description: Merged fastq file
pattern: "*.{merged.fastq.gz}" pattern: "*.{merged.fastq.gz}"
- versions: - versions:
type: file type: file
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@joseespinosa" - "@joseespinosa"
- "@drpatelh" - "@drpatelh"

62
modules/cellranger/count/meta.yml
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@ -1,40 +1,40 @@
name: cellranger_count name: cellranger_count
description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
keywords: keywords:
- align - align
- count - count
- reference - reference
tools: tools:
- cellranger: - cellranger:
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
doi: "" doi: ""
licence: 10x Genomics EULA licence: 10x Genomics EULA
input: input:
- meta: - meta:
type: map type: map
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 ]
- reads: - reads:
type: file type: file
description: | description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data, List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. respectively.
- reference: - reference:
type: folder type: folder
description: Folder containing all the reference indices needed by Cell Ranger description: Folder containing all the reference indices needed by Cell Ranger
output: output:
- outs: - outs:
type: file type: file
description: Files containing the outputs of Cell Ranger description: Files containing the outputs of Cell Ranger
pattern: "sample-${meta.gem}/outs/*" pattern: "sample-${meta.gem}/outs/*"
- versions: - versions:
type: file type: file
description: File containing software version description: File containing software version
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@ggabernet" - "@ggabernet"
- "@Emiller88" - "@Emiller88"

46
modules/cellranger/mkfastq/meta.yml
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@ -7,31 +7,31 @@ keywords:
- illumina - illumina
- bcl2fastq - bcl2fastq
tools: tools:
- cellranger: - cellranger:
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
doi: "" doi: ""
licence: 10x Genomics EULA licence: 10x Genomics EULA
input: input:
- bcl: - bcl:
type: file type: file
description: Base call files description: Base call files
pattern: "*.bcl.bgzf" pattern: "*.bcl.bgzf"
- csv: - csv:
type: file type: file
description: Sample sheet description: Sample sheet
pattern: "*.csv" pattern: "*.csv"
output: output:
- fastq: - fastq:
type: file type: file
description: Unaligned FastQ files description: Unaligned FastQ files
pattern: "*.fastq.gz" pattern: "*.fastq.gz"
- versions: - versions:
type: file type: file
description: File containing software version description: File containing software version
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@ggabernet" - "@ggabernet"
- "@Emiller88" - "@Emiller88"

44
modules/cellranger/mkgtf/meta.yml
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@ -1,31 +1,31 @@
name: cellranger_mkgtf name: cellranger_mkgtf
description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command. description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
keywords: keywords:
- reference - reference
- mkref - mkref
- index - index
tools: tools:
- cellranger: - cellranger:
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
doi: "" doi: ""
licence: 10x Genomics EULA licence: 10x Genomics EULA
input: input:
- gtf: - gtf:
type: file type: file
description: description:
pattern: "*.gtf" pattern: "*.gtf"
output: output:
- gtf: - gtf:
type: folder type: folder
description: gtf transcriptome file description: gtf transcriptome file
pattern: "*.filtered.gtf" pattern: "*.filtered.gtf"
- versions: - versions:
type: file type: file
description: File containing software version description: File containing software version
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@ggabernet" - "@ggabernet"
- "@Emiller88" - "@Emiller88"

58
modules/cellranger/mkref/meta.yml
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@ -1,37 +1,37 @@
name: cellranger_mkref name: cellranger_mkref
description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command. description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
keywords: keywords:
- reference - reference
- mkref - mkref
- index - index
tools: tools:
- cellranger: - cellranger:
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
doi: "" doi: ""
licence: 10x Genomics EULA licence: 10x Genomics EULA
input: input:
- fasta: - fasta:
type: file type: file
description: fasta genome file description: fasta genome file
pattern: "*.{fasta,fa}" pattern: "*.{fasta,fa}"
- gtf: - gtf:
type: file type: file
description: gtf transcriptome file description: gtf transcriptome file
pattern: "*.gtf" pattern: "*.gtf"
- reference_name: - reference_name:
type: val type: val
description: name to give the reference folder description: name to give the reference folder
pattern: str pattern: str
output: output:
- reference: - reference:
type: folder type: folder
description: Folder containing all the reference indices needed by Cell Ranger description: Folder containing all the reference indices needed by Cell Ranger
- versions: - versions:
type: file type: file
description: File containing software version description: File containing software version
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@ggabernet" - "@ggabernet"

2
modules/checkm/lineagewf/meta.yml
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@ -19,7 +19,7 @@ tools:
documentation: https://github.com/Ecogenomics/CheckM/wiki documentation: https://github.com/Ecogenomics/CheckM/wiki
tool_dev_url: https://github.com/Ecogenomics/CheckM tool_dev_url: https://github.com/Ecogenomics/CheckM
doi: "10.1101/gr.186072.114" doi: "10.1101/gr.186072.114"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

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modules/chromap/chromap/meta.yml
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name: chromap_chromap name: chromap_chromap
description: | description: |
Performs preprocessing and alignment of chromatin fastq files to Performs preprocessing and alignment of chromatin fastq files to
fasta reference files using chromap. fasta reference files using chromap.
keywords: keywords:
- chromap - chromap
- alignment - alignment
- map - map
- fastq - fastq
- bam - bam
- sam - sam
- hi-c - hi-c
- atac-seq - atac-seq
- chip-seq - chip-seq
- trimming - trimming
- duplicate removal - duplicate removal
tools: tools:
- chromap: - chromap:
description: Fast alignment and preprocessing of chromatin profiles description: Fast alignment and preprocessing of chromatin profiles
@ -21,7 +21,7 @@ tools:
documentation: https://github.com/haowenz/chromap documentation: https://github.com/haowenz/chromap
tool_dev_url: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap
doi: "" doi: ""
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:
type: map type: map

10
modules/chromap/index/meta.yml
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@ -1,10 +1,10 @@
name: chromap_index name: chromap_index
description: Indexes a fasta reference genome ready for chromatin profiling. description: Indexes a fasta reference genome ready for chromatin profiling.
keywords: keywords:
- index - index
- fasta - fasta
- genome - genome
- reference - reference
tools: tools:
- chromap: - chromap:
description: Fast alignment and preprocessing of chromatin profiles description: Fast alignment and preprocessing of chromatin profiles
@ -12,7 +12,7 @@ tools:
documentation: https://github.com/haowenz/chromap documentation: https://github.com/haowenz/chromap
tool_dev_url: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap
doi: "" doi: ""
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- fasta: - fasta:

2
modules/clonalframeml/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: https://github.com/xavierdidelot/clonalframeml/wiki documentation: https://github.com/xavierdidelot/clonalframeml/wiki
tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML
doi: "10.1371/journal.pcbi.1004041" doi: "10.1371/journal.pcbi.1004041"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

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modules/cmseq/polymut/meta.yml
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@ -17,7 +17,7 @@ tools:
homepage: https://github.com/SegataLab/cmseq homepage: https://github.com/SegataLab/cmseq
documentation: https://github.com/SegataLab/cmseq documentation: https://github.com/SegataLab/cmseq
tool_dev_url: https://github.com/SegataLab/cmseq tool_dev_url: https://github.com/SegataLab/cmseq
licence: ['MIT License'] licence: ["MIT License"]
input: input:
- meta: - meta:

14
modules/cnvkit/batch/meta.yml
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@ -10,7 +10,7 @@ tools:
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
homepage: https://cnvkit.readthedocs.io/en/stable/index.html homepage: https://cnvkit.readthedocs.io/en/stable/index.html
documentation: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html
licence: ['Apache-2.0'] licence: ["Apache-2.0"]
params: params:
- outdir: - outdir:
type: string type: string
@ -85,9 +85,9 @@ output:
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@kaurravneet4123" - "@kaurravneet4123"
- "@KevinMenden" - "@KevinMenden"
- "@MaxUlysse" - "@MaxUlysse"
- "@drpatelh" - "@drpatelh"
- "@fbdtemme" - "@fbdtemme"
- "@lassefolkersen" - "@lassefolkersen"

2
modules/cooler/cload/meta.yml
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@ -9,7 +9,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540" doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-clause'] licence: ["BSD-3-clause"]
input: input:
- meta: - meta:

2
modules/cooler/digest/meta.yml
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@ -10,7 +10,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540" doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-Clause'] licence: ["BSD-3-Clause"]
input: input:
- fasta: - fasta:

2
modules/cooler/dump/meta.yml
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@ -9,7 +9,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540" doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-Clause'] licence: ["BSD-3-Clause"]
input: input:
- meta: - meta:

2
modules/cooler/merge/meta.yml
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@ -9,7 +9,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540" doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-clause'] licence: ["BSD-3-clause"]
input: input:
- meta: - meta:

2
modules/cooler/zoomify/meta.yml
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@ -9,7 +9,7 @@ tools:
documentation: https://cooler.readthedocs.io/en/latest/index.html documentation: https://cooler.readthedocs.io/en/latest/index.html
tool_dev_url: https://github.com/open2c/cooler tool_dev_url: https://github.com/open2c/cooler
doi: "10.1093/bioinformatics/btz540" doi: "10.1093/bioinformatics/btz540"
licence: ['BSD-3-clause'] licence: ["BSD-3-clause"]
input: input:
- meta: - meta:

2
modules/csvtk/concat/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: http://bioinf.shenwei.me/csvtk documentation: http://bioinf.shenwei.me/csvtk
tool_dev_url: https://github.com/shenwei356/csvtk tool_dev_url: https://github.com/shenwei356/csvtk
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

6
modules/csvtk/split/meta.yml
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@ -7,13 +7,13 @@ keywords:
tools: tools:
- csvtk: - csvtk:
description: description:
CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
that allows rapid data investigation and manipulation. that allows rapid data investigation and manipulation.
homepage: https://bioinf.shenwei.me/csvtk/ homepage: https://bioinf.shenwei.me/csvtk/
documentation: https://bioinf.shenwei.me/csvtk/ documentation: https://bioinf.shenwei.me/csvtk/
tool_dev_url: https://github.com/shenwei356/csvtk tool_dev_url: https://github.com/shenwei356/csvtk
doi: "" doi: ""
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map

2
modules/custom/dumpsoftwareversions/meta.yml
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@ -8,7 +8,7 @@ tools:
description: Custom module used to dump software versions within the nf-core pipeline template description: Custom module used to dump software versions within the nf-core pipeline template
homepage: https://github.com/nf-core/tools homepage: https://github.com/nf-core/tools
documentation: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools
licence: ['MIT'] licence: ["MIT"]
input: input:
- versions: - versions:
type: file type: file

3
modules/custom/getchromsizes/meta.yml
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@ -11,7 +11,7 @@ tools:
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
tool_dev_url: https://github.com/samtools/samtools tool_dev_url: https://github.com/samtools/samtools
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT'] licence: ["MIT"]
input: input:
- fasta: - fasta:
@ -33,7 +33,6 @@ output:
description: File containing software version description: File containing software version
pattern: "versions.yml" pattern: "versions.yml"
authors: authors:
- "@tamara-hodgetts" - "@tamara-hodgetts"
- "@chris-cheshire" - "@chris-cheshire"

2
modules/cutadapt/meta.yml
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@ -11,7 +11,7 @@ tools:
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
documentation: https://cutadapt.readthedocs.io/en/stable/index.html documentation: https://cutadapt.readthedocs.io/en/stable/index.html
doi: DOI:10.14806/ej.17.1.200 doi: DOI:10.14806/ej.17.1.200
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:
type: map type: map

2
modules/damageprofiler/meta.yml
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@ -18,7 +18,7 @@ tools:
documentation: https://damageprofiler.readthedocs.io/ documentation: https://damageprofiler.readthedocs.io/
tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler
doi: "10.1093/bioinformatics/btab190" doi: "10.1093/bioinformatics/btab190"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

5
modules/dastool/dastool/meta.yml
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@ -20,7 +20,7 @@ tools:
documentation: https://github.com/cmks/DAS_Tool documentation: https://github.com/cmks/DAS_Tool
tool_dev_url: https://github.com/cmks/DAS_Tool tool_dev_url: https://github.com/cmks/DAS_Tool
doi: "10.1038/s41564-018-0171-1" doi: "10.1038/s41564-018-0171-1"
licence: ['BSD'] licence: ["BSD"]
input: input:
- meta: - meta:
@ -47,7 +47,6 @@ input:
type: val type: val
description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond] description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond]
output: output:
- meta: - meta:
type: map type: map
@ -84,7 +83,7 @@ output:
pattern: "*.proteins.faa" pattern: "*.proteins.faa"
- fasta_archaea_scg: - fasta_archaea_scg:
type: file type: file
description: Results of archaeal single-copy-gene prediction description: Results of archaeal single-copy-gene prediction
pattern: "*.archaea.scg" pattern: "*.archaea.scg"
- fasta_bacteria_scg: - fasta_bacteria_scg:
type: file type: file

2
modules/dastool/scaffolds2bin/meta.yml
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@ -20,7 +20,7 @@ tools:
documentation: https://github.com/cmks/DAS_Tool documentation: https://github.com/cmks/DAS_Tool
tool_dev_url: https://github.com/cmks/DAS_Tool tool_dev_url: https://github.com/cmks/DAS_Tool
doi: "10.1038/s41564-018-0171-1" doi: "10.1038/s41564-018-0171-1"
licence: ['BSD'] licence: ["BSD"]
input: input:
- meta: - meta:

4
modules/dedup/meta.yml
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@ -14,7 +14,7 @@ tools:
documentation: https://dedup.readthedocs.io/en/latest/ documentation: https://dedup.readthedocs.io/en/latest/
tool_dev_url: https://github.com/apeltzer/DeDup tool_dev_url: https://github.com/apeltzer/DeDup
doi: "10.1186/s13059-016-0918-z" doi: "10.1186/s13059-016-0918-z"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:
@ -54,7 +54,5 @@ output:
description: Dedup log information description: Dedup log information
pattern: "*log" pattern: "*log"
authors: authors:
- "@jfy133" - "@jfy133"

2
modules/deeparg/downloaddata/meta.yml
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@ -14,7 +14,7 @@ tools:
documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
doi: "10.1186/s40168-018-0401-z" doi: "10.1186/s40168-018-0401-z"
licence: ['MIT'] licence: ["MIT"]
input: input:
- none: There is no input. This module downloads a pre-built database for use with deepARG. - none: There is no input. This module downloads a pre-built database for use with deepARG.

2
modules/deeparg/predict/meta.yml
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@ -16,7 +16,7 @@ tools:
documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
doi: "10.1186/s40168-018-0401-z" doi: "10.1186/s40168-018-0401-z"
licence: ['MIT'] licence: ["MIT"]
input: input:
- meta: - meta:

2
modules/deeptools/computematrix/meta.yml
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@ -12,7 +12,7 @@ tools:
documentation: https://deeptools.readthedocs.io/en/develop/index.html documentation: https://deeptools.readthedocs.io/en/develop/index.html
tool_dev_url: https://github.com/deeptools/deepTools tool_dev_url: https://github.com/deeptools/deepTools
doi: "10.1093/nar/gku365" doi: "10.1093/nar/gku365"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

2
modules/deeptools/plotfingerprint/meta.yml
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@ -12,7 +12,7 @@ tools:
documentation: https://deeptools.readthedocs.io/en/develop/index.html documentation: https://deeptools.readthedocs.io/en/develop/index.html
tool_dev_url: https://github.com/deeptools/deepTools tool_dev_url: https://github.com/deeptools/deepTools
doi: "10.1093/nar/gku365" doi: "10.1093/nar/gku365"
licence: ['GPL v3'] licence: ["GPL v3"]
input: input:
- meta: - meta:

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