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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>
This commit is contained in:
Matthias Hörtenhuber 2022-02-15 12:15:27 +01:00 committed by GitHub
parent 12b0bc5aa9
commit e745e167c1
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426 changed files with 4713 additions and 4665 deletions
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12
.github/workflows/code-linting.yml vendored
View file

@ -12,9 +12,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: "10"
- uses: actions/setup-node@v2
- name: Install markdownlint
run: npm install -g markdownlint-cli
@ -27,9 +25,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v1
with:
node-version: "10"
- uses: actions/setup-node@v2
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
@ -44,9 +40,7 @@ jobs:
uses: actions/checkout@v2
- name: Install NodeJS
uses: actions/setup-node@v1
with:
node-version: "10"
uses: actions/setup-node@v2
- name: Install yaml-lint
run: npm install -g yaml-lint

6
.gitpod.yml
View file

@ -1,14 +1,14 @@
image: nfcore/gitpod:latest
vscode:
extensions: # based on nf-core.nf-core-extensionpack
extensions: # based on nf-core.nf-core-extensionpack
- 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
- 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
- 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
# - nextflow.nextflow # Nextflow syntax highlighting
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code

2
.markdownlint.yml
View file

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

5
.yamllint.yml Normal file
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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
tool_dev_url: None
doi: "10.1093/bioinformatics/btp347"
licence: ['GPL v2-or-later']
licence: ["GPL v2-or-later"]
input:
- meta:

80
modules/adapterremoval/meta.yml
View file

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

2
modules/agrvate/meta.yml
View file

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

2
modules/amps/meta.yml
View file

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

2
modules/arriba/meta.yml
View file

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

2
modules/artic/guppyplex/meta.yml
View file

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

8
modules/artic/minion/meta.yml
View file

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

2
modules/assemblyscan/meta.yml
View file

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

2
modules/ataqv/ataqv/meta.yml
View file

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

2
modules/bakta/meta.yml
View file

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

2
modules/bamaligncleaner/meta.yml
View file

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

9
modules/bamcmp/meta.yml
View file

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

2
modules/bamtools/convert/meta.yml
View file

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

2
modules/bamtools/split/meta.yml
View file

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

2
modules/bamutil/trimbam/meta.yml
View file

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

74
modules/bandage/image/meta.yml
View file

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

12
modules/bbmap/align/meta.yml
View file

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

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/
tool_dev_url: None
doi: ""
licence: ['UC-LBL license (see package)']
licence: ["UC-LBL license (see package)"]
input:
- meta:
@ -20,14 +20,14 @@ input:
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- contaminants:
type: file
description: |
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
type: file
description: |
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
output:
- meta:

2
modules/bbmap/bbsplit/meta.yml
View file

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

2
modules/bbmap/index/meta.yml
View file

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

68
modules/bcftools/concat/meta.yml
View file

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

84
modules/bcftools/consensus/meta.yml
View file

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

68
modules/bcftools/filter/meta.yml
View file

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

2
modules/bcftools/index/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://samtools.github.io/bcftools/howtos/index.html
tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/gigascience/giab008"
licence: ['MIT', 'GPL-3.0-or-later']
licence: ["MIT", "GPL-3.0-or-later"]
input:
- meta:

84
modules/bcftools/isec/meta.yml
View file

@ -1,49 +1,49 @@
name: bcftools_isec
description: Apply set operations to VCF files
keywords:
- variant calling
- intersect
- union
- complement
- VCF
- variant calling
- intersect
- union
- complement
- VCF
tools:
- isec:
description: |
Computes intersections, unions and complements of VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
- isec:
description: |
Computes intersections, unions and complements of VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcfs:
type: files
description: |
List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis:
type: files
description: |
List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcfs:
type: files
description: |
List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis:
type: files
description: |
List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: directory
description: Folder containing the set operations results perform on the vcf files
pattern: "${prefix}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: directory
description: Folder containing the set operations results perform on the vcf files
pattern: "${prefix}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

80
modules/bcftools/merge/meta.yml
View file

@ -1,47 +1,47 @@
name: bcftools_merge
description: Merge VCF files
keywords:
- variant calling
- merge
- VCF
- variant calling
- merge
- VCF
tools:
- merge:
description: |
Merge VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
- merge:
description: |
Merge VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcfs:
type: files
description: |
List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis:
type: files
description: |
List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcfs:
type: files
description: |
List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis:
type: files
description: |
List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF merged output file
pattern: "*.{vcf.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF merged output file
pattern: "*.{vcf.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

100
modules/bcftools/mpileup/meta.yml
View file

@ -1,57 +1,57 @@
name: bcftools_mpileup
description: Compresses VCF files
keywords:
- variant calling
- mpileup
- VCF
- variant calling
- mpileup
- VCF
tools:
- mpileup:
description: |
Generates genotype likelihoods at each genomic position with coverage.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
- mpileup:
description: |
Generates genotype likelihoods at each genomic position with coverage.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Input BAM file
pattern: "*.{bam}"
- fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
- save_mpileup:
type: boolean
description: Save mpileup file generated by bcftools mpileup
patter: "*.mpileup"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Input BAM file
pattern: "*.{bam}"
- fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
- save_mpileup:
type: boolean
description: Save mpileup file generated by bcftools mpileup
patter: "*.mpileup"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF gzipped output file
pattern: "*.{vcf.gz}"
- tbi:
type: file
description: tabix index file
pattern: "*.{tbi}"
- stats:
type: file
description: Text output file containing stats
pattern: "*{stats.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF gzipped output file
pattern: "*.{vcf.gz}"
- tbi:
type: file
description: tabix index file
pattern: "*.{tbi}"
- stats:
type: file
description: Text output file containing stats
pattern: "*{stats.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

70
modules/bcftools/norm/meta.yml
View file

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

96
modules/bcftools/query/meta.yml
View file

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

2
modules/bcftools/reheader/meta.yml
View file

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

2
modules/bcftools/sort/meta.yml
View file

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

70
modules/bcftools/stats/meta.yml
View file

@ -1,42 +1,42 @@
name: bcftools_stats
description: Generates stats from VCF files
keywords:
- variant calling
- stats
- VCF
- variant calling
- stats
- VCF
tools:
- stats:
description: |
Parses VCF or BCF and produces text file stats which is suitable for
machine processing and can be plotted using plot-vcfstats.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
- stats:
description: |
Parses VCF or BCF and produces text file stats which is suitable for
machine processing and can be plotted using plot-vcfstats.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF input file
pattern: "*.{vcf}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF input file
pattern: "*.{vcf}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- stats:
type: file
description: Text output file containing stats
pattern: "*_{stats.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- stats:
type: file
description: Text output file containing stats
pattern: "*_{stats.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

110
modules/bcftools/view/meta.yml
View file

@ -1,63 +1,63 @@
name: bcftools_view
description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
keywords:
- variant calling
- view
- bcftools
- VCF
- variant calling
- view
- bcftools
- VCF
tools:
- view:
description: |
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
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
- view:
description: |
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
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: |
The vcf file to be inspected.
e.g. 'file.vcf'
- index:
type: file
description: |
The tab index for the VCF file to be inspected.
e.g. 'file.tbi'
- regions:
type: file
description: |
Optionally, restrict the operation to regions listed in this file.
e.g. 'file.vcf'
- targets:
type: file
description: |
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
e.g. 'file.vcf'
- samples:
type: file
description: |
Optional, file of sample names to be included or excluded.
e.g. 'file.tsv'
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: |
The vcf file to be inspected.
e.g. 'file.vcf'
- index:
type: file
description: |
The tab index for the VCF file to be inspected.
e.g. 'file.tbi'
- regions:
type: file
description: |
Optionally, restrict the operation to regions listed in this file.
e.g. 'file.vcf'
- targets:
type: file
description: |
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
e.g. 'file.vcf'
- samples:
type: file
description: |
Optional, file of sample names to be included or excluded.
e.g. 'file.tsv'
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF normalized output file
pattern: "*.{vcf.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF normalized output file
pattern: "*.{vcf.gz}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@abhi18av"
- "@abhi18av"

62
modules/bedtools/bamtobed/meta.yml
View file

@ -1,38 +1,38 @@
name: bedtools_bamtobed
description: Converts a bam file to a bed12 file.
keywords:
- bam
- bed
- bam
- bed
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Input BAM file
pattern: "*.{bam}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Input BAM file
pattern: "*.{bam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed file containing genomic intervals.
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed file containing genomic intervals.
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@yuukiiwa"
- "@drpatelh"
- "@yuukiiwa"
- "@drpatelh"

72
modules/bedtools/complement/meta.yml
View file

@ -1,43 +1,43 @@
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.
keywords:
- bed
- complement
- bed
- complement
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input BED file
pattern: "*.{bed}"
- sizes:
type: file
description: File which defines the chromosome lengths for a given genome
pattern: "*.{sizes}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input BED file
pattern: "*.{bed}"
- sizes:
type: file
description: File which defines the chromosome lengths for a given genome
pattern: "*.{sizes}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"

88
modules/bedtools/genomecov/meta.yml
View file

@ -1,51 +1,51 @@
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.
keywords:
- bed
- bam
- genomecov
- bed
- bam
- genomecov
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- scale:
type: 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
- sizes:
type: file
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
- extension:
type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- scale:
type: 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
- sizes:
type: file
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
- extension:
type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- genomecov:
type: file
description: Computed genome coverage file
pattern: "*.${extension}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- genomecov:
type: file
description: Computed genome coverage file
pattern: "*.${extension}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"
- "@chris-cheshire"
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"
- "@chris-cheshire"

52
modules/bedtools/getfasta/meta.yml
View file

@ -1,34 +1,34 @@
name: bedtools_getfasta
description: extract sequences in a FASTA file based on intervals defined in a feature file.
keywords:
- bed
- fasta
- getfasta
- bed
- fasta
- getfasta
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ["MIT"]
input:
- bed:
type: file
description: Bed feature file
pattern: "*.{bed}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
- bed:
type: file
description: Bed feature file
pattern: "*.{bed}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
output:
- fasta:
type: file
description: Output fasta file with extracted sequences
pattern: "*.{fa}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fasta:
type: file
description: Output fasta file with extracted sequences
pattern: "*.{fa}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

80
modules/bedtools/intersect/meta.yml
View file

@ -1,47 +1,47 @@
name: bedtools_intersect
description: Allows one to screen for overlaps between two sets of genomic features.
keywords:
- bed
- intersect
- bed
- intersect
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals1:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- intervals2:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- extension:
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.).
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals1:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- intervals2:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- extension:
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.).
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intersect:
type: file
description: File containing the description of overlaps found between the two features
pattern: "*.${extension}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intersect:
type: file
description: File containing the description of overlaps found between the two features
pattern: "*.${extension}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"

2
modules/bedtools/makewindows/meta.yml
View file

@ -11,7 +11,7 @@ tools:
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
tool_dev_url: None
doi: "10.1093/bioinformatics/btq033"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

72
modules/bedtools/maskfasta/meta.yml
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@ -1,44 +1,44 @@
name: bedtools_maskfasta
description: masks sequences in a FASTA file based on intervals defined in a feature file.
keywords:
- bed
- fasta
- maskfasta
- bed
- fasta
- maskfasta
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed feature file
pattern: "*.{bed}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed feature file
pattern: "*.{bed}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Output masked fasta file
pattern: "*.{fa}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Output masked fasta file
pattern: "*.{fa}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

64
modules/bedtools/merge/meta.yml
View file

@ -1,39 +1,39 @@
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.
keywords:
- bed
- merge
- bed
- merge
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input BED file
pattern: "*.{bed}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input BED file
pattern: "*.{bed}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Overlapped bed file with combined features
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Overlapped bed file with combined features
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"

64
modules/bedtools/slop/meta.yml
View file

@ -1,39 +1,39 @@
name: bedtools_slop
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
keywords:
- bed
- slopBed
- bed
- slopBed
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input BED file
pattern: "*.{bed}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Input BED file
pattern: "*.{bed}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Slopped BED file
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Slopped BED file
pattern: "*.{bed}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"

72
modules/bedtools/sort/meta.yml
View file

@ -1,46 +1,46 @@
name: bedtools_sort
description: Sorts a feature file by chromosome and other criteria.
keywords:
- bed
- sort
- bed
- sort
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals:
type: file
description: BED/BEDGRAPH
pattern: "*.{bed|bedGraph}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals:
type: file
description: BED/BEDGRAPH
pattern: "*.{bed|bedGraph}"
- extension:
type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
- extension:
type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- sorted:
type: file
description: Sorted output file
pattern: "*.${extension}"
- sorted:
type: file
description: Sorted output file
pattern: "*.${extension}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@chris-cheshire"
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@chris-cheshire"

18
modules/bedtools/subtract/meta.yml
View file

@ -1,16 +1,16 @@
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.
keywords:
- bed
- gff
- vcf
- subtract
- bed
- gff
- vcf
- subtract
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
licence: ['MIT']
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
licence: ["MIT"]
input:
- meta:

74
modules/biobambam/bammarkduplicates2/meta.yml
View file

@ -1,44 +1,44 @@
name: biobambam_bammarkduplicates2
description: Locate and tag duplicate reads in a BAM file
keywords:
- markduplicates
- bam
- cram
- markduplicates
- bam
- cram
tools:
- biobambam:
description: |
biobambam is a set of tools for early stage alignment file processing.
homepage: https://gitlab.com/german.tischler/biobambam2
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
doi: 10.1186/1751-0473-9-13
licence: ['GPL v3']
- biobambam:
description: |
biobambam is a set of tools for early stage alignment file processing.
homepage: https://gitlab.com/german.tischler/biobambam2
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
doi: 10.1186/1751-0473-9-13
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file with duplicate reads marked/removed
pattern: "*.{bam}"
- metrics:
type: file
description: Duplicate metrics file generated by biobambam
pattern: "*.{metrics.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file with duplicate reads marked/removed
pattern: "*.{bam}"
- metrics:
type: file
description: Duplicate metrics file generated by biobambam
pattern: "*.{metrics.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@muffato"
- "@muffato"

104
modules/bismark/align/meta.yml
View file

@ -1,59 +1,59 @@
name: bismark_align
description: Performs alignment of BS-Seq reads using bismark
keywords:
- bismark
- 3-letter genome
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
- bismark
- 3-letter genome
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: dir
description: Bismark genome index directory
pattern: "BismarkIndex"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: dir
description: Bismark genome index directory
pattern: "BismarkIndex"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- unmapped:
type: file
description: Output FastQ file(s) containing unmapped reads
pattern: "*.{fq.gz}"
- report:
type: file
description: Bismark alignment reports
pattern: "*{report.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- unmapped:
type: file
description: Output FastQ file(s) containing unmapped reads
pattern: "*.{fq.gz}"
- report:
type: file
description: Bismark alignment reports
pattern: "*{report.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"
- "@phue"

90
modules/bismark/deduplicate/meta.yml
View file

@ -1,52 +1,52 @@
name: bismark_deduplicate
description: |
Removes alignments to the same position in the genome
from the Bismark mapping output.
Removes alignments to the same position in the genome
from the Bismark mapping output.
keywords:
- bismark
- 3-letter genome
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
- bismark
- 3-letter genome
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file containing read alignments
pattern: "*.{bam}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file containing read alignments
pattern: "*.{bam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Deduplicated output BAM file containing read alignments
pattern: "*.{deduplicated.bam}"
- report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Deduplicated output BAM file containing read alignments
pattern: "*.{deduplicated.bam}"
- report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"
- "@phue"

60
modules/bismark/genomepreparation/meta.yml
View file

@ -1,37 +1,37 @@
name: bismark_genomepreparation
description: |
Converts a specified reference genome into two different bisulfite
converted versions and indexes them for alignments.
Converts a specified reference genome into two different bisulfite
converted versions and indexes them for alignments.
keywords:
- bismark
- 3-letter genome
- index
- methylation
- 5mC
- methylseq
- bisulphite
- fasta
- bismark
- 3-letter genome
- index
- methylation
- 5mC
- methylseq
- bisulphite
- fasta
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file
description: Input genome fasta file
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: dir
description: Bismark genome index directory
pattern: "BismarkIndex"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- index:
type: dir
description: Bismark genome index directory
pattern: "BismarkIndex"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"
- "@phue"

120
modules/bismark/methylationextractor/meta.yml
View file

@ -1,67 +1,67 @@
name: bismark_methylationextractor
description: Extracts methylation information for individual cytosines from alignments.
keywords:
- bismark
- consensus
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
- bedGraph
- bismark
- consensus
- map
- methylation
- 5mC
- methylseq
- bisulphite
- bam
- bedGraph
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file containing read alignments
pattern: "*.{bam}"
- index:
type: dir
description: Bismark genome index directory
pattern: "BismarkIndex"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file containing read alignments
pattern: "*.{bam}"
- index:
type: dir
description: Bismark genome index directory
pattern: "BismarkIndex"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedgraph:
type: file
description: Bismark output file containing coverage and methylation metrics
pattern: "*.{bedGraph.gz}"
- methylation_calls:
type: file
description: Bismark output file containing strand-specific methylation calls
pattern: "*.{txt.gz}"
- coverage:
type: file
description: Bismark output file containing coverage metrics
pattern: "*.{cov.gz}"
- report:
type: file
description: Bismark splitting reports
pattern: "*_{splitting_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{M-bias.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedgraph:
type: file
description: Bismark output file containing coverage and methylation metrics
pattern: "*.{bedGraph.gz}"
- methylation_calls:
type: file
description: Bismark output file containing strand-specific methylation calls
pattern: "*.{txt.gz}"
- coverage:
type: file
description: Bismark output file containing coverage metrics
pattern: "*.{cov.gz}"
- report:
type: file
description: Bismark splitting reports
pattern: "*_{splitting_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{M-bias.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"
- "@phue"

106
modules/bismark/report/meta.yml
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@ -1,60 +1,60 @@
name: bismark_report
description: Collects bismark alignment reports
keywords:
- bismark
- qc
- methylation
- 5mC
- methylseq
- bisulphite
- report
- bismark
- qc
- methylation
- 5mC
- methylseq
- bisulphite
- report
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- align_report:
type: file
description: Bismark alignment reports
pattern: "*{report.txt}"
- splitting_report:
type: file
description: Bismark splitting reports
pattern: "*{splitting_report.txt}"
- dedup_report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{txt}"
- fasta:
type: file
description: Input genome fasta file
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- align_report:
type: file
description: Bismark alignment reports
pattern: "*{report.txt}"
- splitting_report:
type: file
description: Bismark splitting reports
pattern: "*{splitting_report.txt}"
- dedup_report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{txt}"
- fasta:
type: file
description: Input genome fasta file
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- report:
type: file
description: Bismark reports
pattern: "*.{html,txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- report:
type: file
description: Bismark reports
pattern: "*.{html,txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"
- "@phue"

94
modules/bismark/summary/meta.yml
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@ -1,54 +1,54 @@
name: bismark_summary
description: |
Uses Bismark report files of several samples in a run folder
to generate a graphical summary HTML report.
Uses Bismark report files of several samples in a run folder
to generate a graphical summary HTML report.
keywords:
- bismark
- qc
- methylation
- 5mC
- methylseq
- bisulphite
- report
- summary
- bismark
- qc
- methylation
- 5mC
- methylseq
- bisulphite
- report
- summary
tools:
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
- bismark:
description: |
Bismark is a tool to map bisulfite treated sequencing reads
and perform methylation calling in a quick and easy-to-use fashion.
homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167
licence: ["GPL-3.0-or-later"]
input:
- bam:
type: file
description: Bismark alignment
pattern: "*.{bam}"
- align_report:
type: file
description: Bismark alignment reports
pattern: "*{report.txt}"
- dedup_report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- splitting_report:
type: file
description: Bismark splitting reports
pattern: "*{splitting_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{txt}"
- bam:
type: file
description: Bismark alignment
pattern: "*.{bam}"
- align_report:
type: file
description: Bismark alignment reports
pattern: "*{report.txt}"
- dedup_report:
type: file
description: Bismark deduplication reports
pattern: "*.{deduplication_report.txt}"
- splitting_report:
type: file
description: Bismark splitting reports
pattern: "*{splitting_report.txt}"
- mbias:
type: file
description: Text file containing methylation bias information
pattern: "*.{txt}"
output:
- summary:
type: file
description: Bismark summary
pattern: "*.{html,txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- summary:
type: file
description: Bismark summary
pattern: "*.{html,txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@phue"
- "@phue"

68
modules/blast/blastn/meta.yml
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@ -1,41 +1,41 @@
name: blast_blastn
description: Queries a BLAST DNA database
keywords:
- fasta
- blast
- blastn
- DNA sequence
- fasta
- blast
- blastn
- DNA sequence
tools:
- blast:
description: |
BLAST finds regions of similarity between biological sequences.
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work']
- blast:
description: |
BLAST finds regions of similarity between biological sequences.
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2
licence: ["US-Government-Work"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Input fasta file containing queries sequences
pattern: "*.{fa,fasta}"
- db:
type: directory
description: Directory containing blast database
pattern: "*"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Input fasta file containing queries sequences
pattern: "*.{fa,fasta}"
- db:
type: directory
description: Directory containing blast database
pattern: "*"
output:
- txt:
type: file
description: File containing blastn hits
pattern: "*.{blastn.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- txt:
type: file
description: File containing blastn hits
pattern: "*.{blastn.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

48
modules/blast/makeblastdb/meta.yml
View file

@ -1,31 +1,31 @@
name: blast_makeblastdb
description: Builds a BLAST database
keywords:
- fasta
- blast
- database
- fasta
- blast
- database
tools:
- blast:
description: |
BLAST finds regions of similarity between biological sequences.
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work']
- blast:
description: |
BLAST finds regions of similarity between biological sequences.
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2
licence: ["US-Government-Work"]
input:
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
output:
- db:
type: directory
description: Output directory containing blast database files
pattern: "*"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- db:
type: directory
description: Output directory containing blast database files
pattern: "*"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

78
modules/bowtie/align/meta.yml
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@ -1,46 +1,46 @@
name: bowtie_align
description: Align reads to a reference genome using bowtie
keywords:
- align
- fasta
- genome
- reference
- align
- fasta
- genome
- reference
tools:
- bowtie:
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
- bowtie:
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ["Artistic-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
authors:
- "@kevinmenden"
- "@kevinmenden"

50
modules/bowtie/build/meta.yml
View file

@ -1,32 +1,32 @@
name: bowtie_build
description: Create bowtie index for reference genome
keywords:
- index
- fasta
- genome
- reference
- index
- fasta
- genome
- reference
tools:
- bowtie:
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
- bowtie:
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ["Artistic-2.0"]
input:
- fasta:
type: file
description: Input genome fasta file
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- index:
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@kevinmenden"
- "@drpatelh"
- "@kevinmenden"
- "@drpatelh"

88
modules/bowtie2/align/meta.yml
View file

@ -1,51 +1,51 @@
name: bowtie2_align
description: Align reads to a reference genome using bowtie2
keywords:
- align
- fasta
- genome
- reference
- align
- fasta
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later']
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
- log:
type: file
description: Aligment log
pattern: "*.log"
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- fastq:
type: file
description: Unaligned FastQ files
pattern: "*.fastq.gz"
- log:
type: file
description: Aligment log
pattern: "*.log"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

52
modules/bowtie2/build/meta.yml
View file

@ -1,33 +1,33 @@
name: bowtie2_build
description: Builds bowtie index for reference genome
keywords:
- build
- index
- fasta
- genome
- reference
- build
- index
- fasta
- genome
- reference
tools:
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later']
- bowtie2:
description: |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences.
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file
description: Input genome fasta file
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.bt2"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- index:
type: file
description: Bowtie2 genome index files
pattern: "*.bt2"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
- "@joseespinosa"
- "@drpatelh"

42
modules/bwa/aln/meta.yml
View file

@ -10,30 +10,30 @@ keywords:
- map
- fastq
tools:
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later']
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
output:
- meta:

50
modules/bwa/index/meta.yml
View file

@ -1,32 +1,32 @@
name: bwa_index
description: Create BWA index for reference genome
keywords:
- index
- fasta
- genome
- reference
- index
- fasta
- genome
- reference
tools:
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file
description: Input genome fasta file
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: file
description: BWA genome index files
pattern: "*.{amb,ann,bwt,pac,sa}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- index:
type: file
description: BWA genome index files
pattern: "*.{amb,ann,bwt,pac,sa}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@maxulysse"
- "@drpatelh"
- "@maxulysse"

86
modules/bwa/mem/meta.yml
View file

@ -1,50 +1,50 @@
name: bwa_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
- mem
- bwa
- alignment
- map
- fastq
- bam
- sam
- mem
- bwa
- alignment
- map
- fastq
- bam
- sam
tools:
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
- bwa:
description: |
BWA is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
- "@jeremy1805"
- "@drpatelh"
- "@jeremy1805"

22
modules/bwa/sampe/meta.yml
View file

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

22
modules/bwa/samse/meta.yml
View file

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

46
modules/bwamem2/index/meta.yml
View file

@ -1,30 +1,30 @@
name: bwamem2_index
description: Create BWA-mem2 index for reference genome
keywords:
- index
- fasta
- genome
- reference
- index
- fasta
- genome
- reference
tools:
- bwa:
description: |
BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
licence: ['MIT']
- bwa:
description: |
BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
licence: ["MIT"]
input:
- fasta:
type: file
description: Input genome fasta file
- fasta:
type: file
description: Input genome fasta file
output:
- index:
type: file
description: BWA genome index files
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- index:
type: file
description: BWA genome index files
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@maxulysse"
- "@maxulysse"

84
modules/bwamem2/mem/meta.yml
View file

@ -1,49 +1,49 @@
name: bwamem2_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
- mem
- bwa
- alignment
- map
- fastq
- bam
- sam
- mem
- bwa
- alignment
- map
- fastq
- bam
- sam
tools:
- bwa:
description: |
BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['MIT']
- bwa:
description: |
BWA-mem2 is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: file
description: BWA genome index files
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@maxulysse"
- "@maxulysse"

90
modules/bwameth/align/meta.yml
View file

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

52
modules/bwameth/index/meta.yml
View file

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

2
modules/cat/cat/meta.yml
View file

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

62
modules/cat/fastq/meta.yml
View file

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

62
modules/cellranger/count/meta.yml
View file

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

46
modules/cellranger/mkfastq/meta.yml
View file

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

44
modules/cellranger/mkgtf/meta.yml
View file

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

58
modules/cellranger/mkref/meta.yml
View file

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

2
modules/checkm/lineagewf/meta.yml
View file

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

28
modules/chromap/chromap/meta.yml
View file

@ -1,19 +1,19 @@
name: chromap_chromap
description: |
Performs preprocessing and alignment of chromatin fastq files to
fasta reference files using chromap.
Performs preprocessing and alignment of chromatin fastq files to
fasta reference files using chromap.
keywords:
- chromap
- alignment
- map
- fastq
- bam
- sam
- hi-c
- atac-seq
- chip-seq
- trimming
- duplicate removal
- chromap
- alignment
- map
- fastq
- bam
- sam
- hi-c
- atac-seq
- chip-seq
- trimming
- duplicate removal
tools:
- chromap:
description: Fast alignment and preprocessing of chromatin profiles
@ -21,7 +21,7 @@ tools:
documentation: https://github.com/haowenz/chromap
tool_dev_url: https://github.com/haowenz/chromap
doi: ""
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:
type: map

10
modules/chromap/index/meta.yml
View file

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

2
modules/clonalframeml/meta.yml
View file

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

2
modules/cmseq/polymut/meta.yml
View file

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

14
modules/cnvkit/batch/meta.yml
View file

@ -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.
homepage: 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:
- outdir:
type: string
@ -85,9 +85,9 @@ output:
description: File containing software versions
pattern: "versions.yml"
authors:
- "@kaurravneet4123"
- "@KevinMenden"
- "@MaxUlysse"
- "@drpatelh"
- "@fbdtemme"
- "@lassefolkersen"
- "@kaurravneet4123"
- "@KevinMenden"
- "@MaxUlysse"
- "@drpatelh"
- "@fbdtemme"
- "@lassefolkersen"

2
modules/cooler/cload/meta.yml
View file

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

2
modules/cooler/digest/meta.yml
View file

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

2
modules/cooler/dump/meta.yml
View file

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

2
modules/cooler/merge/meta.yml
View file

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

2
modules/cooler/zoomify/meta.yml
View file

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

2
modules/csvtk/concat/meta.yml
View file

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

6
modules/csvtk/split/meta.yml
View file

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

2
modules/custom/dumpsoftwareversions/meta.yml
View file

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

3
modules/custom/getchromsizes/meta.yml
View file

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

2
modules/cutadapt/meta.yml
View file

@ -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.
documentation: https://cutadapt.readthedocs.io/en/stable/index.html
doi: DOI:10.14806/ej.17.1.200
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/damageprofiler/meta.yml
View file

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

5
modules/dastool/dastool/meta.yml
View file

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

2
modules/dastool/scaffolds2bin/meta.yml
View file

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

4
modules/dedup/meta.yml
View file

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

2
modules/deeparg/downloaddata/meta.yml
View file

@ -14,7 +14,7 @@ tools:
documentation: 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"
licence: ['MIT']
licence: ["MIT"]
input:
- none: There is no input. This module downloads a pre-built database for use with deepARG.

2
modules/deeparg/predict/meta.yml
View file

@ -16,7 +16,7 @@ tools:
documentation: 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"
licence: ['MIT']
licence: ["MIT"]
input:
- meta:

2
modules/deeptools/computematrix/meta.yml
View file

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

2
modules/deeptools/plotfingerprint/meta.yml
View file

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

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