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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
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
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

5
.yamllint.yml Normal file
View file

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

2
modules/abacas/meta.yml
View file

@ -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:

2
modules/adapterremoval/meta.yml
View file

@ -10,7 +10,7 @@ tools:
description: The AdapterRemoval v2 tool for merging and clipping reads.
homepage: https://github.com/MikkelSchubert/adapterremoval
documentation: https://adapterremoval.readthedocs.io
licence: ['GPL v3']
licence: ["GPL v3"]
input:
- meta:

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:

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

@ -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

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:

5
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,
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:

2
modules/bandage/image/meta.yml
View file

@ -11,7 +11,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
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:

2
modules/bbmap/bbduk/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:
- 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:

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

@ -13,7 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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

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

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

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

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:

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

@ -13,7 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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

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

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

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

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

@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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:

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

@ -12,7 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -13,7 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -9,7 +9,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -9,7 +9,7 @@ tools:
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']
licence: ["MIT"]
input:
- bed:
type: file

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

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

@ -9,7 +9,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -10,7 +10,7 @@ tools:
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']
licence: ["MIT"]
input:
- meta:

2
modules/biobambam/bammarkduplicates2/meta.yml
View file

@ -11,7 +11,7 @@ tools:
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']
licence: ["GPL v3"]
input:
- meta:
type: map

2
modules/bismark/align/meta.yml
View file

@ -17,7 +17,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/bismark/deduplicate/meta.yml
View file

@ -19,7 +19,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/bismark/genomepreparation/meta.yml
View file

@ -19,7 +19,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file

2
modules/bismark/methylationextractor/meta.yml
View file

@ -18,7 +18,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/bismark/report/meta.yml
View file

@ -16,7 +16,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/bismark/summary/meta.yml
View file

@ -19,7 +19,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- bam:
type: file

2
modules/blast/blastn/meta.yml
View file

@ -12,7 +12,7 @@ tools:
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']
licence: ["US-Government-Work"]
input:
- meta:
type: map

2
modules/blast/makeblastdb/meta.yml
View file

@ -11,7 +11,7 @@ tools:
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']
licence: ["US-Government-Work"]
input:
- fasta:
type: file

2
modules/bowtie/align/meta.yml
View file

@ -13,7 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
licence: ["Artistic-2.0"]
input:
- meta:
type: map

2
modules/bowtie/build/meta.yml
View file

@ -13,7 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
licence: ["Artistic-2.0"]
input:
- fasta:
type: file

2
modules/bowtie2/align/meta.yml
View file

@ -13,7 +13,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/bowtie2/build/meta.yml
View file

@ -14,7 +14,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file

2
modules/bwa/aln/meta.yml
View file

@ -17,7 +17,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- meta:

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

@ -13,7 +13,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- fasta:
type: file

2
modules/bwa/mem/meta.yml
View file

@ -16,7 +16,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

2
modules/bwa/sampe/meta.yml
View file

@ -18,7 +18,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- meta:

2
modules/bwa/samse/meta.yml
View file

@ -19,7 +19,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324"
licence: ['GPL-3.0-or-later']
licence: ["GPL-3.0-or-later"]
input:
- meta:

2
modules/bwamem2/index/meta.yml
View file

@ -12,7 +12,7 @@ tools:
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']
licence: ["MIT"]
input:
- fasta:
type: file

2
modules/bwamem2/mem/meta.yml
View file

@ -16,7 +16,7 @@ tools:
homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

2
modules/bwameth/align/meta.yml
View file

@ -19,7 +19,7 @@ tools:
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
licence: ['MIT']
licence: ["MIT"]
input:
- meta:
type: map

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

@ -15,7 +15,7 @@ tools:
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
licence: ['MIT']
licence: ["MIT"]
input:
- fasta:
type: file

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

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

@ -8,7 +8,7 @@ tools:
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']
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map

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:

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

@ -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

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

@ -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:

2
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

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:

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

@ -13,7 +13,7 @@ tools:
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:

3
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

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:

2
modules/deeptools/plotheatmap/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/plotprofile/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/deepvariant/meta.yml
View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/google/deepvariant
tool_dev_url: https://github.com/google/deepvariant
doi: "https://doi.org/10.1038/nbt.4235"
licence: ['BSD-3-clause']
licence: ["BSD-3-clause"]
input:
- meta:

2
modules/delly/call/meta.yml
View file

@ -13,7 +13,7 @@ tools:
documentation: https://github.com/dellytools/delly/blob/master/README.md
tool_dev_url: None
doi: "DOI:10.1093/bioinformatics/bts378"
licence: ['BSD-3-Clause']
licence: ["BSD-3-Clause"]
input:
- meta:

2
modules/diamond/blastp/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://github.com/bbuchfink/diamond/wiki
tool_dev_url: https://github.com/bbuchfink/diamond
doi: "doi:10.1038/s41592-021-01101-x"
licence: ['GPL v3.0']
licence: ["GPL v3.0"]
input:
- meta:

2
modules/diamond/blastx/meta.yml
View file

@ -12,7 +12,7 @@ tools:
documentation: https://github.com/bbuchfink/diamond/wiki
tool_dev_url: https://github.com/bbuchfink/diamond
doi: "doi:10.1038/s41592-021-01101-x"
licence: ['GPL v3.0']
licence: ["GPL v3.0"]
input:
- meta:

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