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Backfill software licenses meta ()

* backfilled modules with meta.yml that had no license identifier

* harmonized BSD license names

* whitespace linting at modules/unzip/meta.yml:12

* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'

* Update modules/bcftools/index/meta.yml

`bcftools` is dual-licensed, use associative array to allow for multiple licenses

Co-authored-by: Michael L Heuer <heuermh@acm.org>

Co-authored-by: Michael L Heuer <heuermh@acm.org>
This commit is contained in:
Kevin 2021-10-22 15:39:54 -07:00 committed by GitHub
parent 32f6191aca
commit 3aacd46da2
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165 changed files with 168 additions and 33 deletions
modules
bandage/image
bcftools
concat
consensus
filter
index
isec
merge
mpileup
norm
query
reheader
stats
view
bedtools
bamtobed
complement
genomecov
getfasta
intersect
makewindows
maskfasta
merge
slop
sort
subtract
bismark
align
deduplicate
genomepreparation
methylationextractor
report
summary
blast
blastn
makeblastdb
bowtie
bowtie2
bwa
bwamem2
bwameth
cat
cnvkit
cooler
custom/dumpsoftwareversions
cutadapt
delly/call
dshbio
exportsegments
filterbed
filtergff3
splitbed
splitgff3
ensemblvep
expansionhunter
fastp
fastqc
gatk4
applybqsr
baserecalibrator
bedtointervallist
calculatecontamination
createsequencedictionary
fastqtosam
getpileupsummaries
haplotypecaller
intervallisttools
learnreadorientationmodel
markduplicates
mergebamalignment
mergevcfs
mutect2
revertsam
samtofastq
splitncigarreads
variantfiltration
genmap
index
mappability
glnexus
graphmap2
gubbins
gunzip
hmmer/hmmalign
homer
annotatepeaks
findpeaks
maketagdirectory
makeucscfile
ismapper
isoseq3
cluster
refine
ivar
consensus
trim
variants
kallisto/index
kraken2/kraken2

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@ -11,6 +11,7 @@ tools:
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
homepage: https://github.com/rrwick/Bandage homepage: https://github.com/rrwick/Bandage
documentation: https://github.com/rrwick/Bandage documentation: https://github.com/rrwick/Bandage
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -13,6 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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

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@ -13,6 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -11,6 +11,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -12,6 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -12,6 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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

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@ -12,6 +12,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -13,6 +13,7 @@ tools:
homepage: http://samtools.github.io/bcftools/bcftools.html homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352 doi: 10.1093/bioinformatics/btp352
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -8,6 +8,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -8,6 +8,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -9,6 +9,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -9,6 +9,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
input: input:
- bed: - bed:
type: file type: file

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@ -8,6 +8,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -11,7 +11,7 @@ tools:
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
tool_dev_url: None tool_dev_url: None
doi: "10.1093/bioinformatics/btq033" doi: "10.1093/bioinformatics/btq033"
licence: ['GPL v2'] licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -9,6 +9,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

View file

@ -8,6 +8,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -8,6 +8,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -8,6 +8,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -10,6 +10,7 @@ tools:
description: | description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
licence: ['MIT']
input: input:
- meta: - meta:

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@ -17,6 +17,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -19,6 +19,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -19,6 +19,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input: input:
- fasta: - fasta:
type: file type: file

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@ -18,6 +18,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -16,6 +16,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -19,6 +19,7 @@ tools:
homepage: https://github.com/FelixKrueger/Bismark homepage: https://github.com/FelixKrueger/Bismark
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
doi: 10.1093/bioinformatics/btr167 doi: 10.1093/bioinformatics/btr167
licence: ['GPL-3.0-or-later']
input: input:
- bam: - bam:
type: file type: file

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@ -12,6 +12,7 @@ tools:
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2 doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work']
input: input:
- meta: - meta:
type: map type: map

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@ -11,6 +11,7 @@ tools:
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
doi: 10.1016/S0022-2836(05)80360-2 doi: 10.1016/S0022-2836(05)80360-2
licence: ['US-Government-Work']
input: input:
- fasta: - fasta:
type: file type: file

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@ -13,6 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/index.shtml homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
input: input:
- meta: - meta:
type: map type: map

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@ -13,6 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/index.shtml homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['Artistic-2.0']
input: input:
- fasta: - fasta:
type: file type: file

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@ -13,6 +13,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923 doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -14,6 +14,7 @@ tools:
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
doi: 10.1038/nmeth.1923 doi: 10.1038/nmeth.1923
licence: ['GPL-3.0-or-later']
input: input:
- fasta: - fasta:
type: file type: file

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@ -17,7 +17,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324" doi: "10.1093/bioinformatics/btp324"
licence: ['GPL v3'] licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:

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@ -13,6 +13,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
input: input:
- fasta: - fasta:
type: file type: file

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@ -16,6 +16,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -18,7 +18,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324" doi: "10.1093/bioinformatics/btp324"
licence: ['GPL v3'] licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:

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@ -19,7 +19,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/
doi: "10.1093/bioinformatics/btp324" doi: "10.1093/bioinformatics/btp324"
licence: ['GPL v3'] licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:

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@ -12,6 +12,7 @@ tools:
a large reference genome, such as the human genome. a large reference genome, such as the human genome.
homepage: https://github.com/bwa-mem2/bwa-mem2 homepage: https://github.com/bwa-mem2/bwa-mem2
documentation: https://github.com/bwa-mem2/bwa-mem2#usage documentation: https://github.com/bwa-mem2/bwa-mem2#usage
licence: ['MIT']
input: input:
- fasta: - fasta:
type: file type: file

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@ -16,6 +16,7 @@ tools:
homepage: http://bio-bwa.sourceforge.net/ homepage: http://bio-bwa.sourceforge.net/
documentation: http://www.htslib.org/doc/samtools.html documentation: http://www.htslib.org/doc/samtools.html
arxiv: arXiv:1303.3997 arxiv: arXiv:1303.3997
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -19,6 +19,7 @@ tools:
homepage: https://github.com/brentp/bwa-meth homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129 arxiv: arXiv:1401.1129
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -15,6 +15,7 @@ tools:
homepage: https://github.com/brentp/bwa-meth homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129 arxiv: arXiv:1401.1129
licence: ['MIT']
input: input:
- fasta: - fasta:
type: file type: file

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

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@ -8,6 +8,7 @@ tools:
description: | description: |
The cat utility reads files sequentially, writing them to the standard output. The cat utility reads files sequentially, writing them to the standard output.
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
homepage: https://cnvkit.readthedocs.io/en/stable/index.html homepage: https://cnvkit.readthedocs.io/en/stable/index.html
documentation: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html
licence: ['Apache-2.0']
params: params:
- outdir: - outdir:
type: string type: string

View file

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

View file

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

View file

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

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@ -11,6 +11,7 @@ tools:
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
documentation: https://cutadapt.readthedocs.io/en/stable/index.html documentation: https://cutadapt.readthedocs.io/en/stable/index.html
doi: DOI:10.14806/ej.17.1.200 doi: DOI:10.14806/ej.17.1.200
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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

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@ -12,6 +12,7 @@ tools:
or later. or later.
homepage: https://github.com/heuermh/dishevelled-bio homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
or later. or later.
homepage: https://github.com/heuermh/dishevelled-bio homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
or later. or later.
homepage: https://github.com/heuermh/dishevelled-bio homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
or later. or later.
homepage: https://github.com/heuermh/dishevelled-bio homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
or later. or later.
homepage: https://github.com/heuermh/dishevelled-bio homepage: https://github.com/heuermh/dishevelled-bio
documentation: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio
licence: ['LGPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -9,6 +9,7 @@ tools:
or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
homepage: https://www.ensembl.org/info/docs/tools/vep/index.html homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
licence: ['Apache-2.0']
params: params:
- use_cache: - use_cache:
type: boolean type: boolean

View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md
tool_dev_url: None tool_dev_url: None
doi: "10.1093/bioinformatics/btz431" doi: "10.1093/bioinformatics/btz431"
licence: ['Apache v2.0'] licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -10,6 +10,7 @@ tools:
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
documentation: https://github.com/OpenGene/fastp documentation: https://github.com/OpenGene/fastp
doi: https://doi.org/10.1093/bioinformatics/bty560 doi: https://doi.org/10.1093/bioinformatics/bty560
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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@ -15,6 +15,7 @@ tools:
overrepresented sequences. overrepresented sequences.
homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
licence: ['GPL-2.0-only']
input: input:
- meta: - meta:
type: map type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -11,6 +11,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

View file

@ -16,6 +16,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -12,6 +12,8 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- fasta: - fasta:
type: file type: file

View file

@ -1,5 +1,5 @@
name: gatk4_fastqtosam name: gatk4_fastqtosam
description: Converts FastQ file to BAM format description: Converts FastQ file to SAM/BAM format
keywords: keywords:
- bam - bam
- fastq - fastq
@ -14,7 +14,7 @@ tools:
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
tool_dev_url: https://github.com/broadinstitute/gatk tool_dev_url: https://github.com/broadinstitute/gatk
doi: "10.1158/1538-7445.AM2017-3590" doi: "10.1158/1538-7445.AM2017-3590"
licence: ['BSD-3-clause'] licence: ['MIT']
input: input:
- meta: - meta:

View file

@ -15,6 +15,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -13,6 +13,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -14,6 +14,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -15,6 +15,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -13,7 +13,7 @@ tools:
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
tool_dev_url: https://github.com/broadinstitute/gatk tool_dev_url: https://github.com/broadinstitute/gatk
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['BSD-3-clause'] licence: ['MIT']
input: input:
- meta: - meta:

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

View file

@ -14,6 +14,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

View file

@ -12,6 +12,7 @@ tools:
homepage: https://gatk.broadinstitute.org/hc/en-us homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590 doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input: input:
- meta: - meta:
type: map type: map

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@ -9,7 +9,7 @@ tools:
documentation: https://github.com/cpockrandt/genmap documentation: https://github.com/cpockrandt/genmap
tool_dev_url: https://github.com/cpockrandt/genmap tool_dev_url: https://github.com/cpockrandt/genmap
doi: "10.1093/bioinformatics/btaa222" doi: "10.1093/bioinformatics/btaa222"
licence: ['BSD'] licence: ['BSD-3-Clause']
input: input:
- fasta: - fasta:

View file

@ -9,7 +9,7 @@ tools:
documentation: https://github.com/cpockrandt/genmap documentation: https://github.com/cpockrandt/genmap
tool_dev_url: https://github.com/cpockrandt/genmap tool_dev_url: https://github.com/cpockrandt/genmap
doi: "10.1093/bioinformatics/btaa222" doi: "10.1093/bioinformatics/btaa222"
licence: ['BSD'] licence: ['BSD-3-Clause']
input: input:
- fasta: - fasta:

View file

@ -10,7 +10,7 @@ tools:
documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
tool_dev_url: None tool_dev_url: None
doi: https://doi.org/10.1101/343970 doi: https://doi.org/10.1101/343970
licence: ['Apache License 2.0'] licence: ['Apache-2.0']
input: input:
- meta: - meta:

View file

@ -12,6 +12,7 @@ tools:
A versatile pairwise aligner for genomic and spliced nucleotide sequences. A versatile pairwise aligner for genomic and spliced nucleotide sequences.
homepage: https://github.com/lbcb-sci/graphmap2 homepage: https://github.com/lbcb-sci/graphmap2
documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
A versatile pairwise aligner for genomic and spliced nucleotide sequences. A versatile pairwise aligner for genomic and spliced nucleotide sequences.
homepage: https://github.com/lbcb-sci/graphmap2 homepage: https://github.com/lbcb-sci/graphmap2
documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
licence: ['MIT']
input: input:
- fasta: - fasta:
type: file type: file

View file

@ -2,6 +2,7 @@ name: gubbins
description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies
loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the
putative point mutations outside of these regions. putative point mutations outside of these regions.
licence: ['GPL-2.0-only']
keywords: keywords:
- recombination - recombination
- alignment - alignment

View file

@ -8,6 +8,7 @@ tools:
description: | description: |
gzip is a file format and a software application used for file compression and decompression. gzip is a file format and a software application used for file compression and decompression.
documentation: https://www.gnu.org/software/gzip/manual/gzip.html documentation: https://www.gnu.org/software/gzip/manual/gzip.html
licence: ['GPL-3.0-or-later']
input: input:
- archive: - archive:
type: file type: file

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@ -9,7 +9,7 @@ tools:
documentation: http://hmmer.org/documentation.html documentation: http://hmmer.org/documentation.html
tool_dev_url: None tool_dev_url: None
doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195" doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
licence: ['BSD'] licence: ['BSD-3-Clause']
input: input:
- meta: - meta:

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@ -10,6 +10,7 @@ tools:
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
documentation: http://homer.ucsd.edu/homer/ documentation: http://homer.ucsd.edu/homer/
doi: 10.1016/j.molcel.2010.05.004. doi: 10.1016/j.molcel.2010.05.004.
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -9,6 +9,7 @@ tools:
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
documentation: http://homer.ucsd.edu/homer/ documentation: http://homer.ucsd.edu/homer/
doi: 10.1016/j.molcel.2010.05.004. doi: 10.1016/j.molcel.2010.05.004.
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -9,6 +9,7 @@ tools:
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
documentation: http://homer.ucsd.edu/homer/ documentation: http://homer.ucsd.edu/homer/
doi: 10.1016/j.molcel.2010.05.004. doi: 10.1016/j.molcel.2010.05.004.
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

View file

@ -10,6 +10,7 @@ tools:
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
documentation: http://homer.ucsd.edu/homer/ documentation: http://homer.ucsd.edu/homer/
doi: 10.1016/j.molcel.2010.05.004. doi: 10.1016/j.molcel.2010.05.004.
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -10,7 +10,7 @@ tools:
documentation: https://github.com/jhawkey/IS_mapper documentation: https://github.com/jhawkey/IS_mapper
tool_dev_url: https://github.com/jhawkey/IS_mapper tool_dev_url: https://github.com/jhawkey/IS_mapper
doi: "https://doi.org/10.1186/s12864-015-1860-2" doi: "https://doi.org/10.1186/s12864-015-1860-2"
licence: ['BSD'] licence: ['BSD-3-Clause']
input: input:
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@ -9,7 +9,7 @@ tools:
documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
doi: "" doi: ""
licence: ['BSD-3-clause-Clear'] licence: ['BSD-3-Clause-Clear']
input: input:
- meta: - meta:

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@ -10,7 +10,7 @@ tools:
documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
doi: "" doi: ""
licence: ['BSD-3-clause-Clear'] licence: ['BSD-3-Clause-Clear']
input: input:
- meta: - meta:

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@ -10,6 +10,7 @@ tools:
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
homepage: https://github.com/andersen-lab/ivar homepage: https://github.com/andersen-lab/ivar
documentation: https://andersen-lab.github.io/ivar/html/manualpage.html documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
licence: ['GPL-3.0-or-later']
input: input:
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type: map type: map

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@ -10,6 +10,7 @@ tools:
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
homepage: https://github.com/andersen-lab/ivar homepage: https://github.com/andersen-lab/ivar
documentation: https://andersen-lab.github.io/ivar/html/manualpage.html documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -10,6 +10,7 @@ tools:
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
homepage: https://github.com/andersen-lab/ivar homepage: https://github.com/andersen-lab/ivar
documentation: https://andersen-lab.github.io/ivar/html/manualpage.html documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
licence: ['GPL-3.0-or-later']
input: input:
- meta: - meta:
type: map type: map

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@ -9,7 +9,7 @@ tools:
documentation: https://pachterlab.github.io/kallisto/manual documentation: https://pachterlab.github.io/kallisto/manual
tool_dev_url: https://github.com/pachterlab/kallisto tool_dev_url: https://github.com/pachterlab/kallisto
doi: "" doi: ""
licence: ['BSD_2_clause'] licence: ['BSD-2-Clause']
input: input:
- fasta: - fasta:

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@ -12,6 +12,7 @@ tools:
homepage: https://ccb.jhu.edu/software/kraken2/ homepage: https://ccb.jhu.edu/software/kraken2/
documentation: https://github.com/DerrickWood/kraken2/wiki/Manual documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
doi: 10.1186/s13059-019-1891-0 doi: 10.1186/s13059-019-1891-0
licence: ['MIT']
input: input:
- meta: - meta:
type: map type: map

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