mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2025-01-10 15:49:37 -05:00
Backfill software licenses meta (#876)
* 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:
parent
32f6191aca
commit
3aacd46da2
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
bowtie
bowtie2
bwa
bwamem2
bwameth
cat
cnvkit
cooler
custom/dumpsoftwareversions
cutadapt
delly/call
dshbio
ensemblvep
expansionhunter
fastp
fastqc
gatk4
applybqsr
baserecalibrator
bedtointervallist
calculatecontamination
createsequencedictionary
fastqtosam
getpileupsummaries
haplotypecaller
intervallisttools
learnreadorientationmodel
markduplicates
mergebamalignment
mergevcfs
mutect2
revertsam
samtofastq
splitncigarreads
variantfiltration
genmap
glnexus
graphmap2
gubbins
gunzip
hmmer/hmmalign
homer
ismapper
isoseq3
ivar
kallisto/index
kraken2/kraken2
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
- meta:
|
- meta:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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
|
||||||
|
|
|
@ -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:
|
||||||
|
|
|
@ -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
|
||||||
|
|
Some files were not shown because too many files have changed in this diff Show more
Loading…
Reference in a new issue