From 3aacd46da2b221ed47aaa05c413a828538d2c2ae Mon Sep 17 00:00:00 2001 From: Kevin Date: Fri, 22 Oct 2021 15:39:54 -0700 Subject: [PATCH] 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 Co-authored-by: Michael L Heuer --- modules/bandage/image/meta.yml | 1 + modules/bcftools/concat/meta.yml | 1 + modules/bcftools/consensus/meta.yml | 1 + modules/bcftools/filter/meta.yml | 1 + modules/bcftools/index/meta.yml | 2 +- modules/bcftools/isec/meta.yml | 1 + modules/bcftools/merge/meta.yml | 1 + modules/bcftools/mpileup/meta.yml | 1 + modules/bcftools/norm/meta.yml | 1 + modules/bcftools/query/meta.yml | 1 + modules/bcftools/reheader/meta.yml | 2 +- modules/bcftools/stats/meta.yml | 1 + modules/bcftools/view/meta.yml | 1 + modules/bedtools/bamtobed/meta.yml | 1 + modules/bedtools/complement/meta.yml | 1 + modules/bedtools/genomecov/meta.yml | 1 + modules/bedtools/getfasta/meta.yml | 1 + modules/bedtools/intersect/meta.yml | 1 + modules/bedtools/makewindows/meta.yml | 2 +- modules/bedtools/maskfasta/meta.yml | 1 + modules/bedtools/merge/meta.yml | 1 + modules/bedtools/slop/meta.yml | 1 + modules/bedtools/sort/meta.yml | 1 + modules/bedtools/subtract/meta.yml | 1 + modules/bismark/align/meta.yml | 1 + modules/bismark/deduplicate/meta.yml | 1 + modules/bismark/genomepreparation/meta.yml | 1 + modules/bismark/methylationextractor/meta.yml | 1 + modules/bismark/report/meta.yml | 1 + modules/bismark/summary/meta.yml | 1 + modules/blast/blastn/meta.yml | 1 + modules/blast/makeblastdb/meta.yml | 1 + modules/bowtie/align/meta.yml | 1 + modules/bowtie/build/meta.yml | 1 + modules/bowtie2/align/meta.yml | 1 + modules/bowtie2/build/meta.yml | 1 + modules/bwa/aln/meta.yml | 2 +- modules/bwa/index/meta.yml | 1 + modules/bwa/mem/meta.yml | 1 + modules/bwa/sampe/meta.yml | 2 +- modules/bwa/samse/meta.yml | 2 +- modules/bwamem2/index/meta.yml | 1 + modules/bwamem2/mem/meta.yml | 1 + modules/bwameth/align/meta.yml | 1 + modules/bwameth/index/meta.yml | 1 + modules/cat/cat/meta.yml | 2 +- modules/cat/fastq/meta.yml | 1 + modules/cnvkit/meta.yml | 1 + modules/cooler/digest/meta.yml | 2 +- modules/cooler/dump/meta.yml | 2 +- modules/custom/dumpsoftwareversions/meta.yml | 2 +- modules/cutadapt/meta.yml | 1 + modules/delly/call/meta.yml | 2 +- modules/dshbio/exportsegments/meta.yml | 1 + modules/dshbio/filterbed/meta.yml | 1 + modules/dshbio/filtergff3/meta.yml | 1 + modules/dshbio/splitbed/meta.yml | 1 + modules/dshbio/splitgff3/meta.yml | 1 + modules/ensemblvep/meta.yml | 1 + modules/expansionhunter/meta.yml | 2 +- modules/fastp/meta.yml | 1 + modules/fastqc/meta.yml | 1 + modules/gatk4/applybqsr/meta.yml | 1 + modules/gatk4/baserecalibrator/meta.yml | 1 + modules/gatk4/bedtointervallist/meta.yml | 1 + modules/gatk4/calculatecontamination/meta.yml | 1 + modules/gatk4/createsequencedictionary/meta.yml | 2 ++ modules/gatk4/fastqtosam/meta.yml | 4 ++-- modules/gatk4/getpileupsummaries/meta.yml | 1 + modules/gatk4/haplotypecaller/meta.yml | 1 + modules/gatk4/intervallisttools/meta.yml | 1 + modules/gatk4/learnreadorientationmodel/meta.yml | 1 + modules/gatk4/markduplicates/meta.yml | 2 +- modules/gatk4/mergebamalignment/meta.yml | 1 + modules/gatk4/mergevcfs/meta.yml | 1 + modules/gatk4/mutect2/meta.yml | 1 + modules/gatk4/revertsam/meta.yml | 1 + modules/gatk4/samtofastq/meta.yml | 1 + modules/gatk4/splitncigarreads/meta.yml | 1 + modules/gatk4/variantfiltration/meta.yml | 1 + modules/genmap/index/meta.yml | 2 +- modules/genmap/mappability/meta.yml | 2 +- modules/glnexus/meta.yml | 2 +- modules/graphmap2/align/meta.yml | 1 + modules/graphmap2/index/meta.yml | 1 + modules/gubbins/meta.yml | 1 + modules/gunzip/meta.yml | 1 + modules/hmmer/hmmalign/meta.yml | 2 +- modules/homer/annotatepeaks/meta.yml | 1 + modules/homer/findpeaks/meta.yml | 1 + modules/homer/maketagdirectory/meta.yml | 1 + modules/homer/makeucscfile/meta.yml | 1 + modules/ismapper/meta.yml | 2 +- modules/isoseq3/cluster/meta.yml | 2 +- modules/isoseq3/refine/meta.yml | 2 +- modules/ivar/consensus/meta.yml | 1 + modules/ivar/trim/meta.yml | 1 + modules/ivar/variants/meta.yml | 1 + modules/kallisto/index/meta.yml | 2 +- modules/kraken2/kraken2/meta.yml | 1 + modules/lima/meta.yml | 2 +- modules/methyldackel/extract/meta.yml | 1 + modules/methyldackel/mbias/meta.yml | 1 + modules/minia/meta.yml | 1 + modules/minimap2/align/meta.yml | 1 + modules/minimap2/index/meta.yml | 1 + modules/mosdepth/meta.yml | 1 + modules/multiqc/meta.yml | 1 + modules/nanolyse/meta.yml | 1 + modules/nanoplot/meta.yml | 1 + modules/optitype/meta.yml | 2 +- modules/pangolin/meta.yml | 1 + modules/pbbam/pbmerge/meta.yml | 2 +- modules/pbccs/meta.yml | 2 +- modules/picard/collectmultiplemetrics/meta.yml | 1 + modules/picard/collectwgsmetrics/meta.yml | 1 + modules/picard/markduplicates/meta.yml | 1 + modules/picard/mergesamfiles/meta.yml | 1 + modules/picard/sortsam/meta.yml | 1 + modules/qcat/meta.yml | 1 + modules/qualimap/bamqc/meta.yml | 1 + modules/quast/meta.yml | 3 ++- modules/rsem/calculateexpression/meta.yml | 1 + modules/rsem/preparereference/meta.yml | 1 + modules/rseqc/bamstat/meta.yml | 1 + modules/rseqc/inferexperiment/meta.yml | 1 + modules/rseqc/innerdistance/meta.yml | 1 + modules/rseqc/junctionannotation/meta.yml | 1 + modules/rseqc/junctionsaturation/meta.yml | 1 + modules/rseqc/readdistribution/meta.yml | 1 + modules/rseqc/readduplication/meta.yml | 1 + modules/salmon/index/meta.yml | 1 + modules/salmon/quant/meta.yml | 1 + modules/samtools/ampliconclip/meta.yml | 1 + modules/samtools/faidx/meta.yml | 1 + modules/samtools/fastq/meta.yml | 1 + modules/samtools/flagstat/meta.yml | 1 + modules/samtools/idxstats/meta.yml | 1 + modules/samtools/index/meta.yml | 1 + modules/samtools/merge/meta.yml | 1 + modules/samtools/mpileup/meta.yml | 1 + modules/samtools/sort/meta.yml | 1 + modules/samtools/stats/meta.yml | 1 + modules/samtools/view/meta.yml | 1 + modules/seacr/callpeak/meta.yml | 1 + modules/seqkit/split2/meta.yml | 1 + modules/sequenzautils/bam2seqz/meta.yml | 2 +- modules/sequenzautils/gcwiggle/meta.yml | 1 + modules/seqwish/induce/meta.yml | 1 + modules/snpeff/meta.yml | 1 + modules/snpsites/meta.yml | 1 + modules/sratools/fasterqdump/meta.yml | 2 +- modules/sratools/prefetch/meta.yml | 2 +- modules/star/align/meta.yml | 1 + modules/star/genomegenerate/meta.yml | 1 + modules/stringtie/merge/meta.yml | 1 + modules/stringtie/stringtie/meta.yml | 1 + modules/tabix/bgzip/meta.yml | 1 + modules/tabix/bgziptabix/meta.yml | 1 + modules/tabix/tabix/meta.yml | 1 + modules/tiddit/sv/meta.yml | 1 + modules/trimgalore/meta.yml | 1 + modules/untar/meta.yml | 1 + modules/unzip/meta.yml | 2 +- modules/variantbam/meta.yml | 2 +- 165 files changed, 168 insertions(+), 33 deletions(-) diff --git a/modules/bandage/image/meta.yml b/modules/bandage/image/meta.yml index 65f47664..1c2b9840 100644 --- a/modules/bandage/image/meta.yml +++ b/modules/bandage/image/meta.yml @@ -11,6 +11,7 @@ tools: Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily homepage: https://github.com/rrwick/Bandage documentation: https://github.com/rrwick/Bandage + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bcftools/concat/meta.yml b/modules/bcftools/concat/meta.yml index e394d18d..b2848595 100644 --- a/modules/bcftools/concat/meta.yml +++ b/modules/bcftools/concat/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/consensus/meta.yml b/modules/bcftools/consensus/meta.yml index 30f4910a..761115a6 100644 --- a/modules/bcftools/consensus/meta.yml +++ b/modules/bcftools/consensus/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/filter/meta.yml b/modules/bcftools/filter/meta.yml index 433b203d..72d28bf0 100644 --- a/modules/bcftools/filter/meta.yml +++ b/modules/bcftools/filter/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/index/meta.yml b/modules/bcftools/index/meta.yml index 6fc7df17..0d5dd3ef 100644 --- a/modules/bcftools/index/meta.yml +++ b/modules/bcftools/index/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://samtools.github.io/bcftools/howtos/index.html tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/gigascience/giab008" - licence: ['GPL'] + licence: ['MIT', 'GPL-3.0-or-later'] input: - meta: diff --git a/modules/bcftools/isec/meta.yml b/modules/bcftools/isec/meta.yml index 6a482257..d0be6dce 100644 --- a/modules/bcftools/isec/meta.yml +++ b/modules/bcftools/isec/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/merge/meta.yml b/modules/bcftools/merge/meta.yml index 056ea37d..c7e3a280 100644 --- a/modules/bcftools/merge/meta.yml +++ b/modules/bcftools/merge/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/mpileup/meta.yml b/modules/bcftools/mpileup/meta.yml index 49f02a40..c31180ee 100644 --- a/modules/bcftools/mpileup/meta.yml +++ b/modules/bcftools/mpileup/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/norm/meta.yml b/modules/bcftools/norm/meta.yml index 760186dc..27978a53 100644 --- a/modules/bcftools/norm/meta.yml +++ b/modules/bcftools/norm/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/query/meta.yml b/modules/bcftools/query/meta.yml index 12b11216..e450f73e 100644 --- a/modules/bcftools/query/meta.yml +++ b/modules/bcftools/query/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/reheader/meta.yml b/modules/bcftools/reheader/meta.yml index 6d7c9f97..ee8cba32 100644 --- a/modules/bcftools/reheader/meta.yml +++ b/modules/bcftools/reheader/meta.yml @@ -11,7 +11,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 - licence: ['GPL'] + licence: ['MIT'] input: - meta: diff --git a/modules/bcftools/stats/meta.yml b/modules/bcftools/stats/meta.yml index 78294ff7..505bf729 100644 --- a/modules/bcftools/stats/meta.yml +++ b/modules/bcftools/stats/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bcftools/view/meta.yml b/modules/bcftools/view/meta.yml index 638a4e4f..df5b0f8f 100644 --- a/modules/bcftools/view/meta.yml +++ b/modules/bcftools/view/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/bamtobed/meta.yml b/modules/bedtools/bamtobed/meta.yml index 0eaf3e2a..e8c67047 100644 --- a/modules/bedtools/bamtobed/meta.yml +++ b/modules/bedtools/bamtobed/meta.yml @@ -8,6 +8,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/complement/meta.yml b/modules/bedtools/complement/meta.yml index 02ddca29..2ad8749c 100644 --- a/modules/bedtools/complement/meta.yml +++ b/modules/bedtools/complement/meta.yml @@ -8,6 +8,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/genomecov/meta.yml b/modules/bedtools/genomecov/meta.yml index bc49ab03..3deb4d6b 100644 --- a/modules/bedtools/genomecov/meta.yml +++ b/modules/bedtools/genomecov/meta.yml @@ -9,6 +9,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/getfasta/meta.yml b/modules/bedtools/getfasta/meta.yml index 89fbea54..38715c3d 100644 --- a/modules/bedtools/getfasta/meta.yml +++ b/modules/bedtools/getfasta/meta.yml @@ -9,6 +9,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html + licence: ['MIT'] input: - bed: type: file diff --git a/modules/bedtools/intersect/meta.yml b/modules/bedtools/intersect/meta.yml index a14bf515..3bcb6ece 100644 --- a/modules/bedtools/intersect/meta.yml +++ b/modules/bedtools/intersect/meta.yml @@ -8,6 +8,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/makewindows/meta.yml b/modules/bedtools/makewindows/meta.yml index 7d86e127..a536d75f 100644 --- a/modules/bedtools/makewindows/meta.yml +++ b/modules/bedtools/makewindows/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html tool_dev_url: None doi: "10.1093/bioinformatics/btq033" - licence: ['GPL v2'] + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/maskfasta/meta.yml b/modules/bedtools/maskfasta/meta.yml index 428d6f57..0b7aa3ed 100644 --- a/modules/bedtools/maskfasta/meta.yml +++ b/modules/bedtools/maskfasta/meta.yml @@ -9,6 +9,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/merge/meta.yml b/modules/bedtools/merge/meta.yml index 39e79cbd..40a42b7b 100644 --- a/modules/bedtools/merge/meta.yml +++ b/modules/bedtools/merge/meta.yml @@ -8,6 +8,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/slop/meta.yml b/modules/bedtools/slop/meta.yml index 709d88c3..a4713936 100644 --- a/modules/bedtools/slop/meta.yml +++ b/modules/bedtools/slop/meta.yml @@ -8,6 +8,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/sort/meta.yml b/modules/bedtools/sort/meta.yml index a0332787..5b8b41d7 100644 --- a/modules/bedtools/sort/meta.yml +++ b/modules/bedtools/sort/meta.yml @@ -8,6 +8,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bedtools/subtract/meta.yml b/modules/bedtools/subtract/meta.yml index e13057bb..b9245a55 100644 --- a/modules/bedtools/subtract/meta.yml +++ b/modules/bedtools/subtract/meta.yml @@ -10,6 +10,7 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html + licence: ['MIT'] input: - meta: diff --git a/modules/bismark/align/meta.yml b/modules/bismark/align/meta.yml index 92a3b1ec..79948e1c 100644 --- a/modules/bismark/align/meta.yml +++ b/modules/bismark/align/meta.yml @@ -17,6 +17,7 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bismark/deduplicate/meta.yml b/modules/bismark/deduplicate/meta.yml index d19a915f..9e28cd22 100644 --- a/modules/bismark/deduplicate/meta.yml +++ b/modules/bismark/deduplicate/meta.yml @@ -19,6 +19,7 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bismark/genomepreparation/meta.yml b/modules/bismark/genomepreparation/meta.yml index 7712d7c2..2a17f1fb 100644 --- a/modules/bismark/genomepreparation/meta.yml +++ b/modules/bismark/genomepreparation/meta.yml @@ -19,6 +19,7 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 + licence: ['GPL-3.0-or-later'] input: - fasta: type: file diff --git a/modules/bismark/methylationextractor/meta.yml b/modules/bismark/methylationextractor/meta.yml index 9fa0f4f4..602fc06d 100644 --- a/modules/bismark/methylationextractor/meta.yml +++ b/modules/bismark/methylationextractor/meta.yml @@ -18,6 +18,7 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bismark/report/meta.yml b/modules/bismark/report/meta.yml index 889d1227..e849e109 100644 --- a/modules/bismark/report/meta.yml +++ b/modules/bismark/report/meta.yml @@ -16,6 +16,7 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bismark/summary/meta.yml b/modules/bismark/summary/meta.yml index 10f71fe4..0494bb8e 100644 --- a/modules/bismark/summary/meta.yml +++ b/modules/bismark/summary/meta.yml @@ -19,6 +19,7 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 + licence: ['GPL-3.0-or-later'] input: - bam: type: file diff --git a/modules/blast/blastn/meta.yml b/modules/blast/blastn/meta.yml index d19d3df6..39acb663 100644 --- a/modules/blast/blastn/meta.yml +++ b/modules/blast/blastn/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 + licence: ['US-Government-Work'] input: - meta: type: map diff --git a/modules/blast/makeblastdb/meta.yml b/modules/blast/makeblastdb/meta.yml index 545cc2a0..c9d18cba 100644 --- a/modules/blast/makeblastdb/meta.yml +++ b/modules/blast/makeblastdb/meta.yml @@ -11,6 +11,7 @@ tools: homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 + licence: ['US-Government-Work'] input: - fasta: type: file diff --git a/modules/bowtie/align/meta.yml b/modules/bowtie/align/meta.yml index 73c65631..07d480be 100644 --- a/modules/bowtie/align/meta.yml +++ b/modules/bowtie/align/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://bowtie-bio.sourceforge.net/index.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 + licence: ['Artistic-2.0'] input: - meta: type: map diff --git a/modules/bowtie/build/meta.yml b/modules/bowtie/build/meta.yml index aa39f32e..016adcfe 100644 --- a/modules/bowtie/build/meta.yml +++ b/modules/bowtie/build/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://bowtie-bio.sourceforge.net/index.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 + licence: ['Artistic-2.0'] input: - fasta: type: file diff --git a/modules/bowtie2/align/meta.yml b/modules/bowtie2/align/meta.yml index f9d54d87..77c9e397 100644 --- a/modules/bowtie2/align/meta.yml +++ b/modules/bowtie2/align/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bowtie2/build/meta.yml b/modules/bowtie2/build/meta.yml index 4531d079..ecc54e9b 100644 --- a/modules/bowtie2/build/meta.yml +++ b/modules/bowtie2/build/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 + licence: ['GPL-3.0-or-later'] input: - fasta: type: file diff --git a/modules/bwa/aln/meta.yml b/modules/bwa/aln/meta.yml index d4a2b19d..d2424a5f 100644 --- a/modules/bwa/aln/meta.yml +++ b/modules/bwa/aln/meta.yml @@ -17,7 +17,7 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" - licence: ['GPL v3'] + licence: ['GPL-3.0-or-later'] input: - meta: diff --git a/modules/bwa/index/meta.yml b/modules/bwa/index/meta.yml index c3c0a8d8..11d62df3 100644 --- a/modules/bwa/index/meta.yml +++ b/modules/bwa/index/meta.yml @@ -13,6 +13,7 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 + licence: ['GPL-3.0-or-later'] input: - fasta: type: file diff --git a/modules/bwa/mem/meta.yml b/modules/bwa/mem/meta.yml index 66238507..61eaddef 100644 --- a/modules/bwa/mem/meta.yml +++ b/modules/bwa/mem/meta.yml @@ -16,6 +16,7 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/bwa/sampe/meta.yml b/modules/bwa/sampe/meta.yml index ec2dfff5..7b530a03 100644 --- a/modules/bwa/sampe/meta.yml +++ b/modules/bwa/sampe/meta.yml @@ -18,7 +18,7 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" - licence: ['GPL v3'] + licence: ['GPL-3.0-or-later'] input: - meta: diff --git a/modules/bwa/samse/meta.yml b/modules/bwa/samse/meta.yml index 1e7ef335..9a9ecb39 100644 --- a/modules/bwa/samse/meta.yml +++ b/modules/bwa/samse/meta.yml @@ -19,7 +19,7 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" - licence: ['GPL v3'] + licence: ['GPL-3.0-or-later'] input: - meta: diff --git a/modules/bwamem2/index/meta.yml b/modules/bwamem2/index/meta.yml index 1b36be8d..e0f6014c 100644 --- a/modules/bwamem2/index/meta.yml +++ b/modules/bwamem2/index/meta.yml @@ -12,6 +12,7 @@ tools: a large reference genome, such as the human genome. homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: https://github.com/bwa-mem2/bwa-mem2#usage + licence: ['MIT'] input: - fasta: type: file diff --git a/modules/bwamem2/mem/meta.yml b/modules/bwamem2/mem/meta.yml index 2fb4449e..58a35e08 100644 --- a/modules/bwamem2/mem/meta.yml +++ b/modules/bwamem2/mem/meta.yml @@ -16,6 +16,7 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bwameth/align/meta.yml b/modules/bwameth/align/meta.yml index 11fc9949..1cd66237 100644 --- a/modules/bwameth/align/meta.yml +++ b/modules/bwameth/align/meta.yml @@ -19,6 +19,7 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/bwameth/index/meta.yml b/modules/bwameth/index/meta.yml index c96fbfbb..352dfd0f 100644 --- a/modules/bwameth/index/meta.yml +++ b/modules/bwameth/index/meta.yml @@ -15,6 +15,7 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 + licence: ['MIT'] input: - fasta: type: file diff --git a/modules/cat/cat/meta.yml b/modules/cat/cat/meta.yml index f1a46ca3..b3f370ee 100644 --- a/modules/cat/cat/meta.yml +++ b/modules/cat/cat/meta.yml @@ -10,7 +10,7 @@ tools: homepage: None documentation: https://man7.org/linux/man-pages/man1/cat.1.html tool_dev_url: None - + licence: ['GPL-3.0-or-later'] input: - files_in: type: file diff --git a/modules/cat/fastq/meta.yml b/modules/cat/fastq/meta.yml index 6c6c397e..1992fa34 100644 --- a/modules/cat/fastq/meta.yml +++ b/modules/cat/fastq/meta.yml @@ -8,6 +8,7 @@ tools: description: | The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/cnvkit/meta.yml b/modules/cnvkit/meta.yml index 30c1b588..3e760d16 100755 --- a/modules/cnvkit/meta.yml +++ b/modules/cnvkit/meta.yml @@ -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. homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html + licence: ['Apache-2.0'] params: - outdir: type: string diff --git a/modules/cooler/digest/meta.yml b/modules/cooler/digest/meta.yml index 4fb85e4f..6ce95ad7 100644 --- a/modules/cooler/digest/meta.yml +++ b/modules/cooler/digest/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-clause'] + licence: ['BSD-3-Clause'] input: - fasta: diff --git a/modules/cooler/dump/meta.yml b/modules/cooler/dump/meta.yml index 1d98a62e..659b06a1 100644 --- a/modules/cooler/dump/meta.yml +++ b/modules/cooler/dump/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-clause'] + licence: ['BSD-3-Clause'] input: - meta: diff --git a/modules/custom/dumpsoftwareversions/meta.yml b/modules/custom/dumpsoftwareversions/meta.yml index 8d4a6ed4..c8310e35 100644 --- a/modules/custom/dumpsoftwareversions/meta.yml +++ b/modules/custom/dumpsoftwareversions/meta.yml @@ -8,7 +8,7 @@ tools: description: Custom module used to dump software versions within the nf-core pipeline template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools - + licence: ['MIT'] input: - versions: type: file diff --git a/modules/cutadapt/meta.yml b/modules/cutadapt/meta.yml index 62c2ccde..b4e6f6e7 100644 --- a/modules/cutadapt/meta.yml +++ b/modules/cutadapt/meta.yml @@ -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. documentation: https://cutadapt.readthedocs.io/en/stable/index.html doi: DOI:10.14806/ej.17.1.200 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/delly/call/meta.yml b/modules/delly/call/meta.yml index 75e5c9c2..56539188 100644 --- a/modules/delly/call/meta.yml +++ b/modules/delly/call/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/dellytools/delly/blob/master/README.md tool_dev_url: None doi: "DOI:10.1093/bioinformatics/bts378" - licence: ["BSD-3-clause"] + licence: ['BSD-3-Clause'] input: - meta: diff --git a/modules/dshbio/exportsegments/meta.yml b/modules/dshbio/exportsegments/meta.yml index b9b145df..da5455c7 100644 --- a/modules/dshbio/exportsegments/meta.yml +++ b/modules/dshbio/exportsegments/meta.yml @@ -12,6 +12,7 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio + licence: ['LGPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/dshbio/filterbed/meta.yml b/modules/dshbio/filterbed/meta.yml index 0e09b392..77054be4 100644 --- a/modules/dshbio/filterbed/meta.yml +++ b/modules/dshbio/filterbed/meta.yml @@ -10,6 +10,7 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio + licence: ['LGPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/dshbio/filtergff3/meta.yml b/modules/dshbio/filtergff3/meta.yml index 2fd916fa..aa1bce43 100644 --- a/modules/dshbio/filtergff3/meta.yml +++ b/modules/dshbio/filtergff3/meta.yml @@ -10,6 +10,7 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio + licence: ['LGPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/dshbio/splitbed/meta.yml b/modules/dshbio/splitbed/meta.yml index 16aec66b..a35ea25f 100644 --- a/modules/dshbio/splitbed/meta.yml +++ b/modules/dshbio/splitbed/meta.yml @@ -10,6 +10,7 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio + licence: ['LGPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/dshbio/splitgff3/meta.yml b/modules/dshbio/splitgff3/meta.yml index 36e37862..fdbbe16a 100644 --- a/modules/dshbio/splitgff3/meta.yml +++ b/modules/dshbio/splitgff3/meta.yml @@ -10,6 +10,7 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio + licence: ['LGPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/ensemblvep/meta.yml b/modules/ensemblvep/meta.yml index 9ec4f6a4..1b819227 100644 --- a/modules/ensemblvep/meta.yml +++ b/modules/ensemblvep/meta.yml @@ -9,6 +9,7 @@ tools: 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 documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html + licence: ['Apache-2.0'] params: - use_cache: type: boolean diff --git a/modules/expansionhunter/meta.yml b/modules/expansionhunter/meta.yml index 54bb3293..17d72bb4 100644 --- a/modules/expansionhunter/meta.yml +++ b/modules/expansionhunter/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md tool_dev_url: None doi: "10.1093/bioinformatics/btz431" - licence: ['Apache v2.0'] + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/fastp/meta.yml b/modules/fastp/meta.yml index cfef4a99..6e133871 100644 --- a/modules/fastp/meta.yml +++ b/modules/fastp/meta.yml @@ -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. documentation: https://github.com/OpenGene/fastp doi: https://doi.org/10.1093/bioinformatics/bty560 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/fastqc/meta.yml b/modules/fastqc/meta.yml index 0ae08aee..b09553a3 100644 --- a/modules/fastqc/meta.yml +++ b/modules/fastqc/meta.yml @@ -15,6 +15,7 @@ tools: overrepresented sequences. homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ['GPL-2.0-only'] input: - meta: type: map diff --git a/modules/gatk4/applybqsr/meta.yml b/modules/gatk4/applybqsr/meta.yml index be815bd8..e09e8c52 100644 --- a/modules/gatk4/applybqsr/meta.yml +++ b/modules/gatk4/applybqsr/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/baserecalibrator/meta.yml b/modules/gatk4/baserecalibrator/meta.yml index 068f8ef1..d579d9e5 100644 --- a/modules/gatk4/baserecalibrator/meta.yml +++ b/modules/gatk4/baserecalibrator/meta.yml @@ -11,6 +11,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: diff --git a/modules/gatk4/bedtointervallist/meta.yml b/modules/gatk4/bedtointervallist/meta.yml index aacca1a6..910f9552 100644 --- a/modules/gatk4/bedtointervallist/meta.yml +++ b/modules/gatk4/bedtointervallist/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/gatk4/calculatecontamination/meta.yml b/modules/gatk4/calculatecontamination/meta.yml index 0d1b9b85..8c843732 100644 --- a/modules/gatk4/calculatecontamination/meta.yml +++ b/modules/gatk4/calculatecontamination/meta.yml @@ -16,6 +16,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/createsequencedictionary/meta.yml b/modules/gatk4/createsequencedictionary/meta.yml index 90f415a2..54f479b3 100644 --- a/modules/gatk4/createsequencedictionary/meta.yml +++ b/modules/gatk4/createsequencedictionary/meta.yml @@ -12,6 +12,8 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] + input: - fasta: type: file diff --git a/modules/gatk4/fastqtosam/meta.yml b/modules/gatk4/fastqtosam/meta.yml index ab56ec53..8bd9eed5 100644 --- a/modules/gatk4/fastqtosam/meta.yml +++ b/modules/gatk4/fastqtosam/meta.yml @@ -1,5 +1,5 @@ name: gatk4_fastqtosam -description: Converts FastQ file to BAM format +description: Converts FastQ file to SAM/BAM format keywords: - bam - fastq @@ -14,7 +14,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" - licence: ['BSD-3-clause'] + licence: ['MIT'] input: - meta: diff --git a/modules/gatk4/getpileupsummaries/meta.yml b/modules/gatk4/getpileupsummaries/meta.yml index bda0ccb1..70158a8d 100644 --- a/modules/gatk4/getpileupsummaries/meta.yml +++ b/modules/gatk4/getpileupsummaries/meta.yml @@ -15,6 +15,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/haplotypecaller/meta.yml b/modules/gatk4/haplotypecaller/meta.yml index 73adc950..6a1bd7ed 100644 --- a/modules/gatk4/haplotypecaller/meta.yml +++ b/modules/gatk4/haplotypecaller/meta.yml @@ -13,6 +13,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/intervallisttools/meta.yml b/modules/gatk4/intervallisttools/meta.yml index 14f7db35..9e2d994f 100644 --- a/modules/gatk4/intervallisttools/meta.yml +++ b/modules/gatk4/intervallisttools/meta.yml @@ -14,6 +14,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/learnreadorientationmodel/meta.yml b/modules/gatk4/learnreadorientationmodel/meta.yml index c15b48cb..4eff6939 100644 --- a/modules/gatk4/learnreadorientationmodel/meta.yml +++ b/modules/gatk4/learnreadorientationmodel/meta.yml @@ -15,6 +15,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/markduplicates/meta.yml b/modules/gatk4/markduplicates/meta.yml index bd5ed5e7..59aaad4d 100644 --- a/modules/gatk4/markduplicates/meta.yml +++ b/modules/gatk4/markduplicates/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 - licence: ['BSD-3-clause'] + licence: ['MIT'] input: - meta: diff --git a/modules/gatk4/mergebamalignment/meta.yml b/modules/gatk4/mergebamalignment/meta.yml index 7823c458..c66c78db 100644 --- a/modules/gatk4/mergebamalignment/meta.yml +++ b/modules/gatk4/mergebamalignment/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/gatk4/mergevcfs/meta.yml b/modules/gatk4/mergevcfs/meta.yml index b20d7bb5..597f9ec6 100644 --- a/modules/gatk4/mergevcfs/meta.yml +++ b/modules/gatk4/mergevcfs/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/gatk4/mutect2/meta.yml b/modules/gatk4/mutect2/meta.yml index 182b6712..4c38a049 100644 --- a/modules/gatk4/mutect2/meta.yml +++ b/modules/gatk4/mutect2/meta.yml @@ -14,6 +14,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/gatk4/revertsam/meta.yml b/modules/gatk4/revertsam/meta.yml index 619450d3..b52dcb36 100644 --- a/modules/gatk4/revertsam/meta.yml +++ b/modules/gatk4/revertsam/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/gatk4/samtofastq/meta.yml b/modules/gatk4/samtofastq/meta.yml index 20033ec2..de4624b5 100644 --- a/modules/gatk4/samtofastq/meta.yml +++ b/modules/gatk4/samtofastq/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml index 9eefb545..f287ede4 100644 --- a/modules/gatk4/splitncigarreads/meta.yml +++ b/modules/gatk4/splitncigarreads/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/gatk4/variantfiltration/meta.yml b/modules/gatk4/variantfiltration/meta.yml index 4dbd71fe..6d4983a6 100644 --- a/modules/gatk4/variantfiltration/meta.yml +++ b/modules/gatk4/variantfiltration/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + licence: ['Apache-2.0'] input: - meta: type: map diff --git a/modules/genmap/index/meta.yml b/modules/genmap/index/meta.yml index adecf3c0..2ab0910d 100644 --- a/modules/genmap/index/meta.yml +++ b/modules/genmap/index/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/cpockrandt/genmap tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" - licence: ['BSD'] + licence: ['BSD-3-Clause'] input: - fasta: diff --git a/modules/genmap/mappability/meta.yml b/modules/genmap/mappability/meta.yml index c28cbd6d..d2835d92 100644 --- a/modules/genmap/mappability/meta.yml +++ b/modules/genmap/mappability/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/cpockrandt/genmap tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" - licence: ['BSD'] + licence: ['BSD-3-Clause'] input: - fasta: diff --git a/modules/glnexus/meta.yml b/modules/glnexus/meta.yml index aec25bb0..5ba17cae 100644 --- a/modules/glnexus/meta.yml +++ b/modules/glnexus/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started tool_dev_url: None doi: https://doi.org/10.1101/343970 - licence: ['Apache License 2.0'] + licence: ['Apache-2.0'] input: - meta: diff --git a/modules/graphmap2/align/meta.yml b/modules/graphmap2/align/meta.yml index a4acb648..9fb1507a 100644 --- a/modules/graphmap2/align/meta.yml +++ b/modules/graphmap2/align/meta.yml @@ -12,6 +12,7 @@ tools: A versatile pairwise aligner for genomic and spliced nucleotide sequences. 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 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/graphmap2/index/meta.yml b/modules/graphmap2/index/meta.yml index e7bd6cb6..92a0a3d7 100644 --- a/modules/graphmap2/index/meta.yml +++ b/modules/graphmap2/index/meta.yml @@ -10,6 +10,7 @@ tools: A versatile pairwise aligner for genomic and spliced nucleotide sequences. 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 + licence: ['MIT'] input: - fasta: type: file diff --git a/modules/gubbins/meta.yml b/modules/gubbins/meta.yml index 84b930a2..f73e2bb0 100644 --- a/modules/gubbins/meta.yml +++ b/modules/gubbins/meta.yml @@ -2,6 +2,7 @@ name: gubbins 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 putative point mutations outside of these regions. +licence: ['GPL-2.0-only'] keywords: - recombination - alignment diff --git a/modules/gunzip/meta.yml b/modules/gunzip/meta.yml index dbec5534..3482f0d2 100644 --- a/modules/gunzip/meta.yml +++ b/modules/gunzip/meta.yml @@ -8,6 +8,7 @@ tools: description: | 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 + licence: ['GPL-3.0-or-later'] input: - archive: type: file diff --git a/modules/hmmer/hmmalign/meta.yml b/modules/hmmer/hmmalign/meta.yml index c9a50bc2..58dc6b92 100644 --- a/modules/hmmer/hmmalign/meta.yml +++ b/modules/hmmer/hmmalign/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://hmmer.org/documentation.html tool_dev_url: None doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195" - licence: ['BSD'] + licence: ['BSD-3-Clause'] input: - meta: diff --git a/modules/homer/annotatepeaks/meta.yml b/modules/homer/annotatepeaks/meta.yml index 39fe4197..c3ab9460 100644 --- a/modules/homer/annotatepeaks/meta.yml +++ b/modules/homer/annotatepeaks/meta.yml @@ -10,6 +10,7 @@ tools: 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/ doi: 10.1016/j.molcel.2010.05.004. + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/homer/findpeaks/meta.yml b/modules/homer/findpeaks/meta.yml index d1450f3c..2aa8db26 100644 --- a/modules/homer/findpeaks/meta.yml +++ b/modules/homer/findpeaks/meta.yml @@ -9,6 +9,7 @@ tools: 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/ doi: 10.1016/j.molcel.2010.05.004. + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/homer/maketagdirectory/meta.yml b/modules/homer/maketagdirectory/meta.yml index 9a88c2e1..802320f9 100644 --- a/modules/homer/maketagdirectory/meta.yml +++ b/modules/homer/maketagdirectory/meta.yml @@ -9,6 +9,7 @@ tools: 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/ doi: 10.1016/j.molcel.2010.05.004. + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/homer/makeucscfile/meta.yml b/modules/homer/makeucscfile/meta.yml index d9123c7e..68d5fcd4 100644 --- a/modules/homer/makeucscfile/meta.yml +++ b/modules/homer/makeucscfile/meta.yml @@ -10,6 +10,7 @@ tools: 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/ doi: 10.1016/j.molcel.2010.05.004. + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/ismapper/meta.yml b/modules/ismapper/meta.yml index 4ca2450a..810c1674 100644 --- a/modules/ismapper/meta.yml +++ b/modules/ismapper/meta.yml @@ -10,7 +10,7 @@ tools: documentation: 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" - licence: ['BSD'] + licence: ['BSD-3-Clause'] input: - meta: diff --git a/modules/isoseq3/cluster/meta.yml b/modules/isoseq3/cluster/meta.yml index 280e0150..4086ab05 100644 --- a/modules/isoseq3/cluster/meta.yml +++ b/modules/isoseq3/cluster/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md doi: "" - licence: ['BSD-3-clause-Clear'] + licence: ['BSD-3-Clause-Clear'] input: - meta: diff --git a/modules/isoseq3/refine/meta.yml b/modules/isoseq3/refine/meta.yml index 81b57c7c..eefd015b 100644 --- a/modules/isoseq3/refine/meta.yml +++ b/modules/isoseq3/refine/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md doi: "" - licence: ['BSD-3-clause-Clear'] + licence: ['BSD-3-Clause-Clear'] input: - meta: diff --git a/modules/ivar/consensus/meta.yml b/modules/ivar/consensus/meta.yml index 389e5fe6..2ee5f2c6 100644 --- a/modules/ivar/consensus/meta.yml +++ b/modules/ivar/consensus/meta.yml @@ -10,6 +10,7 @@ tools: iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/ivar/trim/meta.yml b/modules/ivar/trim/meta.yml index 4798c25f..44bc742e 100644 --- a/modules/ivar/trim/meta.yml +++ b/modules/ivar/trim/meta.yml @@ -10,6 +10,7 @@ tools: iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/ivar/variants/meta.yml b/modules/ivar/variants/meta.yml index a689ffeb..fd3fce9e 100644 --- a/modules/ivar/variants/meta.yml +++ b/modules/ivar/variants/meta.yml @@ -10,6 +10,7 @@ tools: iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/kallisto/index/meta.yml b/modules/kallisto/index/meta.yml index a4fb08c3..dd952e33 100644 --- a/modules/kallisto/index/meta.yml +++ b/modules/kallisto/index/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto doi: "" - licence: ['BSD_2_clause'] + licence: ['BSD-2-Clause'] input: - fasta: diff --git a/modules/kraken2/kraken2/meta.yml b/modules/kraken2/kraken2/meta.yml index 5b849c3e..4b894705 100644 --- a/modules/kraken2/kraken2/meta.yml +++ b/modules/kraken2/kraken2/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/lima/meta.yml b/modules/lima/meta.yml index d77246c6..567632df 100644 --- a/modules/lima/meta.yml +++ b/modules/lima/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://lima.how/ tool_dev_url: https://github.com/pacificbiosciences/barcoding/ doi: "" - licence: ['BSD-3-clause-Clear'] + licence: ['BSD-3-Clause-Clear'] input: - meta: diff --git a/modules/methyldackel/extract/meta.yml b/modules/methyldackel/extract/meta.yml index 6c87f7c9..3c1dfb2a 100644 --- a/modules/methyldackel/extract/meta.yml +++ b/modules/methyldackel/extract/meta.yml @@ -17,6 +17,7 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/methyldackel/mbias/meta.yml b/modules/methyldackel/mbias/meta.yml index 4bc8f016..e66cde50 100644 --- a/modules/methyldackel/mbias/meta.yml +++ b/modules/methyldackel/mbias/meta.yml @@ -18,6 +18,7 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/minia/meta.yml b/modules/minia/meta.yml index 255bcc20..397a1d49 100644 --- a/modules/minia/meta.yml +++ b/modules/minia/meta.yml @@ -9,6 +9,7 @@ tools: a human genome on a desktop computer in a day. The output of Minia is a set of contigs. homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia + licence: ['AGPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/minimap2/align/meta.yml b/modules/minimap2/align/meta.yml index 35ed411b..9994fb05 100644 --- a/modules/minimap2/align/meta.yml +++ b/modules/minimap2/align/meta.yml @@ -13,6 +13,7 @@ tools: A versatile pairwise aligner for genomic and spliced nucleotide sequences. homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide + licence: ['MIT'] input: - meta: type: map diff --git a/modules/minimap2/index/meta.yml b/modules/minimap2/index/meta.yml index e8450add..78a39bdd 100644 --- a/modules/minimap2/index/meta.yml +++ b/modules/minimap2/index/meta.yml @@ -10,6 +10,7 @@ tools: A versatile pairwise aligner for genomic and spliced nucleotide sequences. homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide + licence: ['MIT'] input: - fasta: type: file diff --git a/modules/mosdepth/meta.yml b/modules/mosdepth/meta.yml index 5627c268..be568aa6 100644 --- a/modules/mosdepth/meta.yml +++ b/modules/mosdepth/meta.yml @@ -11,6 +11,7 @@ tools: Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/multiqc/meta.yml b/modules/multiqc/meta.yml index a54f95ac..63c75a45 100644 --- a/modules/multiqc/meta.yml +++ b/modules/multiqc/meta.yml @@ -11,6 +11,7 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ + licence: ['GPL-3.0-or-later'] input: - multiqc_files: type: file diff --git a/modules/nanolyse/meta.yml b/modules/nanolyse/meta.yml index c59607fa..326fc221 100644 --- a/modules/nanolyse/meta.yml +++ b/modules/nanolyse/meta.yml @@ -8,6 +8,7 @@ tools: DNA contaminant removal using NanoLyse homepage: https://github.com/wdecoster/nanolyse documentation: https://github.com/wdecoster/nanolyse#nanolyse + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/nanoplot/meta.yml b/modules/nanoplot/meta.yml index 0527624f..52ebb622 100644 --- a/modules/nanoplot/meta.yml +++ b/modules/nanoplot/meta.yml @@ -13,6 +13,7 @@ tools: alignment. homepage: http://nanoplot.bioinf.be documentation: https://github.com/wdecoster/NanoPlot + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/optitype/meta.yml b/modules/optitype/meta.yml index 15912125..37654463 100644 --- a/modules/optitype/meta.yml +++ b/modules/optitype/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/FRED-2/OptiType documentation: https://github.com/FRED-2/OptiType doi: "10.1093/bioinformatics/btu548" - licence: ['BSD'] + licence: ['BSD-3-Clause'] input: - meta: diff --git a/modules/pangolin/meta.yml b/modules/pangolin/meta.yml index 29878ef0..a2c0979a 100644 --- a/modules/pangolin/meta.yml +++ b/modules/pangolin/meta.yml @@ -10,6 +10,7 @@ tools: Phylogenetic Assignment of Named Global Outbreak LINeages homepage: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/pbbam/pbmerge/meta.yml b/modules/pbbam/pbmerge/meta.yml index c483ca40..7042d86b 100644 --- a/modules/pbbam/pbmerge/meta.yml +++ b/modules/pbbam/pbmerge/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://pbbam.readthedocs.io/en/latest/tools/pbmerge.html tool_dev_url: https://github.com/pacificbiosciences/pbbam/ doi: "" - licence: ['BSD-3-clause-Clear'] + licence: ['BSD-3-Clause-Clear'] input: - meta: diff --git a/modules/pbccs/meta.yml b/modules/pbccs/meta.yml index b476c829..ef0899a1 100644 --- a/modules/pbccs/meta.yml +++ b/modules/pbccs/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://ccs.how/ tool_dev_url: https://github.com/PacificBiosciences/ccs doi: "" - licence: ['BSD-3-clause-Clear'] + licence: ['BSD-3-Clause-Clear'] input: - meta: diff --git a/modules/picard/collectmultiplemetrics/meta.yml b/modules/picard/collectmultiplemetrics/meta.yml index 587983a1..613afc62 100644 --- a/modules/picard/collectmultiplemetrics/meta.yml +++ b/modules/picard/collectmultiplemetrics/meta.yml @@ -14,6 +14,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ + licence: ['MIT'] input: - meta: type: map diff --git a/modules/picard/collectwgsmetrics/meta.yml b/modules/picard/collectwgsmetrics/meta.yml index 7ae2d41d..5b4d8139 100644 --- a/modules/picard/collectwgsmetrics/meta.yml +++ b/modules/picard/collectwgsmetrics/meta.yml @@ -13,6 +13,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ + licence: ['MIT'] input: - meta: type: map diff --git a/modules/picard/markduplicates/meta.yml b/modules/picard/markduplicates/meta.yml index 13f2d350..c9a08b36 100644 --- a/modules/picard/markduplicates/meta.yml +++ b/modules/picard/markduplicates/meta.yml @@ -14,6 +14,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ + licence: ['MIT'] input: - meta: type: map diff --git a/modules/picard/mergesamfiles/meta.yml b/modules/picard/mergesamfiles/meta.yml index f732daf4..3d010c3c 100644 --- a/modules/picard/mergesamfiles/meta.yml +++ b/modules/picard/mergesamfiles/meta.yml @@ -12,6 +12,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ + licence: ['MIT'] input: - meta: type: map diff --git a/modules/picard/sortsam/meta.yml b/modules/picard/sortsam/meta.yml index 3e0fb450..aa90e456 100644 --- a/modules/picard/sortsam/meta.yml +++ b/modules/picard/sortsam/meta.yml @@ -11,6 +11,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ + licence: ['MIT'] input: - meta: diff --git a/modules/qcat/meta.yml b/modules/qcat/meta.yml index 938bc337..e0ab6a0f 100644 --- a/modules/qcat/meta.yml +++ b/modules/qcat/meta.yml @@ -9,6 +9,7 @@ tools: A demultiplexer for Nanopore samples homepage: https://github.com/nanoporetech/qcat documentation: https://github.com/nanoporetech/qcat#qcat + licence: ['MPL-2.0'] input: - meta: type: map diff --git a/modules/qualimap/bamqc/meta.yml b/modules/qualimap/bamqc/meta.yml index cc0471fc..6888d30e 100644 --- a/modules/qualimap/bamqc/meta.yml +++ b/modules/qualimap/bamqc/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://qualimap.bioinfo.cipf.es/ documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 + licence: ['GPL-2.0-only'] input: - meta: type: map diff --git a/modules/quast/meta.yml b/modules/quast/meta.yml index 8b692e9e..05faa8b8 100644 --- a/modules/quast/meta.yml +++ b/modules/quast/meta.yml @@ -9,7 +9,8 @@ tools: description: | QUAST calculates quality metrics for genome assemblies homepage: http://bioinf.spbau.ru/quast - doi: + doi: https://doi.org/10.1093/bioinformatics/btt086 + licence: ['GPL-2.0-only'] input: - consensus: type: file diff --git a/modules/rsem/calculateexpression/meta.yml b/modules/rsem/calculateexpression/meta.yml index e2fb8f6d..fdfaa0c4 100644 --- a/modules/rsem/calculateexpression/meta.yml +++ b/modules/rsem/calculateexpression/meta.yml @@ -11,6 +11,7 @@ tools: homepage: https://github.com/deweylab/RSEM documentation: https://github.com/deweylab/RSEM doi: https://doi.org/10.1186/1471-2105-12-323 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rsem/preparereference/meta.yml b/modules/rsem/preparereference/meta.yml index 94f7cc05..062f0256 100644 --- a/modules/rsem/preparereference/meta.yml +++ b/modules/rsem/preparereference/meta.yml @@ -10,6 +10,7 @@ tools: homepage: https://github.com/deweylab/RSEM documentation: https://github.com/deweylab/RSEM doi: https://doi.org/10.1186/1471-2105-12-323 + licence: ['GPL-3.0-or-later'] input: - fasta: type: file diff --git a/modules/rseqc/bamstat/meta.yml b/modules/rseqc/bamstat/meta.yml index 64a0b9e4..561ba195 100644 --- a/modules/rseqc/bamstat/meta.yml +++ b/modules/rseqc/bamstat/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rseqc/inferexperiment/meta.yml b/modules/rseqc/inferexperiment/meta.yml index 63710d7b..88eabc8a 100644 --- a/modules/rseqc/inferexperiment/meta.yml +++ b/modules/rseqc/inferexperiment/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rseqc/innerdistance/meta.yml b/modules/rseqc/innerdistance/meta.yml index 7eea1350..27bcf242 100644 --- a/modules/rseqc/innerdistance/meta.yml +++ b/modules/rseqc/innerdistance/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rseqc/junctionannotation/meta.yml b/modules/rseqc/junctionannotation/meta.yml index 5562b0b7..56364232 100644 --- a/modules/rseqc/junctionannotation/meta.yml +++ b/modules/rseqc/junctionannotation/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rseqc/junctionsaturation/meta.yml b/modules/rseqc/junctionsaturation/meta.yml index ffa359ab..05d814ad 100644 --- a/modules/rseqc/junctionsaturation/meta.yml +++ b/modules/rseqc/junctionsaturation/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rseqc/readdistribution/meta.yml b/modules/rseqc/readdistribution/meta.yml index d12ad600..4c736878 100644 --- a/modules/rseqc/readdistribution/meta.yml +++ b/modules/rseqc/readdistribution/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/rseqc/readduplication/meta.yml b/modules/rseqc/readduplication/meta.yml index 98d25ea4..3623de80 100644 --- a/modules/rseqc/readduplication/meta.yml +++ b/modules/rseqc/readduplication/meta.yml @@ -11,6 +11,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/salmon/index/meta.yml b/modules/salmon/index/meta.yml index c956f15c..3b0cd853 100644 --- a/modules/salmon/index/meta.yml +++ b/modules/salmon/index/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 + licence: ['GPL-3.0-or-later'] input: - genome_fasta: type: file diff --git a/modules/salmon/quant/meta.yml b/modules/salmon/quant/meta.yml index 47e81229..223ca82b 100644 --- a/modules/salmon/quant/meta.yml +++ b/modules/salmon/quant/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/samtools/ampliconclip/meta.yml b/modules/samtools/ampliconclip/meta.yml index 7aa8c6bd..8959b98d 100644 --- a/modules/samtools/ampliconclip/meta.yml +++ b/modules/samtools/ampliconclip/meta.yml @@ -15,6 +15,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: diff --git a/modules/samtools/faidx/meta.yml b/modules/samtools/faidx/meta.yml index 6e63b671..16c0b334 100644 --- a/modules/samtools/faidx/meta.yml +++ b/modules/samtools/faidx/meta.yml @@ -12,6 +12,7 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - fasta: type: file diff --git a/modules/samtools/fastq/meta.yml b/modules/samtools/fastq/meta.yml index 9a45886b..91fd476d 100644 --- a/modules/samtools/fastq/meta.yml +++ b/modules/samtools/fastq/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/flagstat/meta.yml b/modules/samtools/flagstat/meta.yml index d408cb76..9bd9ff89 100644 --- a/modules/samtools/flagstat/meta.yml +++ b/modules/samtools/flagstat/meta.yml @@ -16,6 +16,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/idxstats/meta.yml b/modules/samtools/idxstats/meta.yml index f4cb613f..ec542f34 100644 --- a/modules/samtools/idxstats/meta.yml +++ b/modules/samtools/idxstats/meta.yml @@ -17,6 +17,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/index/meta.yml b/modules/samtools/index/meta.yml index 5f4dd3fb..988e8f53 100644 --- a/modules/samtools/index/meta.yml +++ b/modules/samtools/index/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/merge/meta.yml b/modules/samtools/merge/meta.yml index 1903cdaa..78b75b36 100644 --- a/modules/samtools/merge/meta.yml +++ b/modules/samtools/merge/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/mpileup/meta.yml b/modules/samtools/mpileup/meta.yml index ce55643a..fac7a5bc 100644 --- a/modules/samtools/mpileup/meta.yml +++ b/modules/samtools/mpileup/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/sort/meta.yml b/modules/samtools/sort/meta.yml index cd47c86d..3402a068 100644 --- a/modules/samtools/sort/meta.yml +++ b/modules/samtools/sort/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/stats/meta.yml b/modules/samtools/stats/meta.yml index d75d73e2..ae41498a 100644 --- a/modules/samtools/stats/meta.yml +++ b/modules/samtools/stats/meta.yml @@ -15,6 +15,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/samtools/view/meta.yml b/modules/samtools/view/meta.yml index 2e66e7cd..29d1ecc1 100644 --- a/modules/samtools/view/meta.yml +++ b/modules/samtools/view/meta.yml @@ -14,6 +14,7 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/seacr/callpeak/meta.yml b/modules/seacr/callpeak/meta.yml index 22db567d..53b3415f 100644 --- a/modules/seacr/callpeak/meta.yml +++ b/modules/seacr/callpeak/meta.yml @@ -17,6 +17,7 @@ tools: (i.e. regions with no read coverage). homepage: https://github.com/FredHutch/SEACR documentation: https://github.com/FredHutch/SEACR + licence: ['GPL-2.0-only'] input: - meta: type: map diff --git a/modules/seqkit/split2/meta.yml b/modules/seqkit/split2/meta.yml index beb676ea..90eec7f9 100644 --- a/modules/seqkit/split2/meta.yml +++ b/modules/seqkit/split2/meta.yml @@ -10,6 +10,7 @@ tools: homepage: https://github.com/shenwei356/seqkit documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/sequenzautils/bam2seqz/meta.yml b/modules/sequenzautils/bam2seqz/meta.yml index 278f9750..e05d2fa9 100755 --- a/modules/sequenzautils/bam2seqz/meta.yml +++ b/modules/sequenzautils/bam2seqz/meta.yml @@ -8,7 +8,7 @@ tools: homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 - + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/sequenzautils/gcwiggle/meta.yml b/modules/sequenzautils/gcwiggle/meta.yml index 4ecba04a..616e073b 100644 --- a/modules/sequenzautils/gcwiggle/meta.yml +++ b/modules/sequenzautils/gcwiggle/meta.yml @@ -8,6 +8,7 @@ tools: homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/seqwish/induce/meta.yml b/modules/seqwish/induce/meta.yml index c5f9d4c7..281e3994 100644 --- a/modules/seqwish/induce/meta.yml +++ b/modules/seqwish/induce/meta.yml @@ -13,6 +13,7 @@ tools: sequences to a variation graph encoding the sequences and their alignments. homepage: https://github.com/ekg/seqwish documentation: https://github.com/ekg/seqwish + licence: ['MIT'] input: - meta: type: map diff --git a/modules/snpeff/meta.yml b/modules/snpeff/meta.yml index ba049c0e..8ba18683 100644 --- a/modules/snpeff/meta.yml +++ b/modules/snpeff/meta.yml @@ -9,6 +9,7 @@ tools: It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ + licence: ['MIT'] params: - use_cache: type: boolean diff --git a/modules/snpsites/meta.yml b/modules/snpsites/meta.yml index 5361aa3e..381d25cc 100644 --- a/modules/snpsites/meta.yml +++ b/modules/snpsites/meta.yml @@ -9,6 +9,7 @@ tools: description: Rapidly extracts SNPs from a multi-FASTA alignment. homepage: https://www.sanger.ac.uk/tool/snp-sites/ documentation: https://github.com/sanger-pathogens/snp-sites + licence: ['GPL-3.0-or-later'] input: - alignment: type: file diff --git a/modules/sratools/fasterqdump/meta.yml b/modules/sratools/fasterqdump/meta.yml index ac61e71f..1478bed8 100644 --- a/modules/sratools/fasterqdump/meta.yml +++ b/modules/sratools/fasterqdump/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/ncbi/sra-tools documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools - licence: ['Public Domain'] + licence: ['US-Government-Work'] input: - meta: diff --git a/modules/sratools/prefetch/meta.yml b/modules/sratools/prefetch/meta.yml index ab0a5ce5..22213b29 100644 --- a/modules/sratools/prefetch/meta.yml +++ b/modules/sratools/prefetch/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/ncbi/sra-tools documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools - licence: ['Public Domain'] + licence: ['US-Government-Work'] input: - meta: diff --git a/modules/star/align/meta.yml b/modules/star/align/meta.yml index 00f955dd..2d78b81a 100644 --- a/modules/star/align/meta.yml +++ b/modules/star/align/meta.yml @@ -13,6 +13,7 @@ tools: homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/star/genomegenerate/meta.yml b/modules/star/genomegenerate/meta.yml index 09728b58..04ade195 100644 --- a/modules/star/genomegenerate/meta.yml +++ b/modules/star/genomegenerate/meta.yml @@ -13,6 +13,7 @@ tools: homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 + licence: ['MIT'] input: - fasta: type: file diff --git a/modules/stringtie/merge/meta.yml b/modules/stringtie/merge/meta.yml index 81eca6dc..02899766 100644 --- a/modules/stringtie/merge/meta.yml +++ b/modules/stringtie/merge/meta.yml @@ -10,6 +10,7 @@ tools: Transcript assembly and quantification for RNA-Seq homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual + licence: ['MIT'] input: - stringtie_gtf: type: file diff --git a/modules/stringtie/stringtie/meta.yml b/modules/stringtie/stringtie/meta.yml index 0074b90f..7e854caa 100644 --- a/modules/stringtie/stringtie/meta.yml +++ b/modules/stringtie/stringtie/meta.yml @@ -12,6 +12,7 @@ tools: Transcript assembly and quantification for RNA-Seq homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual + licence: ['MIT'] input: - meta: type: map diff --git a/modules/tabix/bgzip/meta.yml b/modules/tabix/bgzip/meta.yml index 0b0787bf..f8318c7c 100644 --- a/modules/tabix/bgzip/meta.yml +++ b/modules/tabix/bgzip/meta.yml @@ -11,6 +11,7 @@ tools: homepage: https://www.htslib.org/doc/tabix.html documentation: http://www.htslib.org/doc/bgzip.html doi: 10.1093/bioinformatics/btp352 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/tabix/bgziptabix/meta.yml b/modules/tabix/bgziptabix/meta.yml index 5b4cc4e8..f2aed84d 100644 --- a/modules/tabix/bgziptabix/meta.yml +++ b/modules/tabix/bgziptabix/meta.yml @@ -12,6 +12,7 @@ tools: homepage: https://www.htslib.org/doc/tabix.html documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/tabix/tabix/meta.yml b/modules/tabix/tabix/meta.yml index 15edf8c3..2e37c4ff 100644 --- a/modules/tabix/tabix/meta.yml +++ b/modules/tabix/tabix/meta.yml @@ -10,6 +10,7 @@ tools: homepage: https://www.htslib.org/doc/tabix.html documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 + licence: ['MIT'] input: - meta: type: map diff --git a/modules/tiddit/sv/meta.yml b/modules/tiddit/sv/meta.yml index 4060a450..f788ffa6 100644 --- a/modules/tiddit/sv/meta.yml +++ b/modules/tiddit/sv/meta.yml @@ -10,6 +10,7 @@ tools: homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: 10.12688/f1000research.11168.1 + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/trimgalore/meta.yml b/modules/trimgalore/meta.yml index 7c46bea9..c7e1df1d 100644 --- a/modules/trimgalore/meta.yml +++ b/modules/trimgalore/meta.yml @@ -13,6 +13,7 @@ tools: MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md + licence: ['GPL-3.0-or-later'] input: - meta: type: map diff --git a/modules/untar/meta.yml b/modules/untar/meta.yml index 2b586c92..51f94995 100644 --- a/modules/untar/meta.yml +++ b/modules/untar/meta.yml @@ -8,6 +8,7 @@ tools: description: | Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ + licence: ['GPL-3.0-or-later'] input: - archive: type: file diff --git a/modules/unzip/meta.yml b/modules/unzip/meta.yml index 57c07f00..7bca1ec2 100644 --- a/modules/unzip/meta.yml +++ b/modules/unzip/meta.yml @@ -9,7 +9,7 @@ tools: homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" - licence: "GNU LPGL" + licence: ['LGPL-2.1-or-later'] input: - archive: diff --git a/modules/variantbam/meta.yml b/modules/variantbam/meta.yml index 9394e418..ddcd0656 100644 --- a/modules/variantbam/meta.yml +++ b/modules/variantbam/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://github.com/walaj/VariantBam#table-of-contents tool_dev_url: https://github.com/walaj/VariantBam doi: 10.1093/bioinformatics/btw111 - licence: ['Apache2'] + licence: ['Apache-2.0'] input: - meta: