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>

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

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

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

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

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:

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

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

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

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

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

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:

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

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

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

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

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

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

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

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

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

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

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

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

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:

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

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

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

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

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

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

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

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

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

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

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

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

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:

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

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

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:

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:

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

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

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

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

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

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

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

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:

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:

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

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

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:

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

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

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

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

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

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

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:

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

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

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:

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:

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

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:

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

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:

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:

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:

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:

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:

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:

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

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

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:

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

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

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

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

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:

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:

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:

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

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

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

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

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:

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

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

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

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

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:

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:

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:

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

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

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

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:

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