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3aacd46da2
* 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>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: bismark_align
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description: Performs alignment of BS-Seq reads using bismark
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keywords:
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- bismark
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- 3-letter genome
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- map
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- bam
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tools:
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- bismark:
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description: |
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Bismark is a tool to map bisulfite treated sequencing reads
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and perform methylation calling in a quick and easy-to-use fashion.
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homepage: https://github.com/FelixKrueger/Bismark
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documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
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doi: 10.1093/bioinformatics/btr167
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licence: ['GPL-3.0-or-later']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: dir
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description: Bismark genome index directory
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pattern: "BismarkIndex"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- unmapped:
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type: file
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description: Output FastQ file(s) containing unmapped reads
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pattern: "*.{fq.gz}"
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- report:
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type: file
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description: Bismark alignment reports
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pattern: "*{report.txt}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@phue"
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