nf-core_modules/modules/bismark/align/meta.yml

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