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
      licence: ["GPL-3.0-or-later"]
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"
