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"