name: bismark_genomepreparation
description: |
    Converts a specified reference genome into two different bisulfite
    converted versions and indexes them for alignments.
keywords:
    - bismark
    - 3-letter genome
    - index
    - methylation
    - 5mC
    - methylseq
    - bisulphite
    - fasta
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:
    - fasta:
        type: file
        description: Input genome fasta file
output:
    - index:
        type: dir
        description: Bismark genome index directory
        pattern: "BismarkIndex"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@phue"