name: bismark_genome_preparation
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
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - singularity_pull_docker_container:
        type: boolean
        description: |
            Instead of directly downloading Singularity images for use with Singularity,
            force the workflow to pull and convert Docker containers instead.
input:
    - fasta:
        type: file
        description: Input genome fasta file
output:
    - index:
        type: dir
        description: Bismark genome index directory
        pattern: "BismarkIndex"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@phue"