name: bwameth_index
description: Performs indexing of c2t converted reference genome
keywords:
    - bwameth
    - 3-letter genome
    - index
    - methylseq
    - bisulphite
    - fasta
tools:
    - bwameth:
        description: |
            Fast and accurate alignment of BS-Seq reads
            using bwa-mem and a 3-letter genome.
        homepage: https://github.com/brentp/bwa-meth
        documentation: https://github.com/brentp/bwa-meth
        arxiv: arXiv:1401.1129
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: file
        description: c2t converted genome BWA index files
        pattern: "*.{bwameth.c2t.amb,bwameth.c2t.ann,bwameth.c2t.bwt,bwameth.c2t.pac,bwameth.c2t.sa}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@phue"