name: bwameth_align
description: Performs alignment of BS-Seq reads using bwameth
keywords:
    - bwameth
    - alignment
    - 3-letter genome
    - map
    - methylation
    - 5mC
    - methylseq
    - bisulphite
    - fastq
    - bam
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
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: Directory containing bwameth genome index
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}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@phue"