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
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:
    - 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: file
        description: BWA genome index files
        pattern: "*.{amb,ann,bwt,pac,sa}"
    - fasta:
        type: file
        description: Input genome fasta file
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}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@phue"