name: bowtie_align
description: Align reads to a reference genome using bowtie
keywords:
    - align
    - fasta
    - genome
    - reference
tools:
    - bowtie:
        description: |
            bowtie is a software package for mapping DNA sequences against
            a large reference genome, such as the human genome.
        homepage: http://bowtie-bio.sourceforge.net/index.shtml
        documentation: http://bowtie-bio.sourceforge.net/manual.shtml
        arxiv: arXiv:1303.3997
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
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: Bowtie genome index files
        pattern: "*.ebwt"
output:
    - index:
        type: file
        description: Bowtie genome index files
        pattern: "*.ebwt"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@kevinmenden"