name: bwa_index
description: Create BWA-mem2 index for reference genome
keywords:
    - index
    - fasta
    - genome
    - reference
tools:
    - bwa:
        description: |
            BWA-mem2 is a software package for mapping DNA sequences against
            a large reference genome, such as the human genome.
        homepage: https://github.com/bwa-mem2/bwa-mem2
        documentation: https://github.com/bwa-mem2/bwa-mem2#usage
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: BWA genome index files
        pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@drpatelh"
    - "@maxulysse"