// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'

params.options = [:]
def options    = initOptions(params.options)

process BWAMEM2_INDEX {
    tag "$fasta"
    label 'process_high'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

    conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.1--he513fc3_0"
    } else {
        container "quay.io/biocontainers/bwa-mem2:2.1--he513fc3_0"
    }

    input:
    path fasta

    output:
    path "bwamem2"      , emit: index
    path "*.version.txt", emit: version

    script:
    def software = getSoftwareName(task.process)
    """
    mkdir bwamem2
    bwa-mem2 index $options.args $fasta -p bwamem2/${fasta}
    echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
    """
}