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

params.options = [:]
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:'index', meta:[:], publish_by_meta:[]) }

    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0"
    } else {
        container "quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0"
    }

    input:
    path fasta

    output:
    path "bwamem2"      , emit: index
    path "versions.yml" , emit: version

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