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

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

process GATK4_SAMTOFASTQ {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
    } else {
        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
    }

    input:
    tuple val(meta), path(bam)

    output:
    tuple val(meta), path('*.fastq.gz')     , emit: fastq
    path  '*.version.txt'                   , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
    def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
    """
    gatk SamToFastq \\
        I=$bam \\
        $output \\
        $options.args

    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
    """
}