nf-core_modules/modules/gatk4/samtofastq/main.nf

process GATK4_SAMTOFASTQ {
    tag "$meta.id"
    label 'process_medium'

    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"

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

    output:
    tuple val(meta), path('*.fastq.gz'), emit: fastq
    path  "versions.yml"               , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def output = meta.single_end ? "--FASTQ ${prefix}.fastq.gz" : "--FASTQ ${prefix}_1.fastq.gz --SECOND_END_FASTQ ${prefix}_2.fastq.gz"

    def avail_mem = 3
    if (!task.memory) {
        log.info '[GATK SamToFastq] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    """
    gatk --java-options "-Xmx${avail_mem}g" SamToFastq \\
        --INPUT $bam \\
        $output \\
        --TMP_DIR . \\
        $args

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
    END_VERSIONS
    """

    stub:
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    touch ${prefix}.fastq.gz
    touch ${prefix}_1.fastq.gz
    touch ${prefix}_2.fastq.gz

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
    END_VERSIONS
    """
}