taxprofiler/modules/nf-core/gunzip/main.nf

process GUNZIP {
    tag "$archive"
    label 'process_single'

    conda "conda-forge::sed=4.7"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
        'docker.io/ubuntu:20.04' }"

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

    output:
    tuple val(meta), path("$gunzip"), emit: gunzip
    path "versions.yml"             , emit: versions

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

    script:
    def args = task.ext.args ?: ''
    gunzip = archive.toString() - '.gz'
    """
    gunzip \\
        -f \\
        $args \\
        $archive

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

    stub:
    gunzip = archive.toString() - '.gz'
    """
    touch $gunzip
    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
    END_VERSIONS
    """
}