main.nf

process GTF2BED {
    tag "$gtf"
    label 'process_low'

    conda "conda-forge::perl=5.26.2"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/perl:5.26.2':
        'biocontainers/perl:5.26.2' }"

    input:
    path gtf

    output:
    path '*.bed'       , emit: bed
    path "versions.yml", emit: versions

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

    script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
    """
    gtf2bed \\
        $gtf \\
        > ${gtf.baseName}.bed

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