nf-core_modules/modules/bedtools/bamtobed/main.nf

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

    conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
        'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"

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

    output:
    tuple val(meta), path("*.bed"), emit: bed
    path  "versions.yml"          , emit: versions

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
    """
    bedtools \\
        bamtobed \\
        $args \\
        -i $bam \\
        | bedtools sort > ${prefix}.bed

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
    END_VERSIONS
    """
}