process BEDTOOLS_BAMTOBED { tag "$meta.id" label 'process_single' conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) container "${ 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 when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${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 """ }