process COOLER_DIGEST { tag "$fasta" label 'process_medium' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' : 'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }" input: path fasta path chromsizes val enzyme output: path "*.bed" , emit: bed path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' """ cooler digest \\ $args \\ -o "${fasta.baseName}_${enzyme.replaceAll(/[^0-9a-zA-Z]+/, '_')}.bed" \\ $chromsizes \\ $fasta \\ $enzyme cat <<-END_VERSIONS > versions.yml "${task.process}": cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //') END_VERSIONS """ }