process COOLER_CLOAD { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null) container "${ 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: tuple val(meta), path(pairs), path(index) val cool_bin path chromsizes output: tuple val(meta), val(cool_bin), path("*.cool"), emit: cool path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : '' """ cooler cload \\ $args \\ $nproc \\ ${chromsizes}:${cool_bin} \\ $pairs \\ ${prefix}.${cool_bin}.cool cat <<-END_VERSIONS > versions.yml "${task.process}": cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //') END_VERSIONS """ }