process BEDTOOLS_GENOMECOV { 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(intervals), val(scale) path sizes val extension output: tuple val(meta), path("*.${extension}"), emit: genomecov path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def args_list = args.tokenize() args += (scale > 0 && scale != 1) ? " -scale $scale" : "" if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } def prefix = task.ext.prefix ?: "${meta.id}" if (intervals.name =~ /\.bam/) { """ bedtools \\ genomecov \\ -ibam $intervals \\ $args \\ > ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ } else { """ bedtools \\ genomecov \\ -i $intervals \\ -g $sizes \\ $args \\ > ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ } }