def MODULE = "bedtools_genomecov" params.publish_dir = MODULE params.publish_results = "default" process BEDTOOLS_GENOMECOV { tag {bam} publishDir "${params.out_dir}/${params.publish_dir}", mode: params.publish_dir_mode, saveAs: { filename -> if (params.publish_results == "none") null else filename } container "docker.pkg.github.com/nf-core/$MODULE" conda "${moduleDir}/environment.yml" input: path (bam) path (chrom_sizes) val (bedtools_genomecov_args) output: path "${bam}.bed", emit: coverage path "*.version.txt", emit: version script: """ bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${bedtools_genomecov_args} > ${bam}.bed bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt """ }