task collapseBed { File bed String sample String docker String disk_size String cluster_config command <<< cat ${bed} | cut -f1-3 > ${sample}.temp.bed /opt/ccdg/bedtools-2.27.1/bin/bedtools merge -i ${sample}.temp.bed > ${sample}.27.homo_ref.consensus.bed >>> runtime { docker:docker cluster:cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File merged_homo_ref_bed = "${sample}.27.homo_ref.consensus.bed" } }