task gvcf_homo_ref { File gvcf String sample String docker String disk_size String cluster_config command <<< awk '{ if ($5 == "") { print } }' ${gvcf} | sed s'/:/\t/'g | awk '{ if($16 >= 30) { print }}' | cut -f1,2,8 | sed s'/END=//g' > ${sample}.filtered.bed bedtools merged -i ${sample}.filtered.bed > ${sample}.homo_ref.bed >>> runtime { docker:docker cluster:cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File filtered_bed = "${sample}.filtered.bed" File homo_ref_bed = "${sample}.homo_ref.bed" } }