task bcf2vcf { File bcf File bcf_index String sample_name String docker String disk_size String cluster_config command <<< set -o pipefail set -e /opt/hall-lab/bcftools-1.9/bin/bcftools view ${bcf} > ${sample_name}.vcf >>> runtime { docker:docker cluster:cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File vcf = "${sample_name}.vcf" } }