task depth { File bam File bam_index String chromosome String sample_name String docker String disk_size String cluster_config command <<< set -o pipefail set -e /opt/conda/bin/samtools depth ${bam} -r ${chromosome} > ${sample_name}.depth.txt >>> runtime { docker:docker cluster:cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File depth = "${sample_name}.depth.txt" } }