task breakChromo { File dedup_bam File dedup_bam_index String chromosome String sample_name String docker String cluster_config String disk_size command <<< set -o pipefail set -e nt=$(nproc) /opt/conda/bin/samtools view -@ $nt -hb ${dedup_bam} ${chromosome} > ${sample_name}_${chromosome}.bam /opt/conda/bin/samtools index ${sample_name}_${chromosome}.bam >>> runtime { docker: docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File chr_bam = "${sample_name}_${chromosome}.bam" File chr_bam_bai = "${sample_name}_${chromosome}.bam.bai" } }