task samtools { File bam_file String bam_id=basename(bam_file) String sample_id String docker String cluster String disk_size command <<< set -o pipefail set -e mkdir -p ${sample_id}/data cp ${bam_file} ${sample_id}/data/${bam_id} samtools index ${sample_id}/data/${bam_id} >>> runtime { docker: docker cluster: cluster systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File bam = "${bam_id}" File bam_index = "${bam_id}.bai" } }