task getBam { File bam File bam_idx String sample String region String docker String cluster_config String disk_size command <<< cat ${region} | whlie read a; do /opt/conda/bin/samtools view -b ${bam} "$a" > $a.${sample}.bam /opt/conda/bin/samtools index $a.${sample}.bam; done >>> runtime { docker:docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { Array[File] region_bam = glob("*.bam") Array[File] region_bai = glob("*.bam.bai") } }