task samtools { File bam_file String bam_id=basename(bam_file) String docker String cluster String disk_size command <<< samtools index --help samtools index -b ${bam_file} > ./${bam_id}.bai cp ${bam_file} ./ >>> runtime { docker: docker cluster: cluster systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File bam="${bam_id}" File bam_index="${bam_id}.bai" } }