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