task extract_info { File vcf String vcf_name = basename(vcf,".vcf") String docker String cluster_config String disk_size command <<< python /opt/extract_vcf_information.py -i ${vcf} -o ${vcf_name}.txt cat ${vcf_name}.txt | cut -f23,25,27,22,12,21,3,18,4,8,11,15 > ${vcf_name}.essential.txt >>> runtime { docker:docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File vcf_info = "${vcf_name}.txt" File vcf_needed_info = "${vcf_name}.essential.txt" } }