task JI { String vcf_a String vcf_b String dir_name File sdf String docker String cluster_config String disk_size command <<< set -o pipefail set -e rtg bgzip ${vcf_a} -c > vcf_a.vcf.gz rtg index vcf_a.vcf.gz rtg bgzip ${vcf_b} -c > vcf_b.vcf.gz rtg index vcf_b.vcf.gz rtg vcfeval -b vcf_a.vcf.gz -c vcf_b.vcf.gz -o ${dir_name} -t ${sdf} mv ${dir_name}/summary.txt ${dir_name}.txt >>> runtime { docker:docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File JI_summary = "${dir_name}.txt" } }