task split_gvcf_files { File gvcf String chromo String docker String cluster_config String disk_size command <<< cat ${gvcf} | grep '#CHROM' | sed s'/\t/\n/g' > name sed -i '1,9d' name for i in {10..133}; do cat ${gvcf}| cut -f1-9,$i > $i.splited.vcf; done ls *splited.vcf | paste - name > rename cat rename | while read a b; do mv $a $b.${chromo}.vcf; done >>> runtime { docker:docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { Array[File] splited_vcf = glob("*.${chromo}.vcf") } }