task votes { File merged_vcf File vcf_dup String sample String prefix String docker String cluster_config String disk_size command <<< python /opt/high_confidence_call_vote.py -vcf ${merged_vcf} -dup ${vcf_dup} -sample ${sample} -prefix ${prefix} cat ${prefix}_annotated.vcf | cut -f1-9,45 | grep -v 'filtered' | grep -v 'confirm for parents' | grep -v 'pcr-free-speicifc' | grep -v 'pcr-speicifc' | grep -v 'dupVar' > ${prefix}_bechmarking_calls.vcf >>> runtime { docker:docker cluster: cluster_config systemDisk: "cloud_ssd 40" dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" } output { File annotated_vcf = "${prefix}_annotated.vcf" File benchmark_call = "${prefix}_bechmarking_calls.vcf" } }