|
- task JI {
- File vcf_a
- File vcf_b
- File dir_name
- File sdf
- String name_a = basename(vcf_a,".vcf")
- String name_b = basename(vcf_b,".vcf")
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- set -o pipefail
- set -e
-
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${vcf_a} -c > ${name_a}.rtg.vcf.gz
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${name_a}.rtg.vcf.gz
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${vcf_a} -c > ${name_b}.rtg.vcf.gz
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${name_b}.rtg.vcf.gz
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b ${name_a}.rtg.vcf.gz -c ${name_b}.rtg.vcf.gz -o ${dir_name} -t ${sdf}
-
- >>>
-
- runtime {
- docker:docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
- output {
- File JI_summary = "${dir_name}/summary.txt"
- }
- }
|
