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- task merge_family {
- File LCL5_vcf_gz
- File LCL5_vcf_idx
- File LCL6_vcf_gz
- File LCL6_vcf_idx
- File LCL7_vcf_gz
- File LCL7_vcf_idx
- File LCL8_vcf_gz
- File LCL8_vcf_idx
- File rename
- String project
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL5_vcf_gz} -o LCL5.vcf.gz
-
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL6_vcf_gz} -o LCL6.vcf.gz
-
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL7_vcf_gz} -o LCL7.vcf.gz
-
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL8_vcf_gz} -o LCL8.vcf.gz
-
- /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.vcf.gz LCL5_vcf_gz LCL6_vcf_gz LCL7_vcf_gz LCL8_vcf_gz
-
- gunzip ${project}.family.vcf.gz
-
- >>>
-
- runtime {
- docker:docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
- output {
- File merged_vcf = "${project}.family.vcf"
- }
- }
-
-
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