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quartet_qc_vcf_input
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quartet_qc_vcf_input/tasks/merge_family.wdl

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  1.  task merge_family {

  2. 	File LCL5_vcf_gz

  3. 	File LCL5_vcf_idx

  4. 	File LCL6_vcf_gz

  5. 	File LCL6_vcf_idx

  6. 	File LCL7_vcf_gz

  7. 	File LCL7_vcf_idx

  8. 	File LCL8_vcf_gz

  9. 	File LCL8_vcf_idx

  10. 	File rename

  11. 	String project

  12. 	String docker

  13. 	String cluster_config

  14. 	String disk_size

  15. 	

  16. 	command <<<

  17. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL5_vcf_gz} -o LCL5.vcf.gz

  18. 

  19. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL6_vcf_gz} -o LCL6.vcf.gz

  20. 

  21. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL7_vcf_gz} -o LCL7.vcf.gz

  22. 

  23. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfannotate --relabel=${rename} -i ${LCL8_vcf_gz} -o LCL8.vcf.gz

  24. 

  25. 		/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

  26. 

  27. 		gunzip ${project}.family.vcf.gz 

  28. 

  29. 	>>>

  30. 

  31. 	runtime {

  32. 		docker:docker

  33. 		cluster: cluster_config

  34. 		systemDisk: "cloud_ssd 40"

  35. 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

  36. 	}

  37. 	output {

  38. 		File merged_vcf = "${project}.family.vcf"

  39. 	}

  40. }

  41.