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quartet_vcf_qc
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quartet_vcf_qc/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 bed

  11. 	String project

  12. 	String docker

  13. 	String cluster_config

  14. 	String disk_size

  15. 	

  16. 	command <<<

  17. 

  18. 		/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}

  19. 

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

  21. 

  22. 

  23. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL5_vcf_gz} --include-bed=${bed} -o LCL5.inside.vcf.gz

  24. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL6_vcf_gz} --include-bed=${bed} -o LCL6.inside.vcf.gz

  25. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL7_vcf_gz} --include-bed=${bed} -o LCL7.inside.vcf.gz

  26. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL8_vcf_gz} --include-bed=${bed} -o LCL8.inside.vcf.gz

  27. 

  28. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.inside.vcf.gz LCL5.inside.vcf.gz LCL6.inside.vcf.gz LCL7.inside.vcf.gz LCL8.inside.vcf.gz

  29. 

  30. 		gunzip ${project}.family.inside.vcf.gz

  31. 

  32. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL5_vcf_gz} --exclude-bed=${bed} -o LCL5.outside.vcf.gz

  33. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL6_vcf_gz} --exclude-bed=${bed} -o LCL6.outside.vcf.gz

  34. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL7_vcf_gz} --exclude-bed=${bed} -o LCL7.outside.vcf.gz

  35. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL8_vcf_gz} --exclude-bed=${bed} -o LCL8.outside.vcf.gz

  36. 

  37. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.outside.vcf.gz LCL5.outside.vcf.gz LCL6.outside.vcf.gz LCL7.outside.vcf.gz LCL8.outside.vcf.gz

  38. 

  39. 		gunzip ${project}.family.outside.vcf.gz

  40. 

  41. 

  42. 

  43. 	>>>

  44. 

  45. 	runtime {

  46. 		docker:docker

  47. 		cluster: cluster_config

  48. 		systemDisk: "cloud_ssd 40"

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

  50. 	}

  51. 	output {

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

  53. 		File outside_vcf = "${project}.family.outside.vcf"

  54. 		File inside_vcf = "${project}.family.inside.vcf"

  55. 	}

  56. }

  57.