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quartet_dna_quality_control_wes_big_pipeline
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quartet_dna_quality_control.../tasks/merge_family.wdl

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  1. task merge_family {

  2. 	File D5_vcf

  3. 	File D6_vcf

  4. 	File F7_vcf

  5. 	File M8_vcf

  6. 	File D5_vcf_tbi

  7. 	File D6_vcf_tbi

  8. 	File F7_vcf_tbi

  9. 	File M8_vcf_tbi

  10. 	String project

  11. 	String docker

  12. 	String cluster_config

  13. 	String disk_size

  14. 	

  15. 	command <<<

  16. 

  17. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.vcf.gz ${D5_vcf} ${D6_vcf} ${F7_vcf} ${M8_vcf}

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

  19. 

  20. 	>>>

  21. 

  22. 	runtime {

  23. 		docker:docker

  24. 		cluster: cluster_config

  25. 		systemDisk: "cloud_ssd 40"

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

  27. 	}

  28. 	output {

  29. 		File family_vcf = "${project}.family.vcf"

  30. 	}

  31. }