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high_confidence_calls_intergration
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high_confidence_calls_inter.../tasks/merge.wdl

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  1. task merge {

  2. 	Array[File] rename_mother_vcf_gz

  3. 	Array[File] rename_mother_vcf_idx

  4. 	Array[File] rename_father_vcf_gz

  5. 	Array[File] rename_father_vcf_idx

  6. 	Array[File] rename_twins_vcf_gz

  7. 	Array[File] rename_twins_vcf_idx

  8. 	String mapper_caller

  9. 	String docker

  10. 	String cluster_config

  11. 	String disk_size

  12. 	

  13. 	command <<<

  14. 		rtg vcfmerge --force-merge-all --no-gzip -o LCL8.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " rename_mother_vcf_gz}

  15. 

  16. 		rtg vcfmerge --force-merge-all --no-gzip -o LCL7.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " rename_father_vcf_gz}

  17. 

  18. 		rtg vcfmerge --force-merge-all --no-gzip -o Twins.${mapper_caller}.sister.consistent.merged.vcf ${sep=" " rename_twins_vcf_gz}

  19. 	>>>

  20. 

  21. 	runtime {

  22. 		docker:docker

  23. 		cluster: cluster_config

  24. 		systemDisk: "cloud_ssd 40"

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

  26. 	}

  27. 	output {

  28. 		File mother_merged_vcf = "LCL8.${mapper_caller}.sister.consistent.merged.vcf"

  29. 		File father_merged_vcf = "LCL7.${mapper_caller}.sister.consistent.merged.vcf"

  30. 		File twins_merged_vcf = "Twins.${mapper_caller}.sister.consistent.merged.vcf"

  31. 	}

  32. }