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high_confidence_calls_intergration
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high_confidence_calls_inter.../tasks/mergeBed.wdl

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  1. task mergeBed {

  2. 	Array[File] snv_true_bed

  3. 	Array[File] snv_false_bed

  4. 	Array[File] indel_true_bed

  5. 	Array[File] indel_false_bed

  6. 	Array[File]	indel_padding

  7. 	Array[File] snv_padding

  8. 	String docker

  9. 	String cluster_config

  10. 	String disk_size

  11. 	

  12. 	command <<<

  13. 

  14. 	/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " snv_true_bed} ${sep=" " indel_true_bed}  > merged.true.bed

  15. 

  16. 	/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " snv_false_bed} ${sep=" " indel_false_bed}  > merged.false.bed

  17. 

  18. 	/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " snv_padding} ${sep=" " indel_padding}  > merged.padding.bed	

  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. 

  29. 	output {

  30. 		File true_bed = "merged.true.bed"

  31. 		File false_bed = "merged.false.bed"

  32. 		File padding = "merged.padding.bed"

  33. 	}

  34. }