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SV_MIE
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SV_MIE/tasks/bedAnnotation.wdl

40 lignes
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Brut Annotations Historique 

  1. task bedAnnotation {

  2. 	File all_info_bed

  3. 	File left_50

  4. 	File left_100

  5. 	File left_150

  6. 	File left_200

  7. 	File left_250

  8. 	File left_300

  9. 	File left_350

  10. 	File left_400

  11. 	File right_50

  12. 	File right_100

  13. 	File right_150

  14. 	File right_200

  15. 	File right_250

  16. 	File right_300

  17. 	File right_350

  18. 	File right_400

  19. 	String sample_name

  20. 	String docker

  21. 	String cluster_config

  22. 	String disk_size

  23. 	

  24. 	command <<<

  25. 

  26. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${all_info_bed} -files ${left_400} ${left_350} ${left_300} ${left_250} ${left_200} ${left_150} ${left_100} ${left_50} ${right_50} ${right_100} ${right_150} ${right_200} ${right_250} ${right_300} ${right_350} ${right_400} > ${sample_name}.info.bed.annotation.txt

  27. 

  28. 	>>>

  29. 

  30. 	runtime {

  31. 		docker:docker

  32. 		cluster: cluster_config

  33. 		systemDisk: "cloud_ssd 40"

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

  35. 	}

  36. 	output {

  37. 		File info_bed_annotation = "${sample_name}.info.bed.annotation.txt"

  38. 	}

  39. }