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SV_MIE
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SV_MIE/tasks/bedCoverage.wdl

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  1. task bedCoverage {

  2. 	File mie_bed

  3. 	File all_bed

  4. 	File left_50

  5. 	File left_100

  6. 	File left_150

  7. 	File left_200

  8. 	File right_50

  9. 	File right_100

  10. 	File right_150

  11. 	File right_200

  12. 	String sample_name

  13. 	String chromo

  14. 	String docker

  15. 	String cluster_config

  16. 	String disk_size

  17. 	

  18. 	command <<<

  19. 

  20. ## MIE

  21. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left50.coverage.txt

  22. 

  23. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left100.coverage.txt

  24. 

  25. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left150.coverage.txt

  26. 

  27. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.left200.coverage.txt

  28. 

  29. 

  30. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right50.coverage.txt

  31. 

  32. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right100.coverage.txt

  33. 

  34. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right150.coverage.txt

  35. 

  36. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${mie_bed} -counts | cut -f4 > ${sample_name}.${chromo}.mie.right200.coverage.txt

  37. 

  38. 		paste ${sample_name}.${chromo}.mie.left200.coverage.txt ${sample_name}.${chromo}.mie.left150.coverage.txt ${sample_name}.${chromo}.mie.left100.coverage.txt ${sample_name}.${chromo}.mie.left50.coverage.txt ${sample_name}.${chromo}.mie.right50.coverage.txt ${sample_name}.${chromo}.mie.right100.coverage.txt ${sample_name}.${chromo}.mie.right150.coverage.txt ${sample_name}.${chromo}.mie.right200.coverage.txt > ${sample_name}.${chromo}.mie.coverage.txt

  39. 

  40. # all variants

  41. 

  42. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_50} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left50.coverage.txt

  43. 

  44. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_100} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left100.coverage.txt

  45. 

  46. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_150} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left150.coverage.txt

  47. 

  48. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_200} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.left200.coverage.txt

  49. 

  50. 

  51. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_50} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right50.coverage.txt

  52. 

  53. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_100} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right100.coverage.txt

  54. 

  55. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_150} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right150.coverage.txt

  56. 

  57. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_200} -b ${all_bed} -counts | cut -f4 > ${sample_name}.${chromo}.all.right200.coverage.txt

  58. 

  59. 		paste ${sample_name}.${chromo}.all.left200.coverage.txt ${sample_name}.${chromo}.all.left150.coverage.txt ${sample_name}.${chromo}.all.left100.coverage.txt ${sample_name}.${chromo}.all.left50.coverage.txt ${sample_name}.${chromo}.all.right50.coverage.txt ${sample_name}.${chromo}.all.right100.coverage.txt ${sample_name}.${chromo}.all.right150.coverage.txt ${sample_name}.${chromo}.all.right200.coverage.txt > ${sample_name}.${chromo}.all.coverage.txt

  60. 

  61. 

  62. 	>>>

  63. 

  64. 	runtime {

  65. 		docker:docker

  66. 		cluster: cluster_config

  67. 		systemDisk: "cloud_ssd 40"

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

  69. 	}

  70. 	output {

  71. 		File mie = "${sample_name}.${chromo}.mie.coverage.txt"

  72. 		File all = "${sample_name}.${chromo}.all.coverage.txt"

  73. 	}

  74. }