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SV_MIE
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SV_MIE/tasks/bedCoverage.wdl

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  1. task bedCoverage {

  2. 	File all_mie_bed

  3. 	File all_all_bed

  4. 	File left_50

  5. 	File left_100

  6. 	File left_150

  7. 	File left_200

  8. 	File left_250

  9. 	File left_300

  10. 	File left_350

  11. 	File left_400

  12. 	File right_50

  13. 	File right_100

  14. 	File right_150

  15. 	File right_200

  16. 	File right_250

  17. 	File right_300

  18. 	File right_350

  19. 	File right_400

  20. 	String sample_name

  21. 	String docker

  22. 	String cluster_config

  23. 	String disk_size

  24. 	

  25. 	command <<<

  26. 

  27. ## MIE

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

  29. 

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

  31. 

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

  33. 

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

  35. 

  36. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_250} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left250.coverage.txt

  37. 

  38. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_300} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left300.coverage.txt

  39. 

  40. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_350} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left350.coverage.txt

  41. 

  42. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_400} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.left400.coverage.txt

  43. 

  44. 

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

  46. 

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

  48. 

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

  50. 

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

  52. 

  53. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_250} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right250.coverage.txt

  54. 

  55. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_300} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right300.coverage.txt

  56. 

  57. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_350} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right350.coverage.txt

  58. 

  59. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_400} -b ${all_mie_bed} -counts | cut -f4 > ${sample_name}.mie.right400.coverage.txt

  60. 

  61. 

  62. 		paste ${sample_name}.mie.left400.coverage.txt ${sample_name}.mie.left350.coverage.txt ${sample_name}.mie.left300.coverage.txt ${sample_name}.mie.left250.coverage.txt ${sample_name}.mie.left200.coverage.txt ${sample_name}.mie.left150.coverage.txt ${sample_name}.mie.left100.coverage.txt ${sample_name}.mie.left50.coverage.txt ${sample_name}.mie.right50.coverage.txt ${sample_name}.mie.right100.coverage.txt ${sample_name}.mie.right150.coverage.txt ${sample_name}.mie.right200.coverage.txt ${sample_name}.mie.right250.coverage.txt ${sample_name}.mie.right300.coverage.txt ${sample_name}.mie.right350.coverage.txt ${sample_name}.mie.right400.coverage.txt > ${sample_name}.mie.coverage.txt

  63. 

  64. # all variants

  65. 

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

  67. 

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

  69. 

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

  71. 

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

  73. 

  74. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_250} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left250.coverage.txt

  75. 

  76. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_300} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left300.coverage.txt

  77. 

  78. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_350} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left350.coverage.txt

  79. 

  80. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${left_400} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.left400.coverage.txt

  81. 

  82. 

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

  84. 

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

  86. 

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

  88. 

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

  90. 

  91. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_250} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right250.coverage.txt

  92. 

  93. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_300} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right300.coverage.txt

  94. 

  95. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_350} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right350.coverage.txt

  96. 

  97. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${right_400} -b ${all_all_bed} -counts | cut -f4 > ${sample_name}.all.right400.coverage.txt

  98. 

  99. 

  100. 		paste ${sample_name}.all.left400.coverage.txt ${sample_name}.all.left350.coverage.txt ${sample_name}.all.left300.coverage.txt ${sample_name}.all.left250.coverage.txt ${sample_name}.all.left200.coverage.txt ${sample_name}.all.left150.coverage.txt ${sample_name}.all.left100.coverage.txt ${sample_name}.all.left50.coverage.txt ${sample_name}.all.right50.coverage.txt ${sample_name}.all.right100.coverage.txt ${sample_name}.all.right150.coverage.txt ${sample_name}.all.right200.coverage.txt ${sample_name}.all.right250.coverage.txt ${sample_name}.all.right300.coverage.txt ${sample_name}.all.right350.coverage.txt ${sample_name}.all.right400.coverage.txt > ${sample_name}.all.coverage.txt

  101. 

  102. 	>>>

  103. 

  104. 	runtime {

  105. 		docker:docker

  106. 		cluster: cluster_config

  107. 		systemDisk: "cloud_ssd 40"

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

  109. 	}

  110. 	output {

  111. 		File mie = "${sample_name}.mie.coverage.txt"

  112. 		File all = "${sample_name}.all.coverage.txt"

  113. 	}

  114. }