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SV_MIE/tasks/diffBed.wdl

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  1. task diffBed {

  2. 	File all_mie_bed

  3. 	File all_all_bed

  4. 	File lcr

  5. 	File centromere

  6. 	File sv_dup

  7. 	File sv_del

  8. 	File sv_inv

  9. 	File easy_region

  10. 	File sv_ins_bp

  11. 	File sv_del_bp

  12. 	File sv_tra_bp

  13. 	File sv_inv_bp

  14. 	File sv_dup_bp

  15. 	String sample_name

  16. 	String docker

  17. 	String cluster_config

  18. 	String disk_size

  19. 	

  20. 	command <<<

  21. 

  22. # mie

  23. 

  24. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${lcr} -b ${all_mie_bed} -counts  > ${sample_name}.mie.lcr.coverage.txt

  25. 

  26. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${centromere} -b ${all_mie_bed} -counts  > ${sample_name}.mie.centromere.coverage.txt

  27. 

  28. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_dup.coverage.txt

  29. 

  30. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_del.coverage.txt

  31. 

  32. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_inv.coverage.txt

  33. 

  34. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_ins_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_ins_bp.coverage.txt

  35. 

  36. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_del_bp.coverage.txt

  37. 

  38. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_tra_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_tra_bp.coverage.txt

  39. 

  40. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_inv_bp.coverage.txt

  41. 

  42. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup_bp} -b ${all_mie_bed} -counts  > ${sample_name}.mie.sv_dup_bp.coverage.txt

  43. 

  44. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${easy_region} -b ${all_mie_bed} -counts  > ${sample_name}.mie.easy_region.coverage.txt

  45. 

  46. 

  47. # all variants

  48. 

  49. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${lcr} -b ${all_all_bed} -counts  > ${sample_name}.all.lcr.coverage.txt

  50. 

  51. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${centromere} -b ${all_all_bed} -counts  > ${sample_name}.all.centromere.coverage.txt

  52. 

  53. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_dup.coverage.txt

  54. 

  55. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_del.coverage.txt

  56. 

  57. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_inv.coverage.txt

  58. 

  59. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_ins_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_ins_bp.coverage.txt

  60. 

  61. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_del_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_del_bp.coverage.txt

  62. 

  63. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_tra_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_tra_bp.coverage.txt

  64. 

  65. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_inv_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_inv_bp.coverage.txt

  66. 

  67. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${sv_dup_bp} -b ${all_all_bed} -counts  > ${sample_name}.all.sv_dup_bp.coverage.txt

  68. 

  69. 		/opt/ccdg/bedtools-2.27.1/bin/bedtools coverage -a ${easy_region} -b ${all_all_bed} -counts  > ${sample_name}.all.easy_region.coverage.txt

  70. 

  71. 

  72. 	>>>

  73. 

  74. 	runtime {

  75. 		docker:docker

  76. 		cluster: cluster_config

  77. 		systemDisk: "cloud_ssd 40"

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

  79. 	}

  80. 	output {

  81. 		File mie_lcr = "${sample_name}.mie.lcr.coverage.txt"

  82. 		File mie_centromere = "${sample_name}.mie.centromere.coverage.txt"

  83. 		File mie_sv_dup = "${sample_name}.mie.sv_dup.coverage.txt"

  84. 		File mie_sv_del = "${sample_name}.mie.sv_del.coverage.txt"

  85. 		File mie_sv_inv = "${sample_name}.mie.sv_inv.coverage.txt"

  86. 		File mie_sv_ins_bp = "${sample_name}.mie.sv_ins_bp.coverage.txt"

  87. 		File mie_sv_del_bp = "${sample_name}.mie.sv_del_bp.coverage.txt"

  88. 		File mie_sv_tra_bp = "${sample_name}.mie.sv_tra_bp.coverage.txt"

  89. 		File mie_sv_inv_bp = "${sample_name}.mie.sv_inv_bp.coverage.txt"

  90. 		File mie_sv_dup_bp = "${sample_name}.mie.sv_dup_bp.coverage.txt"

  91. 		File mie_easy_region = "${sample_name}.mie.easy_region.coverage.txt"

  92. 		File all_lcr = "${sample_name}.all.lcr.coverage.txt"

  93. 		File all_centromere = "${sample_name}.all.centromere.coverage.txt"

  94. 		File all_sv_dup = "${sample_name}.all.sv_dup.coverage.txt"

  95. 		File all_sv_del = "${sample_name}.all.sv_del.coverage.txt"

  96. 		File all_sv_inv = "${sample_name}.all.sv_inv.coverage.txt"

  97. 		File all_sv_ins_bp = "${sample_name}.all.sv_ins_bp.coverage.txt"

  98. 		File all_sv_del_bp = "${sample_name}.all.sv_del_bp.coverage.txt"

  99. 		File all_sv_tra_bp = "${sample_name}.all.sv_tra_bp.coverage.txt"

  100. 		File all_sv_inv_bp = "${sample_name}.all.sv_inv_bp.coverage.txt"

  101. 		File all_sv_dup_bp = "${sample_name}.all.sv_dup_bp.coverage.txt"

  102. 		File all_easy_region = "${sample_name}.all.easy_region.coverage.txt"

  103. 	}

  104. }