renluyao
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repeat_validation
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repeat_validation/tasks/validation.wdl

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  1. task validation {

  2. 	File sub_vcf

  3. 	File sub_vcf_idx

  4. 

  5. 	File satellite

  6. 	File simple_repeat

  7. 	File SINE

  8. 	File LINE

  9. 	File LTR

  10. 	File low_complexity

  11. 	File SD

  12. 	File ins_breakpoint

  13. 	File del_breakpoint

  14. 	File mhc

  15. 

  16. 	File sdf

  17. 	File D5_10X

  18. 	File D5_10X_idx

  19. 

  20. 	String sample_name

  21. 	String tag

  22. 	String docker

  23. 	String cluster_config

  24. 	String disk_size

  25. 	

  26. 	command <<<

  27. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.satellite.vcf.gz --include-bed=${satellite}

  28. 

  29. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.simple_repeat.vcf.gz --include-bed=${simple_repeat}

  30. 

  31. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.SINE.vcf.gz --include-bed=${SINE}

  32. 

  33. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.LINE.vcf.gz --include-bed=${LINE}

  34. 

  35. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.LTR.vcf.gz --include-bed=${LTR}

  36. 

  37. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.low_complexity.vcf.gz --include-bed=${low_complexity}

  38. 

  39. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.SD.vcf.gz --include-bed=${SD}

  40. 

  41. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.ins_breakpoint.vcf.gz --include-bed=${ins_breakpoint}

  42. 

  43. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.del_breakpoint.vcf.gz --include-bed=${del_breakpoint}

  44. 

  45. 		rtg vcffilter -i ${sub_vcf} -o ${sample_name}.${tag}.mhc.vcf.gz --include-bed=${mhc}

  46. 

  47. 

  48. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.satellite.vcf.gz -o ${sample_name}.${tag}.satellite -t ${sdf}

  49. 

  50. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.simple_repeat.vcf.gz -o ${sample_name}.${tag}.simple_repeat -t ${sdf}

  51. 

  52. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.SINE.vcf.gz -o ${sample_name}.${tag}.SINE -t ${sdf}

  53. 

  54. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.LINE.vcf.gz -o ${sample_name}.${tag}.LINE -t ${sdf}

  55. 

  56. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.LTR.vcf.gz -o ${sample_name}.${tag}.LTR -t ${sdf}

  57. 

  58. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.low_complexity.vcf.gz -o ${sample_name}.${tag}.low_complexity -t ${sdf}

  59. 

  60. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.SD.vcf.gz -o ${sample_name}.${tag}.SD -t ${sdf}

  61. 

  62. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.ins_breakpoint.vcf.gz -o ${sample_name}.${tag}.ins_breakpoint -t ${sdf}

  63. 

  64. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.del_breakpoint.vcf.gz -o ${sample_name}.${tag}.del_breakpoint -t ${sdf}	

  65. 

  66. 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.mhc.vcf.gz -o ${sample_name}.${tag}.mhc -t ${sdf}	

  67. 

  68. 

  69. 		cp ${sample_name}.${tag}.satellite/summary.txt > ${sample_name}.${tag}.satellite.summary.txt

  70. 		cp ${sample_name}.${tag}.simple_repeat/summary.txt > ${sample_name}.${tag}.simple_repeat.summary.txt

  71. 		cp ${sample_name}.${tag}.SINE/summary.txt > ${sample_name}.${tag}.SINE.summary.txt

  72. 		cp ${sample_name}.${tag}.LINE/summary.txt > ${sample_name}.${tag}.LINE.summary.txt

  73. 		cp ${sample_name}.${tag}.LTR/summary.txt > ${sample_name}.${tag}.LTR.summary.txt

  74. 		cp ${sample_name}.${tag}.low_complexity/summary.txt > ${sample_name}.${tag}.low_complexity.summary.txt

  75. 		cp ${sample_name}.${tag}.SD/summary.txt > ${sample_name}.${tag}.SD.summary.txt

  76. 		cp ${sample_name}.${tag}.ins_breakpoint/summary.txt > ${sample_name}.${tag}.ins_breakpoint.summary.txt

  77. 		cp ${sample_name}.${tag}.del_breakpoint/summary.txt > ${sample_name}.${tag}.del_breakpoint.summary.txt

  78. 		cp ${sample_name}.${tag}.mhc/summary.txt > ${sample_name}.${tag}.mhc.summary.txt

  79. 

  80. 

  81. 	>>>

  82. 

  83. 	runtime {

  84. 		docker:docker

  85. 		cluster: cluster_config

  86. 		systemDisk: "cloud_ssd 40"

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

  88. 	}

  89. 	output {

  90. 		File satellite_vcf = "${sample_name}.${tag}.satellite.vcf.gz"

  91. 		File simple_repeat_vcf = "${sample_name}.${tag}.simple_repeat.vcf.gz"

  92. 		File SINE_vcf = "${sample_name}.${tag}.SINE.vcf.gz"

  93. 		File LINE_vcf = "${sample_name}.${tag}.LINE.vcf.gz"

  94. 		File LTR_vcf = "${sample_name}.${tag}.LTR.vcf.gz"

  95. 		File low_complexity_vcf = "${sample_name}.${tag}.low_complexity.vcf.gz"

  96. 		File SD_vcf = "${sample_name}.${tag}.SD.vcf.gz"

  97. 		File ins_breakpoint_vcf = "${sample_name}.${tag}.ins_breakpoint.vcf.gz"

  98. 		File del_breakpoint_vcf = "${sample_name}.${tag}.del_breakpoint.vcf.gz"

  99. 		File mhc_vcf = "${sample_name}.${tag}.mhc.vcf.gz"

  100. 		File satellite_summary = "${sample_name}.${tag}.satellite.summary.txt"

  101. 		File simple_repeat_summary = "${sample_name}.${tag}.simple_repeat.summary.txt"

  102. 		File SINE_summary = "${sample_name}.${tag}.SINE.summary.txt"

  103. 		File LINE_summary = "${sample_name}.${tag}.LINE.summary.txt"

  104. 		File LTR_summary = "${sample_name}.${tag}.LTR.summary.txt"

  105. 		File low_complexity_summary = "${sample_name}.${tag}.low_complexity.summary.txt"

  106. 		File SD_summary = "${sample_name}.${tag}.SD.summary.txt"

  107. 		File ins_breakpoint_summary = "${sample_name}.${tag}.ins_breakpoint.summary.txt"

  108. 		File del_breakpoint_summary = "${sample_name}.${tag}.del_breakpoint.summary.txt"

  109. 		File mhc_summary = "${sample_name}.${tag}.mhc.summary.txt"

  110. 	}

  111. }