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  1. import "./tasks/mapping.wdl" as mapping
  2. import "./tasks/Metrics.wdl" as Metrics
  3. import "./tasks/Dedup.wdl" as Dedup
  4. import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
  5. import "./tasks/Realigner.wdl" as Realigner
  6. import "./tasks/BQSR.wdl" as BQSR
  7. import "./tasks/Haplotyper.wdl" as Haplotyper
  8. workflow {{ project_name }} {
  9. File fastq_1
  10. File fastq_2
  11. String SENTIEON_INSTALL_DIR
  12. String sample
  13. String docker
  14. String fasta
  15. File ref_dir
  16. File dbmills_dir
  17. String db_mills
  18. File dbsnp_dir
  19. String dbsnp
  20. String disk_size
  21. String cluster_config
  22. call mapping.mapping as mapping {
  23. input:
  24. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  25. group=sample,
  26. sample=sample,
  27. pl="ILLUMINAL",
  28. fasta=fasta,
  29. ref_dir=ref_dir,
  30. fastq_1=fastq_1,
  31. fastq_2=fastq_2,
  32. docker=docker,
  33. disk_size=disk_size,
  34. cluster_config=cluster_config
  35. }
  36. call Metrics.Metrics as Metrics {
  37. input:
  38. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  39. fasta=fasta,
  40. ref_dir=ref_dir,
  41. sorted_bam=mapping.sorted_bam,
  42. sorted_bam_index=mapping.sorted_bam_index,
  43. sample=sample,
  44. docker=docker,
  45. disk_size=disk_size,
  46. cluster_config=cluster_config
  47. }
  48. call Dedup.Dedup as Dedup {
  49. input:
  50. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  51. sorted_bam=mapping.sorted_bam,
  52. sorted_bam_index=mapping.sorted_bam_index,
  53. sample=sample,
  54. docker=docker,
  55. disk_size=disk_size,
  56. cluster_config=cluster_config
  57. }
  58. call deduped_Metrics.deduped_Metrics as deduped_Metrics {
  59. input:
  60. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  61. fasta=fasta,
  62. ref_dir=ref_dir,
  63. Dedup_bam=Dedup.Dedup_bam,
  64. Dedup_bam_index=Dedup.Dedup_bam_index,
  65. sample=sample,
  66. docker=docker,
  67. disk_size=disk_size,
  68. cluster_config=cluster_config
  69. }
  70. call Realigner.Realigner as Realigner {
  71. input:
  72. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  73. fasta=fasta,
  74. ref_dir=ref_dir,
  75. Dedup_bam=Dedup.Dedup_bam,
  76. Dedup_bam_index=Dedup.Dedup_bam_index,
  77. db_mills=db_mills,
  78. dbmills_dir=dbmills_dir,
  79. sample=sample,
  80. docker=docker,
  81. disk_size=disk_size,
  82. cluster_config=cluster_config
  83. }
  84. call BQSR.BQSR as BQSR {
  85. input:
  86. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  87. fasta=fasta,
  88. ref_dir=ref_dir,
  89. realigned_bam=Realigner.realigner_bam,
  90. realigned_bam_index=Realigner.realigner_bam_index,
  91. db_mills=db_mills,
  92. dbmills_dir=dbmills_dir,
  93. dbsnp=dbsnp,
  94. dbsnp_dir=dbsnp_dir,
  95. sample=sample,
  96. docker=docker,
  97. disk_size=disk_size,
  98. cluster_config=cluster_config
  99. }
  100. call Haplotyper.Haplotyper as Haplotyper {
  101. input:
  102. SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
  103. fasta=fasta,
  104. ref_dir=ref_dir,
  105. recaled_bam=BQSR.recaled_bam,
  106. recaled_bam_index=BQSR.recaled_bam_index,
  107. dbsnp=dbsnp,
  108. dbsnp_dir=dbsnp_dir,
  109. sample=sample,
  110. docker=docker,
  111. disk_size=disk_size,
  112. cluster_config=cluster_config
  113. }
  114. }