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  1. import "./tasks/mendelian.wdl" as mendelian
  2. import "./tasks/sister.wdl" as sister
  3. import "./tasks/merge.wdl" as merge
  4. workflow {{ project_name }} {
  5. File inputSamplesFile
  6. Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
  7. File sdf
  8. String cluster_config
  9. String disk_size
  10. scatter (sample in inputSamples){
  11. call mendelian.mendelian as mendelian {
  12. input:
  13. mother_vcf_gz=sample[0],
  14. father_vcf_gz=sample[1],
  15. child_vcf_gz=sample[2],
  16. mother_vcf_idx=sample[4],
  17. father_vcf_idx=sample[5],
  18. child_vcf_idx=sample[6],
  19. mother_name=sample[8],
  20. father_name=sample[9],
  21. child_name=sample[10],
  22. family_name=sample[11],
  23. sdf=sdf,
  24. cluster_config=cluster_config,
  25. disk_size=disk_size
  26. }
  27. call sister.sister as sister {
  28. input:
  29. violation_vcf_gz=mendelian.violation_vcf_gz,
  30. violation_vcf_idx=mendelian.violation_vcf_idx,
  31. consistent_vcf_gz=mendelian.consistent_vcf_gz,
  32. consistent_vcf_idx=mendelian.consistent_vcf_idx,
  33. sister_vcf_gz=sample[3],
  34. sister_vcf_idx=sample[7],
  35. sdf=sdf,
  36. family_name=sample[11],
  37. cluster_config=cluster_config,
  38. disk_size=disk_size
  39. }
  40. }
  41. call merge.merge as merge {
  42. input:
  43. child_violation_sister=sister.child_violation_sister,
  44. child_violation_sister_idx=sister.child_violation_sister_idx,
  45. child_violation_nonsister=sister.child_violation_nonsister,
  46. child_violation_nonsister_idx=sister.child_violation_nonsister_idx,
  47. child_consistent_sister=sister.child_consistent_sister,
  48. child_consistent_sister_idx=sister.child_consistent_sister_idx,
  49. child_consistent_nonsister=sister.child_consistent_nonsister,
  50. child_consistent_nonsister_idx=sister.child_consistent_nonsister_idx,
  51. cluster_config=cluster_config,
  52. disk_size=disk_size
  53. }
  54. }