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  1. import "./tasks/starfusion.wdl" as starfusion
  2. import "./tasks/fastp.wdl" as fastp
  3. import "./tasks/arriba.wdl" as arriba
  4. workflow {{ project_name }} {
  5. String sample_id
  6. File fastq1
  7. File fastq2
  8. File starfusion_database_dir
  9. String starfusion_docker
  10. String starfusion_cluster
  11. String disk_size
  12. String fastp_docker
  13. String fastp_cluster
  14. String adapter_sequence
  15. String adapter_sequence_r2
  16. String umi_loc
  17. Int trim_front1
  18. Int trim_tail1
  19. Int max_len1
  20. Int trim_front2
  21. Int trim_tail2
  22. Int max_len2
  23. Int disable_adapter_trimming
  24. Int length_required
  25. Int umi_len
  26. Int UMI
  27. Int qualified_quality_phred
  28. Int length_required1
  29. Int disable_quality_filtering
  30. File STAR_INDEX_DIR
  31. File ASSEMBLY_FA
  32. File ANNOTATION_GTF
  33. String arriba_docker
  34. String arriba_cluster
  35. call fastp.fastp as fastp {
  36. input:
  37. read1=fastq1,
  38. read2=fastq2,
  39. sample_id=sample_id,
  40. docker=fastp_docker,
  41. cluster=fastp_cluster,
  42. disk_size=disk_size,
  43. adapter_sequence=adapter_sequence,
  44. adapter_sequence_r2=adapter_sequence_r2,
  45. umi_loc=umi_loc,
  46. trim_front1=trim_front1,
  47. trim_tail1=trim_tail1,
  48. max_len1=max_len1,
  49. trim_front2=trim_front2,
  50. trim_tail2=trim_tail2,
  51. max_len2=max_len2,
  52. disable_adapter_trimming=disable_adapter_trimming,
  53. length_required=length_required,
  54. umi_len=umi_len,
  55. UMI=UMI,
  56. qualified_quality_phred=qualified_quality_phred,
  57. length_required1=length_required1,
  58. disable_quality_filtering=disable_quality_filtering
  59. }
  60. call starfusion.starfusion as starfusion {
  61. input:
  62. sample_id=sample_id,
  63. fastq1=fastp.Trim_R1,
  64. fastq2=fastp.Trim_R2,
  65. database_dir=starfusion_database_dir,
  66. docker=starfusion_docker,
  67. cluster=starfusion_cluster,
  68. disk_size=disk_size
  69. }
  70. call arriba.arriba as arriba {
  71. input:
  72. sample_id=sample_id,
  73. fastq1=fastp.Trim_R1,
  74. fastq2=fastp.Trim_R2,
  75. STAR_INDEX_DIR=STAR_INDEX_DIR,
  76. ASSEMBLY_FA=ASSEMBLY_FA,
  77. ANNOTATION_GTF=ANNOTATION_GTF,
  78. disk_size=disk_size,
  79. docker=arriba_docker,
  80. cluster=arriba_cluster
  81. }
  82. }