室间质评
Nevar pievienot vairāk kā 25 tēmas Tēmai ir jāsākas ar burtu vai ciparu, tā var saturēt domu zīmes ('-') un var būt līdz 35 simboliem gara.

78 rindas
1.6KB

  1. import "./tasks/fastqc.wdl" as fastqc
  2. import "./tasks/fastqscreen.wdl" as fastqscreen
  3. import "./tasks/bamqc.wdl" as bamqc
  4. import "./tasks/benchmark.wdl" as benchmark
  5. import "./tasks/multiqc.wdl" as multiqc
  6. import "./tasks/vcfstat.wdl" as vcfstat
  7. import "./tasks/mergeNum.wdl" as mergeNum
  8. #import "./tasks/jaccard_index.wdl" as JI
  9. workflow {{ project_name }} {
  10. File inputSamplesFile
  11. Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
  12. # File inputJIpiarsFile
  13. # Array[Array[File]] inputJIpairs = read_tsv(inputJIpiarsFile)
  14. File screen_ref_dir
  15. File fastq_screen_conf
  16. File benchmarking_dir
  17. File ref_dir
  18. String fasta
  19. scatter (sample in inputSamples){
  20. call fastqc.fastqc as fastqc {
  21. input:
  22. read1=sample[0],
  23. read2=sample[1]
  24. }
  25. call fastqscreen.fastq_screen as fastqscreen {
  26. input:
  27. read1=sample[0],
  28. read2=sample[1],
  29. screen_ref_dir=screen_ref_dir,
  30. fastq_screen_conf=fastq_screen_conf
  31. }
  32. call bamqc.bamqc as bamqc {
  33. input:
  34. bam=sample[2],
  35. bai=sample[3]
  36. }
  37. call benchmark.benchmark as benchmark {
  38. input:
  39. vcf=sample[4],
  40. benchmarking_dir=benchmarking_dir,
  41. ref_dir=ref_dir,
  42. sample_mark=sample[5],
  43. fasta=fasta
  44. }
  45. call vcfstat.vcfstat as vcfstat {
  46. input:
  47. rtg_vcf=benchmark.rtg_vcf,
  48. rtg_vcf_index=benchmark.rtg_vcf_index
  49. }
  50. }
  51. call multiqc.multiqc as multiqc {
  52. input:
  53. read1_zip=fastqc.read1_zip,
  54. read2_zip=fastqc.read2_zip,
  55. txt1=fastqscreen.txt1,
  56. txt2=fastqscreen.txt2,
  57. zip=bamqc.zip,
  58. summary=benchmark.summary
  59. }
  60. call mergeNum.mergeNum as mergeNum {
  61. input:
  62. vcfnumber=vcfstat.vcfnumber
  63. }
  64. }