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fastp
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fastp/workflow.wdl

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  1. import "./tasks/fastp.wdl" as fastp

  2. workflow {{ project_name }} {	

  3. 	File inputSamplesFile

  4. 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)

  5. 	String fastp_docker

  6. 	String adapter_sequence

  7. 	String adapter_sequence_r2

  8. 	String fastp_cluster

  9. 	String umi_loc	

  10. 	Int trim_front1 

  11. 	Int trim_tail1 

  12. 	Int max_len1 

  13. 	Int trim_front2 

  14. 	Int trim_tail2  

  15. 	Int max_len2 

  16. 	Int disable_adapter_trimming

  17. 	Int length_required

  18. 	Int umi_len

  19. 	Int UMI

  20. 	Int qualified_quality_phred

  21. 	Int length_required1

  22. 	Int disable_quality_filtering

  23. 

  24. 	scatter (quartet in inputSamples){

  25. 		call fastp.fastp as fastp {

  26. 		input: 

  27. 		sample_id=quartet[2],

  28. 		read1=quartet[0], 

  29. 		read2=quartet[1],

  30. 		docker = fastp_docker,

  31. 		cluster = fastp_cluster

  32. 		}

  33. 	}

  34. }