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RNA_Datapotal
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RNA_Datapotal/workflow.wdl

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Neapstrādāts Vainot Vēsture 

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

  2. import "./tasks/hisat2.wdl" as hisat2

  3. import "./tasks/samtools.wdl" as samtools

  4. import "./tasks/stringtie.wdl" as stringtie

  5. import "./tasks/fastqc.wdl" as fastqc

  6. import "./tasks/fastqscreen.wdl" as fastqscreen

  7. import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc

  8. import "./tasks/qualimapRNAseq.wdl" as qualimapRNAseq

  9. import "./tasks/multiqc.wdl" as multiqc

  10. 

  11. workflow {{ project_name }} {

  12. 	

  13. 	

  14. 	String stringtie_docker

  15. 	String stringtie_cluster

  16. 	String multiqc_cluster_config

  17. 	String multiqc_docker

  18. 	Int multiqc_disk_size

  19. 	Int trim_front1 

  20. 	Int trim_tail1 

  21. 	Int max_len1 

  22. 	Int trim_front2 

  23. 	Int trim_tail2  

  24. 	Int max_len2 

  25. 	Int disable_adapter_trimming

  26. 	Int length_required

  27. 	Int umi_len

  28. 	Int UMI

  29. 	Int qualified_quality_phred

  30. 	Int length_required1

  31. 	Int disable_quality_filtering

  32. 	Int pen_cansplice

  33. 	Int pen_noncansplice

  34. 	Int min_intronlen

  35. 	Int max_intronlen

  36. 	Int maxins

  37. 	Int minins

  38. 	Int fastqc_disk_size

  39. 	Int fastqscreen_disk_size

  40. 	Int qualimapBAMqc_disk_size

  41. 	Int qualimapRNAseq_disk_size

  42. 	Int insert_size

  43. 	Int minimum_length_allowed_for_the_predicted_transcripts

  44.     	Int Junctions_no_spliced_reads

  45.    	Float minimum_isoform_abundance

  46.     	Float maximum_fraction_of_muliplelocationmapped_reads

  47. }