YaqingLiu
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bedtools-multicov
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Calculate the bed coverage of multiple BAM files before and after dedup
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bedtools-multicov/workflow.wdl

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

  2. 

  3. workflow {{ project_name }} {

  4. 

  5. 	File input_bam_file

  6. 	File input_bai_file

  7. 	File bed_file

  8. 	Boolean include_dup

  9. 	Array[File] bam = read_lines(input_bam_file)

  10. 	Array[File] bai = read_lines(input_bai_file)

  11. 	

  12. 	call bedtools.bedtools as bedtools {

  13. 		input:

  14. 		bam=bam,

  15. 		bai=bai,

  16. 		include_dup=include_dup,

  17. 		bed_file=bed_file

  18. 	}

  19. }