RNA-Seq/cwl/RNA-seq-wf.cwl

   1 cwlVersion: v1.2
   2 class: Workflow
   3 label: RNAseq workflow
   4
   5 inputs:
   6   fqdir: Directory
   7   genome: Directory
   8   gtf: File
   9
  10 steps:
  11   alignment:
  12     run: helper/alignment.cwl
  13     scatter: fq
  14     in:
  15       fq:
  16         valueFrom: $(inputs.fq.listing)
  17       genome: genome
  18       gtf: gtf
  19     out: [qc_html, bam_sorted_indexed]
  20
  21   featureCounts:
  22     requirements:
  23       ResourceRequirement:
  24         ramMin: 500
  25     run: helper/featureCounts.cwl
  26     in:
  27       counts_input_bam: alignment/bam_sorted_indexed
  28       gtf: gtf
  29     out: [featurecounts]
  30
  31   output-subdirs:
  32     run: helper/subdirs.cwl
  33     in:
  34       fq:
  35        valueFrom: $(inputs.fq.listing)
  36       bams: alignment/bam_sorted_indexed
  37       qc: alignment/qc_html
  38     out: [dirs]
  39
  40 outputs:
  41   dirs:
  42     type: Directory[]
  43     outputSource: output-subdirs/dirs
  44
  45   featurecounts:
  46     type: File
  47     outputSource: featureCounts/featurecounts
  48
  49 requirements:
  50   SubworkflowFeatureRequirement: {}
  51   ScatterFeatureRequirement: {}
  52
  53 hints:
  54   LoadListingRequirement:
  55     loadListing: shallow_listing