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

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