assets/answers/ep5/part4/main.cwl

   1 cwlVersion: v1.2
   2 class: Workflow
   3 label: RNAseq CWL practice workflow
   4
   5 ### 2. Scattering
   6 inputs:
   7   fq: File[]
   8   genome: Directory
   9   gtf: File
  10
  11 steps:
  12   alignment:
  13     run: alignment.cwl
  14     scatter: fq
  15     in:
  16       fq: fq
  17       genome: genome
  18       gtf: gtf
  19     out: [qc_html, bam_sorted_indexed]
  20
  21   ### 4. Combining results
  22   featureCounts:
  23     requirements:
  24       ResourceRequirement:
  25         ramMin: 500
  26     run: featureCounts.cwl
  27     in:
  28       counts_input_bam: alignment/bam_sorted_indexed
  29       gtf: gtf
  30     out: [featurecounts]
  31
  32 outputs:
  33   qc_html:
  34     type: File[]
  35     outputSource: alignment/qc_html
  36   bam_sorted_indexed:
  37     type: File[]
  38     outputSource: alignment/bam_sorted_indexed
  39
  40   ### 4. Combining results
  41   featurecounts:
  42     type: File
  43     outputSource: featureCounts/featurecounts
  44
  45 requirements:
  46   SubworkflowFeatureRequirement: {}
  47   ScatterFeatureRequirement: {}