lesson5/answers/main.cwl

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