RNA-Seq/cwl/RNA-seq-wf.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: helper/alignment.cwl
  13     scatter: fq
  14     in:
  15       fq: fq
  16       genome: genome
  17       gtf: gtf
  18     out: [qc_html, bam_sorted_indexed]
  19
  20   featureCounts:
  21     requirements:
  22       ResourceRequirement:
  23         ramMin: 500
  24     run: helper/featureCounts.cwl
  25     in:
  26       counts_input_bam: alignment/bam_sorted_indexed
  27       gtf: gtf
  28     out: [featurecounts]
  29
  30   output-subdirs:
  31     run: helper/subdirs.cwl
  32     in:
  33       fq: fq
  34       bams: alignment/bam_sorted_indexed
  35       qc: alignment/qc_html
  36     out: [dirs]
  37
  38 outputs:
  39   dirs:
  40     type: Directory[]
  41     outputSource: output-subdirs/dirs
  42
  43   featurecounts:
  44     type: File
  45     outputSource: featureCounts/featurecounts
  46
  47 requirements:
  48   SubworkflowFeatureRequirement: {}
  49   ScatterFeatureRequirement: {}