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   splitDir:
  14     in:
  15       fqdir: fqdir
  16     run: helper/splitDir.cwl
  17     out: [fq]
  18
  19   alignment:
  20     run: helper/alignment.cwl
  21     scatter: fq
  22     in:
  23       fq: splitDir/fq
  24       genome: genome
  25       gtf: gtf
  26     out: [qc_html, bam_sorted_indexed]
  27
  28   featureCounts:
  29     requirements:
  30       ResourceRequirement:
  31         ramMin: 500
  32     run: helper/featureCounts.cwl
  33     in:
  34       counts_input_bam: alignment/bam_sorted_indexed
  35       gtf: gtf
  36     out: [featurecounts]
  37
  38   output-subdirs:
  39     run: helper/subdirs.cwl
  40     in:
  41       fq: splitDir/fq
  42       bams: alignment/bam_sorted_indexed
  43       qc: alignment/qc_html
  44     out: [dirs]
  45
  46 outputs:
  47   dirs:
  48     type: Directory[]
  49     outputSource: output-subdirs/dirs
  50
  51   featurecounts:
  52     type: File
  53     outputSource: featureCounts/featurecounts
  54
  55 requirements:
  56   SubworkflowFeatureRequirement: {}
  57   ScatterFeatureRequirement: {}
  58   StepInputExpressionRequirement: {}