cwlVersion: v1.2
class: Workflow
label: RNAseq CWL practice workflow

inputs:
  fq: File
  genome: Directory
  gtf: File

### 1. Subworkflows
steps:
  alignment:
    run: alignment.cwl
    in:
      fq: fq
      genome: genome
      gtf: gtf
    out: [qc_html, bam_sorted_indexed, featurecounts]

outputs:
  qc_html:
    type: File
    outputSource: alignment/qc_html
  bam_sorted_indexed:
    type: File
    outputSource: alignment/bam_sorted_indexed
  featurecounts:
    type: File
    outputSource: alignment/featurecounts

requirements:
  SubworkflowFeatureRequirement: {}