#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

inputs:
- id: sh_script
  type: File
  inputBinding:
    position: 0
- id: arc_root
  type: string
  inputBinding:
    position: 1
- id: out_folder
  type: string
  inputBinding:
    position: 2
- id: in_kallisto_index
  type: string
  inputBinding:
    position: 3
- id: in_fastq_folder
  type: string
  inputBinding:
    position: 4
- id: kallisto_bootstrap
  type: int
  inputBinding:
    position: 5
- id: kallisto_threads
  type: int
  inputBinding:
    position: 6
- id: kallisto_fragmentLength
  type: int
  inputBinding:
    position: 7
- id: kallisto_stdDev
  type: int
  inputBinding:
    position: 8

outputs:
- id: outdir
  type:
    type: array
    items: Directory
  outputBinding:
    glob: $(runtime.outdir)/$(inputs.out_folder)

baseCommand:
- bash