foo.json

{
    "hello_input": {
        "class": "File",
        "path": "/home/dyuen/consonance/consonance-arch/./datastore/launcher-03ad4441-c074-4893-b5bd-6d14aabb4995/inputs/0e129840-fa77-4cec-a885-19b1e538507a/hello_input"
    },
    "hello_output": {
        "class": "File",
        "path": "/home/dyuen/consonance/consonance-arch/./datastore/launcher-03ad4441-c074-4893-b5bd-6d14aabb4995/outputs/hello_output"
    },
    "ref_file_1": {
        "class": "File",
        "path": "/home/dyuen/consonance/consonance-arch/./datastore/launcher-03ad4441-c074-4893-b5bd-6d14aabb4995/inputs/d2816fb8-7773-4b2a-bd31-ee4a7efa8e04/ref_file_1"
    },
    "ref_file_2": {
        "class": "File",
        "path": "/home/dyuen/consonance/consonance-arch/./datastore/launcher-03ad4441-c074-4893-b5bd-6d14aabb4995/inputs/0bf6ab9f-83a8-4b72-ad67-460eb696bd64/ref_file_2"
    }
}

image-descriptor.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool
description: "Markdown description text here"
id: "HelloWorld"
label: "HelloWorld Tool"

dct:creator:
  "@id": "http://orcid.org/0000-0003-3566-7705"
  foaf:name: Peter Amstutz
  foaf:mbox: "mailto:peter.amstutz@curoverse.com"

requirements:
  - class: DockerRequirement
    dockerPull: "quay.io/collaboratory/workflow-helloworld:1.0.0"
  - { import: node-engine.cwl }

hints:
  - class: ResourceRequirement
    coresMin: 8
    ramMin: 8092
    outdirMin: 512000
    description: "these parameters are used to locate a VM with appropriate resources"

inputs:
  - id: "#ref_file_1"
    type: File
    description: "this describes a large reference file that does not change between runs"
    default:
      class: File
      path: 8e888694-9c56-4529-a750-d6bfbd4a74e7.txt

  - id: "#ref_file_2"
    type: File
    description: "this describes a large reference file that does not change between runs"
    default:
      class: File
      path: b4cdad91-676a-446c-a635-57453f17617a.txt

  - id: "#hello_input"
    type: File
    description: "this describes an input file that should be provided before execution"

outputs:
  - id: "#hello_output"
    type: File
    outputBinding:
      glob: hello-output.txt
    description: "this describes an output file that should be saved after execution"

baseCommand: ["bash", "-c"]
arguments:
  - valueFrom:
      engine: node-engine.cwl
      script: |
        "cat " + $job.hello_input.path + " > hello-output.txt &&"
            + " ls " + $job.ref_file_1.path + " >> hello-output.txt && "
            + " head -20 " + $job.ref_file_2.path + " >> hello-output.txt"

node-engine.cwl

class: ExpressionEngineRequirement
requirements:
  - class: DockerRequirement
    dockerPull: commonworkflowlanguage/nodejs-engine
engineCommand: cwlNodeEngine.js