Unable to run packed workflow [revsort.cwl available in the public repository]

[FarahZKhan]

Expected Behavior

Workflow should run as I am using a packed.cwl file generated by cwltool --pack command.

Actual Behavior

Error as follows:

../../cwltool.py 1.0.20170720184656
[provenance] Temporary research object: /var/folders/tl/1j6jy66x3nvfbxt8ycs_q21m0000gn/T/tmpLU5UWw
Resolved 'packed.cwl' to 'file:///Users/farahkhan/Desktop/cwltool/fred/workflow/packed.cwl'
I'm sorry, I couldn't load this CWL file.  The error was:
Traceback (most recent call last):
  File "/Users/farahkhan/Desktop/cwltool/cwltool/main.py", line 813, in main
    args.ro.packed_workflow(print_pack(document_loader, processobj, uri, metadata))
  File "/Users/farahkhan/Desktop/cwltool/cwltool/main.py", line 650, in print_pack
    packed = pack(document_loader, processobj, uri, metadata)
  File "/Users/farahkhan/Desktop/cwltool/cwltool/pack.py", line 144, in pack
    v = rewrite[r]

Workflow Code

{
    "cwlVersion": "v1.0", 
    "$schemas": [
        "file:///Users/farahkhan/Desktop/cwltool/tests/wf/empty.ttl"
    ], 
    "$graph": [
        {
            "class": "Workflow", 
            "doc": "Reverse the lines in a document, then sort those lines.", 
            "hints": [
                {
                    "class": "DockerRequirement", 
                    "dockerPull": "debian:8"
                }
            ], 
            "inputs": [
                {
                    "type": "File", 
                    "doc": "The input file to be processed.", 
                    "default": {
                        "class": "File", 
                        "location": "file:///Users/farahkhan/Desktop/cwltool/tests/wf/hello.txt"
                    }, 
                    "id": "#main/input"
                }, 
                {
                    "type": "boolean", 
                    "default": true, 
                    "doc": "If true, reverse (decending) sort", 
                    "id": "#main/reverse_sort"
                }
            ], 
            "outputs": [
                {
                    "type": "File", 
                    "outputSource": "#main/sorted/output", 
                    "doc": "The output with the lines reversed and sorted.", 
                    "id": "#main/output"
                }
            ], 
            "steps": [
                {
                    "in": [
                        {
                            "source": "#main/input", 
                            "id": "#main/rev/input"
                        }
                    ], 
                    "out": [
                        "#main/rev/output"
                    ], 
                    "run": "#revtool.cwl", 
                    "id": "#main/rev"
                }, 
                {
                    "in": [
                        {
                            "source": "#main/rev/output", 
                            "id": "#main/sorted/input"
                        }, 
                        {
                            "source": "#main/reverse_sort", 
                            "id": "#main/sorted/reverse"
                        }
                    ], 
                    "out": [
                        "#main/sorted/output"
                    ], 
                    "run": "#sorttool.cwl", 
                    "id": "#main/sorted"
                }
            ], 
            "id": "#main"
        }, 
        {
            "class": "CommandLineTool", 
            "doc": "Reverse each line using the `rev` command", 
            "inputs": [
                {
                    "type": "File", 
                    "inputBinding": {}, 
                    "id": "#revtool.cwl/input"
                }
            ], 
            "outputs": [
                {
                    "type": "File", 
                    "outputBinding": {
                        "glob": "output.txt"
                    }, 
                    "id": "#revtool.cwl/output"
                }
            ], 
            "baseCommand": "rev", 
            "stdout": "output.txt", 
            "id": "#revtool.cwl"
        }, 
        {
            "class": "CommandLineTool", 
            "doc": "Sort lines using the `sort` command", 
            "inputs": [
                {
                    "id": "#sorttool.cwl/reverse", 
                    "type": "boolean", 
                    "inputBinding": {
                        "position": 1, 
                        "prefix": "--reverse"
                    }
                }, 
                {
                    "id": "#sorttool.cwl/input", 
                    "type": "File", 
                    "inputBinding": {
                        "position": 2
                    }
                }
            ], 
            "outputs": [
                {
                    "id": "#sorttool.cwl/output", 
                    "type": "File", 
                    "outputBinding": {
                        "glob": "output.txt"
                    }
                }
            ], 
            "baseCommand": "sort", 
            "stdout": "output.txt", 
            "id": "#sorttool.cwl"
        }
    ]
}

Full Traceback

../../cwltool.py 1.0.20170720184656
Resolved 'packed.cwl' to 'file:///Users/farahkhan/Desktop/cwltool/fred/workflow/packed.cwl'
Tool definition failed initialization:
Tool file contains graph of multiple objects, must specify one of #main, #revtool.cwl, #sorttool.cwl
Traceback (most recent call last):
  File "/Users/farahkhan/Desktop/cwltool/cwltool/main.py", line 832, in main
    makeTool, make_tool_kwds)
  File "/Users/farahkhan/Desktop/cwltool/cwltool/load_tool.py", line 239, in make_tool
    urllib.parse.urldefrag(i["id"])[1] for i in resolveduri
WorkflowException: Tool file contains graph of multiple objects, must specify one of #main, #revtool.cwl, #sorttool.cwl

Your Environment

• cwltool version: 1.0.20170720184656

[mr-c]

Hello @FarahZKhan,

Did you try appending #main as requested in the error message?

[FarahZKhan]

Hi Michael,
From the look of the packed file, #main is appended already?
Where do you suggest adding it in addition to the existing #main tags?

[FarahZKhan]

Hi @mr-c This error was resolved when we run as:
cwltool packed.cwl#main. Thanks for your help.