`--single-process` does not work for steps in nested workflows

[jdidion]

I am trying to using --single-process to execute a step in a subworkflow in the packed form of https://github.com/common-workflow-language/cwl-v1.2/tree/main/tests/count-lines8-wf.cwl. No matter how I specify the step cwltool cannot find it:

cwltool --debug --single-process count-lines-wf/step1 test/cwl_conformance/workflows/count-lines8-wf.cwl.json foo.json
INFO /Users/jdidion/.pyenv/versions/3.6.14/envs/dxc/bin/cwltool 3.1.20210901184224
INFO Resolved 'test/cwl_conformance/workflows/count-lines8-wf.cwl.json' to 'file:///Users/jdidion/projects/dxCompiler/test/cwl_conformance/workflows/count-lines8-wf.cwl.json'
ERROR I'm sorry, I couldn't load this CWL file.
The error was: 
Traceback (most recent call last):
  File "/Users/jdidion/.pyenv/versions/3.6.14/envs/dxc/lib/python3.6/site-packages/cwltool/main.py", line 1117, in main
    ctool = choose_process(args, tool, loadingContext)
  File "/Users/jdidion/.pyenv/versions/3.6.14/envs/dxc/lib/python3.6/site-packages/cwltool/main.py", line 854, in choose_process
    loadingContext.loader.idx,
  File "/Users/jdidion/.pyenv/versions/3.6.14/envs/dxc/lib/python3.6/site-packages/cwltool/subgraph.py", line 202, in get_process
    raise Exception(f"Step {step_id} was not found")
Exception: Step file:///Users/jdidion/projects/dxCompiler/test/cwl_conformance/workflows/count-lines8-wf.cwl.json#main/count-lines-wf/step1 was not found

{
    "$graph": [
        {
            "class": "Workflow",
            "inputs": [
                {
                    "type": "File",
                    "id": "#count-lines1-wf.cwl/file1"
                }
            ],
            "outputs": [
                {
                    "type": "int",
                    "outputSource": "#count-lines1-wf.cwl/step2/output",
                    "id": "#count-lines1-wf.cwl/count_output"
                }
            ],
            "steps": [
                {
                    "run": "#wc-tool.cwl",
                    "in": [
                        {
                            "source": "#count-lines1-wf.cwl/file1",
                            "id": "#count-lines1-wf.cwl/step1/file1"
                        }
                    ],
                    "out": [
                        "#count-lines1-wf.cwl/step1/output"
                    ],
                    "id": "#count-lines1-wf.cwl/step1"
                },
                {
                    "run": "#parseInt-tool.cwl",
                    "in": [
                        {
                            "source": "#count-lines1-wf.cwl/step1/output",
                            "id": "#count-lines1-wf.cwl/step2/file1"
                        }
                    ],
                    "out": [
                        "#count-lines1-wf.cwl/step2/output"
                    ],
                    "id": "#count-lines1-wf.cwl/step2"
                }
            ],
            "id": "#count-lines1-wf.cwl"
        },
        {
            "class": "Workflow",
            "inputs": [
                {
                    "type": "File",
                    "id": "#main/file1"
                }
            ],
            "outputs": [
                {
                    "type": "int",
                    "outputSource": "#main/step1/count_output",
                    "id": "#main/count_output"
                }
            ],
            "requirements": [
                {
                    "class": "SubworkflowFeatureRequirement"
                }
            ],
            "steps": [
                {
                    "run": "#count-lines1-wf.cwl",
                    "in": [
                        {
                            "source": "#main/file1",
                            "id": "#main/step1/file1"
                        }
                    ],
                    "out": [
                        "#main/step1/count_output"
                    ],
                    "id": "#main/step1"
                }
            ],
            "id": "#main"
        },
        {
            "class": "ExpressionTool",
            "requirements": [
                {
                    "class": "InlineJavascriptRequirement"
                }
            ],
            "inputs": [
                {
                    "type": "File",
                    "loadContents": true,
                    "id": "#parseInt-tool.cwl/file1"
                }
            ],
            "outputs": [
                {
                    "type": "int",
                    "id": "#parseInt-tool.cwl/output"
                }
            ],
            "expression": "$({'output': parseInt(inputs.file1.contents)})",
            "id": "#parseInt-tool.cwl"
        },
        {
            "class": "CommandLineTool",
            "inputs": [
                {
                    "type": "File",
                    "id": "#wc-tool.cwl/file1"
                }
            ],
            "outputs": [
                {
                    "type": "File",
                    "outputBinding": {
                        "glob": "output"
                    },
                    "id": "#wc-tool.cwl/output"
                }
            ],
            "baseCommand": [
                "wc",
                "-l"
            ],
            "stdin": "$(inputs.file1.path)",
            "stdout": "output",
            "id": "#wc-tool.cwl"
        }
    ],
    "cwlVersion": "v1.2"
}

[mr-c]

Using #1558

$ cwltool --print-targets https://github.com/common-workflow-language/cwl-v1.2/raw/1f3ef888d9ef2306c828065c460c1800604f0de4/tests/count-lines8-wf.cwl
INFO /home/michael/cwltool/env3.10/bin/cwltool 3.1.20211030003340
INFO  Output targets:
  count_output
INFO  Input targets:
  file1
INFO  steps targets:
  step1
INFO step1 Output targets:
  step1/count_output
INFO step1 Input targets:
  step1/file1
INFO step1 steps targets:
  step1/step1
INFO step1 Output targets:
  step1/output
INFO step1 Input targets:
  step1/file1
  step1/step2
INFO step2 Output targets:
  step2/output
INFO step2 Input targets:
  step2/file1

$ cwltool --single-process step1/step1  https://github.com/common-workflow-language/cwl-v1.2/raw/1f3ef888d9ef2306c828065c460c1800604f0de4/tests/count-lines8-wf.cwl --file1 README.rst 
INFO /home/michael/cwltool/env3.10/bin/cwltool 3.1.20211030003340
INFO [job wc-tool.cwl] /tmp/0ur527tu$ wc \
    -l < /tmp/v33z8mkn/stg903c385d-7f82-4144-a6c4-b3fcf1ba835a/README.rst > /tmp/0ur527tu/output
INFO [job wc-tool.cwl] completed success
{
    "output": {
        "location": "file:///home/michael/cwltool/output",
        "basename": "output",
        "class": "File",
        "checksum": "sha1$91b38232e72e15fd0ab9a483232d6cb65f4403e2",
        "size": 4,
        "path": "/home/michael/cwltool/output"
    }
}
INFO Final process status is success

[jdidion]

Still does not work with the packed workflow.