Changed outputSource refScope from 0 to 1

[GlassOfWhiskey]

This change allows a corret id reference in the outputSource field of WorkflowOutputParameter objects

[codecov]

Codecov Report

Merging #1714 (9407590) into main (0e2ced5) will decrease coverage by 12.03%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##             main    #1714       +/-   ##
===========================================
- Coverage   66.58%   54.54%   -12.04%     
===========================================
  Files          89       45       -44     
  Lines       15850     7950     -7900     
  Branches     4188     2059     -2129     
===========================================
- Hits        10553     4336     -6217     
+ Misses       4207     3090     -1117     
+ Partials     1090      524      -566     

Impacted Files	Coverage Δ
cwltool/provenance_constants.py
cwltool/pack.py
cwltool/udocker.py
cwltool/main.py
cwltool/errors.py
cwltool/cuda.py
cwltool/checker.py
cwltool/argparser.py
cwltool/docker.py
cwltool/mpi.py
... and 34 more

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[GlassOfWhiskey]

This PR allows to unify the behaviour of cwltool.load_tool parser and the schema_salad generated parser in cwl-utils. Indeed, consider the simple Workflow example

cwlVersion: v1.2
class: Workflow
id: a
inputs:
  a: int
outputs:
  a:
    type: int
    outputSource: a
steps: []

In this case, with cwltool we have

{
    "class": "Workflow",
    "cwlVersion": "v1.2",
    "id": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a",
    "inputs": [
        {
            "id": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a/a",
            "type": "int"
        }
    ],
    "outputs": [
        {
            "id": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a/a",
            "outputSource": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a/a",
            "type": "int"
        }
    ],
    "steps": []
}

while with the schema_salad parser we have

{
    "class": "Workflow",
    "cwlVersion": "v1.2",
    "id": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a",
    "inputs": [
        {
            "id": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a/a",
            "type": "int"
        }
    ],
    "outputs": [
        {
            "id": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a/a",
            "outputSource": "file:///home/glassofwhiskey/Projects/streamflow/source/examples/a.cwl#a/a/a",
            "type": "int"
        }
    ],
    "steps": []
}

The cwltool behaviour is correct, while the schema_salad parser puts an additional scope level in the outputSource field, which references an element that does not exist.
Note however that the clash between input and output (and potentially step) ids is present in both cwltool and schema_salad parser, but it is not related to the outputSource scope.

[mr-c]

Closing; this will get fixed in CWL v1.2.1