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CWL steps given in alphabetical order rather than the order in the CWL file #326

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almanilsson opened this issue Oct 19, 2024 · 0 comments

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@almanilsson
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almanilsson commented Oct 19, 2024

If I load a CWL workflow using load_document_by_uri then the object .steps are in alphabetical order rather than the order they were given in the file.

For example parsing the attached file

cwl_obj = load_document_by_uri(cwl_filename)
for step in cwl_obj.steps:
    print( step.id.split("#")[-1])

will output
'ProteinProphet_02', 'StPeter_04', 'XTandem_01', 'XTandem_03'
instead of
'XTandem_01', 'ProteinProphet_02', 'XTandem_03', 'StPeter_04'

File contents:

# WorkflowNo_22
# This workflow is generated by APE (https://github.com/sanctuuary/APE).
cwlVersion: v1.2
class: Workflow

label: WorkflowNo_22
doc: A workflow including the tool(s) XTandem, ProteinProphet, XTandem, StPeter.

inputs:
  input_1:
    type: File
    format: "http://edamontology.org/format_3244" # mzML
  input_2:
    type: File
    format: "http://edamontology.org/format_1929" # FASTA
steps:
  XTandem_01:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/xtandem/xtandem.cwl
    in:
      XTandem_in_1: input_1
      XTandem_in_2: input_2
    out: [XTandem_out_1]
  ProteinProphet_02:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/proteinprophet/proteinprophet.cwl
    in:
      ProteinProphet_in_1: XTandem_01/XTandem_out_1
      ProteinProphet_in_2: input_2
    out: [ProteinProphet_out_1, ProteinProphet_out_2]
  XTandem_03:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/xtandem/xtandem.cwl
    in:
      XTandem_in_1: input_1
      XTandem_in_2: input_2
    out: [XTandem_out_1]
  StPeter_04:
    run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/stpeter/stpeter.cwl
    in:
      StPeter_in_1: ProteinProphet_02/ProteinProphet_out_1
      StPeter_in_2: XTandem_03/XTandem_out_1
      StPeter_in_3: input_1
    out: [StPeter_out_1]
outputs:
  output_1:
    type: File
    format: "http://edamontology.org/format_3747" # protXML
    outputSource: StPeter_04/StPeter_out_1
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