common-workflow-language / common-workflow-language/cwltool
error with checker.py
- Dominant language
- Python
- Stars
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- 2d 7h
- Merged PRs (30d)
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Description
`cwltool --validate --debug https://github.com/genome/analysis-workflows/raw/fa0bf2a51b72cd0869253943b67aa8e271633945/definitions/pipelines/germline_wgs.cwl`
```
I'm sorry, I couldn't load this CWL file.
The error was:
Traceback (most recent call last):
File "/home/michael/cwltool/cwltool/main.py", line 675, in main
tool = make_tool(uri, loadingContext)
File "/home/michael/cwltool/cwltool/load_tool.py", line 351, in make_tool
tool = loadingContext.construct_tool_object(processobj, loadingContext)
File "/home/michael/cwltool/cwltool/workflow.py", line 55, in default_make_tool
return Workflow(toolpath_object, loadingContext)
File "/home/michael/cwltool/cwltool/workflow.py", line 535, in __init__
loadingContext.prov_obj))
File "/home/michael/cwltool/cwltool/workflow.py", line 569, in make_workflow_step
return WorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv)
File "/home/michael/cwltool/cwltool/workflow.py", line 630, in __init__
toolpath_object["run"], loadingContext)
File "/home/michael/cwltool/cwltool/load_tool.py", line 373, in load_tool
loadingContext)
File "/home/michael/cwltool/cwltool/load_tool.py", line 351, in make_tool
tool = loadingContext.construct_tool_object(processobj, loadingContext)
File "/home/michael/cwltool/cwltool/workflow.py", line 55, in default_make_tool
return Workflow(toolpath_object, loadingContext)
File "/home/michael/cwltool/cwltool/workflow.py", line 560, in __init__
static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs, param_to_step)
File "/home/michael/cwltool/cwltool/checker.py", line 168, in static_checker
raise exc
File "/home/michael/cwltool/cwltool/checker.py", line 164, in static_checker
sinksf = sorted([p["pattern"] for p in sink.get("secondaryFiles", []) if p.get("required", True)])
File "/home/michael/cwltool/cwltool/checker.py", line 164, in
sinksf = sorted([p["pattern"] for p in sink.get("secondaryFiles", []) if p.get("required", True)])
AttributeError: 'str' object has no attribute 'get'
```
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