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awslabs / amazon-omics-tools

Apache License 2.0
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run analyzer fails when workflow doesn't exist #75

Open avigailmo opened 4 days ago

avigailmo commented 4 days ago

this line: https://github.com/awslabs/amazon-omics-tools/blob/main/omics/cli/run_analyzer/__main__.py#L574

fails if the HealthOmics workflow was already deleted Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File ".venv/lib/python3.11/site-packages/omics/cli/run_analyzer/main.py", line 574, in engine = omics.get_workflow(id=wfid)["engine"] botocore.errorfactory.ResourceNotFoundException: An error occurred (ResourceNotFoundException) when calling the GetWorkflow operation: Workflow 3910207 not found

The workflow engine is used when --write-config flag is on (only in nextflow) but this failure happens also when it not used.

markjschreiber commented 3 days ago

Thanks for the bug report. Can you share the command line that produced the error? What flags (if any) were set on the command line? Was the tool running in Batch mode?

avigailmo commented 3 days ago

Thanks for the bug report. Can you share the command line that produced the error? What flags (if any) were set on the command line? Was the tool running in Batch mode?

I get the error even when running the simplest command without any flag: python -m omics.cli.run_analyzer 3048418 non batch mode