galaxyproject / galaxyproject/loom
Workflow invocation mangles empty/optional parameters (ConnectedValue object stringified into the value)
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Description
Reported via Orbit beta feedback (0.3.0).
Invoking a workflow with an empty/unset optional parameter sends the literal Python repr of a Galaxy `ConnectedValue` object as the value instead of leaving it empty. fastp then rejects it:
ERROR: the adapter can only have bases in {A, T, C, G},
but the given sequence is: XX
So an empty `adapter_sequence` gets serialized as the placeholder object's repr rather than an empty string / omitted field. The tester worked around it by retrying with empty adapters cleared.
This is in the workflow-invocation input construction (the `galaxy_invoke_workflow` payload mapping): when a step input is connected but has no literal value, we pass the placeholder object through as a string. Empty/optional params should be omitted or sent empty, not stringified.
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