If a workflow fails during a test, test fail steps are not exited - Githubissues

PMCC-BioinformaticsCore / janis

[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows

https://janis.readthedocs.io/

GNU General Public License v3.0

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If a workflow fails during a test, test fail steps are not exited #37

Open illusional opened 3 years ago

illusional commented 3 years ago

FYI @junyk

I believe this is because a SystemExit error is raised (by calling sys.exit) if the workflow / tool fails to run: https://github.com/PMCC-BioinformaticsCore/janis-assistant/blob/fbcefc665a9a23073830acb8f87cc41ea58bcf8f/janis_assistant/management/workflowmanager.py#L595-L598.

These need to be caught separately.