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Unexpected behavior of onstart & onsuccess with modules: Inner onstart overwrites outer ones #3920

@jonasfreimuth

Description

@jonasfreimuth

Snakemake version

v9.14.6

Describe the bug

When using a module (via the module: directive), which contains onstart / onsuccess directives, these directives will overwrite the onstart / onsuccess directives of the importing workflow. This is unexpected and potentially undesirable behavior as the code for a module may not be under the control of the importing workflow's developer. As far as I can tell the configuration seems to not indicate any expected behavior on this.

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Minimal example

A test has been added in https://github.com/TRON-Bioinformatics/snakemake/tree/check-module-onstart-onsuccess. Run it via pixi run -e dev pytest tests/tests.py::test_module_onstart_onsuccess.

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