Snakemake-Profiles / slurm

Cookiecutter for snakemake slurm profile
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Making days optional in _get_cluster_config #18

Closed brand-fabian closed 5 years ago

brand-fabian commented 5 years ago

For #17:

Fix _get_cluster_configuration by adding a default value and making the days capture group otherwise optional.

In order to get the unit tests running with newer versions of the slurm image I had to do some modification to the setup_sacctmgr function, to include a shorter queue and also remove the gres gpu lines present in the slurm config.

Note on test-environment.yml:

percyfal commented 5 years ago

Hi,

thanks for looking into the issues regarding the unit tests and updated packages. I had started to write a fix prior to the summer holidays but didn't have time to finish them then. Merging these fixes will resolve the issue of pytest_namespace and other things. See additional comments to code.

Cheers