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Snakemake-Profiles / slurm

Cookiecutter for snakemake slurm profile
MIT License
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Update tests #58

Closed percyfal closed 4 years ago

percyfal commented 4 years ago

This a major rewrite of the testing infrastructure with the aim of making the tests more accessible and easy to use. Among other things, tests can now be run on a HPC running the SLURM scheduler.

The documentation has been expanded with examples of how to use the profile, and on how tests are setup.

There are also a couple of bug fixes / feature improvements.

percyfal commented 4 years ago

@mwort Following up on the discussion previously this year (https://github.com/Snakemake-Profiles/slurm/pull/33#issuecomment-594412731), I have now finally gotten round to rewriting the test suite. Now it should be possible to run tests locally on a HPC with SLURM. Would you mind trying out the features in this branch before I merge? I'm not asking for a code review as such, but rather would like some feedback on whether this does what you wanted in terms of running tests on a HPC. Of course, suggestions for improvements to code and/or documentation are also very welcome!

EDIT: there still are some issues with the github actions where tests fail, but that seems to have more to do with problems setting up the docker stack - I manage to run the tests locally without problem.

Cheers,

Per