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refactor: unify snakemake versions between envs #16
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As mentioned in #11, the GH Action for miniconda had some random problems with the installation. I have fixed that in this PR by removing the miniconda version fix in the CI workflow. It will always download the most recent one, which is good. I updated the snakemake version in the conda env but then it required mamba too for package management within the zarp workflow (for automatic env generation). So I have added mamba as a dependency and let it run.
This would suggest we need to use different expected output for conda and singularity executions<?> |
What I described above (#16 (comment)) is a separate issue, linked to conda->mamba improvement. I have now fixed the configuration so that we always use conda frontend, as we have always been. |
Sorry @AngryMaciek I did not see the notifications earlier. I will have a look at the open PRs soon. |
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Based on the points mentioned in the discussion, these changes look reasonable to me. Given that the tests pass, I would tend to say let's merge this. But I'm not an expert on Conda, Singularity or Snakemake execution, so I think we should wait for @fgypas review as well
@fgypas : could you plese review the change? |
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Did you also test the cluster execution with the current version?
Yes, the outcome is the same as for local tests. |
Update older snakemake version for the root-dedicated conda env.
Fixes #10