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Conventions around snakemake
#5103
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Thanks for looking into the Snakemake workflow and giving input. For 1.: For 2.: |
In closing this PR, I had a look at the Snakemake workflows here and there are a few things I stumbled across:
There is a best practices page in the Snakemake docs suggesting amongst other things to use
snakemake --lint
snakefmt
Snakemake provides its own environment management/deployment as well as batch system abstraction (as a plugin). This is functionality that significantly overlaps with
tbg
and both of these are delicate issues in the fragile and diverse HPC ecosystems we run in.In the current stage, our usage does not conform to any of these standards. If our strategic decisions imply to professionalise the use of Snakemake, I think there would be value in moving more into that direction. However, my personal experience is that these things are awfully fiddly to setup on a cluster and their adoption would create tensions with
tbg
. (There are, of course, some low-hanging fruits like the adoption of the directory structure and formatter, e.g., inpre-commit
.)This issue is supposed to spark a discussion and trigger a conscious decision about such things. It is by no means intended as a suggestion to implement the above ideas. Involved in this discussion should probably be at least @psychocoderHPC, @PrometheusPi, @JessicaTiebel.
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