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skinniderlab / CLM

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changes to snakemake README; snakemake can be run with zero configuration changes #178

Closed vineetbansal closed 1 month ago

vineetbansal commented 1 month ago

In preparing the documentation for our summer work, I made some changes to the README, generated the dag/rulegraph again, and made config_fast.json consistent with what tests/test_snakemake.py is doing, so it can be run in reasonable time.

Since we're shipping some sample data with our code anyway, I made Snakefile pick up these files by default. I think it's important that a new developer be able to run the workflow as a first step without having to download/configure anything, even if the results are not interpretable.

vineetbansal commented 1 month ago

In the second commit here, I've converted config.json to config.yaml and updated its references. This should help in inline documentation going forward.