Init Project Structure - Githubissues

roshankern commented 1 month ago

In this PR we set up the tool structure and an example analysis for further development. We add:

Main Snakefile that will be the entry point for all other BrieFlow rules
Example analysis with:
- config.yml and associated sbs/phenotype sample tsvs.
- Jupyter notebook to create sbs/phenotype sample tsvs.
- run_analysis.sh script that runs main Snakefile with config

@mat10d this is ready for review! Let me know if you have questions about this setup.

Note: I plan on including no data on this repo until we set up integration/unit tests with the proper data.

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mat10d commented 1 month ago

Overall, this looks good. You may need to think harder about how to reshape the preprocessing pipeline based on the .tsvs, but this will come next.

A good question is if we want jupyter notebooks that are outputting these files for each step--these could be good things to have in the _example notebooks.

cheeseman-lab / brieflow

Init Project Structure #1