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CONTRIBUTING.md

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Contributing

Helping Out

There are TODOs that better enhance the reproducability of datasets or analysis of algorithm outputs, as well as open resolvable issues.

Adding a dataset

To add a dataset (see datasets/yeast-osmotic-stress as an example of a dataset):

  1. Check that your dataset provider isn't already added (some of these datasets act as providers for multiple datasets)
  2. Create a new folder under datasets/<your-dataset>
  3. Add a raw folder containing your data
  4. Add an attached Snakefile that converts your raw data to processed data.
    • Make sure to use uv here. See yeast-osmotic-stress's Snakefile for an example.
  5. Add your Snakefile to the top-level run_snakemake.sh file.
  6. Add your datasets to the appropiate configs
    • If your dataset has gold standards, make sure to include them here.

Adding an algorithm

If you want to add an algorithm, refer to the SPRAS repository instead. If you want to test your new algorithm you PRed to SPRAS, you can swap out the spras submodule that this repository uses with your fork of SPRAS.