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@@ -52,10 +52,11 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
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-`user/`: files that should be provided by users. Document them well!
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-`automatic/`: files that the module downloads or prepares in intermediate steps.
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-`results/`: files generated by the module's algorithms that are relevant to the user.
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- Pre-made integration test setup for your module.
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- Pre-made integration setup for your module.
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- Continuous Integration (CI) settings, ready for [pre-commit.ci](https://pre-commit.ci/).
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- GitHub actions to automate chores during pull requests and releases.
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- Premade `pytest` setup.
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-Optional auto-generated documentation, ready for [Read the Docs](https://about.readthedocs.com/) or [Github Pages](https://pages.github.com/).
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-Documentation setup, ready for [Read the Docs](https://about.readthedocs.com/) or [Github Pages](https://pages.github.com/).
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> [!IMPORTANT]
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>
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> -`config/config.yaml`: a basic functioning example of how to configure this module.
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> -`workflow/internal/config.schema.yaml`: the module's configuration schema, used by `snakemake` for [validation](https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html).
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> -`AUTHORS` / `CITATION.cff` / `LICENSE`: licensing and attribution of this module's code and methods.
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> - If the optional auto-generated documentation was selected, `docs/hooks/clio_standard.py` will use these files to automatically generate a basic Read the Docs website.
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