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+# Developer guide
+
+## CI
+
+Checks are automatically run on certain pushed commits for testing and linting
+purposes. Some are defined by [.github/workflows/ci.yaml][] while others are
+configured outside of this repository.
+
+[.github/workflows/ci.yaml]: ./.github/workflows/ci.yaml
+
+## Pre-commit
+
+[pre-commit][] is used for various checks (see [configuration][]).
+
+You can either [install it yourself][] to catch issues before pushing or look
+for the [pre-commit.ci run][] after pushing.
+
+[pre-commit]: https://pre-commit.com/
+[configuration]: ./.pre-commit-config.yaml
+[install it yourself]: https://pre-commit.com/#install
+[pre-commit.ci run]: https://results.pre-commit.ci/repo/github/493877605
+
+## Snakemake formatting
+
+We use [`snakefmt`](https://github.com/snakemake/snakefmt) to ensure consistency in style across Snakemake files in this project.
+
+### Installing
+
+- Using mamba/bioconda:
+
+```bash
+mamba install -c bioconda snakefmt
+```
+
+- Using pip:
+
+```bash
+pip install snakefmt
+```
+
+### IDE-independent
+
+1. Check for styling issues with `snakefmt --check .`
+1. Automatically fix styling issues with `snakefmt .`
+
+### Using VSCode extension
+
+1. Install the [VSCode extension](https://marketplace.visualstudio.com/items?itemName=tfehlmann.snakefmt)
+1. Check for styling issues with `Ctrl+Shift+P` and select `snakefmt: Check`
+1. Automatically fix styling issues with `Ctrl+Shift+P` and select `Format document`