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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.

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.

Snakemake formatting

We use snakefmt to ensure consistency in style across Snakemake files in this project.

Installing

  • Using mamba/bioconda:
mamba install -c bioconda snakefmt
  • Using pip:
pip install snakefmt

IDE-independent

  1. Check for styling issues with snakefmt --check .
  2. Automatically fix styling issues with snakefmt .

Using VSCode extension

  1. Install the VSCode extension
  2. Check for styling issues with Ctrl+Shift+P and select snakefmt: Check
  3. Automatically fix styling issues with Ctrl+Shift+P and select Format document