snakehooks

git hooks for snakemake pipelines

Getting started

Writing maintainable pipelines requires automatic checks to ensure:

• That the syntax is OK.
• That the scripts and source code adheres to some type of language conventions to prevent smelly code.
• That the documente

Prerequisites

• snakemake,
• shellcheck,
• yamllint>=1.11.1: the --strict option happens here
• pylint

Installing

Link or move pre-commit to .git/hooks/, or run ./src/snakehooks/link_hooks supposing that this repo is installed in src/.

Running it

git commit

That's all. The tests will be run in the following order:

• snakemake clean to remove previous builds,
• snakemake --dryrun to check the snakefiles,
• pylint over the Snakefiles and the subworkflows in src/snakefiles/,
• pylint over *.py scripts that are not in src/snakefiles/,
• yamllint over *.{yaml, yml} files, and
• snakemake to run the pipeline from beginning to end.

Contributing

Do you want to propose another tool? To modify an existing one? Fork and make a PR!