static code analysis

[AngryMaciek]

Is your feature request related to a problem? Please describe.
Not so much of a problem, but the code style is currently not enofrced at all. It would be good to keep consistent good coding practice throughout the repo, especially if it has multiple Py/R scripts.

Describe the solution you'd like
It is relatively easy to introduce another GitHub Actions workflow that would run static code analysis with every commit. There are linters dedicated to Python (flake8) and R (lintr) and one can set them up such that they check all the scripts upon each push. If they detect anything that should be corrected they return with an error exit code, thus triggering a fail for the whole CI workflow.

Describe alternatives you've considered
Alternatively one can hook up the repo to a service like codefactor but then the developer has less flexibility around the code analysis setup.

[dominikburri]

Snakemake also provides an own linter: https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html. So at least checking the individual rules should be covered.
Need to bump the Snakemake version though.