Apply best practices across all modules

[sreichl]

1. add test data/configs
2. add quick start
3. containerize with Snakemake
4. lint & format
5. add GitHub actions for lint, test, container generation, environment pinnning,...

[sreichl]

double check if that makes sense as best-practice and then systematically implement everywhere (maybe separate issue)
Do not hardcode input paths
Use rules.<rule name>.output.<output name>
One can change the output path without worrying about breaking the pipeline