Reorganize workflow according to best practices

[Peter9192]

Following guides at https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html
and https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html

To do:

• make sure all reads from the resources folder work correctly
• reconsider the use of the working directory? reconsider the use of the working directory #26
• run snakemake linter
• test workflow
• add license, .gitignore, and other files in example project structure
• Move to separate repo? Renamed this one and moved other files out
• another attempt at slurm? Another attempt at slurm #27
• Include analysis notebooks in workflow Include analysis notebooks in workflow #28
• insert link to blog post once published. insert link to blog post once published #29

[Peter9192]

[Peter9192]

As discussed, I'll merge this now and open follow-up issues for the remainig todo's. Blog post will be published tomorrow, this will make sure the repo is in a good state by then.