I’ve been spending alot of time using snakemake recently, and I absoutly love it. It makes processing a ton of files relativly easy, and does a ton of the self documenting itself. Paired with this is that it’s far more pliable than a bash script.
That being said, I feel like I revisit the same 20 stack overflow examples. So, here’s an ever updating list of examples I find useful
How to mix Globbing and Wilcards https://www.bioinformatics.stackexchange.com/questions/7184/mix-globbing-and-wildcards-when-specifying-rule-input
How to use a nested YAML file Long but worth it https://www.stackoverflow.com/questions/50198628/snakemake-confusion-on-how-to-access-config-files-properly