The (Unofficial) Snakemake Book
Working heavily on finishing the book now, check back in a few months
The stuff at gitbook is really outdated, currently working on a latex version
Several non-coding biologists (who want to become coding biologists) have told me they would like to learn Snakemake. Therefore, I have started writing a book with exercises.
I hope the community will make PRs to improve the language, code examples, explanations, structure (both high- and low-level) and anything else you can think of.
Note that some knowledge of coding in Python and using the shell is required. See Learn Python The Hard Way for a free introduction. Don't worry about the title, that book is probably the friendliest introduction to programming you can find! It also has an appendix with a crash course in shell usage.
If there is something you do not understand, or you have suggestions for improvements please create an issue here: https://github.com/endrebak/snakemake-book/issues I'd like to continually improve the book, and your feedback will make it much, much easier!
The code is available at
https://github.com/endrebak/snakemake-book
and the book itself at