This lesson is still being designed and assembled (Pre-Alpha version)

Snakemake for Bioinformatics

A lesson in using Snakemake for bioinformatics analysis.


BASH shell (TODO - check exact prerequisites)


Setup Download files required for the lesson
00:00 1. Running commands with Snakemake How do I run a simple command with Snakemake?
00:30 2. Placeholders and Wildcards How do I make a generic rule?
00:30 3. Chaining rules How do I combine rules into a workflow?
How do I make a rule with multiple inputs and outputs?
00:30 4. How snakemake chooses what jobs to run How do I visualise a Snakemake workflow?
How does Snakemake avoid unecessary work?
How do I control what steps will be run?
00:30 5. Processing lists of inputs How do I process multiple files at once?
How do I make Snakemake decide what to process?
How do I combine multiple outputs together?
00:30 6. Quoting How do I make my Snakefiles robust?
00:30 7. Snakemake execution stages and the DAG How do I visualize what Snakemake is doing?
How do I understand and debug the errors?
00:30 8. Configuration files and parameters How do I separate my rules from my configuration?
00:30 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.