Integrating Workflows with Snakemake
Integrating Workflows with Snakemake
This unit introduces Snakemake as a way to turn analysis scripts, notebooks, and expected files into reproducible workflows. Learners first build static rules that run code and track outputs, then generalize those workflows with wildcards, expand(), and glob_wildcards() so one workflow can scale across many related files.
Sessions
Static Workflows with Snakemake
Build Snakemake rules that run code, declare outputs, and connect inputs into simple reproducible workflows.
Generalizing Workflows with Wildcards
Use wildcards, expand(), and glob_wildcards() to scale Snakemake workflows across repeated filenames and connected rules.