How to force Snakemake to rerun a rule and visualize a pipeline (CC257)

October 17, 2022 • PD Schloss • 1 min read • •

In this Code Club, Pat shares how to visualize the structure of a Snakemake pipeline and force Snakemake to rerun a rule. In this application we are rerunning a rule because we need to pull fresh data from the NOAA website. After getting fresh data, Pat refactors the R code that he wrote in the last episode for calculating the z-score of the amount of monthly precipitation relative to the same month over the past century. He does this using filter, group_by, mutate, and select. The overall goal of this project is to highlight reproducible research practices using a number of tools. The specific output from this project will be a map-based visual that shows the level of drought across the globe.

Code

You can browse the state of the repository at the

• beginning of the episode
• end of the episode