Snakemake Local Example

Minimal Snakemake workflow that:

• runs PyDESeq2 on real RNA-seq counts from GSE240671
• uses R + ggpubr to make an MA-plot and a top-gene boxplot

Setup

Create an environment with Snakemake and Conda (needed for --use-conda):

mamba env create -f environment.yml
mamba activate snakemake-example

This gives you a shell where you can run snakemake. When the workflow runs, Snakemake will create the Python and R environments it needs from the small files in envs/.

Run the workflow

From the repo root:

snakemake --use-conda -j 1

To have Snakemake use mamba (faster) when creating rule envs, add --conda-frontend mamba.

This will write:

• a DE results table for GSE240671
• an MA-plot PNG and a top-gene boxplot PNG

Files in this example

• Snakefile – defines the rules.
• config.yml – small config with data paths.
• envs/ – tiny Conda env files used by each rule.
• scripts/ – Python and R scripts called by the rules.
• results/ – output folder created by Snakemake.
• logs/ – text logs and simple timing info for each rule.