Overview

Instructor(s): Dr. Wes Brashear

Time: Friday, October 24, 2025 — 1:30PM-4:00PM CT

Location: Blocker 220

Prerequisite(s): Active HPRC account

Snakemake is a Python-based workflow management system for creating reproducible and scalable data science pipelines. Snakemake workflows can help manage software versioning, parameter selection, and generate interactive, shareable, browser-based reports. Students will learn best practices on how to incorporate Snakemake in their workflows on HPRC systems and complete hands-on exercises creating simple Snakemake workflows to more complex, multi-step pipelines culminating in descriptive workflow reports. Examples in this course will utilize common bioinformatic workflows, but the concepts covered can be applied to any pipelines incorporating data science.

Course Materials

Presentation slides

The presentation slides will be made available as downloadable PDF files.

Learning Objectives

Participants will be able to:

• Explain Snakemake workflow management system
• Explain best practices for using Snakemake on HPRC systems
• Create and execute Snakemake workflows
• Use Snakemake to generate interactive workflow reports

Note: During the class sessions many aspects of the material will be illustrated live via a login to an HPRC Cluster. Attendees will log into the Grace cluster using their own computers to follow along and complete exercises.

You are encouraged to contact the HPRC helpdesk with any questions regarding HPRC clusters.