Overview

Instructor(s): Dr. Wes Brashear

Time: April 2026

Location: Online using Zoom

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.

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Course Materials

• Incorporating Snakemake in HPC Workflows (Fall 2025): PDF

Participation

During the training, attendees are expected to log in to an HPRC cluster using their own computer and complete the instructor-led examples and exercises.

Learning Objectives and Agenda

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