Automated & Reproducible Workflows with Snakemake

Name: Automated & Reproducible Workflows with Snakemake
Start: 2026-11-18T17:00:00+00:00
End: 2026-11-18T21:00:00+00:00
Location: Effie Mona Mack (EMM) 100

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When: Wednesday, November 18, 20269:00 AM – 1:00 PM PSTAdd to calendar Google Calendar
Where: Effie Mona Mack (EMM) 100Open in Maps

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Career & InternshipsComputer Science & Tech

About

Prerequisites

Comfortable working in UNIX, or the Beginner and Intermediate UNIX workshops (Nov 2 and 4)Basic understanding of Docker or the Docker workshop (Nov 9)Familiarity with Python is helpful for Snakemake syntax but not requiredLaptop running macOS, Linux, or Windows (tablets and Chromebooks won’t work)This hands-on workshop introduces Snakemake, a workflow management system for building automated, reproducible, and scalable data analysis pipelines. Learn how to organize complex analyses, manage software dependencies, and efficiently run multi-step workflows. Using a bioinformatics workflow as an example, you’ll develop pipelines that simplify complex analyses and improve reproducibility.

What you'll learn

Understand the principles of workflow automation and reproducible computational researchBuild rule-based workflows with Snakemake, including wildcards, inputs, outputs, and dependenciesAutomate multi-step analyses and manage parallel executionManage software dependencies with Conda environments and containersIntegrate Docker containers into Snakemake workflows for portable, reproducible pipelinesMonitor workflow execution, troubleshoot errors, and rerun failed or incomplete steps

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