Workshop 3 Introduction Slides

Workflow Automation with Snakemake

• Make your genome analysis reproducible and shareable
• Refactor your previous scripts into a Snakemake workflow
• Use LLMs to help design, implement, and debug your workflow

Problem Statement

• Refactor your scripts from previous workshops into a Snakemake workflow
• Automate steps for downloading data, running sequence analysis, and summarizing results
• Run your workflow on the compute cluster
• Summarize your workflow and findings for your PI

Why Use Workflow Management?

• Ensures reproducibility and transparency
• Automates complex, multi-step analyses
• Facilitates collaboration and sharing

What is Snakemake?

• A workflow management system for reproducible data analysis
• Uses a simple, readable syntax to define rules and dependencies
• Integrates easily with Python scripts and cluster computing

Workshop Workflow: Problem → Prompt → Code → Debug → Result

• Problem: Define the workflow challenge
• Prompt: Craft an effective LLM prompt
• Code: Generate and run Snakemake rules
• Debug: Identify and fix errors (locally and on the cluster)
• Result: Summarize and interpret findings

Getting Started: Example LLM Prompt

I need to refactor my genome analysis scripts into a Snakemake
workflow that downloads an ancient genome FASTA file, computes
sequence statistics, and summarizes the results. Please generate
a Snakefile and example rule for running the analysis on a compute
cluster.