Reproducible Bioinformatics with Pixi, Nextflow & Snakemake
1 👋 Welcome
Welcome to the workshop on Reproducible Bioinformatics Using Pixi, Nextflow, and Snakemake.
This training focuses on making bioinformatics 💻 workflows:
✅ Reproducible
✅ Portable
✅ Automated
✅ Easy to share
2 🎯 Objectives
By the end of this workshop you will:
- Understand why reproducibility matters
- Know how to use Pixi for environment & workflow management
- Build multi-step automated workflows
- Run pipelines with Nextflow and/or Snakemake
- Generate QC and reproducible reports
3 📅 Schedule
| Time | Session | Duration | Topics Covered |
|---|---|---|---|
| 09:00-09:10 | 📖 Session 1 — Introduction | 10 min | - What is reproducibility? - Why Conda fails - Why Pixi fixes it |
| 09:10-09:55 | 📦 Session 2 — Pixi Basics | 45 min | Creating projects Adding packages Running tasks Hands-on exercise |
| 09:55-10:35 | 🔧 Session 3 — Pipelines | 40 min | Creating QC workflow Task dependencies Automation best practices |
| 10:35-10:45 | ☕ Break | 10 min | — |
| 10:45-11:15 | 🔄 Session 4 — Nextflow + Pixi | 30 min | Per-process envs Running full workflows |
| 11:15-11:45 | 🐍 Session 5 — Snakemake + Pixi | 30 min | Rule-based automation Conda/envs |
| 11:45-12:00 | ✅ Wrap-up | 15 min | Quiz Q&A Git/GitHub sharing |
Use the navigation bar to explore each module.