A hands-on course that takes you from limited bioinformatics experience to running your own nf-core pipelines.
Everything runs in the browser via GitHub Codespaces — nothing to install.
🌐 Prefer a rendered site? Take the course at eco-flow.github.io/training
Work through it top to bottom — or jump to whatever you need.
| Part | Lesson | Type | What you'll do |
|---|---|---|---|
| 0 | Setup | Practical | Get your environment ready with GitHub Codespaces, so you can run everything from your browser. |
| 1 | Command line basics | Practical · optional | A gentle introduction to the command line. Skip this part if you're already comfortable in a terminal. |
| 2 | Pipelines with Nextflow | Lecture | What Nextflow and nf-core are, and why pipelines matter for reproducible, scalable science. |
| 3 | Run an nf-core RNA-Seq pipeline | Practical | Hands-on — run a real nf-core/rnaseq analysis end to end, from raw reads to results. |
🚧 Coming soon — Part 4 · Differential expression (Practical · R): analyse the gene counts from Part 3 with DESeq2 to find differentially expressed genes. (Draft — still in progress.)
- Click Open in GitHub Codespaces above (or use the green Code → Codespaces button).
- Wait a minute or two for the environment to build — Nextflow, Java, Docker and all the data are pre-installed.
- Begin with Part 0 · Setup.
Eco-Flow builds reproducible bioinformatics pipelines and provides foundational, hands-on Nextflow and nf-core training. Want to hear about future courses? Email us to join the mailing list: ecoflow . ucl @ gmail . com
- Official Nextflow training — https://training.nextflow.io/
- nf-core community & pipelines — https://nf-co.re/
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