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. |
| 4 | Differential expression | Practical · R | Analyse the gene counts from Part 3 with DESeq2 to find differentially expressed genes. |
| 5 | Run an nf-core ampliseq pipeline | Practical · 🚧 draft | Run a real nf-core/ampliseq analysis on amplicon sequencing data. |
| 6 | Run nanoporemetabarcoding pipeline | Practical | Run the nanopore metabarcoding pipeline. |
| 7 | Interacting with code on GitHub | Practical | Issues, Pull Requests, READMEs and Claude Code — how to report, fix and contribute changes, using the nanopore pipeline as the example. |
| 8 | Running a pipeline on an HPC | Practical · optional | Turn your Codespace into a working Slurm cluster and run an nf-core pipeline through it — submit and watch jobs, let Nextflow do the submitting, keep a run alive, then see what changes on your own cluster. No HPC account needed. |
| 9 | Monitoring runs with Seqera Platform | Practical · optional | Follow your runs live in the browser with Seqera Platform, from Codespaces or your HPC, plus an overview of launching pipelines from it. |
| ★ | Advanced: setting up Nextflow for your HPC | Advanced · optional | Write a config for a Slurm/SGE cluster that doesn't have one yet — talk to your admin, adapt a config, and test it. |
🚧 Part 5 is still a draft, and the ★ Advanced HPC page is optional reference material for people setting up a cluster config — if you just want to run a pipeline on your cluster, start with Part 8.
- 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/
🌳 🌳 🌳