Eco-Flow Basic Nextflow Training
A hands-on course that takes you from limited bioinformatics experience to running your own nf-core pipelines. It's pitched at beginners — no prior Nextflow experience is needed, and only basic command-line familiarity is assumed (Part 1 covers the terminal from scratch if you're new to it; the later differential-expression part assumes a little R). Everything runs in the browser via GitHub Codespaces, so there's nothing to install.
This course was developed with the support of
Work through it, step by step
Each part opens right here on the site. Start at the top — or jump to whatever you need.
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0
Setup Practical
Get your environment ready with GitHub Codespaces, so you can run everything from your browser.
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1
Command line basics Practical · optional
A gentle introduction to the command line. Skip this part if you're already comfortable in a terminal.
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2
Pipelines with Nextflow Lecture
What Nextflow and nf-core are, and why pipelines matter for reproducible, scalable science.
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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.
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4
Differential gene expression Practical
Take the counts from the RNA-Seq pipeline and find what changed — normalise with DESeq2, run differential expression, and interpret the results in R.
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Running a pipeline on an HPC Reference
A conceptual guide to moving a pipeline onto a High-Performance Computing cluster — what to ask your HPC team, where to find configs, and how to test one. Reading, not a hands-on run.
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Dive into the material
Grab the full course (data, scripts and Codespaces config) on GitHub, or try the official Nextflow training to go further.