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.
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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 · R
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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5
Run an nf-core ampliseq pipeline Practical
Hands-on — run nf-core/ampliseq on 16S amplicon data from river and soil samples, from raw reads to taxonomic classification, diversity stats and a QC report.
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6
Run the nanopore metabarcoding pipeline Practical
Hands-on — run Eco-Flow's nanoporemetabarcoding pipeline end to end, from raw Nanopore reads to a taxonomically-annotated community table.
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7
Interacting with code on GitHub Practical
Issues, pull requests, READMEs and Claude Code — how to report, fix and contribute changes to a pipeline, using nanoporemetabarcoding as the worked example.
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8
Running a pipeline on an HPC Practical · optional
Run an nf-core pipeline on a Slurm/SGE cluster that's already set up — get the pipeline, submit and watch jobs, keep Nextflow alive, and avoid common mistakes. Practise on a mini Slurm cluster in Codespaces.
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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.
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Advanced: setting up Nextflow for your HPC Advanced
Advanced material for people setting up Nextflow on a cluster with no ready-made config — what to ask your HPC team, where to find configs, and how to adapt and test one. Reading and reference, 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.