A global community effort to collect a curated set of open‑source analysis pipelines built using Nextflow.

For facilities

Highly optimised pipelines with excellent reporting. Validated releases ensure reproducibility.

For users

Portable, documented and easy to use workflows.
Pipelines that you can trust.

For developers

Companion templates and tools help to validate your code and simplify common tasks.

nf-core is published in Nature Biotechnology! Nat Biotechnol 38, 276-278 (2020).

Nextflow is an incredibly powerful and flexible workflow language.

nf-core pipelines adhere to strict guidelines - if one works, they all will.

Fully featured pipelines

Documentation

Extensive documentation covering installation, usage and description of output files ensures that you won't be left in the dark.

Stable Releases

nf-core pipelines use GitHub releases to tag stable versions of the code and software. Pipelines are exceptionally well tested and easy to run.

Open source

All nf-core code is licensed under the MIT license and is available on GitHub. Pipelines can be used, modified, and forked - by anyone.

CI Testing

Every time a change is made to the pipeline code, nf-core pipelines use continuous-integration testing to ensure that nothing has broken.

Run anywhere

Pipelines are ultra-portable and run on most laptops, HPCs and clouds. Tests run on AWS after every release: you can browse results on the website and use for your own benchmarking.

Packaged software

Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda or others. No need for any software installations.

All nf-core code is community owned.

Everyone is welcome to use, contribute to, and help maintain nf-core.

How to get involved

Everyone is welcome to contribute, in any way!

Contribute ideas and code directly via GitHub, or come talk to us in Slack.

Start small or go big

You start wherever you like: Typo fixes in docs? No module for your favourite tool? Missing a pipeline? We are looking for all types of contributions!

Develop with the community

Join forces with others! We promote collaboration over duplication: before you start coding, please propose your idea in Slack.

Start from the template

Pipelines, modules and subworkflows are based on a template, created using nf-core tools. An automated sync keeps pipelines up to date.

Get started in minutes

Nextflow lets you run nf-core pipelines on virtually any computing environment.

The nf-core companion tool makes it easy to list all available nf-core pipelines and shows which are available locally. Local versions are checked against the latest available release.

The nf-core companion tool also provides a range of helper functions to make it easier to work with nf-core pipelines, such as downloading pipelines for offline use, an interactive command-line launch wizard and helper functions to generate commented config file templates for any pipeline.

# Install nextflow
curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/

# Launch the RNAseq pipeline
nextflow run nf-core/rnaseq \
    --input samplesheet.csv \
    --output ./results/ \
    --genome GRCh37 \
    -profile docker

# Install nf-core tools
pip install nf-core

# List all nf-core pipelines and show available updates
nf-core pipelines list

See what's available

Check out the available pipelines to see if we have what you need. Each comes with release details, keywords and a description.

Available pipelines

Run a pipeline

Read the quickstart tutorial to learn how to get set up with the required software and tools, and how to launch a nf-core pipeline.

Quickstart Tutorial

Get into the code

If you're interested in contributing to nf-core, take a look at the developer documentation to see what's required.

Developer docs

See a complete list » Used by groups all over the world

The nf-core community is spread all over the globe and includes a large number of contributing users.

See a complete list »