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.
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.
Upcoming Events
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 listSee 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 pipelinesRun 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 TutorialGet 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 docsSee 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.
