A community effort to collect a curated set of 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.

Documentation

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

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.

Stable Releases

nf-core pipelines use GitHub releases to tag stable versions of the code and software, making pipeline runs totally reproducable.

Docker

Software dependencies are always available in a bundled docker container, which Nextflow can automatically download from dockerhub.

Singularity

If you're not able to use Docker, built-in support for Singularity can solve your HPC container problems. These are built from the docker containers.

Bioconda

Where possible, pipelines come with a bioconda environment file, allowing you to set up a new environment for the pipeline in a single command.

Get started in minutes

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

nf-core pipelines come with built-in support for AWS iGenomes with common species.

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.

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

# Launch the RNAseq pipeline
nextflow run nf-core/RNAseq \
    -profile standard,docker \
    --genome GRCh37 \
    --reads "data/*_{R1,R2}.fastq.gz"

# Install nf-core tools
pip install nf-core

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

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 all »