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Nextflow

Data-driven computational pipelines

Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.

Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.

Find out more

Zero config

Zero config

Just download and play with it. No installation is required.

Polyglot

Polyglot

Are you a Python geek or a Perl hacker?
You can start fast with it.

Concurrency

Concurrency

Lightweight processes with message passing, no shared memory

Scale easily

Scale easily

Develop on your laptop, run in the grid or scale-out in the cloud with no changes.


Features

Nextflow is built around the idea that Linux is the lingua franca of data science.

Fast prototyping

Nextflow allows you to write a computational pipeline by making it simpler to put together many different tasks.

You may reuse your existing scripts and tools and you don't need to learn a new language or API to start using it.

Reproducibility

Nextflow supports Docker and Singularity containers technology.

This, along with the integration of the GitHub code sharing platform, allows you to write self-contained pipelines, manage versions and to rapidly reproduce any former configuration.

Portable

Nextflow provides an abstraction layer between your pipeline's logic and the execution layer, so that it can be executed on multiple platforms without it changing.

It provides out of the box executors for SGE, LSF, SLURM, PBS and HTCondor batch schedulers and for Kubernetes and Amazon AWS cloud platforms.

Unified parallelism

Nextflow is based on the dataflow programming model which greatly simplifies writing complex distributed pipelines.

Parallelisation is implicitly defined by the processes input and output declarations. The resulting applications are inherently parallel and can scale-up or scale-out, transparently, without having to adapt to a specific platform architecture.

Continuous checkpoints

All the intermediate results produced during the pipeline execution are automatically tracked.

This allows you to resume its execution, from the last successfully executed step, no matter what the reason was for it stopping.

Stream oriented

Nextflow extends the Unix pipes model with a fluent DSL, allowing you to handle complex stream interactions easily.

It promotes a programming approach, based on functional composition, that results in resilient and easily reproducible pipelines.


Getting started

It can be used on any POSIX compatible system (Linux, Solaris, OS X, etc).
Simply follow these three steps.

Check prerequisites

Java 8 is required

1
Make sure 8 is installed
on your computer by using the command:
java -version
Note: version numbers "1.8.y_z" and "8" identify the same Java release.

Set up

Dead easy to install

2
Enter this command in your terminal:
curl -s https://get.nextflow.io | bash
(it creates a file nextflow in the current dir)
Note: it can also be downloaded from GitHub or installed by using Homebrew or Bioconda package managers.

Launch

Try a simple demo

3
Run the classic Hello world
by entering the following command:
./nextflow run hello



What's next

  • Confused? Ask the community

    A Nextflow discussion group is available on Google groups. Just click the above link.
  • Report bugs

    Bug reports help Nextflow improve, so please report any issue you may have!
  • Applications showcase

    A collection of Nextflow applications developed by the Nextflow users community.