gongyixiao / nextflow

A DSL for data-driven computational pipelines

"Dataflow variables are spectacularly expressive in concurrent programming"
Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum

Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It is based on the dataflow programming model, which greatly simplifies the writing of parallel and distributed pipelines, allowing you to focus on the flow of data and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, AWS Batch, Azure Batch, Google Cloud Batch, and Kubernetes. Additionally, it supports many ways to manage your software dependencies, including Conda, Spack, Docker, Podman, Singularity, and more.

Quick start

Install Nextflow with a single command:

curl -fsSL https://get.nextflow.io | bash

It creates the nextflow executable file in the current directory. You can then move it to a directory in your $PATH to run it from anywhere.

Nextflow can also be installed from Bioconda:

conda install -c bioconda nextflow

Documentation

The Nextflow documentation is available for the latest stable and edge releases.

Community

You can post questions and get help in the Nextflow community forum or the Nextflow Slack. Bugs and feature requests should be reported as GitHub issues.

The Nextflow community is highly active with regular community meetings, events, a podcast and more. You can view much of this material on the Nextflow and nf-core YouTube channels.

The nf-core project is a community effort aggregating high quality Nextflow workflows which can be used by everyone.

Contributing

Contributions are more than welcome. See the CONTRIBUTING file for details.

License

Nextflow is released under the Apache 2.0 license. Nextflow is a registered trademark.

Citations

If you use Nextflow in your work, please cite:

P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:10.1038/nbt.3820

Credits

Nextflow is built on two *great* open-source software projects, Groovy and GPars.

YourKit is kindly supporting Nextflow with its fully-featured Java Profiler.