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https://github.com/nextflow-io/nextflow

A DSL for data-driven computational pipelines
https://github.com/nextflow-io/nextflow

aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine

Last synced: 6 days ago
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A DSL for data-driven computational pipelines

Host: GitHub
URL: https://github.com/nextflow-io/nextflow
Owner: nextflow-io
License: apache-2.0
Created: 2013-03-27T11:17:33.000Z (almost 12 years ago)
Default Branch: master
Last Pushed: 2024-10-28T16:43:41.000Z (3 months ago)
Last Synced: 2024-10-28T18:08:03.527Z (3 months ago)
Topics: aws, bioinformatics, cloud, dataflow, docker, groovy, hello, hpc, nextflow, pipeline, pipeline-framework, reproducible-research, reproducible-science, sge, singularity, singularity-containers, slurm, workflow-engine
Language: Groovy
Homepage: http://nextflow.io
Size: 55 MB
Stars: 2,742
Watchers: 88
Forks: 626
Open Issues: 453
Metadata Files:
- Readme: README.md
- Changelog: changelog.txt
- Contributing: CONTRIBUTING.md
- License: COPYING
- Code of conduct: CODE-OF-CONDUCT.md
- Citation: CITATION.cff
- Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

Awesome-Bioinformatics - Nextflow - A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ [paper-2018](https://pubmed.ncbi.nlm.nih.gov/29412134) | [web](http://nextflow.io) ] (Next Generation Sequencing / Workflow Managers)
jimsghstars - nextflow-io/nextflow - A DSL for data-driven computational pipelines (Groovy)
awesome - nextflow - driven computational pipelines | 13 hours ago | ([Groovy](#groovy))
StarryDivineSky - nextflow-io/nextflow - core的YouTube频道上查看大部分内容。nf-core项目是一个社区努力，汇集了高质量的Nextflow工作流程，供所有人使用。 (其他_机器学习与深度学习)
awesome-starred - nextflow-io/nextflow - A DSL for data-driven computational pipelines (bioinformatics)
awesome-list-docker - nextflow - driven computational pipelines (workflow-engine)
awesome - nextflow-io/nextflow - A DSL for data-driven computational pipelines (docker)

README

        
  

  

  

*"Dataflow variables are spectacularly expressive in concurrent programming"*


[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)

[![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)

[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)

[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=58bd9f&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)

[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=58bd9f&style=popout)](https://www.nature.com/articles/nbt.3820)

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=58bd9f&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)

[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)

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:

```bash

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:

```bash

conda install -c bioconda nextflow

```

## Documentation

The Nextflow documentation is available for the latest [stable](https://nextflow.io/docs/latest/) and [edge](https://nextflow.io/docs/edge/) releases.

## Community

You can post questions and get help in the [Nextflow community forum](https://community.seqera.io) or the [Nextflow Slack](https://www.nextflow.io/slack-invite.html). Bugs and feature requests should be reported as [GitHub issues](https://github.com/nextflow-io/nextflow/issues/new/choose).

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](https://www.youtube.com/@Nextflow) and [nf-core](https://www.youtube.com/@nf-core) YouTube channels.

The [nf-core](https://nf-co.re/) 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](CONTRIBUTING.md) file for details.

## License

Nextflow is released under the Apache 2.0 license. Nextflow is a [registered trademark](https://github.com/nextflow-io/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](http://www.nature.com/nbt/journal/v35/n4/full/nbt.3820.html)

## 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.