205 lines
5.4 KiB
Markdown
205 lines
5.4 KiB
Markdown
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# Nextflow
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*"Dataflow variables are spectacularly expressive in concurrent programming"*
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<br />[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)
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[](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
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[](https://github.com/nextflow-io/nextflow/releases/latest)
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[](https://twitter.com/nextflowio)
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[](https://www.nature.com/articles/nbt.3820)
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[](http://bioconda.github.io/recipes/nextflow/README.html)
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[](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
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Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It uses a dataflow programming model that simplifies writing parallel and distributed pipelines by allowing you to focus on data flow and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, and cloud. Additionally, Nextflow supports a range of compute environments, software container runtimes, and package managers, allowing workflows to be executed in reproducible and isolated environments.
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## Get started
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To get started with Nextflow:
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1. See the Nextflow {ref}`overview <overview-page>` to learn key concepts.
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2. Download and {ref}`install <install-page>` Nextflow.
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3. Set up an {ref}`environment <devenv-page>` with the {ref}`Nextflow VS Code extension <devenv-nextflow>`.
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4. Run {ref}`your first script <your-first-script>`.
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To continue learning about Nextflow, visit the [Nextflow community training portal](https://training.nextflow.io/latest/) and find a training course that is right for you. Seqera, the company that develops Nextflow, also runs a variety of training events. See [Seqera Events](https://seqera.io/events/) for more information.
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## Community
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You can post questions 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).
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The Nextflow community is highly active with regular community meetings, events, a podcast, and more. You can view this material on the [Nextflow](https://www.youtube.com/@Nextflow) YouTube channel.
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The [nf-core](https://nf-co.re/) project is a community effort aggregating high-quality Nextflow workflows that can be used by everyone.
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## Contributing
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Contributions to Nextflow are welcome. See {ref}`Contributing <contributing-page>` for more details.
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## License
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Nextflow is released under the Apache 2.0 license. Nextflow is a [registered trademark](https://github.com/nextflow-io/trademark).
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## Citations
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If you use Nextflow in your work, please cite:
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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)
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```{toctree}
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:hidden:
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:caption: Get started
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:maxdepth: 1
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overview
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install
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developer-env
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your-first-script
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```
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```{toctree}
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:hidden:
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:caption: Running pipelines
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:maxdepth: 1
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cli
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config
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executor
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cache-and-resume
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reports
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```
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```{toctree}
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:hidden:
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:caption: Developing pipelines
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:maxdepth: 1
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script
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working-with-files
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process
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process-typed
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workflow
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workflow-typed
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notifications
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secrets
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sharing
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vscode
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```
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```{toctree}
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:hidden:
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:caption: Modules
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:maxdepth: 1
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modules/modules
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modules/using-modules
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modules/developing-modules
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modules/module-registry
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```
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```{toctree}
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:hidden:
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:caption: Software dependencies
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:maxdepth: 1
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git
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container
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conda
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spack
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wave
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```
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```{toctree}
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:hidden:
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:caption: Compute & storage
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:maxdepth: 1
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aws
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amazons3
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azure
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google
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kubernetes
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fusion
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```
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```{toctree}
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:hidden:
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:caption: Plugins
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:maxdepth: 1
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plugins/plugins
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plugins/using-plugins
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plugins/developing-plugins
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plugins/plugin-registry
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```
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```{toctree}
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:hidden:
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:caption: Language Reference
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:maxdepth: 1
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reference/feature-flags
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reference/syntax
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reference/stdlib
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reference/process
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reference/channel
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reference/operator-typed
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reference/operator
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```
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```{toctree}
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:hidden:
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:caption: Runtime Reference
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:maxdepth: 1
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reference/cli
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reference/config
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reference/env-vars
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```
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```{toctree}
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:hidden:
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:caption: Updates
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:maxdepth: 1
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updating-nextflow
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strict-syntax
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migrations/index
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```
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```{toctree}
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:hidden:
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:caption: Contributing
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:maxdepth: 1
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developer/index
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developer/diagram
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developer/config-scopes
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developer/packages
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```
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```{toctree}
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:hidden:
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:caption: Tutorials
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:maxdepth: 1
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tutorials/rnaseq-nf
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tutorials/data-lineage
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tutorials/workflow-outputs
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tutorials/static-types
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tutorials/static-types-operators
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tutorials/metrics
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tutorials/flux
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```
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```{toctree}
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:hidden:
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:caption: Guides
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:maxdepth: 1
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guides/aws-java-sdk-v2
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guides/gradle-plugin
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guides/migrate-plugin
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guides/updating-spot-retries
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```
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