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# nextflow pipeline

This repository is a template and a library repository to help you build nextflow pipeline.
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You can fork this repository to build your own pipeline.
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## Getting the last updates

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To get the last commits from this repository into your fork use the following commands:

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For the first time:
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```sh
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Laurent Modolo committed
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git remote add upstream git@gitbio.ens-lyon.fr:LBMC/nextflow.git
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git pull upstream master
```
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Then to make an update:
```sh
git pull upstream master
git merge upstream/master
```

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## Getting Started

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These instructions will get you a copy of the project as a template when you want to build your own pipeline.
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[you can follow them here.](doc/getting_started.md)
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## Building your pipeline

You can follow the [building your pipeline guide](./doc/building_your_pipeline.md) for a gentle introduction to `nextflow` and taking advantage of this template to build your pipelines.

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## Existing Nextflow pipeline

Before starting a new project, you can check if someone else didn’t already to the work !
- [on the nextflow project page](./doc/nf_projects.md)
- [on the nf-core project](https://nf-co.re/pipelines)

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## Contributing

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If you want to add more tools to this project, please read the [CONTRIBUTING.md](CONTRIBUTING.md).
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## Authors

* **Laurent Modolo** - *Initial work*

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See also the list of [contributors](https://gitbio.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
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## License

This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details