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

```sh
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git remote add upstream gitlab_lbmc:pipelines/nextflow.git
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git pull upstream master
```
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**If you created your `.config` file before version `0.4.0` you need to run the script `src/.update_config.sh` to use the latest docker, singularity and conda configuration (don't forget to check your config files afterward for typos).**
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## Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

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[you can follow them here.](doc/getting_started.md)
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## Available tools

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[The list of available tools.](doc/available_tools.md)
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## Projects using nextflow

[A list of projects using nextflow at the LBMC.](doc/nf_projects.md)

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## Contributing

Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.

## Versioning

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We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags).
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## Authors

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

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

## License

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