This repository is a template and a library repository to help you build nextflow pipeline.
## 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.
### Prerequisites
To run nextflow on you computer you need to have java (>= 1.8) installed.
```sh
java --version
```
To be able to easily test tools already implemented for nextflow on your computer (`src/nf_modules/` to see their list). You need to have docker installed.
```sh
docker run hello-world
```
### Installing
To install nextflow on you computer simply run the following command:
```sh
src/install_nextflow.sh
```
Then to initialise a given tools run the following command:
for example to initialise `file_handle` version `0.1.1`, run:
```sh
src/nf_modules/file_handle/0.1.1/docker_init.sh
```
## Running the tests
Explain how to run the automated tests for this system
### Break down into end to end tests
Explain what these tests test and why
```
Give an example
```
### And coding style tests
Explain what these tests test and why
```
Give an example
```
## Contributing
Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.
## Versioning
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).
## 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
