**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).**
## 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.
These instructions will get you a copy of the project as a template when you want to build your own pipeline.
[you can follow them here.](doc/getting_started.md)
## Available tools
## Building your pipeline
[The list of available tools.](doc/available_tools.md)
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.
## Projects using nextflow
## Existing Nextflow pipeline
[A list of projects using nextflow at the LBMC.](doc/nf_projects.md)
Before starting a new project, you can check if someone else didn’t already do the work !
-[on the nextflow project page](./doc/nf_projects.md)
-[on the nf-core project](https://nf-co.re/pipelines)
- You can use the [nf_core utility](https://gitbio.ens-lyon.fr/LBMC/hub/PSMN/nfcore_utility) to create a psmn config file in order to launch nf-core pipeline on the PSMN
## 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://gitbio.ens-lyon.fr/pipelines/nextflow/tags).
If you want to add more tools to this project, please read the [CONTRIBUTING.md](CONTRIBUTING.md).
