README.md: add upstream mergin commands

README.md

@@ -4,33 +4,29 @@ This repository is a template and a library repository to help you build nextflo
 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:
 
+For the first time:
 ```sh
 git remote add upstream git@gitbio.ens-lyon.fr::pipelines/nextflow.git
 git pull upstream master
 ```
+
+Then to make an update:
+```sh
+git pull upstream master
+git merge upstream/master
+```
+
 **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
-
-[The list of available tools.](doc/available_tools.md)
-
-## Projects using nextflow
-
-[A list of projects using nextflow at the LBMC.](doc/nf_projects.md)
-
 ## 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).
 
 ## Authors