@@ -23,6 +23,8 @@ For this we are going to build a small RNASeq analysis pipeline that should run
You are going to build a pipeline for you or your team. So the first step is to create your own project.
## Forking
Instead of reinventing the wheel, you can use the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) as a template.
To easily do so, go to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) repository and click on the [**fork**](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/forks/new) button.
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@@ -32,4 +34,27 @@ In git, the [action of forking](https://git-scm.com/book/en/v2/GitHub-Contributi
## Project organisation
This project (and yours) follow the [guide of good practices for the LBMC](http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC)
You are now on the main page of your fork of the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow). You can explore this project, all the code in it is under the CeCILL lience (in the [LICENCE](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/LICENSE) file).
The [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file contains instructions to run your pipeline and test it's installation.
The [CONTRIBUTING.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/CONTRIBUTING.md) file contains guidelines to follow if you want to contribute to the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow)(making a merge request for example).
The [data](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/data) folder will be the place were you store the raw data for your analysis.
The [results](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/results) folder will be the place were you store the results of your analysis.
Note that the content of these two folders should never be saved on git.
The [doc](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/doc) folder contains the documentation of this practical course.
And most interestingly for you, the [src](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src) contains code to wrapp tools. This folder contains two subdirectory. A `nf_modules` and a `sge_modules` folder.
