TP_experimental_biologists.md

title: "TP for experimental biologists"
author: Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)
date: 6 Jun 2018
output:
  pdf_document:
    toc: true
    toc_depth: 3
    number_sections: true
    highlight: tango
    latex_engine: xelatex

The Goal of this practical is to learn how to build your own pipeline with nextflow and using the tools already wrapped. For this we are going to build a small RNASeq analysis pipeline that should run the following steps:

• remove Illumina adaptors
• trim reads by quality
• build the index of a reference genome
• estimate the number of RNA fragments mapping to the transcript of this genome

Initialize your own project

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 as a template. To easily do so, go to the pipelines/nextflow repository and click on the fork button.

In git, the action of forking means that you are going to make your own private copy of a repository. You can then write modifications in your project, and if they are of interest for the source repository (here pipelines/nextflow) create a merge request. Merge request are send to the source repository to ask the maintainers to integrate modifications.

Project organisation

This project (and yours) follow the guide of good practices for the LBMC

You are now on the main page of your fork of the pipelines/nextflow. You can explore this project, all the code in it is under the CeCILL lience (in the LICENCE file).

The README.md file contains instructions to run your pipeline and test it's installation.

The CONTRIBUTING.md file contains guidelines to follow if you want to contribute to the pipelines/nextflow (making a merge request for example).

The data folder will be the place were you store the raw data for your analysis. The 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 folder contains the documentation of this practical course.

And most interestingly for you, the src contains code to wrapp tools. This folder contains two subdirectory. A nf_modules and a sge_modules folder.