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

TP for experimental biologists

The Goal of this practical is to learn how to build your own pipeline with nextflow and using the tools already wrapped in Docker and SGE. 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.

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.