building_your_pipeline.md

Building your own pipeline

The goal of this guide is to walk you through the Nextflow pipeline building process you will learn:

1. How to use this git repository (LBMC/nextflow) as a template for your project.
2. The basis of Nextflow the pipeline manager that we use at the lab.
3. How to build a simple pipeline for the transcript-level quantification of RNASeq data
4. How to run the exact same pipeline on a computing center (PSMN)

This guide assumes that you followed the Git basis, training course.

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 LBMC/nextflow as a template. To easily do so, go to the LBMC/nextflow repository and click on the fork button (you need to log-in).

In git, the action of forking means that you are going to make your own private copy of a repository. This repository will keep a link with the original LBMC/nextflow project from which you will be able to