RNA-Seq pipeline

This example shows how to put together a basic RNA-Seq pipeline. It maps a collection of read-pairs to a given reference genome and outputs the respective transcript model.

Try it in your computer

To run this pipeline on your computer, you will need:

Unix-like operating system
Java 11 (or higher)
Docker

Install Nextflow by entering the following command in the terminal:

$ curl -fsSL get.nextflow.io | bash

Then launch the pipeline with this command:

$ nextflow run rnaseq-nf -with-docker

It will automatically download the pipeline GitHub repository and the associated Docker images, thus the first execution may take a few minutes to complete depending on your network connection.

NOTE: To run this example with versions of Nextflow older than 22.04.0, you must include the -dsl2 flag with nextflow run.