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