Getting Started

This page will walk you through how to set up Nextflow and run the longGWAS pipeline.

Requirements

Hardware

The pipeline is meant to be run on a server with considerable resources, and it is not meant to be run on a local machine.

The minimum hardware specifications are:

4 CPUs
12GB RAM

Software

The pipeline requires the following software prerequisites and has been tested on a Linux Ubuntu 18.04 environment:

1. Java JRE 11

To use Nextflow, you will require a Java Runtime Environment (JRE) version 11 or higher. You can learn how to install Java from the Nextflow website or download the latest Java JDK directly from the Oracle website. Once installed, check the version using java -version.

2. Nextflow

You can install Nextflow following the instructions on the Nextflow website. Once installed, check that it is installed properly by running nextflow run hello.

3. Docker

You can install Docker Engine from the Docker documentation. Once installed, check that it is installed properly by running docker run hello-world.

4. Git

We run the longGWAS pipeline hosted on GitHub at michael-ta/longitudinal-GWAS-pipeline. Therefore, we will require Git to be installed for Nextflow to pull the software from GitHub. Additionally, we have made available some test data on a separate GitHub repository, which can be cloned into your system using Git. To install Git, run sudo apt-get install git-all.

Basic Usage

For a quick example of how to run Nextflow, we will download some example data from our testdata repository:

git clone https://github.com/AMCalejandro/testdata

Then, we can run the longGWAS analysis with the default parameters using these Nextflow commands:

nextflow run michael-ta/longitudinal-GWAS-pipeline -profile standard -r main

Note: To learn more about the Nextflow command line interface (CLI), please refer to the Nextflow documentation.