Quick Start

Installation

Requirements

  • Nextflow

    Check that nextflow is installed on your cluster and load it.

Preferred version:

21.10 or greater

  • Singularity

    Singularity has now been changed to Apptainer, but most clusters to run it as singularity. We’ll need singularity to pull the gencall docker container from our dockerhub account as a singularity image file.

    Check if singularity is installed on your cluster and load it.

Preferred version:

3.5 or greater

Install

Navigate to the path where you would like to run the workflow from and run the code below.

wget https://github.com/GeneMAP-Research/genemapgwas/archive/refs/tags/v0.1.tar.gz
tar zxvf v0.1.tar.gz
rm v0.1.tar.gz
cd genemapgwas-0.1

Go to Convert IDAT to VCF workflow

Go to GWAS Analysis workflow

under development