Getting Started

This page will walk you through the process of building the docker image and setting up Nextflow to run the GWAS pipeline. If running this pipeline from ADWB, skip the installation section and go to the basic usage section.

Installation

Requirements

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

Nextflow
Docker
Java JRE 8

To enable Nextflow to manage memory resources within Docker containers set the following option in /etc/default/grub

GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"

Clone the Repository

The repository for the pipeline can be found at https://github.com/michael-ta/longitudinal-GWAS-pipeline. Run the command below to clone the repository

git clone https://github.com/michael-ta/longitudinal-GWAS-pipeline.git 

Build the Docker Image

This repository comes with the Dockerfile and local resources needed to build the docker image used by the pipeline. After cloning the repository, you can build the image with

cd longitudinal-GWAS-pipeline
sudo docker build --build-arg BUILD_VAR=$(date +%Y%m%d-%H%M%S) -t gwas-pipeline .

The parameter BUILD_VAR sets the environment variable IMAGE_BUILD_VAR to the date and time of the current build. This can be used to track different versions of the Docker image once built. Using the default nextflow.config the pipeline will launch containers using a local image with the label gwas-pipeline. This behavior can be adjusted by changing the nextflow.config or setting the option at runtime. For more details, see the Nextflow Configuration page.

Note: invoking sudo is not necessary if the Docker user has been previously added to sudoers

Basic Usage

Once the Docker image is built, the pipeline can be called by running the following command within the local cloned irepository

sudo nextflow gwas-pipeline.nf \
  --input_vcf "example/data/genetic/*.vcf" \
  --covarfile "examples/basic/covar.tsv" \
  --phenofile "examples/basic/pheno.tsv"

The outputs from the pipeline will be saved to the directory defined by the environment variable GWAS_OUTPUT_DIR in the Nextflow configuration. Within the output directory you'll see the following folders and files after running the pipeline on the basic example files

results/
  cor_timestamp/
    *.linear
    plots/
      *.

cache/
  p1_run_cache/
  p2_qc_pipeline_cache/ 