Overview of the h3aGWAS pipeline
h3aGWAS is a simple human GWAS analysis workflow built by the [Pan-African Bioinformatics Network for H4 Africa] (http://www.h3abionet.org) for data quality control (QC) and basic association testing. It takes away the need for having to enter individual commands at the unix prompt and rather organizes GWAS tasks sequentially (facilitated via Nextflow) for submission to an underlying computing infrastructure. h3aGWAS is highly portable and uses Nextlow's versatile features to be able to run on a variety of infrastructures, just by changing a few parameters. As examples, we have run the workflow on
- laptops and servers with and without Docker
- clusters, with and without Docker
- a DockerSwarm built using OpenNebula
- Amazon EC2 Nextflow supports execution on all these platforms and more.
The pipeline has been dockerised, simplifying the setup and execution of the pipeline. Using docker allows the pipeline to be run easily on any platform, since the pipeline is run through the docker container. See the link in the sidebar to the right for more information. We provide Docker images, so if your computer or cluster supports Docker, you do not need to install any bioinformatics software. Some people will not want or be able to use Docker: all the software we use is standard bioinformatics software. We give instructions below on how to install.
h3aGWAS was based on an earlier pipline using Rubra developed by Lerato Magosi (http://magosil86.github.io/witsGWAS/)
#Quick Wiki Navigation
| Overview | Setting up h3aGWAS | Running pipelines | Extending pipelines | FAQ |
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| Why we use h3aGWAS | Getting started | Running pipelines | Extending pipelines | [Getting help] (https://github.com/magosil86/witsGWAS/wiki/witsGWAS-FAQ) |
| What problem does h3aGWAS solve | Installing witsGWAS | A step-by-step guide with examples on running witsGWAS | A step-by-step guide on modifying witsGWAS pipelines and creating new ones | Trouble- shooting tips |
Please see the sidebar on the right for a detailed view of the topics.