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witsGWAS is a simple human GWAS analysis workflow built at the Sydney Brenner Institute 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 Ruffus) for submission to a distributed PBS Torque cluster (managed via Rubra). Furthermore, witsGWAS monitors (using flag files) the progress of jobs/tasks submitted to the cluster on behalf of the user, courteously waiting for one job to finish before sending another one.
The pipeline has been "dockerized", 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.
#Quick Wiki Navigation
| Overview | Setting up witsGWAS | Running pipelines | Extending pipelines | FAQ |
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| About witsGWAS | Getting started | Running pipelines | Extending pipelines | [Getting help] (https://github.com/magosil86/witsGWAS/wiki/witsGWAS-FAQ) |
| What problem does witsGWAS 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.