Workflow Tip: Simplifying Public Health Bioinformatics with Terra

Our Public Health Bioinformatics (PHB) v1.0.0 workflows are now available! These workflows are designed specifically for Terra, making them easily accessible to everyone, but can be also used on the command-line with Cromwell or miniWDL. These workflows are designed for pathogen characterization, genomic epidemiology, and the preparation and submission of NGS data to internationally-accessible repositories such as NCBI and GISAID.

PHB v1.0.0 was designed to improve efficiency and reduce errors in maintaining our repositories. We consolidated the PHVG, PHBG, and Terra Utilities repositories to eliminate code redundancies that complicated the implementation of updates and bug fixes. In addition, we have established stricter organization and enforced a style guide to enhance readability and simplify maintenance. These updates have made the PHB repository more adaptable to the ever-changing needs of the public health community.

All workflows in the PHB repository now have the suffix “_PHB” to distinguish them from their previous versions in the PHBG, PHVG, and Terra Utilities repositories. We have also created a PHB Dockstore collection, which organizes all of the PHB workflows together for seamless integration into your Terra workspaces. When importing these workflows from Dockstore, please be sure to choose the version with the “_PHB” suffix!

A huge thank you to our public health partners for using our tools and providing critical feedback that continues to guide our development priorities. Your invaluable support and insights are driving advancements in public health bioinformatics!

You can find more information about these workflows on our Theiagen Public Health Resources Page.

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