Episode 89: What do we do with WDL?

The microbinfie podcast explores Workflow Description Language (WDL), a critical tool for standardizing and simplifying bioinformatics pipeline development and deployment across different computational environments.

Highlights of the Episode

• Introduction to WDL: The podcast delves into the functionality of WDL, a language commonly used to describe bioinformatics pipelines in a portable and cross-environmental manner. WDL's strength lies in its ability to effectively connect pre-containerized tools, standardizing bioinformatics processes which enhances reproducibility and scalability. By doing this, it minimizes the need for complex CIS (Computer Information Systems) admin work, allowing researchers to concentrate more on scientific inquiries.

• Unique Features of WDL: Despite the existence of various workflow languages, WDL stands out due to its formal specification and its compatibility with common implementations used for execution.

• Public Health Bioinformatics: Joel and Danny discuss the implications of workflow languages in the realm of public health bioinformatics, particularly addressing challenges related to version control and quality management. They introduce the StaphB community, which unites state-level public health bioinformaticians to address challenges and foster connections between academia and state public health departments.

• Narratives from the Guests: Danny shares his journey of discovering WDL and realizing its suitability for pipeline portability. Conversely, Joel talks about choosing WDL for its public health applications and support from the Broad Institute. They agree that their choice of workflow language is influenced by the operational environment and suitability to their specific needs.

Conclusion

The episode underscores the critical role workflow languages like WDL play in bridging the gap between bioinformatics and public health. The choice of such a language is crucial and should align with the intended practical environment. Both guests advocate strongly for WDL, emphasizing how it has streamlined their bioinformatics workflows.