89 What do we do with WDL?

Micro binfie podcast

Today on the @microbinfie podcast, we talk about WDL with @sevinsky and @DannyJPark. We learn what widdle means to Andrew and his kids. Joel takes a shot at Lyve-SET and you'll never guess what happens next. In the MicroBinfie podcast, we discuss the workflow description language (WDL) commonly used to describe bioinformatics pipelines in a portable and cross-environmental way. The starting point is the presumption that tools are already containerized, and WDL helps to bind them together. The guests highlighted that this standardizes bioinformatics in the field, making it more reproducible and scalable. It also helps remove the need for excessive CIS admin work, enabling researchers to spend more time on scientific questions. Despite having many workflow languages available, WDL is unique in its formal specification and its orthogonality to the common implementations that are used in executing those things. In the second part of the podcast discussion, guests Joel and Danny talked about workflow languages and public health bioinformatics. They highlighted the challenge of version control to quality management and its effects on the field of bioinformatics. They spoke about the origins of the community, StaphB, which comprises state-level public health bioinformaticians. The community discusses various challenges and contributes to creating links between academia and state public health departments. WDL is a workflow language used for bioinformatics work that the hosts use. Danny shared his story of how they came to use Whittle and how they realized it was the perfect language for portability of pipelines. On the other hand, Joel talked about how they chose WDL for its applicability to public health and the support it received from its creators, particularly the Broad Institute. They both agreed that the choice of workflow language was driven by the environment they could work in and which language was best suited to their needs. In conclusion, the discussion focused on the vital role of workflow languages such as WDL in bridging the gap between bioinformatics and public health. The choice of workflow language was critical and would depend heavily on the environment in which the language was used. Finally, they expressed their support for WDL and how it had helped them streamline their bioinformatics workflows.