[2021 July] Demo: How to incorporate your R code into a WDL

Anton Kovalsky
  • Updated

This demo was given by Charlie Condon on July 27, 2021 to a cohort of fellows using BioData Catalyst powered by Terra. Working in Alexander Bick's research group, he and his team extended a publicly available WDL workflow for Mutect2 to do annotation and filtering for CHIP driver mutations. They migrated R code they had previously written locally, into a WDL task in order to run the full pipeline as a batch job. 

In the video, Charlie explains the pro's and con's for directly inserting your R code into a WDL task versus running it as a separate R script. He covers developing Docker files with the necessary dependencies for your R scripts, and how to run those R scripts from inside of a WDL task.

You can download the slides and samples of scripts from the presentation [here].




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