Prior to GATK4 we supported two ways of writing GATK pipelines, Queue and Cromwell + WDL. Here's a point-by-point comparison. Note that Queue was phased out in favor of Cromwell+WDL, and support for Queue was permanently discontinued upon release of GATK 4 in January 2018.
|Scala, high learning curve||WDL, more user-friendly|
|Execution||Local + cluster through job scheduler (LSF, GridEngine etc)||Local + cloud through Cromwell (cluster not yet supported)|
|Support||Discontinued (we are no longer using Queue)||Active (we use Cromwell+WDL in production)|
|Documentation||Queue forum||WDL website and forum|
|Toy examples in Github repository||Working examples on the WDL website
(+ Broad production pipeline scripts coming soon)
|Distribution||Integrated with GATK in "Queue.jar"
(see WDL website)
|Source code||GATK public module||WDL and Cromwell|
|License||Open source (MIT)||Open source (BSD)|