Pipelining Options
Tools and scripts for analysis pipelines

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 Download)
Available separately
(see WDL website)
Source code GATK public module WDL and Cromwell
License Open source (MIT) Open source (BSD)