We currently support two ways of writing GATK pipelines (pick anything else, you're on your own). Here's a point-by-point comparison. Note that Queue is being phased out in favor of Cromwell+WDL, and support for Queue will be discontinued upon release of GATK 4 (expected ~June 2017).
|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||Limited (we are moving away from Queue)||Active (we use Crom+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)|