Pipelining Options
Tools and scripts for analysis pipelines

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