Add use statements for WorkflowBuilder
Make command for getting the vcf-result from DV2 at runtime

We couldn't pass this in when we launch the workflow because it hasn't
been created yet at that point.
Params shouldn't be listed as inputs for commands

They are for SoftwareResults, but not for commands
Integrate Annotation Plan into Somatic Validation/Variation builds
Remove unused (dummy) input from GetInitialVcfResult
Create Dag module to generate the annotation-dag

This will soon replace the MasterCommand->dag method
Remove MasterCommand
Make sure we create the output_directory
Replaced temp-variables with methods
Bugfix: stop use_ok'ing non-existent class
Move base class

We have to 'hide' this base class in a folder to keep the
model define subcommand factory from attempting to generate a
subcommand.