Remove dependency on external GATK jar file, deprecate conda
The pipeline currently depends on the user to specify an external GATK jar file, due to licencing issues around GATK3.7. However, the broadinstitute does provide a docker image which contains GATK3.7. By using this docker image, we can remove the dependency on an external .jar file altogether when using singularity.
Since hutspot has been running successfully with singularity for some time now, conda should be deprecated as well.