Merge branch 'fix-scatter' into 'develop'

Fix scatter

Fixes scattering in shiva.

This should fix failing tests here:
http://ci.sasc.nl:8080/job/Biopet-Functional-Tests/36/

See merge request !289

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -8,11 +8,12 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.Output
+import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
 
+  @Gather(enabled = false)
   @Output(required = false)
   protected var vcfIndex: File = _
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -8,10 +8,11 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.Output
+import org.broadinstitute.gatk.utils.commandline.{Gather, Output}
 
 class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
 
+  @Gather(enabled = false)
   @Output(required = false)
   protected var vcfIndex: File = _