Updated Executable

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala

@@ -7,12 +7,12 @@ package nl.lumc.sasc.biopet.core
 
 object BiopetExecutableProtected extends BiopetExecutable {
   def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
-    nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
     nl.lumc.sasc.biopet.pipelines.gatk.ShivaGatk,
+    nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcallingGatk,
     nl.lumc.sasc.biopet.pipelines.basty.Basty)
 
   def tools = BiopetExecutablePublic.tools

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

@@ -27,7 +27,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.kopisu.ConiferPipeline,
     nl.lumc.sasc.biopet.pipelines.carp.Carp,
     nl.lumc.sasc.biopet.pipelines.toucan.Toucan,
-    nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
+    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
   )
 
   def tools: List[MainCommand] = List(

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -193,7 +193,6 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
         addAll(bamMetrics.functions)
         addSummaryQScript(bamMetrics)
 
-
         if (config("single_sample_variantcalling", default = false).asBoolean) {
           val vc = makeVariantcalling(multisample = false)
           vc.sampleId = Some(sampleId)

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -5,7 +5,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.tools.{VcfStats, VcfFilter, MpileupToVcf}
+import nl.lumc.sasc.biopet.tools.{ VcfStats, VcfFilter, MpileupToVcf }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.Input