Switch to biopet scattering

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

@@ -26,7 +26,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, LocusScatterFunction }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -50,7 +50,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.Argument
 import org.broadinstitute.gatk.utils.commandline.Gather
 import org.broadinstitute.gatk.utils.commandline.Input

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

@@ -28,7 +28,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, ReadScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 //TODO: check gathering

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

@@ -26,7 +26,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
 
 class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -26,7 +26,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class CombineVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -49,7 +49,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -79,7 +79,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk._
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
 
 class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -34,7 +34,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ BamGatherFunction, GATKScatterFunction, ReadScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class IndelRealigner(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -26,7 +26,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ BamGatherFunction, GATKScatterFunction, ReadScatterFunction }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline._
 
 class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -28,7 +28,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, _ }
 
 class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -26,7 +26,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
 
 class SelectVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -60,7 +60,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
 
 class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {

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

@@ -26,10 +26,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.extensions.gatk.{ CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile }
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
+import org.broadinstitute.gatk.queue.extensions.gatk.{CatVariantsGatherer, GATKScatterFunction, LocusScatterFunction, TaggedFile}
+import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Output, _}
 
 class VariantAnnotator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
   analysisName = "VariantAnnotator"

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

+package nl.lumc.sasc.biopet.core
+
+/**
+  * Created by pjvan_thof on 4/26/16.
+  */
+trait ScatterGatherableFunction extends BiopetCommandLineFunction
+  with org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction {
+  scatterCount = config("scatter_count", freeVar = true)
+}