Commit 298ca175 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switch to biopet scattering

parent 85bf7a10
......@@ -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 {
......
......@@ -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
......
......@@ -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
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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"
......
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)
}
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