Commit 3fc3e1c5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Disable scattering

parent 7570f55a
......@@ -31,11 +31,13 @@ import org.broadinstitute.gatk.queue.extensions.gatk.{ GATKScatterFunction, Read
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
//TODO: check gathering
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with ScatterGatherableFunction */ {
analysisName = "BaseRecalibrator"
analysis_type = "BaseRecalibrator"
scatterClass = classOf[ReadScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
//TODO: check gathering
//scatterClass = classOf[ReadScatterFunction]
//setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
/** A database of known polymorphic sites */
@Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites", required = false, exclusiveOf = "", validation = "")
......@@ -46,8 +48,8 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with Scat
private var knownSitesIndexes: Seq[File] = Nil
/** The output recalibration table file to create */
@Output(fullName = "out", shortName = "o", doc = "The output recalibration table file to create", required = true, exclusiveOf = "", validation = "")
@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
@Output(fullName = "out", shortName = "o", doc = "The output recalibration table file to create", required = true, exclusiveOf = "", validation = "") //TODO: check gathering
//@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
var out: File = _
/**
......
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