Commit d1b10c50 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switch gatk parts to new memory limits

parent 13e4d93a
......@@ -9,9 +9,6 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
memoryLimit = Option(4)
override val defaultVmem = "8G"
if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)
if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").asString)
if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)
......
......@@ -15,7 +15,7 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
jarFile = config("gatk_jar")
override val defaultVmem = "7G"
override val defaultCoreMemory = 4.0
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
......
......@@ -9,10 +9,6 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
memoryLimit = Option(4)
override val defaultVmem = "8G"
if (config.contains("scattercount")) scatterCount = config("scattercount")
}
......
......@@ -9,9 +9,6 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
override val defaultVmem = "6G"
memoryLimit = Some(2.5)
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("known")) known ++= config("known").asFileList
......
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