Changed default max threads

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

@@ -12,10 +12,12 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
   scatterCount = config("scattercount", default = 0)
 
+  override val defaultThreads = 3
+
   override def beforeGraph() {
     super.beforeGraph()
 
-    nt = Option(getThreads(3))
+    nt = Option(getThreads)
     memoryLimit = Option(nt.getOrElse(1) * 2)
 
     import org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode

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

@@ -9,6 +9,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
 
 class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
+
+  override val defaultThreads = 1
+
   min_mapping_quality_score = config("minMappingQualityScore", default = 20)
   scatterCount = config("scattercount", default = 1)
   if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
@@ -41,7 +44,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
       threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
     }
-    nct = Some(getThreads(1))
+    nct = Some(getThreads)
     memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
   }
 

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

@@ -26,11 +26,13 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
     }
   }
 
+  override val defaultThreads = 1
+
   override def beforeGraph() {
     super.beforeGraph()
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
-    nct = Some(getThreads(1))
+    nct = Some(getThreads)
     memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
   }
 }

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

@@ -11,7 +11,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 
 class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantRecalibrator with GatkGeneral {
-  nt = Option(getThreads(4))
+  override val defaultThreads = 4
+
+  nt = Option(getThreads)
   memoryLimit = Option(nt.getOrElse(1) * 2)
 
   if (config.contains("dbsnp")) resource :+= new TaggedFile(config("dbsnp").asString, "known=true,training=false,truth=false,prior=2.0")

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

@@ -199,13 +199,15 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     BiopetCommandLineFunctionTrait.versionCache.get(versionCommand)
   }
 
+  def getThreads = getThreads(defaultThreads)
+
   /**
    * Get threads from config
    * @param default default when not found in config
    * @return number of threads
    */
   def getThreads(default: Int): Int = {
-    val maxThreads: Int = config("maxthreads", default = 8)
+    val maxThreads: Int = config("maxthreads", default = 24)
     val threads: Int = config("threads", default = default)
     if (maxThreads > threads) threads
     else maxThreads
@@ -218,7 +220,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
    * @return number of threads
    */
   def getThreads(default: Int, module: String): Int = {
-    val maxThreads: Int = config("maxthreads", default = 8, submodule = module)
+    val maxThreads: Int = config("maxthreads", default = 24, submodule = module)
     val threads: Int = config("threads", default = default, submodule = module)
     if (maxThreads > threads) threads
     else maxThreads

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

@@ -74,7 +74,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
   /** Sets correct output files to job */
   override def beforeGraph() {
     require(w != null)
-    if (threads == 0) threads = getThreads(defaultThreads)
+    if (threads == 0) threads = getThreads
     executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
     super.beforeGraph()
     out :::= List(Some(getInfoFile), getBestTreeFile, getBootstrapFile, getBipartitionsFile).flatten