Switch to CommandLineResources

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

@@ -14,8 +14,8 @@ class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk
 
   override val defaultThreads = 3
 
-  override def beforeGraph() {
-    super.beforeGraph()
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
 
     nt = Option(getThreads)
     memoryLimit = Option(nt.getOrElse(1) * 2)

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

@@ -20,7 +20,6 @@ object BaseRecalibrator {
     val br = new BaseRecalibrator(root)
     br.input_file :+= input
     br.out = output
-    br.beforeGraph()
     br
   }
 }
\ No newline at end of file

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

@@ -5,17 +5,19 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ CommandLineResources, Reference, BiopetJavaCommandLineFunction }
 import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
-trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
+trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference {
   memoryLimit = Option(3)
 
   override def subPath = "gatk" :: super.subPath
 
   jarFile = config("gatk_jar")
 
+  reference_sequence = referenceFasta()
+
   override def defaultCoreMemory = 4.0
   override def faiRequired = true
 
@@ -33,14 +35,9 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
 
-  override def versionRegex = """(.*)""".r
-  override def versionExitcode = List(0, 1)
-  override def versionCommand = executable + " -jar " + jarFile + " -version"
-
-  override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
+  //override def versionRegex = """(.*)""".r
+  //override def versionExitcode = List(0, 1)
+  //override def versionCommand = executable + " -jar " + jarFile + " -version"
 
-  override def beforeGraph(): Unit = {
-    super.beforeGraph()
-    if (reference_sequence == null) reference_sequence = referenceFasta()
-  }
+  //override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
 }

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

@@ -38,8 +38,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     stand_emit_conf = config("stand_emit_conf", default = 0)
   }
 
-  override def beforeGraph() {
-    super.beforeGraph()
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
     if (bamOutput != null && nct.getOrElse(1) > 1) {
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
     }

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

@@ -28,8 +28,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
 
   override val defaultThreads = 1
 
-  override def beforeGraph() {
-    super.beforeGraph()
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
     nct = Some(getThreads)

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

@@ -10,9 +10,6 @@ import java.io.File
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-  override def beforeGraph() {
-    super.beforeGraph()
-  }
 }
 
 object VariantEval {
@@ -22,7 +19,6 @@ object VariantEval {
     vareval.eval = Seq(sample)
     vareval.comp = Seq(compareWith)
     vareval.out = output
-    vareval.beforeGraph()
     vareval
   }
 
@@ -36,7 +32,6 @@ object VariantEval {
     vareval.ST = ST
     vareval.noEV = true
     vareval.EV = EV
-    vareval.beforeGraph()
     vareval
   }