Fixe namespaces

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

@@ -13,7 +13,7 @@ import java.io.FileInputStream
 import java.security.MessageDigest
 
 trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
-  analysisName = getClass.getSimpleName
+  analysisName = configName
 
   @Input(doc = "deps", required = false)
   var deps: List[File] = Nil
@@ -38,7 +38,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   override def freezeFieldValues() {
     checkExecutable
     afterGraph
-    jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + analysisName + ".out")
+    jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
 
     if (threads == 0) threads = getThreads(defaultThreads)
     if (threads > 1) nCoresRequest = Option(threads)
@@ -48,7 +48,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
       if (vmem == null && !defaultVmem.isEmpty) vmem = defaultVmem
     }
     if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
-    jobName = this.analysisName + ":" + firstOutput.getName
+    jobName = configName + ":" + firstOutput.getName
 
     super.freezeFieldValues()
   }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -6,9 +6,9 @@ import org.broadinstitute.gatk.queue.util.Logging
 trait Configurable extends Logging {
   val root: Configurable
   val globalConfig: Config = if (root != null) root.globalConfig else new Config()
-  val configPath: List[String] = if (root != null) root.configFullPath else List()
-  protected val configName = getClass.getSimpleName.toLowerCase
-  protected val configFullPath = configName :: configPath
+  def configPath: List[String] = if (root != null) root.configFullPath else List()
+  protected lazy val configName = getClass.getSimpleName.toLowerCase
+  protected lazy val configFullPath = configName :: configPath
   var defaults: scala.collection.mutable.Map[String,Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray:_*)
                                                           else scala.collection.mutable.Map()
   

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

@@ -18,8 +18,8 @@ class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gat
 object VariantRecalibrator {
   def apply(root: Configurable, input:File, recal_file:File, tranches_file:File, indel: Boolean = false): VariantRecalibrator = {
     val vr = new VariantRecalibrator(root) {
-      override val configName = "variantrecalibrator"
-      override val configFullPath = (if (indel) "indel" else "snp") :: configName :: configPath
+      override lazy val configName = "variantrecalibrator"
+      override def configPath:  List[String] = (if (indel) "indel" else "snp") :: super.configPath
       if (indel) {
         mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
         defaults ++= Map("ts_filter_level" -> 99.0)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -92,18 +92,22 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
         val allBamfiles = for ((sampleID,sampleOutput) <- samplesOutput;
                                 file <- sampleOutput.variantcalling.bamFiles) yield file
         val allRawVcfFiles = for ((sampleID,sampleOutput) <- samplesOutput) yield sampleOutput.variantcalling.rawFilterVcfFile
-        val hcDiscorvery = new HaplotypeCaller(this)
+        val hcDiscorvery = new HaplotypeCaller(this) {
+          override protected lazy val configName = "haplotypecaller"
+          override def configPath:  List[String] = "multisample" :: super.configPath
+        }
         hcDiscorvery.input_file = allBamfiles.toSeq
-        hcDiscorvery.scatterCount = config("scattercount", submodule = "multisample")
         hcDiscorvery.out = outputDir + "variantcalling/hc.vcf.gz"
         add(hcDiscorvery)
 
         val cvRaw = CombineVariants(this, allRawVcfFiles.toList, outputDir + "variantcalling/raw.vcf.gz")
         add(cvRaw)
 
-        val hcRaw = new HaplotypeCaller(this)
+        val hcRaw = new HaplotypeCaller(this) {
+          override protected lazy val configName = "haplotypecaller"
+          override def configPath:  List[String] = "multisample" :: super.configPath
+        }
         hcRaw.input_file = allBamfiles.toSeq
-        hcRaw.scatterCount = config("scattercount", submodule = "multisample")
         hcRaw.out = outputDir + "variantcalling/raw_genotype.vcf.gz"
         hcRaw.alleles = cvRaw.out
         hcRaw.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES