Automatic class name conversion

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

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core
 
 trait PipelineCommand extends MainCommand {
 
-  val pipeline = ""
+  def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
 
   def main(args: Array[String]): Unit = {
     var argv: Array[String] = Array()

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -73,8 +73,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
 }
 
 object BamMetrics extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.class"
-
   def apply(root: Configurable, bamFile: File, outputDir: String): BamMetrics = {
     val bamMetrics = new BamMetrics(root)
     bamMetrics.inputBam = bamFile

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -55,6 +55,4 @@ class Basty (val root: Configurable) extends QScript with MultiSampleQScript {
   }
 }
 
-object Basty extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/basty/Basty.class"  
-}
+object Basty extends PipelineCommand

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -272,6 +272,4 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   }
 }
 
-object Flexiprep extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.class"
-}
+object Flexiprep extends PipelineCommand

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

@@ -58,6 +58,4 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
   }
 }
 
-object GatkBenchmarkGenotyping extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.class"
-}
+object GatkBenchmarkGenotyping extends PipelineCommand

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

@@ -57,6 +57,4 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   }
 }
 
-object GatkGenotyping extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.class"
-}
+object GatkGenotyping extends PipelineCommand

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

@@ -214,6 +214,4 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 }
 
-object GatkPipeline extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.class"  
-}
+object GatkPipeline extends PipelineCommand

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

@@ -73,6 +73,4 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
   }
 }
 
-object GatkVariantRecalibration extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.class"
-}
+object GatkVariantRecalibration extends PipelineCommand

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

@@ -221,8 +221,6 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
 }
 
 object GatkVariantcalling extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.class"
-  
   class ScriptOutput {
     var bamFiles: List[File] = _
     var gvcfFile: File = _

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

@@ -87,6 +87,4 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
   }
 }
 
-object GatkVcfSampleCompare extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.class"
-}
+object GatkVcfSampleCompare extends PipelineCommand

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -76,6 +76,4 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
   }
 }
 
-object Gentrap extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.class"
-}
+object Gentrap extends PipelineCommand

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -278,8 +278,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
 }
 
 object Mapping extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.class"
-
   def loadFromLibraryConfig(root: Configurable, runConfig: Map[String, Any], sampleConfig: Map[String, Any], runDir: String): Mapping = {
     val mapping = new Mapping(root)
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -197,6 +197,4 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   }
 }
 
-object Sage extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/sage/Sage.class"
-}
+object Sage extends PipelineCommand