Sync with develop changes

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala

@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.extensions.kraken
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 /** Extension for Kraken */
-class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
+class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   @Input(doc = "Input: FastQ or FastA")
   var input: List[File] = _
@@ -46,9 +46,9 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
   var paired: Boolean = config("paired", default = false)
 
   executable = config("exe", default = "kraken")
-  override def versionRegex = """^Kraken version ([\d\w\-\.]+)""".r
+  def versionRegex = """^Kraken version ([\d\w\-\.]+)""".r
   override def versionExitcode = List(0, 1)
-  override def versionCommand = executable + " --version"
+  def versionCommand = executable + " --version"
 
   override def defaultCoreMemory = 8.0
   override def defaultThreads = 4

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala

@@ -15,17 +15,17 @@
  */
 package nl.lumc.sasc.biopet.extensions.sambamba
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 
 /** General Sambamba extension */
-abstract class Sambamba extends BiopetCommandLineFunction {
+abstract class Sambamba extends BiopetCommandLineFunction with Version {
   override def defaultCoreMemory = 2.0
   override def defaultThreads = 2
 
   override def subPath = "sambamba" :: super.subPath
 
   executable = config("exe", default = "sambamba", submodule = "sambamba")
-  override def versionCommand = executable
-  override def versionRegex = """sambamba v(.*)""".r
+  def versionCommand = executable
+  def versionRegex = """sambamba v(.*)""".r
   override def versionExitcode = List(0, 1)
 }
\ No newline at end of file

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala

@@ -3,21 +3,20 @@ package nl.lumc.sasc.biopet.extensions.tools
 /**
  * Created by waiyileung on 05-10-15.
  */
-
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
+import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
 
 /**
  * KrakenReportToJson function class for usage in Biopet pipelines
  *
  * @param root Configuration object for the pipeline
  */
-class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+class KrakenReportToJson(val root: Configurable) extends ToolCommandFunction with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.KrakenReportToJson
 
   @Input(doc = "Input Kraken Full report", shortName = "inputReport", required = true)
@@ -31,10 +30,11 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
 
   override def defaultCoreMemory = 1.0
 
-  override def cmdLine = super.cmdLine +
-    required("-i", inputReport) +
-    required("-o", output) +
-    conditional(skipNames, "--skipnames")
+  override def cmdLine =
+    super.cmdLine +
+      required("-i", inputReport) +
+      required("-o", output) +
+      conditional(skipNames, "--skipnames")
 
   def summaryStats: Map[String, Any] = {
     ConfigUtils.fileToConfigMap(output)