Change getVersion to Option[String]

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

@@ -135,10 +135,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   protected val versionExitcode = List(0)
 
   /** Executes the version command */
-  private def getVersionInternal: String = {
-    if (versionCommand == null || versionRegex == null) return "N/A"
+  private def getVersionInternal: Option[String] = {
+    if (versionCommand == null || versionRegex == null) return None
     val exe = new File(versionCommand.trim.split(" ")(0))
-    if (!exe.exists()) return "N/A"
+    if (!exe.exists()) return None
     val stdout = new StringBuffer()
     val stderr = new StringBuffer()
     def outputLog = "Version command: \n" + versionCommand +
@@ -147,25 +147,28 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
     if (!versionExitcode.contains(process.exitValue)) {
       logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
-      return "N/A"
+      return None
     }
     for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
       line match {
-        case versionRegex(m) => return m
+        case versionRegex(m) => return Some(m)
         case _               =>
       }
     }
     logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
-    return "N/A"
+    return None
   }
 
   /** Get version from cache otherwise execute the version command  */
-  def getVersion: String = {
+  def getVersion: Option[String] = {
     if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
       preProcesExecutable
-    if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
-      BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
-    return BiopetCommandLineFunctionTrait.versionCache(executable)
+    if (!BiopetCommandLineFunctionTrait.versionCache.contains(versionCommand))
+      getVersionInternal match {
+        case Some(version) => BiopetCommandLineFunctionTrait.versionCache += versionCommand -> version
+        case _             =>
+      }
+    BiopetCommandLineFunctionTrait.versionCache.get(versionCommand)
   }
 
   /**

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

@@ -64,8 +64,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       // otherwise, use default contaminants file (depending on FastQC version)
       case None =>
         val defaultContams = getVersion match {
-          case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
-          case _         => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+          case Some("v0.11.2") => new File(fastqcDir + "/Configuration/contaminant_list.txt")
+          case _               => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
         }
         config("contaminants", default = defaultContams)
     }
@@ -76,8 +76,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       // otherwise, check if adapters are already present (depending on FastQC version)
       case None =>
         val defaultAdapters = getVersion match {
-          case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
-          case _         => None
+          case Some("v0.11.2") => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+          case _               => None
         }
         defaultAdapters.collect { case adp => config("adapters", default = adp) }
     }