changed version command to def

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

@@ -18,6 +18,8 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
   var fastq_output: File = _
   
   executeble = config("exe","cutadapt")
+  override def versionCommand = executeble + " --version"
+  override val versionRegex = """(.*)""".r
   
   var default_clip_mode:String = config("default_clip_mode", "3")
   var opt_adapter: Set[String] = config("adapter", Nil)
@@ -27,15 +29,9 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
   var opt_discard: Boolean = config("discard",false)
   var opt_minimum_length: String = config("minimum_length", 1)
   var opt_maximum_length: String = config("maximum_length", null)
-  
-  override val versionRegex = """(.*)""".r
-  
-  override def afterGraph() {
-    versionCommand = executeble + " --version"
-  }
-  
+    
   override def beforeCmd() {
-    this.getContamsFromFile
+    getContamsFromFile
   }
   
   def cmdLine = {

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

@@ -31,9 +31,10 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
     this.checkExecuteble
     val fastqcDir = executeble.substring(0, executeble.lastIndexOf("/"))
     if (contaminants == null) contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
-    versionCommand = executeble + " --version"
   }
-    
+  
+  override def versionCommand = executeble + " --version"
+  
   def cmdLine = {
     required(executeble) + 
       optional("--java", java_exe) +

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala

@@ -38,10 +38,10 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
   override def afterGraph {
     if (defaultQualityType == null) defaultQualityType = config("defaultqualitytype", "sanger")
     if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
-    
-    versionCommand = executeble + " --version"
   }
   
+  override def versionCommand = executeble + " --version"
+  
   override def beforeCmd {
     qualityType = getQualityTypeFromFile
   }

mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala

@@ -19,18 +19,17 @@ class Bwa(val root:Configurable) extends BiopetCommandLineFunction {
   @Output(doc="Output file SAM", shortName="output")
   var output: File = _
   
-  executeble = config("exe", "bwa")
-  
   var RG: String = _
   var M: Boolean = config("M", true)
   
+  executeble = config("exe", "bwa")
+  override val versionRegex = """Version: (.*)""".r
+  override val versionExitcode = List(0,1)
+  
   override val defaultVmem = "6G"
   override val defaultThreads = 8
-  override val versionRegex = """Version: (.*)""".r
   
-  override def beforeCmd() {
-    versionCommand = executeble
-  }
+  override def versionCommand = executeble
   
   def cmdLine = {
     required(executeble) +