Change name checkExecutable to preProcesExecutable

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

@@ -57,7 +57,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
    * Set default output file, threads and vmem for current job
    */
   override def freezeFieldValues() {
-    checkExecutable
+    preProcesExecutable
     beforeGraph
     if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
 
@@ -77,7 +77,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   /**
    * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
    */
-  protected[core] def checkExecutable {
+  protected[core] def preProcesExecutable {
     if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
       try if (executable != null) {
         if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -119,7 +119,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
    * executes checkExecutable method and fill job report
    */
   final protected def preCmdInternal {
-    checkExecutable
+    preProcesExecutable
 
     beforeCmd
 
@@ -170,7 +170,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   /** Get version from cache otherwise execute the version command  */
   def getVersion: String = {
     if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
-      checkExecutable
+      preProcesExecutable
     if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
       BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
     return BiopetCommandLineFunctionTrait.versionCache(executable)

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

@@ -71,7 +71,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
     }
     for (function <- functions) function match {
       case f: BiopetCommandLineFunctionTrait => {
-        f.checkExecutable
+        f.preProcesExecutable
         f.beforeGraph
         f.commandLine
       }

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

@@ -49,7 +49,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   override val defaultThreads = 4
 
   override def beforeGraph {
-    this.checkExecutable
+    this.preProcesExecutable
 
     val fastqcDir = new File(executable).getParent
 

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

@@ -29,7 +29,7 @@ class ConiferExport(val root: Configurable) extends Conifer {
   var output: File = _
 
   override def beforeGraph {
-    this.checkExecutable
+    this.preProcesExecutable
   }
 
   override def cmdLine = super.cmdLine +