Changes ; to &&, is saver

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

@@ -87,7 +87,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
 
   /** Returns command to execute */
   def cmdLine = {
-    var cmd: String = required("cd", outputDir) + "&&" + required(executable)
+    var cmd: String = required("cd", outputDir) + " && " + required(executable)
     if (runmode != null && runmode == "genomeGenerate") { // Create index
       cmd += required("--runMode", runmode) +
         required("--genomeFastaFiles", reference)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala

@@ -30,7 +30,7 @@ class Bowtie2Build(val root: Configurable) extends BiopetCommandLineFunction {
     outputFiles ::= new File(reference.getParentFile, baseName + ".2.bt2")
   }
 
-  def cmdLine = required("cd", reference.getParentFile) + "; " +
+  def cmdLine = required("cd", reference.getParentFile) + " && " +
     required(executable) +
     required(reference) +
     required(baseName)

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

@@ -30,7 +30,7 @@ class BowtieBuild(val root: Configurable) extends BiopetCommandLineFunction {
     outputFiles ::= new File(reference.getParentFile, baseName + ".2.ebwt")
   }
 
-  def cmdLine = required("cd", reference.getParentFile) + "; " +
+  def cmdLine = required("cd", reference.getParentFile) + " && " +
     required(executable) +
     required(reference) +
     required(baseName)