moved preLoad config to PipelineCommand

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

@@ -92,14 +92,6 @@ object BiopetExecutable extends Logging {
         println("version: " + getVersion)
       }
       case Array(module, name, passArgs @ _*) => {
-        // Reading config files
-        val argsSize = passArgs.size
-        for (t <- 0 until argsSize) {
-          if (passArgs(t) == "-config" || args(t) == "--config_file") {
-            if (t >= argsSize) throw new IllegalStateException("-config needs a value")
-            Config.global.loadConfigFile(new File(passArgs(t + 1)))
-          }
-        }
         getCommand(module, name).main(passArgs.toArray)
       }
       case Array(module) => {

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

 package nl.lumc.sasc.biopet.core
 
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 
 trait PipelineCommand extends MainCommand with GatkLogging {
@@ -8,6 +10,14 @@ trait PipelineCommand extends MainCommand with GatkLogging {
   def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
 
   def main(args: Array[String]): Unit = {
+    val argsSize = args.size
+    for (t <- 0 until argsSize) {
+      if (args(t) == "-config" || args(t) == "--config_file") {
+        if (t >= argsSize) throw new IllegalStateException("-config needs a value")
+        Config.global.loadConfigFile(new File(args(t + 1)))
+      }
+    }
+
     var argv: Array[String] = Array()
     argv ++= Array("-S", pipeline)
     argv ++= args