Fixed jobOutputFile

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

@@ -78,6 +78,13 @@ trait BiopetQScript extends Configurable with GatkLogging {
       case f: ScatterGatherableFunction => f.scatterCount = 1
       case _                            =>
     }
+
+    this match {
+      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+        logger.info("Write report is skipped because sample flag is used")
+      case _ => reportClass.foreach(add(_))
+    }
+
     for (function <- functions) function match {
       case f: BiopetCommandLineFunction =>
         f.preProcessExecutable()
@@ -96,11 +103,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
       else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
     }
 
-    this match {
-      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
-        logger.info("Write report is skipped because sample flag is used")
-      case _ => reportClass.foreach(add(_))
-    }
+    functions.filter(_.jobOutputFile == null).foreach(f => {
+      if (f.jobOutputFile == null && f.firstOutput != null)
+        f.jobOutputFile = new File(f.firstOutput.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + configName + ".out")
+      else throw new IllegalStateException(s"Can't generate a jobOutputFile for $f")
+    })
 
     if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
 

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

@@ -58,9 +58,6 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
       case e: NullPointerException => null
     }
 
-    if (jobOutputFile == null && firstOutput != null)
-      jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
-
     nCoresRequest = Option(threads)
 
     /** The 1e retry does not yet upgrade the memory */