Still executes multisample jobs when all samples are given with --sample flag

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

@@ -87,8 +87,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
     else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
 
     this match {
-      case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
-        logger.info("Write summary is skipped because sample flag is used")
+      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(_))
     }
 

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

@@ -131,7 +131,7 @@ trait MultiSampleQScript extends SummaryQScript {
 
   /** Runs addAndTrackJobs method for each sample */
   final def addSamplesJobs() {
-    if (onlySamples.isEmpty) {
+    if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
       samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
       addMultiSampleJobs()
     } else onlySamples.foreach(sampleId => samples.get(sampleId) match {

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

@@ -136,7 +136,7 @@ trait SummaryQScript extends BiopetQScript {
       addChecksum(file)
 
     this match {
-      case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
+      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
         logger.info("Write summary is skipped because sample flag is used")
       case _ => add(writeSummary)
     }