Fix summary when --sample flag is used in multisample pipelines

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

@@ -86,7 +86,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
       globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
     else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
 
-    reportClass.foreach(add(_))
+    this match {
+      case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
+        logger.info("Write summary is skipped because sample flag is used")
+      case _ => reportClass.foreach(add(_))
+    }
 
     Logging.checkErrors()
   }

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

@@ -26,7 +26,7 @@ trait MultiSampleQScript extends SummaryQScript {
   qscript =>
 
   @Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
-  private val onlySamples: List[String] = Nil
+  private[core] val onlySamples: List[String] = Nil
 
   require(globalConfig.map.contains("samples"), "No Samples found in config")
 

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

@@ -135,7 +135,11 @@ trait SummaryQScript extends BiopetQScript {
     for ((_, file) <- this.summaryFiles)
       addChecksum(file)
 
-    add(writeSummary)
+    this match {
+      case q: MultiSampleQScript if (q.onlySamples.nonEmpty) =>
+        logger.info("Write summary is skipped because sample flag is used")
+      case _ => add(writeSummary)
+    }
   }
 }