Hide QC from report when flexiprep is not executed

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -143,14 +143,16 @@ object ShivaReport extends MultisampleReportBuilder {
 
   /** Library page */
   def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
-    ReportPage(List(
-      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
-      "QC" -> FlexiprepReport.flexiprepPage
-    ), List(
-      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
-      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
-    ), args)
+    val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
+    ReportPage(
+      "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)) ::
+        (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
+        ), "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
+        (if (flexiprepExecuted) List(
+          "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+          "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+        )
+        else Nil), args)
   }
 
   /** Name of the report */