Hide insertsize plot on single end runs

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -61,6 +61,8 @@ object BammetricsReport extends ReportBuilder {
     val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
     val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
 
+    val insertsizeMetrics = summary.getValue(sampleId, libId, metricsTag, "stats", "CollectInsertSizeMetrics", "metrics").isDefined
+
     val targets = (
       summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
       summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
@@ -77,9 +79,9 @@ object BammetricsReport extends ReportBuilder {
         targets.map(t => t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> Some(t)))),
         Map())),
       List(
-        "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
-      ) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+        "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp")) ++
+        (if (insertsizeMetrics) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
+      ) else Nil) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
           Map("showPlot" -> true)))
         else Nil) ++
         (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala

@@ -28,6 +28,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
 
     val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
     val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
+    val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_.isDefined)
     val flexiprepExecuted = summary.getLibraryValues("flexiprep")
       .exists { case ((sample, lib), value) => value.isDefined }
 
@@ -44,9 +45,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
         "Report" -> frontSection,
         "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
-        ),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
-          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) ++
+        )) ++
+        (if (insertsizeExecuted) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
+          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))else Nil) ++
         (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
         else Nil) ++