Skipping parts of report when they are skipped in the pipeline

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

@@ -35,18 +35,22 @@ object MappingReport extends ReportBuilder {
 
   /** Root page for single BamMetrcis report */
   def indexPage = {
-    val bamMetricsPage = BammetricsReport.bamMetricsPage(summary, sampleId, libId)
-    ReportPage(List("QC" -> FlexiprepReport.flexiprepPage) ::: bamMetricsPage.subPages ::: List(
-      "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-      )), Map()),
-      "Files" -> ReportPage(List(), List(
-        "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
-        "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
-        "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
-      ), Map())
-    ), List(
+    val skipFlexiprep = summary.getValue(sampleId, libId, "mapping", "settings", "skip_flexiprep").getOrElse(false) == true
+    val bamMetricsPage = if (summary.getValue(sampleId, libId, "mapping", "settings", "skip_metrics").getOrElse(false) == true) {
+      Some(BammetricsReport.bamMetricsPage(summary, sampleId, libId))
+    } else None
+    ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) :::
+      bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: List(
+        "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+        )), Map()),
+        "Files" -> ReportPage(List(), (if (skipFlexiprep) Nil else List(
+          "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
+          "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"))) :::
+          List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
+          ), Map())
+      ), List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp")
-    ) ::: bamMetricsPage.sections,
+    ) ::: bamMetricsPage.map(_.sections).getOrElse(Nil),
       Map()
     )
   }