Merge branch 'fix-mapping_report' into 'develop'

Skipping parts of report when they are skipped in the pipeline

Report of mapping fail when skip_flexiprep or skip_metrics is enabled, this should fix it.

See merge request !216

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * Extension for Tophat
  */
-class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
+class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Reference {
 
   executable = config("exe", default = "tophat", freeVar = false)
 

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()
     )
   }