Merge branch 'fix-merge_issues' into 'develop'

Fix merge issues



See merge request !321

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/LazyCheck.scala

@@ -7,9 +7,9 @@ class LazyCheck[T](function: => T) {
   private var _isSet = false
   def isSet = _isSet
   lazy val value = {
-    val chache = function
+    val cache = function
     _isSet = true
-    chache
+    cache
   }
   def apply() = value
   def get = value

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -177,7 +177,7 @@ class Gentrap(val root: Configurable) extends QScript
     if (removeRibosomalReads && ribosomalRefFlat().isEmpty)
       Logging.addError("removeRibosomalReads is enabled but no ribosomalRefFlat is given")
 
-    executedMeasures.foreach(x => x.outputDir = new File(outputDir, "expresion_measures" + File.separator + x.name))
+    executedMeasures.foreach(x => x.outputDir = new File(outputDir, "expression_measures" + File.separator + x.name))
   }
 
   /** Pipeline run for multiple samples */
@@ -208,8 +208,8 @@ class Gentrap(val root: Configurable) extends QScript
       val job = new WipeReads(qscript)
       job.inputBam = bamFile.get
       ribosomalRefFlat().foreach(job.intervalFile = _)
-      job.outputBam = createFile(".cleaned.bam")
-      job.discardedBam = createFile(".rrna.bam")
+      job.outputBam = createFile("cleaned.bam")
+      job.discardedBam = createFile("rrna.bam")
       add(job)
       Some(job.outputBam)
     } else bamFile

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

@@ -21,6 +21,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
   /** Front section for the report */
   def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp")
 
+  def additionalSections: List[(String, ReportSection)] = Nil
+
   def pipelineName = "multisamplemapping"
 
   /** Root page for the carp report */
@@ -42,8 +44,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
           )), Map())
         ),
       List(
-        "Report" -> frontSection,
-        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+        "Report" -> frontSection) ++
+        additionalSections ++
+        List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
           Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
         )) ++
         (if (insertsizeExecuted) List("Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",

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

@@ -47,16 +47,16 @@ object ShivaReport extends MultisampleMappingReportTrait {
   override def extFiles = super.extFiles ++ List("js/gears.js")
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
+  override def additionalSections = super.additionalSections ++ (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
+    Map("showPlot" -> true, "showTable" -> false)))
+  else Nil)
+
   /** Root page for the shiva report */
   override def indexPage = {
-    val variantcallingSection = (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
-      Map("showPlot" -> true, "showTable" -> false)))
-    else Nil)
-
     val regions = regionsPage
     val oldPage = super.indexPage
 
-    oldPage.copy(sections = oldPage.sections.head :: variantcallingSection ::: oldPage.sections.tail, subPages = oldPage.subPages ++ regionsPage)
+    oldPage.copy(subPages = oldPage.subPages ++ regionsPage)
   }
 
   /** Generate a page with all target coverage stats */