Merge branch 'fix-renames' into 'develop'

Fix renames

Some naming fixes for consistency.

See merge request !309

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

@@ -107,7 +107,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   )
 
   /** File to add to the summary */
-  def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,
+  def summaryFiles: Map[String, File] = Map("output_bam" -> finalBamFile, "input_R1" -> input_R1,
     "reference" -> referenceFasta()) ++
     (if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map())
 

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

@@ -66,7 +66,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
     "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)),
     "Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
-      Map("pipelineName" -> pipelineName, "fileTag" -> "preProcessBam"))), Map())
+      Map("pipelineName" -> pipelineName, "fileTag" -> "output_bam_preprocess"))), Map())
 
   /** Single sample page */
   def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {

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

@@ -62,7 +62,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
     class Library(libId: String) extends AbstractLibrary(libId) {
       def summaryFiles: Map[String, File] = (inputR1.map("input_R1" -> _) :: inputR2.map("input_R2" -> _) ::
         inputBam.map("input_bam" -> _) :: bamFile.map("output_bam" -> _) ::
-        preProcessBam.map("output_preProcessBam" -> _) :: Nil).flatten.toMap
+        preProcessBam.map("output_bam_preprocess" -> _) :: Nil).flatten.toMap
 
       def summaryStats: Map[String, Any] = Map()
 
@@ -159,7 +159,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
     }
 
     def summaryFiles: Map[String, File] = (bamFile.map("output_bam" -> _) ::
-      preProcessBam.map("output_preProcessBam" -> _) :: Nil).flatten.toMap
+      preProcessBam.map("output_bam_preprocess" -> _) :: Nil).flatten.toMap
 
     def summaryStats: Map[String, Any] = Map()