diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala index 559c15ff35fbf1fdc9649db8cb3ed4ac166d9559..a9be0fc1ce44a6fd445cd12156549a42cd52948e 100644 --- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala +++ b/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()) diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala index 496ee2260d83757d8913b95e13080cc0f25080e3..19348061dbe29285437ab08c48cd43786d03aca6 100644 --- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala +++ b/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()