diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala index 79bab74f383b6b38db5a38ee1109ea47898ebffd..a5000b2f94a73d4d01dad86757273d6853561777 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala @@ -85,7 +85,9 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza "output_chart" -> chartOutput ).collect { case (key, Some(value)) => key -> value } - def summaryStats = Picard.getMetrics(output).getOrElse(Map()) + def summaryStats = Map( + "metrics" -> Picard.getMetrics(output).getOrElse(Map()), + "histogram" -> Picard.getHistogram(output).getOrElse(Map())) override def commandLine = super.commandLine + required("INPUT=", input, spaceSeparated = false) +