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 eb8e53730c45c35f0c45bc810ad085274ce6a95a..2c2345528fbf97da5e6111e3f35d9819e9ca627e 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 @@ -71,10 +71,8 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza "metrics" -> output, "annotation" -> refFlat ) ++ Map( - "ribosomal_intervals" -> ribosomalIntervals - // TODO: this is disabled now since the file *may* not exist (e.g. when gene coverage is low) - // and it breaks the summary md5 creation - //"output_chart" -> chartOutput + "ribosomal_intervals" -> ribosomalIntervals, + "output_chart" -> chartOutput ).collect { case (key, Some(value)) => key -> value } def summaryStats: Map[String, Any] = Picard.getMetrics(output) match {