diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala index b2114c72598dc873e6028eac8d3c96800b7612af..340d5e098d85679d556fd1155545890bfd9d3cc2 100644 --- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala +++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala @@ -48,7 +48,7 @@ class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl. case Some(n) => n -> Map("sequence" -> seq, "count" -> count) // adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter // sequences come from FastQC - case None => + case _ => throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in 'clipping_$readName'.") } }.toMap @@ -58,7 +58,7 @@ class Cutadapt(root: Configurable, fastqc: Fastqc, readName: String) extends nl. Map.empty[String, Map[String, Any]] } // "adapters" key not found ~ something went wrong in our part - case None => throw new RuntimeException(s"Required key 'adapters' not found in stats entry 'clipping_$readName'.") + case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry 'clipping_$readName'.") } initStats.updated("adapters", adapterCounts) }