@@ -74,6 +74,9 @@ class Bowtie(val parent: Configurable)
s"No index files found for bowtie in: $indexDir with basename: $basename")
}
}
if(R2.nonEmpty&&maxins.isEmpty){
Logging.addError("The parameter 'maxins' that specifies the maximum allowed insert size, is missing in the configuration. Please note that Bowtie won't align reads coming from inserts longer than this value.")