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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

@@ -282,7 +282,8 @@ class Tophat(val parent: Configurable)
                .exists(_.endsWith(".bt2")))
       throw new IllegalArgumentException("No bowtie2 index found for tophat")
     if (R2.nonEmpty && mateInnerDist.isEmpty) {
-      logger.warn("The parameter 'mate_inner_dist' is not set in the configuration, TopHat will use it's default value - 50bp, please check if this value for inner mate distance is correct for the current data.")
+      logger.warn(
+        "The parameter 'mate_inner_dist' is not set in the configuration, TopHat will use it's default value - 50bp, please check if this value for inner mate distance is correct for the current data.")
     }
   }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala

@@ -75,7 +75,8 @@ class Bowtie(val parent: Configurable)
       }
     }
     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.")
+      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.")
     }
   }