let's test fail on format/git issues

Jenkinsfile

@@ -21,6 +21,10 @@ node('local') {
             junit '*/target/surefire-reports/*.xml'
         }
 
+        stage('Check git on changes') {
+            sh 'if [ $(git diff | wc -l) -eq 0 ]; then true; else echo "[ERROR] Git is not clean anymore after build"; false; fi'
+        }
+
         stage('Check Documentation') {
             sh 'mkdocs build --clean --strict'
         }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -30,7 +30,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   var inputR1: File = _
 
   @Input(doc = "R2 fastq file (gzipped allowed)", shortName = "R2", fullName = "inputR2", required = false)
-  var inputR2: Option[File] = None
+  var inputR2:     Option[File] = None
 
   /** Skip Trim fastq files */
   var skipTrim: Boolean = config("skip_trim", default = false)