trying to fix weird error in testing

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -154,6 +154,7 @@ class BamMetrics(val parent: Configurable) extends QScript
       val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
         output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
         minOverlap = config("strict_intersect_overlap", default = 1.0))
+      biStrict.jobOutputFile = new File(targetDir, ".biStrict.Bedtools.out")
       val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
       addSummarizable(biopetFlagstatStrict, targetName + "_flagstats_strict")
       add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
@@ -161,6 +162,7 @@ class BamMetrics(val parent: Configurable) extends QScript
       val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
         output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
         minOverlap = config("loose_intersect_overlap", default = 0.01))
+      biLoose.jobOutputFile = new File(targetDir, ".biLoose.Bedtools.out")
       val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
       addSummarizable(biopetFlagstatLoose, targetName + "_flagstats_loose")
       add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

@@ -23,13 +23,13 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
 
   @Input(doc = "Input file (bed/gff/vcf/bam)")
-  var input: File = null
+  var input: File = _
 
   @Input(doc = "Intersect file (bed/gff/vcf)")
-  var intersectFile: File = null
+  var intersectFile: File = _
 
   @Output(doc = "output File")
-  var output: File = null
+  var output: File = _
 
   @Argument(doc = "Min overlap", required = false)
   var minOverlap: Option[Double] = config("minoverlap")
@@ -46,7 +46,8 @@ class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
   }
 
   /** Returns command to execute */
-  def cmdLine = required(executable) + required("intersect") +
+  def cmdLine: String = required(executable) +
+    required("intersect") +
     required(inputTag, input) +
     required("-b", intersectFile) +
     optional("-f", minOverlap) +