Fixing null pointer

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

@@ -154,7 +154,6 @@ 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)))
@@ -162,7 +161,6 @@ 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-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     beforeGraph()
     internalBeforeGraph()
 
-    this.commandDirectory = this.jobOutputFile.getParentFile
+    if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
 
     super.freezeFieldValues()
   }