diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index c8b81c0c4d31d6424db74390390c758096478838..cbe6fd6eb56e9d7eab647cad238456717d10a6b8 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -173,19 +173,22 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
   }
 
   def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: File) {
-    val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.sense.coverage"),
+    val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed,
+      output = Some(new File(outputDir, outputPrefix + ".genome.sense.coverage")),
       depth = false, sameStrand = true, diffStrand = false)
     val countSense = new BedtoolsCoverageToCounts(this)
     countSense.input = bedtoolsSense.output
     countSense.output = new File(outputDir, outputPrefix + ".genome.sense.counts")
 
-    val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.antisense.coverage"),
+    val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed,
+      output = Some(new File(outputDir, outputPrefix + ".genome.antisense.coverage")),
       depth = false, sameStrand = false, diffStrand = true)
     val countAntisense = new BedtoolsCoverageToCounts(this)
     countAntisense.input = bedtoolsAntisense.output
     countAntisense.output = new File(outputDir, outputPrefix + ".genome.antisense.counts")
 
-    val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.coverage"),
+    val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed,
+      output = Some(new File(outputDir, outputPrefix + ".genome.coverage")),
       depth = false, sameStrand = false, diffStrand = false)
     val count = new BedtoolsCoverageToCounts(this)
     count.input = bedtools.output