diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index 3a11baa99e9358827f218c8bd03e70877b6a926b..aadf3f64b5ea0935211b150282713ee4bf192342 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -123,7 +123,9 @@ class GearsSingle(val parent: Configurable)
       if (r1.size == 1) r1.head
       else {
         val outputFile = new File(outputDir, "merged.R1.fq.gz")
-        add(Zcat(this, r1) | new Gzip(this) > outputFile)
+        val merge = Zcat(this, r1) | new Gzip(this) > outputFile
+        merge.isIntermediate = true
+        add(merge)
         outputFile
       }