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 }