Fix gzip

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -40,6 +40,8 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction with Versio
 object Gzip {
   def apply(root: Configurable): Gzip = new Gzip(root)
 
+  def apply(root: Configurable, input: File, output: File): Gzip = Gzip(root, List(input), output)
+
   def apply(root: Configurable, input: List[File], output: File): Gzip = {
     val gzip = new Gzip(root)
     gzip.input = input

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala

@@ -37,7 +37,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     centrifuge.isIntermediate = true
     add(centrifuge)
 
-    add(centrifuge.output :<: new Gzip(this) > centrifugeOutput)
+    add(Gzip(this, centrifuge.output, centrifugeOutput))
 
     makeKreport(List(centrifuge.output), "centrifuge", unique = false)
     makeKreport(List(centrifuge.output), "centrifuge_unique", unique = true)