Fixing bug with freebayes

79b42eea · Peter van 't Hof · 33d98997 · 79b42eea
Commit 79b42eea authored Aug 11, 2016 by Peter van 't Hof
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala ...src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala +1 -1

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--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
@@ -30,7 +30,7 @@ class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
  var output: File = null

  var f: Boolean = config("f", default = false)
-  executable = config("exe", default = "bgzip")
+  executable = config("exe", default = "bgzip", freeVar = false)

  def cmdLine = required(executable) +
    conditional(f, "-f") +