diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala index 05b4dcae4bdc66189f3269f738c1fe74ac107985..026f9ef27e72a655cc141f9a5dacc595f9f85d1b 100644 --- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala +++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala @@ -21,6 +21,10 @@ class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction { override val defaultVmem = (memory * 2 / 1000) + "G" override val defaultThreads = 2 + override def beforeCmd { + memory = memory * threads + } + def cmdLine = required(executeble) + conditional(decomrpess, "-d") + conditional(!decomrpess, "-z") +