diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala index 4f6236179755659b3b42d74cef6c722713fbf4c9..1d7b45ec9617091a457f073e4110ff5e01932e24 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala @@ -50,6 +50,8 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction { @Argument(doc = "Output directory", required = true) var w: String = _ + var noBfgs: Boolean = config("no_bfgs", default = false) + @Input(required = false) var t: File = _ @@ -101,5 +103,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction { optional("-f", f) + optional("-t", t) + optional("-z", z) + + conditional(noBfgs, "--no-bgfs") + required("-T", threads) }