From 0999885a07fd38d3890aad1621e14e66bcd15d2b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Feb 2015 14:08:48 +0100
Subject: [PATCH] Add --no-bgfs option
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala | 3 +++
1 file changed, 3 insertions(+)
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 4f6236179..1d7b45ec9 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)
}
--
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