From 42b5a99133aa117c52c252d9702f3e879708e533 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Wed, 20 Jan 2016 15:15:09 +0100
Subject: [PATCH] Fix bwa bug using freeVar=false
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index 91037fa4e..80743e00d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -94,7 +94,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
var trimPrimer: Boolean = config("trim_primer", default = false)
var stripF3: Boolean = config("strip_f3", default = false)
var maq: Boolean = config("maq", default = false)
- var bwa: Boolean = config("bwa", default = false)
+ var bwa: Boolean = config("bwa", default = false, freeVar = false)
var noZeroCap: Boolean = config("no_zero_cap", default = false)
var zeroCap: Boolean = config("zero_cap", default = false)
--
GitLab