From 43748908994dd164cb54a97b60db0a664b9d987b Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Fri, 15 Jan 2016 16:54:32 +0100
Subject: [PATCH] bgzip piping went wrong fix with if stdout else >
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
index 321cb8b9c..a43fc4734 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
@@ -36,5 +36,5 @@ class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
def cmdLine = required(executable) +
conditional(f, "-f") +
" -c " + repeat(input) +
- " > " + required(output)
+ (if (outputAsStsout) "" else " > " + required(output))
}
--
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