From 937247103c92112ed7c4c6bff4b7dfabf1e8c6c6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 22 Sep 2015 12:04:32 +0200
Subject: [PATCH] Made output of bwamem pipeable
---
.../main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 31c652528..5cbd73852 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -111,6 +111,6 @@ class BwaMem(val root: Configurable) extends Bwa with Reference {
required(reference) +
required(R1) +
optional(R2) +
- " > " + required(output)
+ (if (outputAsStsout) "" else " > " + required(output))
}
}
--
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