From eb23b56ee20bbdc2dc0a55c8a1c398926b2f7d2e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 May 2014 14:07:29 +0200
Subject: [PATCH] - fixed namespaceing in AddOrReplaceReadGroups
---
.../lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 0fc8ea9ee..a2f59eca1 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -119,12 +119,12 @@ class Mapping(private var globalConfig: Config) extends QScript {
this.nCoresRequest = 2
this.jobResourceRequests :+= "h_vmem=4G"
- this.RGLB = RGLB
- this.RGPL = RGPL
- this.RGPU = RGPU
- this.RGSM = RGSM
- if (RGCN != null) this.RGCN = RGCN
- if (RGDS != null) this.RGDS = RGDS
+ this.RGLB = qscript.RGLB
+ this.RGPL = qscript.RGPL
+ this.RGPU = qscript.RGPU
+ this.RGSM = qscript.RGSM
+ if (RGCN != null) this.RGCN = qscript.RGCN
+ if (RGDS != null) this.RGDS = qscript.RGDS
}
add(addOrReplaceReadGroups)
--
GitLab