From 66f989dff7834e6cda79e00b30a2f6b6e35ac062 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 6 Aug 2014 17:58:52 +0200
Subject: [PATCH] Added sample and library to flexiprep
---
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 90557d3e8..1fd236b24 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -160,6 +160,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
if (chunking) flexiprep.skipSummary = true
+ flexiprep.sampleName = this.RGSM
+ flexiprep.libraryName = this.RGLB
flexiprep.init
flexiprep.runInitialJobs
//flexiprep.biopetScript
--
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