From ef3b8eb63c2e2bb4895d9c40744e143464297c1f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 28 Oct 2015 18:07:32 +0100
Subject: [PATCH] Added args
---
.../scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 1b1107f4a..212bdc29e 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -181,6 +181,8 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
aorrg.RGID = sampleId + "-" + libId
aorrg.RGLB = libId
aorrg.RGSM = sampleId
+ aorrg.RGPL = "unknown"
+ aorrg.RGPU = "na"
aorrg.isIntermediate = true
qscript.add(aorrg)
} else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
--
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