From d90761b674001d220beb4e63f5e60b0ef98d1f7c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 7 Aug 2014 14:18:06 +0200
Subject: [PATCH] Added metrics pipeline
---
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
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 1fd236b24..47774f2ea 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
@@ -201,7 +201,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile = new File(outputDir + outputName + ".dedup.bam")
add(MarkDuplicates(this, bamFiles, bamFile))
} else if (skipMarkduplicates && chunking) bamFile = addMergeBam(bamFiles, new File(outputDir + outputName + ".bam"), outputDir)
-
+
+ addAll(BamMetrics.apply(this, bamFile, outputDir + "metrics/").functions)
+
outputFiles += ("finalBamFile" -> bamFile)
}
--
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