From 2a64a1d61c04aaf35d34862647d9f75f65fc7904 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 11 Nov 2015 18:59:12 +0100
Subject: [PATCH] Add fixme
---
.../scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 1 +
1 file changed, 1 insertion(+)
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 b90a3b9b7..5c243df86 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
@@ -262,6 +262,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
md.input = input
md.output = new File(sampleDir, sampleId + ".dedup.bam")
md.outputMetrics = new File(sampleDir, sampleId + ".dedup.metrics")
+ //FIXME: making this file intermediate make the pipeline restart unnessery jobs
//md.isIntermediate = isIntermediate
add(md)
addSummarizable(md, "mark_duplicates")
--
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