From dc0495a6bc748541eeebca829095dcdd2a4ca1f1 Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Tue, 9 May 2017 15:46:23 +0200
Subject: [PATCH] Change fastq to intermediate
---
.../nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index 3a11baa99..aadf3f64b 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -123,7 +123,9 @@ class GearsSingle(val parent: Configurable)
if (r1.size == 1) r1.head
else {
val outputFile = new File(outputDir, "merged.R1.fq.gz")
- add(Zcat(this, r1) | new Gzip(this) > outputFile)
+ val merge = Zcat(this, r1) | new Gzip(this) > outputFile
+ merge.isIntermediate = true
+ add(merge)
outputFile
}
--
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