From 46f8b1b580c79eafd7acb05a6f696da3ff1a80bd Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 Oct 2015 13:24:25 +0200
Subject: [PATCH] Change to compressed output
---
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
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 7d8a04d4f..5e80f114c 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
@@ -144,8 +144,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
config("bam_to_fastq", default = false).asBoolean match {
case true =>
val samToFastq = SamToFastq(qscript, config("bam"),
- new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
- new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
+ new File(libDir, sampleId + "-" + libId + ".R1.fq.gz"),
+ new File(libDir, sampleId + "-" + libId + ".R2.fq.gz"))
samToFastq.isIntermediate = true
qscript.add(samToFastq)
mapping.foreach(mapping => {
--
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