From fbff5f3d9b54d7d721c358c472c51a306bd8d08d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 10 Nov 2014 12:04:51 +0100
Subject: [PATCH] Change default threads to 1
---
.../nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index f9d1dd146..00904552a 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -11,7 +11,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
- nct = config("threads", default = 3)
+ nct = config("threads", default = 1)
bamOutput = config("bamOutput")
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 96cc08149..75105f1b2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -10,7 +10,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
- nct = config("threads", default = 3)
+ nct = config("threads", default = 1)
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
--
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