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Commit cd4a8f4c authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix merge file

parent f069ee1e
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @ cd4a8f4c
...@@ -75,7 +75,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait { ...@@ -75,7 +75,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
} }
} }
override def keepMergedFiles: Boolean = config("keep_merged_files", default = false) override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner) override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner)
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