Commit 6d672983 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing temp files

parent d2c7fc48
......@@ -187,7 +187,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
Some(makeVariantcalling(multisample = false, sample = Some(sampleId)))
} else None
override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner || (libraries.size == 1))
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
......
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