Commit 8b2b1732 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed summary output file

parent 95e63289
......@@ -179,7 +179,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
override def preProcessBam: Option[File] = if (useIndelRealigner && libraries.values.flatMap(_.preProcessBam).size > 1) {
override def preProcessBam: Option[File] = if (useIndelRealigner) {
bamFile.map(swapExt(sampleDir, _, ".bam", ".realign.bam"))
} else bamFile
......
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