Commit b770117f authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed intermediates

parent af816bfa
......@@ -122,7 +122,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
if (useBaseRecalibration) {
addBaseRecalibrator(bamFile.get, libDir, libraries.size > 1, usePrintReads)
addBaseRecalibrator(bamFile.get, libDir, useIndelRealigner || libraries.size > 1, usePrintReads)
variantcalling.foreach(vc => {
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