Commit 894af898 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix cores on bamOutput option

parent 31822f0a
......@@ -42,6 +42,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
if (bamOutput != null && nct.getOrElse(1) > 1) {
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
nCoresRequest = Some(1)
nct = Some(getThreads)
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
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