Commit 0267b656 authored by bow's avatar bow
Browse files

Default to disabling MarkDuplicates in Gentrap

parent 16422010
......@@ -93,7 +93,9 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
// avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
"picard" -> Map(
"programrecordid" -> "null"
// disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
"mapping" -> Map("skip_markduplicates" -> true)
), super.defaults)
/** Adds output merge jobs for the given expression mode */
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