diff --git a/src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala b/src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala index 4a9bfc610..f14644d82 100644 --- a/src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala +++ b/src/main/scala/com/fulcrumgenomics/umi/CallMolecularConsensusReads.scala @@ -121,7 +121,7 @@ class CallMolecularConsensusReads """) val maxReads: Option[Int] = None, @arg(flag='B', doc="If true produce tags on consensus reads that contain per-base information.") val outputPerBaseTags: Boolean = DefaultProducePerBaseTags, - @arg(flag='S', doc="The sort order of the output, if `:none:` then the same as the input.") val sortOrder: Option[SamOrder] = None, + @arg(flag='S', doc="The sort order of the output, the same as the input if not given.") val sortOrder: Option[SamOrder] = None, @arg(flag='D', doc="Turn on debug logging.") val debug: Boolean = false, @arg(doc="The number of threads to use while consensus calling.") val threads: Int = 1 ) extends FgBioTool with LazyLogging {