diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala index 59a51db96..7567434e2 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala @@ -48,7 +48,7 @@ class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommand @Output(doc="The output bam index", shortName = "out_index", fullName = "output_bam_index_file", required = false) var outputIndex: File = _ - @Output(doc="File to write duplication metrics to", shortName = "out_metrics", fullName = "output_metrics_file", required = false) + @Output(doc="File to write duplication metrics to", shortName = "out_metrics", fullName = "output_metrics_file", required = true) var metrics: File = new File(output + ".metrics") @Argument(doc="If true do not write duplicates to the output file instead of writing them with appropriate flags set.", shortName = "remdup", fullName = "remove_duplicates", required = false)