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Making metrics a required parameter in MarkDuplicates 

As requested by user (forum)
This commit is contained in:
Mauricio Carneiro 2013-01-25 17:49:15 -05:00
parent 99cb8d68e9
commit e7c9e3639e
1 changed files with 1 additions and 1 deletions
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2
public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
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@ -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)