Commit a7b9890f authored by bow's avatar bow
Browse files

Use correct flag annotations for Picard CollectRnaSeqMetrics

parent 80353a70
......@@ -34,11 +34,14 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
@Input(doc = "Gene annotations in refFlat form", required = true)
var refFlat: File = null
@Input(doc = "Location of rRNA sequences in interval list format", required = false)
var ribosomalIntervals: Option[File] = config("ribosomal_intervals")
@Output(doc = "Output metrics file", required = true)
var output: File = null
@Argument(doc = "Location of rRNA sequences in interval list format", required = false)
var ribosomalIntervals: Option[File] = config("ribosomal_intervals")
@Output(doc = "PDF output of the coverage chart", required = false)
var chartOutput: Option[File] = config("chart_output")
@Argument(doc = "Strand specificity", required = false)
var strandSpecificity: Option[String] = config("strand_specificity")
......@@ -46,9 +49,6 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
@Argument(doc = "Minimum length of transcripts to use for coverage-based values calculation", required = false)
var minimumLength: Option[Int] = config("minimum_length")
@Argument(doc = "PDF output of the coverage chart", required = false)
var chartOutput: Option[File] = config("chart_output")
@Argument(doc = "Sequences to ignore for mapped reads", required = false)
var ignoreSequence: Option[String] = config("ignore_sequence")
......
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