Commit 36568da0 authored by bow's avatar bow
Browse files

Use correct alignment file for per-sample CollectRnaSeqMetrics job

parent 12b2af39
......@@ -619,7 +619,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
/** Picard CollectRnaSeqMetrics job */
private def collectRnaSeqMetricsJob: CollectRnaSeqMetrics = {
val job = new CollectRnaSeqMetrics(qscript)
job.input = alnFileDirty
job.input = alnFile
job.output = createFile(".rna_metrics")
job.refFlat = annotationRefFlat
job.chartOutput = Option(createFile(".coverage_bias.pdf"))
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