Commit 77d06f6e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix output bam files of mapping

parent 73995acb
......@@ -51,6 +51,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
mapping.sampleId = Some(sampleId)
mapping.libId = Some(libId)
mapping.outputDir = libDir
mapping.outputName = sampleId + "-" + libId
(Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile))
}
......@@ -187,7 +188,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
val bamMetrics = new BamMetrics(root)
bamMetrics.sampleId = Some(sampleId)
bamMetrics.inputBam = preProcessBam.get
bamMetrics.outputDir = outputDir
bamMetrics.outputDir = sampleDir
bamMetrics.init
bamMetrics.biopetScript
addAll(bamMetrics.functions)
......
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