Commit ef5ea6ce authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added bammetrics when start from bam file

parent 3d73d611
......@@ -197,6 +197,16 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
val bamLn = Ln(qscript, oldBamFile, bamFile.get)
bamLn.deps :+= baiLn.output
add(bamLn)
val bamMetrics = new BamMetrics(qscript)
bamMetrics.sampleId = Some(sampleId)
bamMetrics.libId = Some(libId)
bamMetrics.inputBam = bamFile.get
bamMetrics.outputDir = new File(libDir, "metrics")
bamMetrics.init()
bamMetrics.biopetScript()
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
}
}
}
......
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