Commit 3a1bd525 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding metrics step on merged bam file

parent d030c0bf
......@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
......@@ -108,6 +109,9 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
add(merge)
}
val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"))
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
addAll(Bam2Wig(qscript, bamFile).functions)
val macs2 = new Macs2CallPeak(qscript)
......
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