Commit d90761b6 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added metrics pipeline

parent 72ac9801
......@@ -201,7 +201,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile = new File(outputDir + outputName + ".dedup.bam")
add(MarkDuplicates(this, bamFiles, bamFile))
} else if (skipMarkduplicates && chunking) bamFile = addMergeBam(bamFiles, new File(outputDir + outputName + ".bam"), outputDir)
addAll(BamMetrics.apply(this, bamFile, outputDir + "metrics/").functions)
outputFiles += ("finalBamFile" -> bamFile)
}
......
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