Commit 9b20e271 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added skipMetrics option

parent f6bbd1b0
......@@ -33,6 +33,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
@Argument(doc = "Skip mark duplicates", shortName = "skipmarkduplicates", required = false)
var skipMarkduplicates: Boolean = false
@Argument(doc = "Skip metrics", shortName = "skipmetrics", required = false)
var skipMetrics: Boolean = false
@Argument(doc = "Alginer", shortName = "ALN", required = false)
var aligner: String = _
......@@ -217,7 +220,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
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)
if (!skipMetrics) addAll(BamMetrics.apply(this, bamFile, outputDir + "metrics/").functions)
outputFiles += ("finalBamFile" -> bamFile)
}
......
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