Commit 11faecb0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Placeholder for library tag counts

parent 8d6d72c9
......@@ -108,8 +108,11 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping.biopetScript
addAll(mapping.functions)
if (config("library_counts", default = false).getBoolean)
if (config("library_counts", default = false).getBoolean) {
this.addBedtoolsCounts(mapping.outputFiles("finalBamFile"), sampleID + "-" + runID, runDir)
// TODO: Tag counts
}
outputFiles += ("FinalBam" -> mapping.outputFiles("finalBamFile"))
} else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
......
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