Commit 2ca6260e authored by pjvan_thof's avatar pjvan_thof

Fixing duplicate metrics

parent 67f8439a
......@@ -231,14 +231,15 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
} else add(Ln.linkBamFile(qscript, inputBam.get, bamFile.get): _*)
}
val bamMetrics = new BamMetrics(qscript)
bamMetrics.sampleId = Some(sampleId)
bamMetrics.libId = Some(libId)
bamMetrics.inputBam = bamFile.get
bamMetrics.outputDir = new File(libDir, "metrics")
bamMetrics.paired = inputR2.isDefined || inputBam.isDefined
add(bamMetrics)
if (!bamToFastq) {
val bamMetrics = new BamMetrics(qscript)
bamMetrics.sampleId = Some(sampleId)
bamMetrics.libId = Some(libId)
bamMetrics.inputBam = bamFile.get
bamMetrics.outputDir = new File(libDir, "metrics")
bamMetrics.paired = inputR2.isDefined || inputBam.isDefined
add(bamMetrics)
}
if (config("execute_bam2wig", default = true)) add(Bam2Wig(qscript, bamFile.get))
} else logger.warn(s"Sample '$sampleId' does not have any input files")
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment