Commit d62a45d8 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing location of bammetrics

parent dc82741a
......@@ -284,6 +284,9 @@ object BammetricsReport extends ReportBuilder {
.getOrElse(throw new IllegalStateException("Sample must be there"))
val libraryName =
library.flatMap(l => Await.result(summary.getLibraryName(l), Duration.Inf))
if (yKeyList.find(x => map.contains(x) && map(x).isDefined).isEmpty) {
""
}
val yKey = yKeyList.find(x => map.contains(x) && map(x).isDefined).get
val xKey = xKeyList.find(x => map.contains(x) && map(x).isDefined).get
Map(
......
......@@ -229,17 +229,18 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
qscript.add(aorrg)
}
} 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
add(bamMetrics)
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
add(bamMetrics)
if (config("execute_bam2wig", default = true)) add(Bam2Wig(qscript, bamFile.get))
if (config("execute_bam2wig", default = true)) add(Bam2Wig(qscript, bamFile.get))
}
} else logger.warn(s"Sample '$sampleId' does not have any input files")
}
}
......
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