Commit ebe731f3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix for -sample commandline argument

parent d46ad182
......@@ -125,15 +125,15 @@ trait MultiSampleQScript extends BiopetQScript {
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */
protected def sampleIds: Set[String] = if (onlySample != Nil) onlySample.toSet else {
ConfigUtils.any2map(Config.global.map("samples")).keySet
}
protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
for ((sampleId, sample) <- samples) {
sample.addAndTrackJobs()
}
if (onlySample.isEmpty) samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
else onlySample.foreach(sampleId => samples.get(sampleId) match {
case Some(sample) => sample.addAndTrackJobs()
case None => logger.warn("sampleId '" + sampleId + "' not found")
})
}
/** Stores sample state */
......
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