Commit 62c1705d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixes #213

parent aca99bf8
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
import org.broadinstitute.gatk.utils.commandline.Argument
/** This trait creates a structured way of use multisample pipelines */
......@@ -90,6 +90,8 @@ trait MultiSampleQScript extends SummaryQScript {
/** Adds sample jobs */
final def addAndTrackJobs(): Unit = {
if (sampleRegex.findFirstIn(sampleId) == None)
Logging.addError(s"Sample '$sampleId' contains illegal chars")
currentSample = Some(sampleId)
addJobs()
qscript.addSummarizable(this, "pipeline", Some(sampleId))
......@@ -129,6 +131,8 @@ trait MultiSampleQScript extends SummaryQScript {
/** Returns a list of all sampleIDs */
protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
protected lazy val sampleRegex = """^[a-zA-Z0-9-_]+$""".r
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
......
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