From 62c1705d64cd48e95305bbe73eb4b35402872d6f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 9 Oct 2015 11:59:46 +0200
Subject: [PATCH] Fixes #213
---
.../scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 17631709f..abeb787a5 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -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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