From bffb8a1bfcb69c6caa0d9454613abc67dc755221 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Jul 2014 15:59:04 +0200
Subject: [PATCH] Fix for outputDir
---
.../nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala b/gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
index c15ee576c..d61fcc2b9 100644
--- a/gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+++ b/gatk-genotyping/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
@@ -33,6 +33,8 @@ class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript {
if (reference == null) reference = config("reference")
if (dbsnp == null && configContains("dbsnp")) dbsnp = config("dbsnp")
if (outputFile == null) outputFile = outputDir + outputName + ".vcf"
+ if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
+ else if (!outputDir.endsWith("/")) outputDir += "/"
}
def biopetScript() {
--
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