Commit bffb8a1b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix for outputDir

parent 94c23ca3
...@@ -33,6 +33,8 @@ class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript { ...@@ -33,6 +33,8 @@ class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript {
if (reference == null) reference = config("reference") if (reference == null) reference = config("reference")
if (dbsnp == null && configContains("dbsnp")) dbsnp = config("dbsnp") if (dbsnp == null && configContains("dbsnp")) dbsnp = config("dbsnp")
if (outputFile == null) outputFile = outputDir + outputName + ".vcf" 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() { def biopetScript() {
......
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