Commit cfae9015 authored by Peter van 't Hof's avatar Peter van 't Hof

OutputName change

parent 7624b929
......@@ -22,11 +22,11 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var dbsnp: File = _
@Argument(doc = "OutputName", required = false)
var outputName: String = "hc"
var outputName: String = _
@Output(doc = "OutputFile", required = false)
var outputFile: File = _
var gvcfMode = true
var singleGenotyping = false
......@@ -35,7 +35,9 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if (!singleGenotyping) singleGenotyping = config("singlegenotyping")
if (reference == null) reference = config("reference", required = true)
if (dbsnp == null) dbsnp = config("dbsnp")
if (outputFile == null) outputFile = outputDir + outputName + (if (gvcfMode) ".gvcf.vcf" else ".vcf")
if (outputFile == null) outputFile = outputDir +
(if (outputName != null && !outputName.endsWith(".")) outputName + "." else outputName) +
(if (gvcfMode) "hc.gvcf.vcf" else ".vcf")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
......
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