Commit db06f6bc authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix error when no mode selected

parent 844ff098
......@@ -73,7 +73,7 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
add(delly)
}
// we need to merge the vcf's
var finalVCF = if (vcfFiles.size > 1) {
val finalVCF = if (vcfFiles.size > 1) {
// do merging
// CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
//TODO: convert to biopet extension
......@@ -83,30 +83,28 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
variants.reference = referenceFasta()
// add the job
add(variants)
this.outputvcf
} else {
Some(outputvcf)
} else if (vcfFiles.size == 1) {
// TODO: pretify this
val ln = Ln(this, vcfFiles.head._2, this.outputvcf, relative = true)
add(ln)
ln.output
}
Some(ln.output)
} else None
outputFiles += ("vcf" -> this.outputvcf)
finalVCF.foreach(file => outputFiles += ("vcf" -> file))
}
private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".delly.vcf"
}
object Delly extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
def apply(root: Configurable, input: File, runDir: File): Delly = {
val dellypipeline = new Delly(root)
dellypipeline.input = input
dellypipeline.workdir = runDir
dellypipeline.init()
dellypipeline.biopetScript()
dellypipeline
val dellyPipeline = new Delly(root)
dellyPipeline.input = input
dellyPipeline.workdir = runDir
dellyPipeline.init()
dellyPipeline.biopetScript()
dellyPipeline
}
}
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