Commit 8fc17a50 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed file names

parent ab0764f7
......@@ -45,11 +45,13 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
@Input(doc = "Input GVCF file", shortName = "gvcf", required = false)
var inputGvcf: Option[File] = None
def outputName = inputVcf.getName.stripSuffix(".vcf.gz")
def outputVcf: File = (gonlVcfFile, exacVcfFile) match {
case (Some(_), Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
case (Some(_), _) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
case (_, Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
case _ => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.vcf.gz")
case (Some(_), Some(_)) => new File(outputDir, s"$outputName.vep.normalized.gonl.exac.vcf.gz")
case (Some(_), _) => new File(outputDir, s"$outputName.vep.normalized.gonl.vcf.gz")
case (_, Some(_)) => new File(outputDir, s"$outputName.vep.normalized.exac.vcf.gz")
case _ => new File(outputDir, s"$outputName.vep.normalized.vcf.gz")
}
lazy val minScatterGenomeSize: Long = config("min_scatter_genome_size", default = 75000000)
......@@ -114,7 +116,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
cv.variant = outputVcfFiles.toList
cv.outputFile = outputVcf
add(cv)
} else runChunk(useVcf, outputDir, "toucan")
} else runChunk(useVcf, outputDir, outputName)
addSummaryJobs()
}
......
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