Commit bc3e6582 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fix

parent 384e5667
...@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk ...@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand } import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter , MergeAlleles} import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, MergeAlleles }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper } import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
...@@ -135,7 +135,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr ...@@ -135,7 +135,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile) mergBuffer += ("9.raw" -> scriptOutput.rawFilterVcfFile)
if (useAllelesOption.get) { if (useAllelesOption.get) {
val mergeAlleles = MergeAlleles(this,mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz.tbi") val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz.tbi")
add(mergeAlleles, isIntermediate = true) add(mergeAlleles, isIntermediate = true)
if (useHaplotypecaller.get) { if (useHaplotypecaller.get) {
......
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