Commit f17e2175 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

added dependency for combinevariants

parent 34024cc5
...@@ -53,6 +53,8 @@ class CombineVariants(val root: Configurable) extends Gatk { ...@@ -53,6 +53,8 @@ class CombineVariants(val root: Configurable) extends Gatk {
case Some("UNIQUIFY") | Some("PRIORITIZE") | Some("UNSORTED") | Some("REQUIRE_UNIQUE") | None => case Some("UNIQUIFY") | Some("PRIORITIZE") | Some("UNSORTED") | Some("REQUIRE_UNIQUE") | None =>
case _ => throw new IllegalArgumentException("Wrong option for genotypeMergeOptions") case _ => throw new IllegalArgumentException("Wrong option for genotypeMergeOptions")
} }
deps :::= inputFiles.filter(_.getName.endsWith("vcf.gz")).map(x => new File(x.getAbsolutePath + ".tbi"))
deps = deps.distinct
} }
override def cmdLine = super.cmdLine + override def cmdLine = super.cmdLine +
......
...@@ -18,15 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva ...@@ -18,15 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag } import nl.lumc.sasc.biopet.core.{Reference, SampleLibraryTag}
import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsMerge, BcftoolsCall } import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats } import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix } import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging } import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.function.CommandLineFunction import org.broadinstitute.gatk.utils.commandline.Input
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** /**
* Common trait for ShivaVariantcalling * Common trait for ShivaVariantcalling
......
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