From f17e2175ce5536f911bd673255c42ff3a94ae187 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 19 Oct 2015 16:13:54 +0200
Subject: [PATCH] added dependency for combinevariants
---
.../biopet/extensions/gatk/CombineVariants.scala | 2 ++
.../pipelines/shiva/ShivaVariantcallingTrait.scala | 13 ++++++-------
2 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
index 144a91f21..8291e667b 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
@@ -53,6 +53,8 @@ class CombineVariants(val root: Configurable) extends Gatk {
case Some("UNIQUIFY") | Some("PRIORITIZE") | Some("UNSORTED") | Some("REQUIRE_UNIQUE") | None =>
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 +
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index 1e49e4c38..c16374327 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -18,15 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsMerge, BcftoolsCall }
+import nl.lumc.sasc.biopet.core.{Reference, SampleLibraryTag}
+import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
-import org.broadinstitute.gatk.queue.function.CommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
+import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
+import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.utils.commandline.Input
/**
* Common trait for ShivaVariantcalling
--
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