From d03ff5ffbb82fdcb5d5d7e9bc97ae71d43329ea3 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 9 May 2016 14:33:18 +0200
Subject: [PATCH] attempt to fix cyclic errors
---
.../nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
index 650340d63..b36bc2988 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
@@ -106,16 +106,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
@Gather(enabled = false)
private var outputIndex: File = _
- @Output
- @Gather(enabled = false)
- private var dbsnpIndex: File = _
-
override def beforeGraph() {
super.beforeGraph()
deps ++= variant.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
outputIndex = VcfUtils.getVcfIndexFile(out)
- dbsnp.foreach(x => dbsnpIndex = VcfUtils.getVcfIndexFile(x))
+ dbsnp.foreach(x => deps :+= VcfUtils.getVcfIndexFile(x))
}
override def cmdLine = super.cmdLine +
--
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