From 2b7c4c64bf2555059c9f8b17b0d0ee504f98d6ed Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 12 Dec 2018 21:17:24 +1100
Subject: gridss: call identifyVariants through bionix tree

---
 tools/gridss-variants.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix
index a838da6..87c2877 100644
--- a/tools/gridss-variants.nix
+++ b/tools/gridss-variants.nix
@@ -90,7 +90,7 @@ rec {
     name = "gridss-annotateVariants";
     buildInputs = [ jre ];
     buildCommand = mkLinks + ''
-      ln -s ${identify} input.vcf
+      ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf
       java -Xmx4g -Dsamjdk.create_index=true \
         -cp ${jar} gridss.AnnotateVariants \
         REFERENCE_SEQUENCE=ref.fa \
-- 
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