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authorJustin Bedo <cu@cua0.org>2018-12-12 21:17:24 +1100
committerJustin Bedo <cu@cua0.org>2018-12-12 21:17:24 +1100
commit2b7c4c64bf2555059c9f8b17b0d0ee504f98d6ed (patch)
tree99a5cd777c4cb145948e6eacafd2a0fbfd0de21b /tools
parent979bf4c65ad668b668750b58eefa9996f51b1242 (diff)
gridss: call identifyVariants through bionix tree
Diffstat (limited to 'tools')
-rw-r--r--tools/gridss-variants.nix2
1 files changed, 1 insertions, 1 deletions
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 \