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| author | Justin Bedo <cu@cua0.org> | 2018-12-12 21:17:24 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-12-12 21:17:24 +1100 |
| commit | 2b7c4c64bf2555059c9f8b17b0d0ee504f98d6ed (patch) | |
| tree | 99a5cd777c4cb145948e6eacafd2a0fbfd0de21b | |
| parent | 979bf4c65ad668b668750b58eefa9996f51b1242 (diff) | |
gridss: call identifyVariants through bionix tree
| -rw-r--r-- | tools/gridss-variants.nix | 2 |
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 \ |