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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-12-12 21:27:54 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-12-12 21:27:54 +1100 |
| commit | 2ec0e115917d194eeea6ef4c1b4b1f7f6a7f416b (patch) | |
| tree | ba8d940de5860e09543d296b2c7ac28e94351476 /tools/gridss-variants.nix | |
| parent | 875d5f28926a2dd3e066a4ce08a2ce18baee4661 (diff) | |
| parent | 2b7c4c64bf2555059c9f8b17b0d0ee504f98d6ed (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss-variants.nix')
| -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 eb5957f..d3070a8 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -91,7 +91,7 @@ rec { name = "gridss-annotateVariants"; buildInputs = [ jre ]; buildCommand = mkLinks + '' - ln -s ${identify} input.vcf + ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.AnnotateVariants \ REFERENCE_SEQUENCE=ref.fa \ |