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| author | l-d-s <l@sdf.org> | 2018-11-12 16:54:30 +1100 |
|---|---|---|
| committer | l-d-s <l@sdf.org> | 2018-11-12 16:54:30 +1100 |
| commit | 4574deb8e1649eaf63df424585d11645c7cfa7dd (patch) | |
| tree | 165478a6535a1b0172f489c03eb2a6d8ac18c023 /tools/gridss-annotateVariants.nix | |
| parent | b46138826260f1ed963ffe18fef7ec4ce70b6de8 (diff) | |
Attempt to integrate config file into GRIDSS stage
Diffstat (limited to 'tools/gridss-annotateVariants.nix')
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix index 4f66c6c..33992c4 100644 --- a/tools/gridss-annotateVariants.nix +++ b/tools/gridss-annotateVariants.nix @@ -8,6 +8,7 @@ , softClipsToSplitReadsAttrs ? {} , identifyVariantsAttrs ? {} , flags ? null +, config ? null }: with nixpkgs; @@ -64,6 +65,7 @@ stdenv.mkDerivation rec { INPUT_VCF=input.vcf \ OUTPUT_VCF=out.vcf \ WORKING_DIR=$TMPDIR/ \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ TMP_DIR=$TMPDIR/ mv out.vcf $out |