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Diffstat (limited to 'tools/gridss-variants.nix')
| -rw-r--r-- | tools/gridss-variants.nix | 3 |
1 files changed, 1 insertions, 2 deletions
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index 4f39b1e..ad4c66d 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -5,7 +5,6 @@ , assemblyAttrs ? {} , collectMetricsAttrs ? {} , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } -, flags ? null , config ? null , heapSize ? "4g" }: @@ -91,7 +90,7 @@ rec { name = "gridss-annotateVariants"; buildInputs = with pkgs; [ jre ]; buildCommand = mkLinks + '' - ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf + ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs config; } inputs} input.vcf java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.AnnotateVariants \ VERBOSITY=WARNING \ |