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Diffstat (limited to 'tools/gridss-variants.nix')
| -rw-r--r-- | tools/gridss-variants.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index fc26c5a..b564725 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -70,6 +70,7 @@ rec { buildCommand = mkLinks + '' java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.IdentifyVariants \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ @@ -93,6 +94,7 @@ rec { 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 \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ |