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| author | Justin Bedo <cu@cua0.org> | 2019-03-28 13:40:31 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-28 13:40:31 +1100 |
| commit | dbbfc5655b840e9cd1d10993b411376ec0a90135 (patch) | |
| tree | 17f3a63cd9ab7c6407eeb6b88ffe0488b9932deb /tools/gridss-variants.nix | |
| parent | 1d01a7faf089bc4ce221a4460abf613dd279e2a7 (diff) | |
gridss: less chatty logs
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} \ |