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author | l-d-s <l@sdf.org> | 2018-11-12 16:54:30 +1100 |
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committer | l-d-s <l@sdf.org> | 2018-11-12 16:54:30 +1100 |
commit | 4574deb8e1649eaf63df424585d11645c7cfa7dd (patch) | |
tree | 165478a6535a1b0172f489c03eb2a6d8ac18c023 /tools/gridss-collectGridssMetrics.nix | |
parent | b46138826260f1ed963ffe18fef7ec4ce70b6de8 (diff) |
Attempt to integrate config file into GRIDSS stage
Diffstat (limited to 'tools/gridss-collectGridssMetrics.nix')
-rw-r--r-- | tools/gridss-collectGridssMetrics.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix index bb8d2e9..86732b8 100644 --- a/tools/gridss-collectGridssMetrics.nix +++ b/tools/gridss-collectGridssMetrics.nix @@ -2,6 +2,7 @@ , nixpkgs , thresholdCoverage ? 10000 , flags ? null +, config ? null }: with nixpkgs; @@ -25,6 +26,7 @@ stdenv.mkDerivation rec { java -Xmx1G -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ ${optionalString sorted "ASSUME_SORTED=true"} \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ I=input.bam \ O=$out \ THRESHOLD_COVERAGE=${toString thresholdCoverage} |