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Diffstat (limited to 'tools/gridss-collectGridssMetrics.nix')
-rw-r--r-- | tools/gridss-collectGridssMetrics.nix | 32 |
1 files changed, 32 insertions, 0 deletions
diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix new file mode 100644 index 0000000..bb8d2e9 --- /dev/null +++ b/tools/gridss-collectGridssMetrics.nix @@ -0,0 +1,32 @@ +{ bionix +, nixpkgs +, thresholdCoverage ? 10000 +, flags ? null +}: + +with nixpkgs; +with lib; +with bionix.types; + +input: + +let + ref = matchFiletype "gridss-collectGridssMetrics" { bam = x: x.ref; } input; + sorted = matchFileSorting "gridss-collectGridssMetrics" { name = _: true; } input; +in + + +stdenv.mkDerivation rec { + name = "gridss-collectGridssMetrics"; + buildInputs = [ jre ]; + buildCommand = '' + mkdir $out + ln -s ${input} input.bam + java -Xmx1G -cp ${bionix.gridss.jar} \ + gridss.analysis.CollectGridssMetrics \ + ${optionalString sorted "ASSUME_SORTED=true"} \ + I=input.bam \ + O=$out \ + THRESHOLD_COVERAGE=${toString thresholdCoverage} + ''; +} |