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|
{ bionix
, nixpkgs
, thresholdCoverage ? 10000
, flags ? null
, config ? 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"} \
${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=input.bam \
O=$out \
THRESHOLD_COVERAGE=${toString thresholdCoverage}
'';
}
|
