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|
{ bionix
, thresholdCoverage ? 10000
, flags ? null
, config ? null
, heapSize ? "1G"
}:
with bionix;
with lib;
with types;
input:
let
ref = matchFiletype "gridss-collectMetrics" { bam = x: x.ref; } input;
in
stage rec {
name = "gridss-collectMetrics";
buildInputs = with pkgs; [ jre R ];
buildCommand = ''
mkdir $out
java -Xmx${heapSize} -cp ${bionix.gridss.jar} \
gridss.analysis.CollectGridssMetrics \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
VERBOSITY=WARNING \
I=${input}\
O=$out/input \
AS=true \
THRESHOLD_COVERAGE=${toString thresholdCoverage} \
${optionalString (flags != null) flags}
# Make the output deterministic by removing timestamps
sed -i '/^# Started on:/d' $out/input.*_metrics
if [ -e $out/input.insert_size_histogram.pdf ] ; then
sed -i 's/(D:[0-9]\+)/(D:19700101000000)/g' $out/input.insert_size_histogram.pdf
fi
'';
}
|
