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{ bionix
, dictIndexAttrs ? {}
, faidxAttrs ? {}
, flags ? null
, unmappedReads ? false
, minClipLength ? 5
, collectMetricsAttrs ? {}
, config ? null
}:
with bionix;
with lib;
with types;
input:
let
ref = matchFiletype "gridss-extractSVReads" { bam = x: x.ref; } input;
in
stage rec {
name = "gridss-extractSVReads";
buildInputs = with pkgs; [ jre R ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
ln -s ${bionix.samtools.dict dictIndexAttrs ref} ref.fa.dict
ln -s ${input} input.bam
for f in ${bionix.gridss.collectMetrics collectMetricsAttrs input}/* ; do
ln -s $f
done
java -Dsamjdk.create_index=true \
-cp ${bionix.gridss.jar} gridss.ExtractSVReads \
VERBOSITY=WARNING \
REFERENCE_SEQUENCE=ref.fa \
I=input.bam \
O=$out \
UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
MIN_CLIP_LENGTH=${toString minClipLength}
'';
passthru.filetype = input.filetype;
}
|
