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{ bionix
, bwaIndexAttrs ? {}
, faidxAttrs ? {}
, flags ? null
, config ? null
, heapSize ? "1G"
}:
with bionix;
with lib;
with types;
input:
let
ref = matchFiletype "gridss-computeSamTags" { bam = x: x.ref; } input;
sorted = matchFileSorting "gridss-computeSamTags" { name = _: true; } input;
in
assert(sorted);
stage rec {
name = "gridss-computeSamTags";
buildInputs = with pkgs; [ jre ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
ln -s $f
done
java -Xmx${heapSize} \
-Dsamjdk.create_index=false \
-cp ${bionix.gridss.jar} gridss.ComputeSamTags \
VERBOSITY=WARNING \
REFERENCE_SEQUENCE=ref.fa \
WORKING_DIR=$TMP_DIR \
TMP_DIR=$TMP_DIR \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
I=${input} \
O=$out \
AS=true
'';
passthru.filetype = input.filetype;
}
|
