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{ bionix
, bwaIndexAttrs ? {}
, faidxAttrs ? {}
, indexAttrs ? {}
, collectMetricsAttrs ? {}
, flags ? null
, config ? null
, heapSize ? "31g"
, workdirs ? []
, jobIndex ? null
, jobNodes ? null
}:
with bionix;
with lib;
with types;
inputs:
let
getref = matchFiletype "gridss-assemble" { bam = x: x.ref; };
ref = getref (head inputs);
sorted = matchFileSorting "gridss-assemble" { coord = _: true; };
homoRef = length (unique (map getref inputs)) == 1;
linkInput = input: ''
BASENAME=$(basename ${input})
WRKDIR="''${BASENAME}.gridss.working"
mkdir $WRKDIR
ln -s ${input} $WRKDIR/$BASENAME.sv.bam
ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
for f in ${bionix.gridss.collectMetrics collectMetricsAttrs input}/* ; do
ln -s $f $WRKDIR/$BASENAME.''${f##*.}
done
'';
in
assert (all sorted inputs);
assert (homoRef);
stage rec {
name = "gridss-assemble";
buildInputs = with pkgs; [ jre bwa ];
outputs = [ "out" "work" ];
buildCommand = ''
TMPDIR=$(pwd)
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
${concatMapStringsSep "\n" linkInput inputs}
mkdir out.gridss.working
${concatMapStringsSep "\n" (w: "cp -r ${w}/* ./out.gridss.working") workdirs}
chmod -R u+rwX out.gridss.working
java -Xmx${heapSize} -Dsamjdk.create_index=true \
-cp ${bionix.gridss.jar} gridss.AssembleBreakends \
VERBOSITY=WARNING \
REFERENCE_SEQUENCE=ref.fa \
${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
WORKER_THREADS=$NIX_BUILD_CORES \
OUTPUT=out \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/ \
${optionalString (jobIndex != null) "JOB_INDEX=${toString jobIndex}"} \
${optionalString (jobIndex != null) "JOB_NODES=${toString jobNodes}"} \
${optionalString (flags != null) flags}
[ -e out ] && cp -r out $out
touch $out
cp -r out.gridss.working $work
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
passthru.multicore = true;
}
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