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{ bionix, indexAttrs ? { }, faidxAttrs ? { }, flags ? "" }:
{ normals ? [ ], tumour ? null }:
with bionix;
with lib;
with types;
let
getref = matchFiletype "manta-call" { bam = x: x.ref; };
refs = map getref normals ++ optionals (tumour != null) [ (getref tumour) ];
ref = head refs;
renameAndIndex = f: stage {
name = "rename";
buildCommand = ''
mkdir $out
ln -s ${f} $out/sample.bam
ln -s ${samtools.index indexAttrs f} $out/sample.bam.bai
'';
};
in
assert (length (unique refs) == 1);
stage {
name = "manta-call";
buildInputs = with pkgs; [ manta strace ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
configManta.py ${optionalString (normals != null) (concatMapStringsSep " " (n: "--bam=${renameAndIndex n}/sample.bam") normals)} \
${optionalString (tumour != null) "--tumourBam=${renameAndIndex tumour}/sample.bam"} \
--runDir=$TMPDIR \
--referenceFasta=ref.fa \
${flags}
./runWorkflow.py -j $NIX_BUILD_CORES
cp -r results $out
'';
passthru.multicore = true;
}
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