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{bionix
,targets ? null
,annotations ? null
,flags ? null
,indexAttrs ? {}}:
{normals ? [], tumours}:
with bionix;
with lib;
with types;
let
getref = f: matchFiletype "cnvkit-batch" { bam = {ref, ...}: ref; } f;
refs = map getref normals ++ map getref tumours;
ref = head refs;
sorted = matchFileSorting "cnvkit-batch" { coord = _: true; };
in
assert (length (unique refs) == 1);
assert (all sorted (normals ++ tumours));
stage {
name = "cnvkit";
buildInputs = with pkgs; [ python2Packages.cnvkit ];
outputs = [ "out" ] ++ builtins.genList (x: "out${toString (x + 1)}") (length tumours);
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
cnvkit.py batch ${concatStringsSep " " tumours} \
${optionalString (normals != []) ("-n " + concatStringsSep " " normals)} \
${optionalString (annotations != null) "--annotate ${annotations}"} \
${if targets != null then "--targets ${targets}" else "-m wgs"} \
-f ref.fa \
-p $NIX_BUILD_CORES \
-d $TMPDIR \
${optionalString (flags != null) flags}
# Copy individual tumour files
mkdir $out
cnt=1
for f in ${concatStringsSep " " tumours} ; do
output="out$cnt"
mkdir ''${!output}
for g in $(basename $f)*.{cnr,cnn,cns} ; do
cp $g ''${!output}/sample-''${g#*-}
done
cnt=$((cnt+1))
ln -s ''${!output} $out/$output
done
'';
passthru.multicore = true;
}
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