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|
{ bionix
, nixpkgs
, ref
, bamOutput ? true
, flags ? null
, indexAttrs ? {}
}:
{ input1
, input2 ? null
}:
with nixpkgs;
with lib;
stdenv.mkDerivation {
name = "bwa-mem";
buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
buildCommand = ''
ln -s ${ref} ref.fa
for f in ${bionix.bwa.index indexAttrs ref}/* ; do
ln -s $f
done
cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
if [[ $cores -lt 1 ]] ; then
>&2 echo "not enough build cores"
exit 1
fi
bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${input1} \
${optionalString (input2 != null) input2} \
${optionalString bamOutput "| samtools view -b"} \
> $out
'';
}
|