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|
{ bionix
, ref
, bamOutput ? true
, flags ? null
, indexAttrs ? { }
, RG ? { }
}:
{ input1
, input2 ? null
}:
with bionix;
with lib;
with types;
with compression;
let
fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
in
stage {
name = "bwa-mem2";
buildInputs = with pkgs; [ bionix.bwa.app2 bc ] ++ optional bamOutput samtools;
buildCommand = ''
ln -s ${fa ref} ref.fa
for f in ${bionix.bwa.index2 indexAttrs ref}/* ; do
ln -s $f
done
cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
if [[ $cores -lt 1 ]] ; then
cores=1
fi
bwa-mem2 mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \
${optionalString (input2 != null) (fq input2)} \
${optionalString (RG ? ID) "-R'@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \
${optionalString bamOutput "| samtools view -b"} \
> $out
'';
passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
passthru.multicore = true;
stripStorePaths = !bamOutput;
}
|
