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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 "bowtie2-ref" { fa = _: f; } f;
fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
in
stage {
name = "bowtie2-align";
buildInputs = with pkgs; [ bowtie2 bc samtools ];
buildCommand = ''
cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
if [[ $cores -lt 1 ]] ; then
cores=1
fi
bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \
${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \
${optionalString (RG ? ID) ''
--rg-id ${RG.ID} ${concatMapAttrsStringsSep " " (k: v: "--rg ${k}:${v}") (filterAttrs (k: _: k != "ID") 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;
}
|
