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|
{ bionix
, ref
, flags ? null
, indexAttrs ? {}
}:
{ input1
, input2 ? null
}:
with bionix;
with lib;
with types;
let
fa = f: matchFiletype "last-ref" { fa = _: f; } f;
fq = f: matchFiletype "last-input" { fq = _: f; } f;
fqfa = f: matchFiletype "last-input" { fq = _: f; fa = _: f; } f;
Q = f: matchFiletype "last-input" { fq = _: 1; fa = _: 0; } f;
parallel = f: matchFiletype "last-input" { fq = _: "parallel-fastq"; fa = _: "parallel-fasta"; } f;
in stage {
name = "last-align";
buildInputs = with pkgs; [ last ];
buildCommand = ''
${if (input2 != null) then "fastq-interleave ${fq input1} ${fq input2}" else "cat ${fa input1}"} | \
${parallel input1} -j $NIX_BUILD_CORES \
lastal -Q${toString (Q input1)} \
${optionalString (input2 != null) "-i1"} \
${optionalString (flags != null) flags} \
${bionix.lastal.index indexAttrs ref}/index \
> tmp
'' + (if input2 == null then ''
cp tmp $out
'' else ''
last-pair-probs tmp > $out
'');
passthru.multicore = true;
}
|
