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|
{ bionix
, ref
, bamOutput ? true
, flags ? null
, indexAttrs ? { }
}:
{ input1
, input2 ? null
}:
with bionix;
with lib;
with types;
with compression;
let
fa = f: matchFiletype "snap-ref" { fa = _: f; } f;
fq = f: matchFiletype "snap-input" { fq = _: f; gz = matchFiletype' "snap-input" { fq = _: f; }; } f;
in
stage {
name = "snap-align";
buildInputs = with pkgs; [ bionix.snap.app bc ] ++ optional bamOutput samtools;
buildCommand = ''
for f in /* ; do
ln -s $f
done
snap-aligner ${if input2 == null then "single" else "paired"} ${bionix.snap.index indexAttrs ref} ${fq input1} \
${optionalString (input2 != null) (fq input2)} \
-o ${if bamOutput then "-bam" else "-sam" } - \
-t $NIX_BUILD_CORES \
${optionalString (flags != null) flags} \
| samtools sort -n > $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 = false;
}
|
