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|
{ bionix
, ref
, flags ? null
, indexAttrs ? { }
, RG ? { }
, type ? 1
}:
{ input1
, input2 ? null
}:
with bionix;
with lib;
with types;
with compression;
let
fa = f: matchFiletype "subread-ref" { fa = _: f; } f;
fq = f: matchFiletype "subread-input" { fq = _: f; gz = matchFiletype' "subread-input" { fq = _: f; }; } f;
in
stage {
name = "subread-align";
buildInputs = with pkgs; [ subread ];
buildCommand = ''
subread-align -i ${bionix.subread.index indexAttrs ref}/ref ${optionalString (flags != null) flags} -T $NIX_BUILD_CORES \
-t ${toString type} \
-r ${fq input1} \
${optionalString (input2 != null) "-R ${fq input2}"} \
${optionalString (RG ? ID) ''
--rg-id ${RG.ID} ${concatMapAttrsStringsSep " " (k: v: "--rg ${k}:${v}") (filterAttrs (k: _: k != "ID") RG)} \
''} \
-o $out
'';
passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
passthru.multicore = true;
stripStorePaths = false;
}
|
