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{bionix
, indexFlags ? {}
, bias ? false
, bootstrapSamples ? 0
, seed ? 42
, plaintext ? false
, fusion ? false
, single ? false
, frStranded ? false
, rfStranded ? false
, fragmentLength ? null
, fragmentSD ? null
, ref}:
with bionix;
with lib;
assert (!single || (fragmentLength != null && fragmentSD != null));
inputs:
let
inherit (bionix.types) matchFiletype';
isFastQ = matchFiletype' "kallisto-quant" {fq = _: true; gz = isFastQ; };
in
assert (all (x: isFastQ (x.filetype)) inputs);
stage {
name = "kallisto-quant";
buildInputs = with pkgs; [ kallisto ];
buildCommand = ''
mkdir $out
kallisto quant \
-i ${bionix.kallisto.index indexFlags ref} \
-o $out \
${optionalString bias "--bias"} \
${optionalString (bootstrapSamples > 0) "-b ${toString bootstrapSamples} --seed=${toString seed}"} \
${optionalString plaintext "--plaintext"} \
${optionalString fusion "--fusion"} \
${optionalString single "--single -l ${toString fragmentLength} -s ${toString fragmentSD}"} \
${optionalString frStranded "--fr-stranded"} \
${optionalString rfStranded "--rf-stranded"} \
-t $NIX_BUILD_CORES \
${concatStringsSep " " inputs}
'';
passthru.multicore = true;
}
|
