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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; };
empty = ./kallisto-quant-empty.h5;
python = pkgs.python3Packages.python.withPackages (p: with p; [ h5py ]);
noStamp = pkgs.writeScript "nostamp.py" ''
#!${python}/bin/python
import h5py
import os
def copy(obj, out, path):
if type(obj) in [h5py._hl.group.Group,h5py._hl.files.File]:
for key in obj.keys():
if key != "start_time":
copy(obj[key], out, path + "/" + key)
elif type(obj)==h5py._hl.dataset.Dataset:
out.create_dataset(path, data=f[path], track_order=False, track_times = False)
with h5py.File(os.environ['out'] + "/abundance.h5", "r") as f:
with h5py.File("repack.h5", "a", track_order = False) as g:
copy(f, g, "")
'';
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}
# Make deterministic by removing timestamps and using hdf5 empty template
cp ${empty} repack.h5
chmod 644 repack.h5
${noStamp}
cp repack.h5 $out/abundance.h5
sed -i $out/run_info.json -e '/"start_time"/d'
sed -i $out/run_info.json -e '/"call"/d'
'';
passthru.multicore = true;
}
|
