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path: root/tools/fastp-check.nix
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{ bionix
, flags ? null
}:

{ input1
, input2 ? null
}:

with bionix;
with lib;
with types;

let
  fq = f: matchFiletype "fastp-input" { fq = _: f; gz = matchFiletype' "fastp-input" { fq = _: f; }; } f;

  out =
    stage {
      name = "fastp";
      buildInputs = [ pkgs.fastp ];
      outputs = [ "out" "fastq1" "json" ] ++ (if input2 != null then [ "fastq2" ] else [ ]);
      buildCommand = ''
        mkdir -p $out
        fastp \
            ${optionalString (flags != null) flags} \
            -i ${fq input1} \
            -o fastq1.fq.gz \
            ${optionalString (input2 != null) ''
                -I ${fq input2} \
                -O fastq2.fq.gz \

                cp fastq2.fq.gz $fastq2
            ''}

            cp fastq1.fq.gz $fastq1
            cp fastp.html $out
            cp fastp.json $json
      '';
    };
  fqgz = { filetype = filetype.gz (filetype.fastq { }); };
in
out // { fastq1 = out.fastq1 // fqgz; } // (if input2 != null then { fastq2 = out.fastq2 // fqgz; } else { })