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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 { })
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