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{ bionix
, flags ? null
} :
{ input1
, input2 ? null
} :
with bionix;
with pkgs.lib;
with types;
# Match input file type—how to do .fq and .fq.gz? Does bz2 work?
let
out =
stage {
name = "fastp";
buildInputs = [ fastp.app ];
outputs = [ "out" "fastq1" "json" ] ++ (if input2 != null then [ "fastq2" ] else []);
buildCommand = ''
mkdir -p $out
fastp \
${optionalString (flags != null) flags} \
-i ${input1} \
-o fastq1.fq.gz \
${optionalString (input2 != null) ''
-I ${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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