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|
{ bionix
, flags ? null
} :
{ input1
, input2 ? null
} :
with bionix;
with pkgs.lib;
# Match input file type—how to do .fq and .fq.gz? Does bz2 work?
stage {
name = "fastp";
buildInputs = [ fastp.app ];
outputs = [ "out" "fastq1" "fastq2" "html" "json" ];
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
ln -s $fastq2 $out/fastq2.fq.gz
''}
cp fastq1.fq.gz $fastq1
cp fastp.html $html
cp fastp.json $json
ln -s $fastq1 $out/fastq1.fq.gz
ln -s $html $out/fastp.html
ln -s $json $out/fastp.json
'';
}
|