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Diffstat (limited to 'tools/fastp-run.nix')
| -rw-r--r-- | tools/fastp-run.nix | 40 |
1 files changed, 0 insertions, 40 deletions
diff --git a/tools/fastp-run.nix b/tools/fastp-run.nix deleted file mode 100644 index c7cbb3c..0000000 --- a/tools/fastp-run.nix +++ /dev/null @@ -1,40 +0,0 @@ -{ 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 - ''; -}
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