diff options
Diffstat (limited to 'tools/fastp-check.nix')
| -rw-r--r-- | tools/fastp-check.nix | 45 |
1 files changed, 23 insertions, 22 deletions
diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix index 06f00ae..9467cd9 100644 --- a/tools/fastp-check.nix +++ b/tools/fastp-check.nix @@ -1,10 +1,10 @@ { bionix , flags ? null -} : +}: { input1 , input2 ? null -} : +}: with bionix; with lib; @@ -15,26 +15,27 @@ let 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 \ + 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 fastq2.fq.gz $fastq2 + ''} - cp fastq1.fq.gz $fastq1 - cp fastp.html $out - cp fastp.json $json - ''; + 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 {}) + fqgz = { filetype = filetype.gz (filetype.fastq { }); }; +in +out // { fastq1 = out.fastq1 // fqgz; } // (if input2 != null then { fastq2 = out.fastq2 // fqgz; } else { }) |