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| author | Justin Bedo <cu@cua0.org> | 2019-05-21 18:23:02 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-05-21 18:23:47 +1000 |
| commit | b714521422af63a910ff660dcc019cbaeb6a5d17 (patch) | |
| tree | 8d621e0b67b5e2efdd1eb19c2fb9e6951c2fc120 /tools | |
| parent | 7b7f7c5eddfb3829cef8df7bf217d8309507cf2d (diff) | |
fastp: input filetypes
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/fastp-check.nix | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/tools/fastp-check.nix b/tools/fastp-check.nix index be807d6..bd522d8 100644 --- a/tools/fastp-check.nix +++ b/tools/fastp-check.nix @@ -7,12 +7,12 @@ } : with bionix; -with pkgs.lib; +with lib; with types; -# Match input file type—how to do .fq and .fq.gz? Does bz2 work? - let + fq = f: matchFiletype "fastp-input" { fq = _: f; gz = matchFiletype' "fastp-input" { fq = _: f; }; } f; + out = stage { name = "fastp"; @@ -22,10 +22,10 @@ let mkdir -p $out fastp \ ${optionalString (flags != null) flags} \ - -i ${input1} \ + -i ${fq input1} \ -o fastq1.fq.gz \ ${optionalString (input2 != null) '' - -I ${input2} \ + -I ${fq input2} \ -O fastq2.fq.gz \ cp fastq2.fq.gz $fastq2 |