diff options
Diffstat (limited to 'tools/pizzly-call.nix')
-rw-r--r-- | tools/pizzly-call.nix | 24 |
1 files changed, 24 insertions, 0 deletions
diff --git a/tools/pizzly-call.nix b/tools/pizzly-call.nix new file mode 100644 index 0000000..72e23bf --- /dev/null +++ b/tools/pizzly-call.nix @@ -0,0 +1,24 @@ +{ bionix, kmerSize ? 31, gtf, cdna, alignScore ? 2, maxInsertSize ? 400 }: + +with bionix; +with pkgs; + +input: +stage { + name = "pizzly"; + buildInputs = [ bionix.pizzly.app ]; + buildCommand = '' + ln -s ${gtf} ref.gtf + ln -s ${cdna} ref.fa + mkdir $out + pizzly \ + -G ref.gtf \ + -C cache \ + -F ref.fa \ + -k ${toString kmerSize} \ + -o $out/output \ + -a ${toString alignScore} \ + -i ${toString maxInsertSize} \ + ${input}/fusion.txt + ''; +} |