{ 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
  '';
}