{
  bionix,
  fast ? false,
  very-fast ? false,
  max-genotypes ? null,
  targets ? null,
  faidxAttrs ? {},
  indexAttrs ? {},
  flags ? "",
}:
assert !fast || !very-fast;
assert max-genotypes == null || max-genotypes > 0;
with bionix;
with lib;
with types;
  inputs: let
    getref = matchFiletype "octopus-call" {
      bam = {ref, ...}: ref;
      cram = {ref, ...}: ref;
    };
    refs = map getref inputs;
    ref = head refs;

    handleTarget = x: let
      type = builtins.typeOf x;
      handler = handlers."${type}" or (builtins.throw "octopus-call:unhandled target type:${type}");
      handlers = {
        string = "-T '${x}'";
        list = let
          file = pkgs.writeText "regions.txt" (concatStringsSep "\n" x);
        in "-t ${file}";
        path = "-t ${x}";
        set = "-t ${x}";
      };
    in
      handler;
  in
    assert (length (unique refs) == 1);
      stage {
        name = "octopus-call";
        buildInputs = with pkgs; [octopus-caller];
        outputs = ["out" "evidence"];
        buildCommand = ''
          ln -s ${ref} ref.fa
          ln -s ${samtools.faidx faidxAttrs ref} ref.fai
          ${concatMapStringsSep "\n" (i: ''
              ln -s ${i} $(basename ${i}).bam
              ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
            '')
            inputs}
          ${optionalString (length inputs > 1) "mkdir $evidence"}
          octopus -R ref.fa -I *.bam -o $out \
            --bamout $evidence \
            --threads=$NIX_BUILD_CORES \
            ${optionalString fast "--fast"} \
            ${optionalString very-fast "--very-fast"} \
            ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
            ${optionalString (targets != null) (handleTarget targets)} \
            ${flags}

          # Strip out octopus ARGV
          sed -i '/^##octopus=/d' $out
        '';
        passthru.filetype = filetype.vcf {inherit ref;};
        passthru.multicore = true;
        stripStorePaths = false;
      }