depot/third_party/nixpkgs/pkgs/development/interpreters/nextflow/default.nix

{ lib
, stdenv
, fetchurl
, makeWrapper
, openjdk17
, wget
, which
, gnused
, gawk
, coreutils
, buildFHSEnv
}:

let
  nextflow =
stdenv.mkDerivation rec {
  pname = "nextflow";
  version = "22.10.6";

  src = fetchurl {
    url = "https://github.com/nextflow-io/nextflow/releases/download/v${version}/nextflow-${version}-all";
    hash = "sha256-zeYsKxWRnzr0W6CD+yjoAXwCN/AbN5P4HhH1oftnrjY=";
  };

  nativeBuildInputs = [
    makeWrapper
    openjdk17
    wget
    which
    gnused
    gawk
    coreutils
  ];

  dontUnpack = true;

  installPhase = ''
    runHook preInstall

    mkdir -p $out/bin
    install -Dm755 $src $out/bin/nextflow

    runHook postInstall
  '';

  postFixup = ''
    wrapProgram $out/bin/nextflow \
      --prefix PATH : ${lib.makeBinPath nativeBuildInputs} \
      --set JAVA_HOME ${openjdk17.home}
  '';

  meta = with lib; {
    description = "DSL for data-driven computational pipelines";
    longDescription = ''
      Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows.

      It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes.

      Additionally, it provides support for manage your workflow dependencies through built-in support for Conda, Docker, Singularity, and Modules.
    '';
    homepage = "https://www.nextflow.io/";
    changelog = "https://github.com/nextflow-io/nextflow/releases";
    license = licenses.asl20;
    maintainers = with maintainers; [ Etjean edmundmiller ];
    mainProgram = "nextflow";
    platforms = platforms.unix;
  };
};
in
if stdenv.isLinux then
  buildFHSEnv
  {
    name = "nextflow";
    targetPkgs = pkgs: [ nextflow ];
    runScript = "nextflow";
  }
else nextflow