nextflow: 22.10.6 -> 24.04.4 + remove buildFHSEnv

{ lib

, stdenv

, fetchurl

, makeWrapper

, openjdk17

, wget

, which

, gnused

, gawk

, coreutils

, buildFHSEnv

{

  lib,

  stdenv,

  fetchFromGitHub,

  makeWrapper,

  openjdk,

  gradle,

  wget,

  which,

  gnused,

  gawk,

  coreutils,

  bash,

}:

let

  nextflow =

stdenv.mkDerivation rec {

stdenv.mkDerivation (finalAttrs: {

  pname = "nextflow";

  version = "22.10.6";

  # 24.08.0-edge is compatible with Java 21. The current (as of 2024-09-19)

  # nextflow release (24.04.4) does not yet support java21, but java19. The

  # latter is not in nixpkgs(-unstable) anymore.

  version = "24.08.0-edge";

  src = fetchurl {

    url = "https://github.com/nextflow-io/nextflow/releases/download/v${version}/nextflow-${version}-all";

    hash = "sha256-zeYsKxWRnzr0W6CD+yjoAXwCN/AbN5P4HhH1oftnrjY=";

  src = fetchFromGitHub {

    owner = "nextflow-io";

    repo = "nextflow";

    rev = "6e866ae81ff3bf8a9729e9dbaa9dd89afcb81a4b";

    hash = "sha256-SA27cuP3iO5kD6u0uTeEaydyqbyJzOkVtPrb++m3Tv0=";

  };

  nativeBuildInputs = [

    makeWrapper

    openjdk17

    wget

    which

    gnused

    gawk

    coreutils

    gradle

  ];

  dontUnpack = true;

  postPatch = ''

    # Nextflow invokes the constant "/bin/bash" (not as a shebang) at

    # several locations so we fix that globally. However, when running inside

    # a container, we actually *want* "/bin/bash". Thus the global fix needs

    # to be reverted for this specific use case.

    substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \

      --replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \

      --replace-fail "if( containerBuilder ) {" "if( containerBuilder ) {

                launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")"

  '';

  mitmCache = gradle.fetchDeps {

    inherit (finalAttrs) pname;

    data = ./deps.json;

  };

  __darwinAllowLocalNetworking = true;

  # During the build, some additional dependencies are downloaded ("detached

  # configuration"). We thus need to run a full build on instead of the default

  # one.

  # See https://github.com/NixOS/nixpkgs/pull/339197#discussion_r1747749061

  gradleUpdateTask = "pack";

  # See Makefile (`make pack`)

  preBuild = ''

    export BUILD_PACK=1

  '';

  gradleBuildTask = "pack";

  installPhase = ''

    runHook preInstall

    mkdir -p $out/bin

    install -Dm755 $src $out/bin/nextflow

    install -Dm755 build/releases/nextflow-${finalAttrs.version}-dist $out/bin/nextflow

    runHook postInstall

  '';

  postFixup = ''

    wrapProgram $out/bin/nextflow \

      --prefix PATH : ${lib.makeBinPath nativeBuildInputs} \

      --set JAVA_HOME ${openjdk17.home}

      --prefix PATH : ${

        lib.makeBinPath [

          coreutils

          gawk

          gnused

          wget

          which

        ]

      } \

      --set JAVA_HOME ${openjdk.home}

  '';

  meta = with lib; {

    homepage = "https://www.nextflow.io/";

    changelog = "https://github.com/nextflow-io/nextflow/releases";

    license = licenses.asl20;

    maintainers = with maintainers; [ Etjean edmundmiller ];

    maintainers = with maintainers; [

      Etjean

      edmundmiller

    ];

    mainProgram = "nextflow";

    platforms = platforms.unix;

  };

};

in

if stdenv.hostPlatform.isLinux then

  buildFHSEnv

  {

    name = "nextflow";

    targetPkgs = pkgs: [ nextflow ];

    runScript = "nextflow";

  }

else nextflow

})