Commit 8d15ee11 authored by Rolf Schröder's avatar Rolf Schröder Committed by Doron Behar
Browse files

tests/nextflow: init

parent e7dac85a

nixos/tests/all-tests.nix

+1 −0
Original line number Diff line number Diff line
@@ -658,6 +658,7 @@ in { 
  # TODO: put in networking.nix after the test becomes more complete

  networkingProxy = handleTest ./networking-proxy.nix {};

  nextcloud = handleTest ./nextcloud {};

  nextflow = handleTest ./nextflow.nix {};

  nextjs-ollama-llm-ui = runTest ./web-apps/nextjs-ollama-llm-ui.nix;

  nexus = handleTest ./nexus.nix {};

  # TODO: Test nfsv3 + Kerberos

nixos/tests/nextflow.nix

0 → 100644
+60 −0
Original line number Diff line number Diff line 
import ./make-test-python.nix (

  { pkgs, ... }:

  let

    bash = pkgs.dockerTools.pullImage {

      imageName = "quay.io/nextflow/bash";

      imageDigest = "sha256:bea0e244b7c5367b2b0de687e7d28f692013aa18970941c7dd184450125163ac";

      sha256 = "161s9f24njjx87qrwq0c9nmnwvyc6iblcxka7hirw78lm7i9x4w5";

      finalImageName = "quay.io/nextflow/bash";

    };



    hello = pkgs.stdenv.mkDerivation {

      name = "nextflow-hello";

      src = pkgs.fetchFromGitHub {

        owner = "nextflow-io";

        repo = "hello";

        rev = "afff16a9b45c8e8a4f5a3743780ac13a541762f8";

        hash = "sha256-c8FirHc+J5Y439g0BdHxRtXVrOAzIrGEKA0m1mp9b/U=";

      };

      installPhase = ''

        cp -r $src $out

      '';

    };

    run-nextflow-pipeline = pkgs.writeShellApplication {

      name = "run-nextflow-pipeline";

      runtimeInputs = [ pkgs.nextflow ];

      text = ''

        export NXF_OFFLINE=true

        for b in false true; do

          echo "docker.enabled = $b" > nextflow.config

          cat nextflow.config

          nextflow run -ansi-log false ${hello}

        done

      '';

    };

  in

  {

    name = "nextflow";



    nodes.machine =

      { ... }:

      {

        environment.systemPackages = [

          run-nextflow-pipeline

          pkgs.nextflow

        ];

        virtualisation = {

          docker.enable = true;

        };

      };



    testScript =

      { nodes, ... }:

      ''

        start_all()

        machine.wait_for_unit("docker.service")

        machine.succeed("docker load < ${bash}")

        machine.succeed("run-nextflow-pipeline >&2")

      '';

  }

)

pkgs/development/interpreters/nextflow/default.nix

+2 −0
Original line number Diff line number Diff line
@@ -12,6 +12,7 @@ 
  coreutils,

  bash,

  testers,

  nixosTests,

}:

stdenv.mkDerivation (finalAttrs: {

  pname = "nextflow";
@@ -83,6 +84,7 @@ stdenv.mkDerivation (finalAttrs: { 
      --set JAVA_HOME ${openjdk.home}

  '';



  passthru.tests.default = nixosTests.nextflow;

  # versionCheckHook doesn't work as of 2024-09-23.

  # See https://github.com/NixOS/nixpkgs/pull/339197#issuecomment-2363495060

  passthru.tests.version = testers.testVersion {