Merge pull request #152961 from Etjean/add-nextflow

nextflow: init at 21.10.6

maintainers/maintainer-list.nix

@@ -3743,6 +3743,12 @@
     githubId = 222467;
     name = "Dmitry Ivanov";
   };
+  Etjean = {
+    email = "et.jean@outlook.fr";
+    github = "Etjean";
+    githubId = 32169529;
+    name = "Etienne Jean";
+  };
   etu = {
     email = "elis@hirwing.se";
     matrix = "@etu:semi.social";

pkgs/development/interpreters/nextflow/default.nix

@@ -0,0 +1,56 @@
+{ lib
+, stdenv
+, fetchurl
+, makeWrapper
+, jre
+, wget
+, which
+, gnused
+, gawk
+, coreutils
+}:
+
+stdenv.mkDerivation rec {
+  pname = "nextflow";
+  version = "21.10.6";
+
+  src = fetchurl {
+    url = "https://github.com/nextflow-io/nextflow/releases/download/v${version}/nextflow-${version}-all";
+    sha256 = "0l9hi51vrhvfx3px2pxw7lp4h21n8ks50x4icfk3hbgl2hwf7fvx";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre 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 buildInputs}
+  '';
+
+  meta = with lib; {
+    description = "A 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 = [ maintainers.Etjean ];
+    mainProgram = "nextflow";
+    platforms = platforms.unix;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -13666,6 +13666,8 @@ with pkgs;
 
   mujs = callPackage ../development/interpreters/mujs { };
 
+  nextflow = callPackage ../development/interpreters/nextflow { };
+
   ngn-k = callPackage ../development/interpreters/ngn-k { };
 
   obb = callPackage ../development/interpreters/clojure/obb.nix { };