{ lib
, stdenv
, fetchurl
, makeWrapper
, openjdk17
, wget
, which
, gnused
, gawk
, coreutils
, buildFHSUserEnv
}:
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 = "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;
};
};
in
if stdenv.isLinux then
buildFHSUserEnv
{
name = "nextflow";
targetPkgs = pkgs: [ nextflow ];
runScript = "nextflow";
}
else nextflow