From fec44452ab8e2aff8b8bb7faf7a7b8b5f805c30d Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Wed, 9 Jul 2025 23:05:40 +0200
Subject: [PATCH] nextflow: fix long run with slurm

Nexflow requires userName, that is obtained from $USER.
The nix derivation somehows reset it.
Here we wrap nextflow command to force userName to $USER
at runtime.
---
 pkgs/by-name/ne/nextflow/package.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/by-name/ne/nextflow/package.nix b/pkgs/by-name/ne/nextflow/package.nix
index 612c1c2913c1..4692617c3efe 100644
--- a/pkgs/by-name/ne/nextflow/package.nix
+++ b/pkgs/by-name/ne/nextflow/package.nix
@@ -87,7 +87,8 @@ stdenv.mkDerivation (finalAttrs: {
           which
         ]
       } \
-      --set JAVA_HOME ${openjdk.home}
+      --set JAVA_HOME ${openjdk.home} \
+      --set NXF_OPTS "-Duser.name=\''${USER}"
   '';
 
   passthru.tests.default = nixosTests.nextflow;