From 1d9da023e6ddb5ee4ec7dd0e4632165b8c4bfa52 Mon Sep 17 00:00:00 2001
From: Manuel Frischknecht <manuel.frischknecht@gmail.com>
Date: Sun, 25 May 2025 15:43:32 +0200
Subject: [PATCH] trimmomatic: fix build by switching to JDK 21

For some reason, the invocation of jre_minimal in conjunction with
JDK 11 leads to failures; `jlink` complains about a version mismatch
with the target JRE version:

```
Running phase: patchPhase
Running phase: updateAutotoolsGnuConfigScriptsPhase
Running phase: configurePhase
no configure script, doing nothing
Running phase: buildPhase
Error: jlink version 21.0 does not match target java.base version 11.0
```

I didn't invest much time into figuring out how this happens, because
simply switching to JDK 21 seems to do at least fix the failing build.
---
 pkgs/top-level/all-packages.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f1905b8625cf..95dcc364fe13 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15635,14 +15635,14 @@ with pkgs;
     ;
 
   trimmomatic = callPackage ../applications/science/biology/trimmomatic {
-    jdk = pkgs.jdk11_headless;
+    jdk = pkgs.jdk21_headless;
     # Reduce closure size
     jre = pkgs.jre_minimal.override {
       modules = [
         "java.base"
         "java.logging"
       ];
-      jdk = pkgs.jdk11_headless;
+      jdk = pkgs.jdk21_headless;
     };
   };