From 990ebda331f3345877e537a2b71eabd3cced8e05 Mon Sep 17 00:00:00 2001
From: mulatta <67085791+mulatta@users.noreply.github.com>
Date: Tue, 13 Jan 2026 01:31:26 +0900
Subject: [PATCH] nextflow: add shellPath() bash patch for trace support

Adds missing patch for shellPath() method to use nix store bash
instead of /bin/bash. This is required for trace wrapper execution
when using -with-trace or resource monitoring features.

Without this patch, trace functionality fails with:
  /bin/bash: No such file or directory

Verified with comparison testing of patched vs unpatched versions.
---
 pkgs/by-name/ne/nextflow/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/ne/nextflow/package.nix b/pkgs/by-name/ne/nextflow/package.nix
index 26d238d6eb76..d3215d58f43b 100644
--- a/pkgs/by-name/ne/nextflow/package.nix
+++ b/pkgs/by-name/ne/nextflow/package.nix
@@ -41,6 +41,7 @@ stdenv.mkDerivation (finalAttrs: {
     # to be reverted for this specific use case.
     substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \
       --replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \
+      --replace-fail '? "/bin/bash"' '? "'${bash}'/bin/bash"' \
       --replace-fail "if( containerBuilder ) {" "if( containerBuilder ) {
                 launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")"
   '';