From a66b09cf1e6e738e106bca2fa8571a544640db8d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 7 Aug 2024 07:19:25 +0200
Subject: [PATCH] shlex quote the working directory

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/tool_util/deps/singularity_util.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/deps/singularity_util.py b/lib/galaxy/tool_util/deps/singularity_util.py
index 2d090fc6237c..081c706fc3c4 100644
--- a/lib/galaxy/tool_util/deps/singularity_util.py
+++ b/lib/galaxy/tool_util/deps/singularity_util.py
@@ -102,7 +102,7 @@ def build_singularity_run_command(
     # the mounting behavior.
     command_parts.append("--contain")
     if working_directory:
-        command_parts.extend(["--pwd", working_directory])
+        command_parts.extend(["--pwd", shlex.quote(working_directory)])
     if cleanenv:
         command_parts.append("--cleanenv")
     if ipc: