diff --git a/cwltool/software_requirements.py b/cwltool/software_requirements.py
index 9854bca38..d5d1b2637 100644
--- a/cwltool/software_requirements.py
+++ b/cwltool/software_requirements.py
@@ -85,6 +85,7 @@ def build_job_script(self, builder: "Builder", command: List[str]) -> str:
         app_config = {
             "conda_auto_install": True,
             "conda_auto_init": True,
+            "debug": builder.debug,
         }
         tool_dependency_manager: "deps.DependencyManager" = deps.build_dependency_manager(
             app_config_dict=app_config,