required env vars override EnvVarRequirement & --preserve-entire-environment

Author: mr-c

cwltool/job.py

@@ -509,11 +509,11 @@ def prepare_environment(
         elif runtimeContext.preserve_environment:
             self._preserve_environment_on_containers_warning(runtimeContext.preserve_environment)
 
+        env.update(self.extract_environment(runtimeContext, envVarReq))
+
         # Set required env vars
         env.update(self._required_env())
 
-        env.update(self.extract_environment(runtimeContext, envVarReq))
-
         # Set on ourselves
         self.environment = env