fix envvar handling

snakemake · Dec 8, 2023 · c9d007b · c9d007b
1 parent 16ee9de
commit c9d007b
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/snakemake_executor_plugin_azure_batch/__init__.py b/snakemake_executor_plugin_azure_batch/__init__.py
@@ -261,7 +261,7 @@ def __post_init__(self):
         self.pool_id = f"snakepool-{ts:s}"
         self.job_id = f"snakejob-{ts:s}"
 
-        self.envvars = list(self.workflow.envvars) or []
+        self.envvars = self.workflow.spawned_job_args_factory.envvars()
 
         # enable autoscale flag
         self.az_batch_enable_autoscale = self.settings.autoscale
@@ -328,10 +328,10 @@ def run_job(self, job: JobExecutorInterface):
         # with job_info being of type
         # snakemake_interface_executor_plugins.executors.base.SubmittedJobInfo.
         envsettings = []
-        for key in self.envvars:
+        for key, value in self.envvars.items():
             try:
                 envsettings.append(
-                    batchmodels.EnvironmentSetting(name=key, value=os.environ[key])
+                    batchmodels.EnvironmentSetting(name=key, value=value)
                 )
             except KeyError:
                 continue