fix: do not pass SNAKEMAKE_PROFILE into cluster-submit (snakemake#1398)

holtgrewe · Feb 17, 2022 · 7255528 · 7255528
1 parent 0593de1
commit 7255528
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/snakemake/executors/__init__.py b/snakemake/executors/__init__.py
@@ -1070,12 +1070,17 @@ def run(self, job, callback=None, submit_callback=None, error_callback=None):
             raise WorkflowError(str(e), rule=job.rule if not job.is_group() else None)
 
         try:
+            # Remove SNAKEMAKE_PROFILE from environment as the snakemake call inside
+            # of the cluster job must run locally (or complains about missing -j).
+            env = dict(os.environ.items())
+            env.pop("SNAKEMAKE_PROFILE", None)
             ext_jobid = (
                 subprocess.check_output(
                     '{submitcmd} "{jobscript}"'.format(
                         submitcmd=submitcmd, jobscript=jobscript
                     ),
                     shell=True,
+                    env=env,
                 )
                 .decode()
                 .split("\n")