Sleep in snakefile.

loculus-project · Jul 12, 2024 · b38506d · b38506d
1 parent 0adfa05
commit b38506d
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Showing 2 changed files with 13 additions and 4 deletions.
diff --git a/ena-submission/Snakefile b/ena-submission/Snakefile
@@ -72,6 +72,17 @@ rule get_ena_submission_list:
                 --log-level {params.log_level} \
         """
 
+rule get_ena_submission_list_and_sleep:
+    input:
+        file="results/ena_submission_list.json"
+    output:
+        file="results/sleep.txt"
+    shell:
+        """
+        sleep 360
+        touch {output.file}
+        """
+
 rule create_project:
     """
     Create a project in ENA

diff --git a/kubernetes/loculus/templates/ena-submission-deployment.yaml b/kubernetes/loculus/templates/ena-submission-deployment.yaml
@@ -71,11 +71,9 @@ spec:
                 secretKeyRef:
                   name: database
                   key: password
-          command:
-            - /bin/sh
-            - -c
           args:
-            - snakemake get_ena_submission_list && sleep 360 # Do not start submission process yet until on pods until better tested. 
+            - snakemake
+            - get_ena_submission_list_and_sleep # Do not start submission process yet until on pods until better tested. 
           volumeMounts:
             - name: loculus-ena-submission-config-volume
               mountPath: /package/config/config.yaml