From b38506d629aad915cfe6ba41a3a4a1f654e4aefa Mon Sep 17 00:00:00 2001
From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com>
Date: Fri, 12 Jul 2024 18:43:14 +0200
Subject: [PATCH] Sleep in snakefile.

---
 ena-submission/Snakefile                              | 11 +++++++++++
 .../loculus/templates/ena-submission-deployment.yaml  |  6 ++----
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/ena-submission/Snakefile b/ena-submission/Snakefile
index f08e62193..63a3f34ae 100644
--- 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
index 08d49a296..450e3f46d 100644
--- 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