Server hotfixes - 230419 (#616)

* Rename gisaid flu workflow folders

* suspend VOC mining for now

* Ignore new update scripts

.gitignore

@@ -105,6 +105,10 @@ server/htpasswd
 # Ignore site deployment scripts
 push_data.sh
 daily_update.sh
+daily_update_new.sh
+daily_update_rsv.sh
+daily_update_sars2_genbank.sh
+daily_update_sars2_gisaid.sh
 update_gisaid.sh
 update_genbank.sh
 filter_list.txt

config/config_flu_gisaid.yaml

@@ -16,7 +16,7 @@ static_data_folder: "static_data/flu"
 # Path to folder with data to use in development
 # This path is relative to the project root
 # Only used for database seeding in development
-example_data_folder: "data_flu_small"
+example_data_folder: "data_gisaid_flu"
 
 # Database for this virus
 postgres_db: "flu_gisaid"

workflow_main/Snakefile

@@ -101,7 +101,7 @@ def sars2_output(wildcards):
     if config['virus'] == 'sars2':
         return [
             rules.build_phylotree_graph.output.graph_table,
-            os.path.join(data_folder, "status", "update_vocs_" + today_str + ".done"),
+            #os.path.join(data_folder, "status", "update_vocs_" + today_str + ".done"),
             os.path.join(data_folder, "spikenuc.fa.gz"),
             os.path.join(data_folder, "spikeaa.fa.gz")
         ]