adding wiredTiger to mongo instance

.dockerignore

@@ -1,2 +1,3 @@
 *.vcf.gz
-ri_tools/vcf/files_to_read/*vcf.gz
+ri_tools/vcf/files_to_read/*vcf.gz
+beacon/connections/mongo/data/datasets/*

beacon/connections/mongo/reindex.py

@@ -33,6 +33,14 @@
     client.beacon.validate_collection("synonyms")
 except Exception:
     db=client.beacon.create_collection(name="synonyms")
+try:
+    client.beacon.validate_collection("caseLevelData")
+except Exception:
+    db=client.beacon.create_collection(name="caseLevelData")
+try:
+    client.beacon.validate_collection("targets")
+except Exception:
+    db=client.beacon.create_collection(name="targets")
 try:
     client.beacon.drop_collection("counts")
 except Exception:

docker-compose.yml

@@ -67,6 +67,7 @@ services:
 
   db:
     image: mongo:5
+    command: --wiredTigerCacheSizeGB 4
     hostname: mongo
     container_name: mongoprod
     ports:

ri-tools/conf/conf.py

@@ -7,6 +7,7 @@
 reference_genome='GRCh37' # Choose one between NCBI36, GRCh37, GRCh38
 datasetId='COVID_pop11_fin_2'
 case_level_data=False
+num_rows=7000000
 
 ### MongoDB parameters ###
 database_host = 'mongo'