Add RSV-B

Author: DrYak

group_vars/srsilo/main.yml

@@ -22,6 +22,7 @@ srsilo_group: srsilo
 srsilo_enabled_viruses:
   - covid
   - rsva
+  - rsvb
 
 # Per-virus configuration overrides
 # Use this to override global defaults for specific viruses
@@ -36,6 +37,11 @@ srsilo_virus_config:
     fetch_max_reads: 50000000     # 50M reads - lower volume expected
     chunk_size: 500000            # Smaller chunks
     docker_memory_limit: 50g
+  rsvb:
+    fetch_days: 120
+    fetch_max_reads: 50000000     # 50M reads - lower volume expected
+    chunk_size: 500000            # Smaller chunks
+    docker_memory_limit: 50g
 
 # =============================================================================
 # Repository Path

playbooks/srsilo/vars/test_vars.yml

@@ -25,6 +25,11 @@ srsilo_virus_config:
     fetch_max_reads: 2000000        # Limit to 2M reads instead of 50M
     chunk_size: 30000               # Reduced for 8GB RAM test environment
     docker_memory_limit: 7g         # 90% of 8GB RAM
+  rsvb:
+    fetch_days: 45                  # Fetch only 45 days instead of 90
+    fetch_max_reads: 2000000        # Limit to 2M reads instead of 50M
+    chunk_size: 30000               # Reduced for 8GB RAM test environment
+    docker_memory_limit: 7g         # 90% of 8GB RAM
 
 # Shared configuration (same as production)
 srsilo_api_base_url: https://api.db.wasap.genspectrum.org

roles/srsilo/defaults/main.yml

@@ -43,6 +43,11 @@ srsilo_viruses:
     instance_name: wise-rsva
     lapis_port: 8084
     silo_port: 8082
+  rsvb:
+    organism: rsvb
+    instance_name: wise-rsvb
+    lapis_port: 8085
+    silo_port: 8086
 
 # List of enabled viruses (for multi-virus playbooks)
 # This controls which viruses are actually processed - override in group_vars

roles/srsilo/files/viruses/rsvb/database_config.yaml

@@ -0,0 +1,28 @@
+schema:
+  metadata:
+    - name: sampleId
+      type: string
+      generateIndex: true
+    - name: batchId
+      type: string
+      generateIndex: true
+    - name: locationCode
+      type: string
+      generateIndex: true
+    - name: samplingDate
+      type: date
+      generateIndex: false
+    - name: locationName
+      type: string
+      generateIndex: true
+    - name: readId
+      type: string
+    - name: sr2siloVersion
+      type: string
+      generateIndex: true
+  opennessLevel: OPEN
+  instanceName: wise-rsvb
+  features:
+    - name: generalizedAdvancedQuery
+  primaryKey: readId
+siloClientThreadCount: 96

roles/srsilo/files/viruses/rsvb/preprocessing_config.yaml

@@ -0,0 +1,2 @@
+ndjsonInputFilename: sorted.ndjson.zst
+withoutUnalignedSequences: true