In the end, I gave up trying to use logstash and used this method of achieving what I desired:
output.elasticsearch:
# Array of hosts to connect to.
hosts: ["localhost:9200"]
# Protocol - either `http` (default) or `https`.
#protocol: "https"
indices:
- index: "filebeat-netflow"
when.equals:
event.module: "netflow"
- index: "filebeat-threatintel"
when.equals:
event.module: "threatintel"