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All the configuration is made with the docker-compose file. I added a custom field in order to process the docker logs to a dedicated index.
This line LOGSTASH_FIELDS: fileset.module=logspout in the Logspout docker-compose allows this output in Logstash:
output { if "logspout" in [fileset.module] { elasticsearch { hosts => ["127.0.0.1:9200"] index => "logspout-%{+YYYY.MM.dd}" }}}
Which will create every day an index named logspout-date_of_the_day