Netflow module stops conf files

After adding below configuration to logstash.yml for Netflow module, Logstash stops listen ports for files from conf.d directory.

- name: netflow
  var.elasticsearch.hosts: "localhost:9200"
  var.input.udp.port: 2055 "localhost:5601"

In logs i can see below message:

[2019-04-22T04:51:45,804][WARN ][logstash.config.source.multilocal] Ignoring the 'pipelines.yml' file because modules or command line options are specified

It works if I comment lines for netflow in logstash.yml, start logstash service then run netflow.var.input.udp.port=2055
But this does not persist reboot.

Can anybody help with this issue?

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