You should be able to use the input type to direct log events to specific 
indexes. For example:

input {
  file { 
    type => "unixlogs"
    path => "/var/log/UNIX/*.log"
  } 
}

output {
  if [type] == "unixlogs" {
    elasticsearch { 
      host => "localhost"
      index => "unix-%{+YYYY.MM.dd}"
    }
  }
}

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