If you want to use custom ids, then yes, you need to use the document_id in your Elasticsearch output.
@metadata fields are not part of the final document that is sent to Elasticsearch, besides that, the _id field is set during the request not from a field in the document., so you would still need to use the document_id option in the output.
Would you know if there is an option in order to avoid a global elasticsearch output plugin configuration ? Not all my log sources are using/needing the fingerprint plugin.
Using multiple pipelines makes management easier because you do not need to rely on multiple conditionals to separate different data sources and log formats.
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