Support for renaming/saving multiple source metadata keys to same destination key

[apetkau]

Suggestion

It would be useful if, when parsing metadata to save and writing to iridanext.output.json.gz, there could be multiple source metadata keys that get saved to the same destination key based on different conditions.

Example

Consider the following config file:

nextflow.config

iridanext {
    output {
        metadata {
            samples {
                rename = [
                    "serotype_sistr": "serotype",
                    "serotype_ectyper": "serotype"
                ]
            }
        }
    }
}

This could be used to save metadata to a sample under the name serotype that is derived from different software (SISTR or ECTyper).

Enhancements

It may be useful to have some way of adding logical statements to define conditions under which one key is chosen over another (e.g., when serotype_sistr is chosen over serotype_ectyper).

Checklist

Currently, the above may work with nf-iridanext as-is, but the following would need to be checked:

• Can multiple keys be specified in the rename section
• If all of the metadata keys exist and there is an attempt to save to the same destination key, will the pipeline properly report an error (e.g., if serotype_sistr and serotype_ectyper both exist and there is an attempt to write both to serotype, will this generate an error).