Geneious operations in the CLI follow the basic format:
geneious -i <input_file_name> --operation <operation_name> <-options> -o <output_file_name>
To see all available operations, type
geneious --list (add --filter <operation type> to filter the list on specific types of operations)
To see all options for a given operation, type
geneious --options-for <operation> (add --advanced to see advanced options)
Note that the command line interface cannot currently access files directly from your Geneious data folder. If you have files currently in Geneious you want to use as input to operations in the CLI, you must export them from geneious so that they are stored as files on your drive. They can be exported in either .geneious format or any of the common sequence formats. You can also use raw sequence files (such as fastq files from your sequencing provider) that have not been imported into Geneious.
To see some examples of how to use the CLI, type
geneious --examples