Stop `prokka` from renaming contigs by default #920

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Run time

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Job	Run time
Run pipeline with test data (AMP and ARG workflows) (23.04.0, --annotation_tool prodigal)	1m 2s
Run pipeline with test data (AMP and ARG workflows) (23.04.0, --annotation_tool prokka)	1m 1s
Run pipeline with test data (AMP and ARG workflows) (23.04.0, --annotation_tool bakta --annotatio...	1m 3s
Run pipeline with test data (AMP and ARG workflows) (latest-everything, --annotation_tool prodigal)	1m 3s
Run pipeline with test data (AMP and ARG workflows) (latest-everything, --annotation_tool prokka)	1m 1s
Run pipeline with test data (AMP and ARG workflows) (latest-everything, --annotation_tool bakta -...	1m 3s
Run pipeline with test data (BGC workflow) (23.04.0, --annotation_tool prodigal)	1m 1s
Run pipeline with test data (BGC workflow) (23.04.0, --annotation_tool prokka)	1m 1s
Run pipeline with test data (BGC workflow) (23.04.0, --annotation_tool bakta --annotation_bakta_d...	1m 2s
Run pipeline with test data (BGC workflow) (latest-everything, --annotation_tool prodigal)	1m 2s
Run pipeline with test data (BGC workflow) (latest-everything, --annotation_tool prokka)	1m 2s
Run pipeline with test data (BGC workflow) (latest-everything, --annotation_tool bakta --annotati...	1m 1s
Run pipeline with test data (DeepARG only workflow) (23.04.0, --annotation_tool bakta --annotatio...	1m 1s
Run pipeline with test data (DeepARG only workflow) (23.04.0, --annotation_tool pyrodigal)	1m 1s
Run pipeline with test data (DeepARG only workflow) (latest-everything, --annotation_tool bakta -...	1m 1s
Run pipeline with test data (DeepARG only workflow) (latest-everything, --annotation_tool pyrodigal)	1m 0s
	16m 25s