Dear Dr. Woodcroft,
We are working in order to include CoverM in Galaxy, and it would be great if you could clarify a few doubts that we have. Could you provide us with some additional details about the cases in which is strictly necessary to use the --reference parameter? Under my understanding, it is only strictly required when providing metagenomic assemblies. Also, it would be great if you could clarify this sentence:

However, while not necessary, --reference can be specified if an alternate reference sequence set is desired.

Thank you so much for your attention.