Right now it keeps the files that are in the salmon_index which doesn't result in an error to use the database but could be confusing later on. I haven't confirmed if this maintains backwards compatibility with salmon v1 but doesn't matter because leviathan will only be using salmon v2.x for the foreseeable future.
Right now it keeps the files that are in the salmon_index which doesn't result in an error to use the database but could be confusing later on. I haven't confirmed if this maintains backwards compatibility with salmon v1 but doesn't matter because leviathan will only be using salmon v2.x for the foreseeable future.