if rename flag not include on inputs with duplicate headers, it quitly fails later #474
Description
Description of the bug
If your input fastas have duplicate headers across the files, that is what the --rename flag is for, to ensure you have unique headers. But if you don't include --rename, it doesn't error out at anypoint, it just finishes with a messed up raw-annotation.tsv file where the input_fasta column is blank. Ideally it should be able to check if you need to run rename and run it automatically, or at least error out immediately if you need to and didn't include it.
System information
beta19
Command used and terminal output
Relevant files
No response