"Minor" feature requests

[dandaman]

Thanks for developing, providing and maintaining orthofinder, it's a milestone tool! Your work on this is greatly appreciated!

Applying it to all kinds of datasets I think these easy to implement features would be very useful:

1. allow to write in the same (custom) output directory - OF generates its own subdir anyway... so why hassle the user with this limitation
2. introduce an optional config file to:

• support/improve repoducibility and FAIR publishing of OF runs i.e. like in snakemake all parameters could be given in the config but overridden on the cmdline
• introduce more fine-grained options to disable some result files e.g. the NxN orthologs subfolders can be a pain in the neck on slow NFS file systems and can be easily inferred from other result files.

Maybe something along the lines of https://stackoverflow.com/questions/3609852/which-is-the-best-way-to-allow-configuration-options-be-overridden-at-the-comman

Best, Daniel