[Feature Request] Allow for passing options to Diamond and other dependencies

[StefanFlaumberg]

Dear OrthoFinder team,

It would be great to have a way to pass free arguments to the sequence search, msa and gene tree building programs. Their default behavior might sometimes be far from optimal. For example, passing a more strict E-value cutoff or coverage cutoffs may decrease the number of false positive findings during blastp search.

This can be realized by introducing something like -So, -Ao and -To options, after which one would write arguments to be passed respectively to the search, alignment or tree program being used. Like writing -S diamond -So '--evalue 1E-5 --matrix BLOSUM45' to use diamond blastp for search and to pass the evalue and matrix arguments to it.

Personally, I'm mostly interested in passing options to the searching program.

I think such an improvement would make OrthoFinder much more flexible)

Best regards, Stefan

[davidemms]

Hi Stefan

You can edit the arguments using the config.json file.

All the best David