I am using OrthoFinder to find orthogroups between species. I am using the latest version unpacked through tar as per their instructions.

Orthofinder creates an output folder according to the current date, ie, Results_Dec25. However, I want to integrate orthofinder in snakemake, so having a stable output directory is necessary. The -o option allows specification of an output prefix, but the dated folder is then created within.

Is it possible to force a given name to the output folder? Or is there a way in snakemake to allow ambiguous output directory names?

I know this would be possible via editing the source code of OrthoFinder, but this workflow needs to be reproducible without faff.

Many thanks

This question has already been asked here but remains unanswered.

Is there an option in Orthofinder to choose the output directory name?


1 Answer 1


The latest version solves the issue.

Source : https://github.com/davidemms/OrthoFinder/issues/403
Latest Version: https://github.com/davidemms/OrthoFinder/releases/tag/2.4.0


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.