Is the output from OrthoFinder depreciated?

Hi everyone,

Sorry, another question.

In the github documentation for OrthoFinder (v 2.5.5), it says the ‘Orthogroups Directory/Orthogroups.tsv’ is depreciated (since v 2.4.0) in favour of ‘Phylogenetic Hierarchical Orthogroups Directory/N0.tsv’, is this followed in the tool?

Looking into this further, it seems that the output is not available but is collected in the tool script:

 <data format="tsv" name="hogs" label="OrthoFinder on ${on_string}: hierarchical orthogroups (tsv)" from_work_dir="results/Phylogenetic_Hierarchical_Orthogroups/N0.tsv">

How can I collect this additional output, or request that it be made available?

It seems I did not perform a full run and so this output was not generated.