Update orthofinder and pick up new orthogroup output

[TomHarrop]

Pick up new "Hierarchical Orthogroups" output

Fixed bioconda recipe (bioconda/bioconda-recipes#45149) and update orthofinder to 2.5.5 (closes #5312)

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• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
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• - This PR adds a new tool or tool collection
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• - This PR does something else (explain below)

[bernt-matthias]

Tests should show if we can really remove this. Has been added here to allow for containerized tests: #2757

[TomHarrop]

Oops. That was a mistake. But it passed the tests using this singularity container (and no other dependencies): bioconda/bioconda-recipes#45149 (comment)

Thanks for spotting that, I will test it again once the new container is on quay.

[TomHarrop]

@bernt-matthias this passes tests with the new biocontainer, run in Apptainer, without the util-linux requirement.

Do you think I should leave util-linux out?

[bgruening]

@TomHarrop is this still Draft?

[TomHarrop]

Yes. According to the manual the main output been deprecated and I have to pick up the new output in the wrapper.

[TomHarrop]

Thanks @bgruening, all done now