[WIP]I have added orthofinder 3 as a separate module

[chriswyatt1]

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Closes #10337 to be completed

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[chriswyatt1]

We need to make sure the output snapshot doesnt just take versions

[SPPearce]

Why is this a separate module, rather than just updating the current orthofinder module?

[chriswyatt1]

People are still actively using the older module. The version 3 is a beta version, so I didn't want to remove the version 2. Is there a better way to solve this issue?

[chriswyatt1]

This is the tool: https://github.com/davidemms/OrthoFinder

[SPPearce]

Looks like the tool is now at https://github.com/OrthoFinder/OrthoFinder
Has the input/output and arguments changed a lot between the two?

[SPPearce]

Nothing in the release notes or README makes me think that the tool is radically different from the previous version.

[chriswyatt1]

You are right, it is still doing the same tasks (mostly), even if it is a big overhaul:

--assign flags to add assign new species to existing runs of orthofinder (using --core). It may be the case that this behaviour warrants its own submodule orthofinder/assign as it is quite different ins/outs. But I have not done that in this module, it just works with the standard input of a protein fasta file store.

I just worry that several users wanted the older version, so should I just tell them to convert the existing 2.5.5 version to a local module, or start adapting to the newer version 3.1.3. I guess thats cleaner than having two modules with separate versions.

Thanks for helping with this, as I was quite unsure which route to take!

[SPPearce]

If people want to keep the older version, they don't have to update.
I agree, it sounds like there should be a separate submodule for the other mode, better that than trying to incorporate multiple distinct modes into one module.

[chriswyatt1]

OK, great. I will change the PR to update the module on nf-core to v3 as default. Not two versions.
Then they still have the old version privately