TreeSummarizedExperiment support

[TuomasBorman]

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Hello!

This PR is related to this issue: #802

Good news is that I found some time to check this thing. Bad news is that I lack sufficient expertise in both ampliseq and Nextflow to successfully lead the effort to implement TreeSE support.

I realized it would be far more efficient if I had more guidance or, ideally, if someone with deeper knowledge could integrate the "main" TreeSE construction file into ampliseq.

It's worth noting that TreeSE is very similar to phyloseq, so most of the workflows for constructing phyloseq objects should be reusable for TreeSE. The only unique component is the treesummarizedexperiment.nf file.

If no one else is able to take this forward, I’m willing to contribute my expertise and help bring it to completion.

-Tuomas

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @TuomasBorman,

It looks like this pull-request is has been made against the TuomasBorman/ampliseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the TuomasBorman/ampliseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[d4straub]

Thanks!
It shouldn't be too complicated to add it into the pipeline if input files are satisfied by the files that are created by the pipeline. In case I find time I'll test it.
In any case, for future work, please work on the dev branch because that is the up to date code. master holds the code of the current release, which had some amendments already.
Best

[d4straub]

Closing in favor of #807