added mgnifyR workflow that uses mia

[Insaynoah]

This is a copy of the existing 'Fetch Analyses metadata for a Study' workflow but using mia instead of phyloseq.

[SandyRogers]

@Insaynoah Thank you very much for this PR and for introducing mia examples to the repository.

Before I do a proper review, is there a particular reason to introduce this as a quarto markdown file rather than as a jupyter notebook? In the current setup, quarto is being used to render all markdown AND jupyter files to the docs.mgnify.org site, however the notebooks.mgnify.org site and the Galaxy.eu tool only show jupyter notebooks (because they're just running Jupyter Lab, and we don't render qmd -> ipynb currently). This looks like a nice example to have as an interactive notebook on the jupyter servers too.

[Insaynoah]

@SandyRogers . The reason it was made in quarto rather than jupyter notebook is because Jupyter notebook only allows R kernels up to version 4.1.2. However mia requires a R version of 4.4 and above if I'm not mistaken. Being unable to set up anything locally, @TuomasBorman and I decided that It would be good to create a quarto markdown first before integrating it as a jupyter notebook in the EBI cloud.

[TuomasBorman]

mia requires 4.3 and MGnifyR 4.4.

There is partial misunderstanding, I thought that we continue developing this notebook inside our lab first. As internship of @Insaynoah is ending, I thought that it is better to get the notebook done so that someone else can continue from there.

Sorry for being unclear

[antagomir]

@SHillman836 could you check if you can finalize this PR as well (move the code from qmd to ipynb)?

[antagomir]

These have been incorporated in #50

[antagomir]

With that, we can close this one.

[antagomir]

@Insaynoah we have incorporated this in #50 now, can you close this PR?