1st Experience: Preprocessing, Integration, Clustering about panpipes HOT 4 CLOSED

I will leave this open to remind myself to remove the "output_logged_mudata" parameter

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Thanks Sarah,

Preprocess:
Did you specify a True/False value here or a path? I believe it is supposed to be a path. But also you are correct that we don't intend to maintain that functionality. Since we are utilising scanpy layers instead.

Integration:
You are correct that "plot_pcas" does not exist as a task. You can always work out what the tasks are called by running panpipes integration show full. I would expect the pcas to be plotted in the preprocess step, did they not plot?

Clustering:
I have referenced the clustree issue in the yml, and in the documentation on the website. https://panpipes-pipelines.readthedocs.io/en/latest/workflows/clustering.html

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Thank you!
Regarding the integration, I ran panpipes integration make plot_pcas --local because it is still mentioned in the README.md: https://github.com/DendrouLab/panpipes/blob/main/README.md, namely: 2. Run panpipes integration make plot_pcas and assess the post filtering qc plots, and pca outputs
But yes, the PCA is plotted in the preprocess step

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