Support converting to AnnData objects with multiplexed libraries

[allyhawkins]

For cell hashing experiments, I slightly altered the workflow to skip exporting AnnData. I think this should be temporary. The problem is that when we add the sample metadata to the colData we need to pick a column that contains the sample_id that we want to use for adding in sample metadata. We have three different ways that we currently do demultiplexing and so three different columns with a potential sample_id to use. I think this might warrant some further discussion about how we may want to deal with joining sample metadata for multiplexed samples later.

Originally posted by @allyhawkins in #414 (comment)

[allyhawkins]

I'm slightly updating this issue to reflect that we do not currently support converting multiplexed libraries to AnnData objects. If we want to do this in the future then we will need to do the following:

• remove the filtering out of multiplexed libraries before the process that converts SCE to AnnData
• Update the script that does the converting to properly format multiplexed SCE objects. This should include deciding how to handle adding in the sample metadata as described above.
• Update the documentation in scpca-nf to note the output of the workflow for multiplexed libraries.