How to handle multiple segmentations in the csv output?

[DenisSch]

We are about to enable a second segmentation module. Should we create:

1. Subfolders in the quantification folder
2. Change the name of the csv file according to the used segmentation

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[ArtemSokolov]

It's not just quantification, right? We need to subdivide prob_maps and segmentation folders too.

[DenisSch]

@ArtemSokolov I think all others will get new folders, since the amount and type of files will change. I was just hoping that we can have csv files with different names instead of same name but different folders. Too dangerous...

[ArtemSokolov]

Oh, I see.

[ArtemSokolov]

If it helps, Nextflow will be keeping track which segmentation method was run on each file, so it can correctly publish resulting files to the proper subfolder. As a consequence, the method name can be provided to quantification, if you want:

python CommandSingleCellExtraction.py ... --seg-method ilastik

[ArtemSokolov]

Addressed in #168 by having segmentation prepend the probability map generator name to its output folder, leading to automatic resolution of any potential name collisions in all downstream modules.