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Paths hardcoded in new preprocess scripts #5

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@aforestsomewhere

I was trying to update my local install of preprocessing, and noticed that in the new scripts (preprocess.new2.py; preprocess.new2.sh) lots of paths are hardcoded to the local setup ("shares/CIBIO-Storage...") - this should be amended or clarified in the documentation for the wider user base if possible please.

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