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The current output of IMP3 is huge, especially the folder Preprocessing/. For a user, it might be difficult to decide which files could be deleted because they are not required later and could be re-created if necessary. For example, <omic>.se1.trimmed.fq.gz and <omic>.se2.trimmed.fq.gz are concatenated into <omic>.se.trimmed.fq.gz but all three are kept after preprocessing.

I would suggest to have a discussion how to best address this issue:

• identify files which could be considered as not or less relevant, and can be re-created if needed
• define how to handle these files, e.g. removing these if a certain flag is set in the config file or provide a list of files so the users can remove them themselves