Output: minimize output size
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