we need to add controls on existing output files.
something like "if trimmed file already exists, do not trim it again".
otherwise when we stop at a given step (like tonight: stopped error at first realignment) we have to start again from the beginning.
idea: ExpFolder, SkipWhatsBeenDone and DeleteIntermediateSteps could be input arguments given by the user, so we don't have to change add commit push and pull every time.
we need to add controls on existing output files. something like "if trimmed file already exists, do not trim it again". otherwise when we stop at a given step (like tonight: stopped error at first realignment) we have to start again from the beginning.