Add flag to optionally cleanup intermediate files

[p-j-smith]

Motivation

The analysis pipeline creates large intermediate files that can be deleted

Pitch

• add a flag --cleanup to the analysis script. If set, all intermediate files will be deleted
• default to not setting the flag

Alternatives

Suggested by Chris via email:

My job failed because I hadn’t specified enough memory. When I tried to rerun it, it failed again because the t1-mni.anat folder already existed which I then had to delete before rerunning I would highly advice to build in an if statement that checks if that folder and necessary files already exist and skip these steps if they exist as having to rerun fsl_anat is quite a waste of time, resources and can alleviate some frustration for the people that have to use the pipeline (on large datasets)

If the --cleanup flag is not set, we could look for and use intermediate files.

Additional context

No response