Implement manual correction strategy

[jcohenadad]

Context

When running automatic pipelines, processing fails in X % of the case. E.g., segmentation leaks. So, we would like to be able to:

• run the pipeline
• manually fix what needs to be fixed
• re-run the pipeline, using what is manually fixed

Suggestions

One way to do it, is to add a suffix -manual to all manual corrections and upload those in the derivatives. Then, the pipeline looks for the file with "-manual" in the derivatives and use them.

Some inspiration from the spine-generic project.

[agahkarakuzu]

SCT is no longer using Nextflow, but the issue may be still relevant. I defer this one to @jcohenadad.

[jcohenadad]

SCT is no longer using Nextflow, but the issue may be still relevant. I defer this one to @jcohenadad.

issue is still relevant-- i removed "NF" in the title