[Internal] [Bug] Resume flag re-runs submission even if completed

[jessicarowell]

Executing the pipeline again, with the resume command, re-runs the full submission subworkflow. It would be better if it only runs the step that didn't finish (e.g., fetching the report) to avoid resubmitting the same samples.

If this is because the steps are all in a subworkflow, we may need to break it up.

Run environment (container, cloud service, HPC, platform, etc.)
All

Command to replicate the error:
Any command including submission.

Any Additional Context or Information?