[Internal] [Feature] Write a new update_submission.py script

[jessicarowell]

Instead of calling the only submission.py script, write a new one and have UPDATE_SUBMISSION module call that.

I did not originally do this because I didn't want to replicate code in two scripts. The original submission.py script needs to fetch report.xml files to get BioSample IDs, etc., so I wanted to re-use the same code in UPDATE_SUBMISSION. The problem there is that it copies all the inputs to a working directory, even the ones it doesn't use. That's really inefficient particularly when fastq files are in the inputs list.

Ideally, we want a separate update_submission.py script that will just take the INITIAL_SUBMISSION working directory as input. But we also want to minimize code replication because that's not a good practice (e.g., having to update code in two places).

Place an ❌ in a Box that Best Matches the Feature's Importance:

• [] 1 - Most important (absolutely integral and will not use codebase at all without it)
• [] 2-4 - Moderate (still using codebase for other functions but is serving as a blocker for future use-cases)
• 5 - Least important (would like to see but there are no stringent expectations nor urgency for current/future use-cases) 

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Helpful Resources to Reference? Screenshots or Links?