[Internal] [Feature] Update README with more detail on parameters

[jessicarowell]

We've added some parameters to the config files (e.g., metadata validation params) so it's time to update the README with a more in-depth portion that discusses all the options.

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?

[RamiyapriyaS]

Add information on different ways of running the pipeline. Include the following:

• metadata validation
• optional annotation with --annotation
• submission, with 2 options: the default is for submitting for the first time, and --update_submission if you want to make changes to an existing submission that's already hosted at NCBI.
• for users' convenience, we have a separate --fetch_reports_only workflow that just looks for the reports associated with a prior submission. It will not submit anything. It just parses your metadata file to know what samples to fetch reports for, then it tries to fetch them and put them in your results directory, and it tries to create a submission_report.csv file from the report.xmls.