[Feat] Deprecate nextclade json parser, add github actions, and update task names

[danpolanco]

This PR:

• Closes [REQUEST] Incorporate Nextclade  #1
• Closes [REQUEST] Rename WDL tasks to be more specific, standardized, or otherwise improved #4

Aim, context, and functionality 🎯

We are removing the nextclade json parser in favor of including the Nextclade results in the summary file. We are also improving WDL task names and variables.

Workflow Changes ✅

Upstream effects

None.

Input changes

None.

Output changes

• nextclade_json_parser.py has been removed and the the output file it produced as well.
• summary.py now includes the columns needed that were originally output by nextclade_json_parser.py.

Downstream effects

None yet as we haven't included RSV results in production datasets or Horizon.

Testing 🛠️

None at the moment.

Developer Checklist 👷‍♀️

• Prior to development, issues were discussed with the bioinformatics team members and approved
• Code has been refactored to sufficiently address the issues this pull request closes
• Testing was performed and the results from testing match the expected results
• All code changes match our style guide
• README has been updated to reflect changes
• Workflow diagrams in READMEs have been updated to reflect changes

Reviewer Checklist 🔍

• Met with developer to review all changes and testing performed
• Code refactoring sufficiently address the issue(s) that this pull request closes
• All code meets style guide criteria
• Confirm testing was sufficient (e.g. correct dataset was used for testing, results match the expected results). If not, the developer will perform additional testing which should be documented in the testing section above.
• New version release number has been decided upon (if applicable)

[danpolanco]

Is this supposed to be "Run_Date" instead of "run_date"?

[danpolanco]

I added initialization to prevent mypy type errors. Also, good practice to declare it in the outer scope here since we use it outside the following if statements.

[danpolanco]

I'm not sure how to handle the type issues where we assign some_variable = np.NaN. I get an error from mypy error: Incompatible types in assignment (expression has type "float", variable has type "int").

[danpolanco]

This pull request now also partially addresses #3 where mypy complains about type issues.

[danpolanco]

Should this be concatenate_seq_results_py or maybe should we shorten it everwhere?

[danpolanco]

@molly-hetheringtonrauth , I tested this in Terra and it works and results match what we expect. I don't think we need a individual meeting about these changes and can just merge them in if that works for you. I'll be making more changes after this pull request to add versioning and fix any Horizon issues anyway.