Use pathogen-repo-build in GH Action workflows

[joverlee521]

Description of proposed changes

Updates all GH Action workflows for running nextstrain build to use the shared pathogen-repo-build workflow.

Resolves #1113

Testing

• rebuild-100k -> 2h18m
• rebuild-country -> the profile itself is borked
• rebuild-gisaid-21L -> 3h38m
• rebuild-gisaid -> 7h22m
• rebuild-open -> 3h11m

TODO

Run times are safely under 12h so we should be good to switch to short-lived sessions.
I'm currently holding off on removing the secrets because it would break @victorlin 's testing for #1106

• remove AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY from repo secrets
• Delete nextstrain-ncov-runner IAM user and associated policies

[joverlee521]

Docs failure unrelated to changes in this PR, it's the same issue as nextstrain/docs.nextstrain.org#209

[joverlee521]

The rebuild-country workflow exited with an error that is unrelated to the GH Action workflow changes.

I can replicate the error locally

$ nextstrain build --envdir ~/Repos/env.d/aws/ . results/nextstrain_country_6m/auspice_config.json --profile nextstrain_profiles/nextstrain-country 
Using profile nextstrain_profiles/nextstrain-country for setting default command line arguments.
Config file defaults/parameters.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Provided resources: concurrent_deploys=2
Conda environments: ignored
Job stats:
job               count
--------------  -------
auspice_config        1
total                 1

Cannot send slack message as the config does not define a channel and/or token.
Select jobs to execute...

[Wed Jun 26 17:47:36 2024]
Job 0: Making a custom auspice config.
Reason: Missing output files: results/nextstrain_country_6m/auspice_config.json

Config file defaults/parameters.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Provided resources: concurrent_deploys=2
Conda environments: ignored
Select jobs to execute...
[Wed Jun 26 17:47:37 2024]
Error in rule auspice_config:
    jobid: 0
    output: results/nextstrain_country_6m/auspice_config.json

RuleException:
ValueError in file /nextstrain/build/workflow/snakemake_rules/export_for_nextstrain.smk, line 146:
too many values to unpack (expected 2)
  File "/nextstrain/build/workflow/snakemake_rules/export_for_nextstrain.smk", line 146, in __rule_auspice_config
  File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

I don't think this profile ever worked as intended, since the build names have three parts delimited by underscores (e.g. nextstrain_country_1m), while our auspice config rule only expects two parts:

ncov/workflow/snakemake_rules/export_for_nextstrain.smk

Lines 145 to 146 in eb488d6

	if "_" in build_name:
	build_region, build_timespan = build_name.split("_")

Also worth noting that I cannot find any history of the rebuild-country GH Action workflow being used. I only see my one trial run in the run history

$ gh run list --workflow rebuild-country.yml
STATUS  TITLE                                   WORKFLOW                 BRANCH                   EVENT              ID          ELAPSED   AGE               
X       Rebuild country-specific phylogenet...  Rebuild country-spec...  use-pathogen-repo-build  workflow_dispatch  9671643994  1h28m21s  about 17 hours ago

---

My plan is to disable the rebuild-country GH Action workflow for now and fix it (or remove it) in a separate PR. Tracking in #1120