Remove Nextstrain profiles#1197
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Better aligns with usage in GitHub Actions workflows.
There has never been a file at this path, so I'm not sure what the reference is for.
This file was removed in "Split Nextstrain open builds to generate "6m" and "all-time" targets" (4a35ef5).
These had no effect because Nextstrain CLI automatically specifies --cores.
These were being overridden by --set-threads in the GitHub Actions workflows.
This is a comprehensive shift from --profile to --configfile, standardizing the preference started in "Remove my_profiles/" (2b88070) and already used by the "100k" workflow (which was misleadingly under "nextstrain_profiles"). Workflow-specific options are translated into command line arguments in the GitHub Actions workflow. Default options are retained in a default profile config, a practice still used across pathogen workflows.
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This PR contains 5 prep commits and 1 main commit with the following message:
This is a comprehensive shift from
--profileto--configfile, standardizing the preference started in "Remove my_profiles/" (2b88070) and already used by the "100k" workflow (which was misleadingly under "nextstrain_profiles").Workflow-specific options are translated into command line arguments in the GitHub Actions workflow. Default options are retained in a default profile config, a practice still used across pathogen workflows.
No user-facing or functional changes, thus no changelog entry.