Pin existing uses of pathogen-repo-ci

[joverlee521]

See #84 for context

Update the existing use of the pathogen-repo-ci across Nextstrain repos to pin them to ef5c51a (since we have not tagged a specific version) v0 so that they continue to run as expected without having to conform the folder structure required by #90.

Searched for pathogen-repo-ci with https://github.com/search?q=org%3Anextstrain+%2Fpathogen-repo-ci%5B.%5Dyaml%40%2F&type=code:

• avian flu -> Pin pathogen-repo-ci to v0 avian-flu#59
• conda-base -> updated as part of Provide GNU coreutils in the runtime conda-base#70
• docker-base -> ci.yaml: Pin pathogen-repo-ci to v0 docker-base#217
• ebola -> ci.yaml: Pin pathogen-repo-ci ebola#8
• lassa -> ci.yaml: Pin pathogen-repo-ci lassa#5
• mumps -> ci.yaml: Pin pathogen-repo-ci mumps#8
• ncov -> ci.yaml: Pin pathogen-repo-ci ncov#1115
• rsv -> ci.yaml: Pin pathogen-repo-ci rsv#64
• rsv-old -> not updating since it's an archived repo
• seasonal-flu -> ci.yaml: Pin pathogen-repo-ci seasonal-flu#170
• tb -> ci.yaml: Pin pathogen-repo-ci tb#11

[genehack]

<suggestion type="gentle">
Maybe instead of pinning to ef5c51a, add a v0 tag to ef5c51a and then pin to that?
</suggestion>

[joverlee521]

Maybe instead of pinning to ef5c51a, add a v0 tag to ef5c51a and then pin to that?

Didn't actually get to this today, since I got distracted by ncov-ingest, will do tomorrow.

Also noting that the commit hash ef5c51a9a3a22bde9243a090bbada0cd3a983f73 was copied over from the old issue. There's since been other updates in the repo before the pathogen-repo-ci update, so the v0 tag should be at baf4c03

[joverlee521]

Search query for pathogen-repo-ci@master only returns .github and seasonal-cov repos now 🎉