CI: Update test-pathogen-repo-ci

Add comments to clearly show the job using pathogen-repo-ci@v0 is for
pathogen repos that do not conform to the standard pathogen repo
structure. Since these are tied to a old tag of the `pathogen-repo-ci`,
the job should not be expected to be updated.

Any new pathogen repos should be added to the `test-pathogen-repo-ci`
job which uses the latest version of `pathogen-repo-ci`.

.github/workflows/ci.yml

@@ -199,7 +199,11 @@ jobs:
         ./devel/copy-images -i ghcr.io -o docker.io -t ${{ needs.build.outputs.tag }} -l
 
   # Run pathogen repo CI builds with the final image
-  test-pathogen-repo-ci:
+  # This is running pathogen-repo-ci@v0 for pathogen repos that do not conform
+  # to the standard pathogen repo structure and is not expected to be updated.
+  # Any new pathogen repos should be added to the job using the latest version
+  # of the pathogen-repo-ci below.
+  test-pathogen-repo-ci-v0:
     # Only one of push-{branch,build} runs for any given workflow run, and
     # we're ok with either of them.
     needs: [build, push-branch, push-build]
@@ -208,7 +212,6 @@ jobs:
       || needs.push-branch.result == 'success'
       || needs.push-build.result == 'success'
     strategy:
-      # XXX TODO: Test on multiple platforms via the matrix too, as above?
       matrix:
         include:
           - { pathogen: avian-flu,       build-args: test_target }
@@ -219,12 +222,7 @@ jobs:
           - { pathogen: rsv }
           - { pathogen: seasonal-flu,    build-args: --configfile profiles/ci/builds.yaml -p }
 
-          # Disable some pathogens that do not conform to pathogen-repo-ci@v0
-          # TODO: Consider adding a separate job that uses pathogen-repo-ci@v1 for these pathogens
-          # - { pathogen: mpox }
-          # - { pathogen: zika }
-
-    name: test-pathogen-repo-ci (${{ matrix.pathogen }})
+    name: test-pathogen-repo-ci-v0 (${{ matrix.pathogen }})
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0
     with:
       repo: nextstrain/${{ matrix.pathogen }}
@@ -237,6 +235,37 @@ jobs:
       continue-on-error: true
     secrets: inherit
 
+  # Run pathogen repo CI builds with the final image
+  # This is running pathogen-repo-ci@master for pathogen repos that _do_ follow
+  # standard pathogen repo structure and new pathogens should be added here
+  # to be supported for future updates such as testing on multiple platforms.
+  test-pathogen-repo-ci:
+    # Only one of push-{branch,build} runs for any given workflow run, and
+    # we're ok with either of them.
+    needs: [build, push-branch, push-build]
+    if: |2
+         success()
+      || needs.push-branch.result == 'success'
+      || needs.push-build.result == 'success'
+    strategy:
+      # XXX TODO: Test on multiple platforms via the matrix too, as above?
+      matrix:
+        pathogen:
+          - mpox
+          - zika
+
+    name: test-pathogen-repo-ci (${{ matrix.pathogen }})
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
+    with:
+      repo: nextstrain/${{ matrix.pathogen }}
+      runtimes: |
+        - docker
+      env: |
+        NEXTSTRAIN_DOCKER_IMAGE: nextstrain/base:${{ needs.build.outputs.tag }}
+      artifact-name: ${{ matrix.pathogen }}-outputs
+      continue-on-error: true
+    secrets: inherit
+
   # Delete the builder and final images from GitHub Container Registry.
   cleanup-registry:
     if: always()