For CI config files, we will use the directory "build-configs" instea…

…d of "profiles". This is consistent with the pathogen-repo-guide. https://github.com/nextstrain/pathogen-repo-guide/tree/5509de0e315eb6acae513d2df4dfab874ff289b5/phylogenetic/build-configs/ci However, note that the `ingest/profiles` does not need to be renamed because it's actually using the Snakemake Profiles feature. https://github.com/snakemake-profiles/doc
nextstrain · Feb 28, 2024 · 7377e53 · 7377e53
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -18,7 +18,7 @@ jobs:
       run: |
         nextstrain build \
           phylogenetic \
-          --configfile profiles/ci/profiles_config.yaml
+          --configfile build-configs/ci/profiles_config.yaml
       artifact-name: output-${{ matrix.runtime }}
       artifact-paths: |
         phylogenetic/auspice/

diff --git a/...genetic/profiles/ci/copy_example_data.smk → ...ic/build-configs/ci/copy_example_data.smk b/...genetic/profiles/ci/copy_example_data.smk → ...ic/build-configs/ci/copy_example_data.smk
diff --git a/...ogenetic/profiles/ci/profiles_config.yaml → ...tic/build-configs/ci/profiles_config.yaml b/...ogenetic/profiles/ci/profiles_config.yaml → ...tic/build-configs/ci/profiles_config.yaml