From 967c80dabac2be74c55fcd829f0c695492772cbe Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Tue, 11 Jun 2024 14:21:03 -0700
Subject: [PATCH] Switch CI to `pathogen-repo-ci` action [#257]

Also add `nextstrain-pathogen.yaml` so that the new workflow triggers.
---
 .github/workflows/ci.yaml | 23 ++---------------------
 .yamlfmt                  |  1 +
 nextstrain-pathogen.yaml  |  5 +++++
 3 files changed, 8 insertions(+), 21 deletions(-)
 create mode 100644 nextstrain-pathogen.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 91325533..13f9c99f 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -8,24 +8,5 @@ on:
   workflow_dispatch:
 
 jobs:
-  pathogen-ci:
-    strategy:
-      matrix:
-        runtime: [docker, conda]
-    permissions:
-      id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
-    secrets: inherit
-    with:
-      runtime: ${{ matrix.runtime }}
-      run: |
-        nextstrain build \
-          phylogenetic \
-          --configfiles build-configs/ci/config.yaml
-      artifact-name: output-${{ matrix.runtime }}
-      artifact-paths: |
-        phylogenetic/auspice/
-        phylogenetic/results/
-        phylogenetic/benchmarks/
-        phylogenetic/logs/
-        phylogenetic/.snakemake/log/
+  ci:
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
diff --git a/.yamlfmt b/.yamlfmt
index dc1213a3..47b78788 100644
--- a/.yamlfmt
+++ b/.yamlfmt
@@ -1,5 +1,6 @@
 exclude:
   - ingest/
+  - nextstrain-pathogen.yaml
 formatter:
   type: basic
   line_ending: lf
diff --git a/nextstrain-pathogen.yaml b/nextstrain-pathogen.yaml
new file mode 100644
index 00000000..b74c50d3
--- /dev/null
+++ b/nextstrain-pathogen.yaml
@@ -0,0 +1,5 @@
+# This is currently an empty file to indicate the top level pathogen repo.
+# The inclusion of this file allows the Nextstrain CLI to run the
+# `nextstrain build` from any directory regardless of runtime.
+#
+# See https://github.com/nextstrain/cli/releases/tag/8.2.0 for more details.