From 9f8d5391e20cd706c6f984dbd8195903dc91f72e Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Mon, 15 Jul 2024 17:10:34 -0700
Subject: [PATCH] CI: Switch CI to `pathogen-repo-ci` workflow

See https://github.com/nextstrain/.github/issues/94 for context
---
 .github/workflows/ci.yaml | 30 +++++++-----------------------
 1 file changed, 7 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5a233e2..520a4ae 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -1,28 +1,12 @@
 name: CI
 
 on:
-  - push
-  - pull_request
+  push:
+    branches:
+      - main
+  pull_request:
+  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: ${{ matrix.runtime }}
-      run: |
-        nextstrain build \
-          phylogenetic \
-          --configfile build-configs/ci/config.yaml
-      artifact-name: output-${{ 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