diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 71149f9..849c056 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -238,6 +238,16 @@ jobs:
           ref: ${{ needs.workflow-context.outputs.sha }}
           path: ${{ env.NEXTSTRAIN_GITHUB_DIR }}
 
+      - name: Verify nextstrain-pathogen.yaml file
+        continue-on-error: false
+        run: >
+          # shellcheck disable=SC2154
+
+          [[ -f nextstrain-pathogen.yaml ]] || (
+               echo "To use this workflow, there must be a 'nextstrain-pathogen.yaml' file present in the repository root" \
+            && exit 1
+          )
+
       - name: Set up Nextstrain runtime ${{ matrix.runtime }}
         uses: ./.git/nextstrain/.github/actions/setup-nextstrain-cli
         with:
diff --git a/actions/run-nextstrain-ci-build/action.yaml b/actions/run-nextstrain-ci-build/action.yaml
index d647307..ecb8c73 100644
--- a/actions/run-nextstrain-ci-build/action.yaml
+++ b/actions/run-nextstrain-ci-build/action.yaml
@@ -33,12 +33,12 @@ runs:
       env:
         DIR: ${{ inputs.directory }}
       run: |
-        if [[ -f nextstrain-pathogen.yaml && -f "$DIR"/Snakefile && -f "$DIR"/build-configs/ci/config.yaml ]]; then
+        if [[ -f "$DIR"/Snakefile && -f "$DIR"/build-configs/ci/config.yaml ]]; then
           nextstrain check-setup ${{ inputs.runtime }} --set-default
           nextstrain build "$DIR" --configfile build-configs/ci/config.yaml
         else
           echo "Skipping $DIR build due to one or more missing files."
-          for i in nextstrain-pathogen.yaml "$DIR"/Snakefile "$DIR"/build-configs/ci/config.yaml; do
+          for i in "$DIR"/Snakefile "$DIR"/build-configs/ci/config.yaml; do
             [[ -f $i ]] || echo missing "$i"
           done
         fi