pathogen-repo-ci: Make example_data/ optional

Assume that if it's missing there's no data setup to do.  Lets us use
this workflow for the ncov repo, which doesn't use example_data/.  Test
with the zika-tutorial, which also doesn't have example_data/ (because
the whole build is an example).

.github/workflows/ci.yaml

@@ -16,3 +16,8 @@ jobs:
     uses: ./.github/workflows/pathogen-repo-ci.yaml
     with:
       repo: nextstrain/zika
+
+  test-pathogen-repo-ci-no-example-data:
+    uses: ./.github/workflows/pathogen-repo-ci.yaml
+    with:
+      repo: nextstrain/zika-tutorial

.github/workflows/pathogen-repo-ci.yaml

@@ -41,14 +41,13 @@ jobs:
       - run: nextstrain check-setup
       - run: nextstrain update
 
-      # Consider conditionalizing the copy from example_data/ on its existence
-      # and assume that if it's missing the calling workflow will setup any
-      # data appropriately first.  Update filePatterns in
-      # workflow-templates/pathogen-repo-ci.properties.json if we do.
-      #   -trs, 1 April 2022
       - name: Copy example data
         run: |
-          mkdir -p data/
-          cp -v example_data/* data/
+          if [[ -d example_data ]]; then
+            mkdir -p data/
+            cp -v example_data/* data/
+          else
+            echo No example data to copy.
+          fi
 
       - run: nextstrain build --docker . ${{ inputs.build-args }}

workflow-templates/pathogen-repo-ci.properties.json

@@ -2,7 +2,6 @@
   "name": "CI for pathogen repos",
   "description": "Basic CI workflow for repos housing Nextstrain pathogen builds",
   "filePatterns": [
-    "^Snakefile$",
-    "^example_data$"
+    "^Snakefile$"
   ]
 }