Add CI workflow and configs [#2]

.github/workflows/ci.yaml

@@ -0,0 +1,12 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ci:
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master

ingest/build-configs/ci/config.yaml

@@ -0,0 +1,6 @@
+custom_rules:
+  - "build-configs/ci/copy_example_data.smk"
+
+# Snakemake requires at least one top level key in a config file, so including
+# a bogus key here that should not be used anywhere in the Snakemake workflow
+bogus_ci_config: "bogus_ci_config"

ingest/build-configs/ci/copy_example_data.smk

@@ -0,0 +1,12 @@
+rule copy_example_data:
+    input:
+        ncbi_dataset="example_data/ncbi_dataset.zip"
+    output:
+        ncbi_dataset=temp("data/ncbi_dataset.zip")
+    shell:
+        """
+        cp -f {input.ncbi_dataset} {output.ncbi_dataset}
+        """
+
+# force this rule over NCBI data fetch
+ruleorder: copy_example_data > fetch_ncbi_dataset_package