Update the CI workflow

Following the pathogen-repo-guide and
nextstrain/zika@efe11e3

.github/workflows/ci.yaml

@@ -5,5 +5,24 @@ on:
   - pull_request
 
 jobs:
-  ci:
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
+  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/

phylogenetic/Snakefile

@@ -9,6 +9,12 @@ include: "rules/construct_phylogeny.smk"
 include: "rules/annotate_phylogeny.smk"
 include: "rules/export.smk"
 
+# Include custom rules defined in the config.
+if "custom_rules" in config:
+    for rule_file in config["custom_rules"]:
+
+        include: rule_file
+
 rule clean:
     """Removing directories: {params}"""
     params:

phylogenetic/build-configs/ci/config.yaml

@@ -0,0 +1,7 @@
+# This configuration file contains the custom configurations parameters
+# for the CI workflow to run with the example data.
+
+# Custom rules to run as part of the CI automated workflow
+# The paths should be relative to the phylogenetic directory.
+custom_rules:
+  - build-configs/ci/copy_example_data.smk

phylogenetic/build-configs/ci/copy_example_data.smk

@@ -0,0 +1,17 @@
+rule copy_example_data:
+    input:
+        sequences="example_data/sequences.fasta",
+        metadata="example_data/metadata.tsv",
+    output:
+        sequences="data/sequences.fasta",
+        metadata="data/metadata.tsv",
+    shell:
+        """
+        cp -f {input.sequences} {output.sequences}
+        cp -f {input.metadata} {output.metadata}
+        """
+
+# Add a Snakemake ruleorder directive here if you need to resolve ambiguous rules
+# that have the same output as the copy_example_data rule.
+
+# ruleorder: copy_example_data > ...