Update the CI workflow

Use the stopgap from mpox (nextstrain/mpox#214) until the pathogen-repo-ci is updated.

.github/workflows/ci.yaml

@@ -5,7 +5,17 @@ on:
   - pull_request
 
 jobs:
-  ci:
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@dec0880059017dac7facf100435c5737bf1386c8
+  pathogen-ci:
+    strategy:
+      matrix:
+        runtime: [docker, conda]
+    permissions:
+      id-token: write
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    secrets: inherit
     with:
-      workflow-root: phylogenetic
+      runtime: ${{ matrix.runtime }}
+      run: |
+        nextstrain build \
+          phylogenetic \
+          --configfile profiles/ci/profiles_config.yaml

phylogenetic/Snakefile

@@ -1,5 +1,4 @@
-if not config:
-    configfile: "config/config_dengue.yaml"
+configfile: "config/config_dengue.yaml"
 
 serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4']
 
@@ -52,6 +51,12 @@ 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/profiles/ci/copy_example_data.smk

@@ -0,0 +1,14 @@
+rule copy_example_data:
+    input:
+        sequences="example_data/sequences_{serotype}.fasta",
+        metadata="example_data/metadata_{serotype}.tsv",
+    output:
+        sequences="data/sequences_{serotype}.fasta",
+        metadata="data/metadata_{serotype}.tsv",
+    shell:
+        """
+        cp -f {input.sequences} {output.sequences}
+        cp -f {input.metadata} {output.metadata}
+        """
+
+ruleorder: copy_example_data > decompress

phylogenetic/profiles/ci/profiles_config.yaml

@@ -0,0 +1,2 @@
+custom_rules:
+  - profiles/ci/copy_example_data.smk