Round-trip ci: block in .nf-core.yml

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nf-core/tools: Changelog
 
+## [unreleased]
+
+### General
+
+- Round-trip the `ci:` block in `.nf-core.yml` so centralised nf-core/actions CI config is not dropped by `sync`/`bump-version` ([#4453](https://github.com/nf-core/tools/pull/4453))
+
 ## [v4.1.0 - Marshalled Mamba](https://github.com/nf-core/tools/releases/tag/4.1.0) - [2026-07-29]
 
 ### General

nf_core/pydantic_models.py

@@ -183,6 +183,13 @@ class NFCoreYamlConfig(BaseModel):
     """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information. """
     container_registry: list[str] | None = Field(default=None, alias="container-registry")
     """ Additional container registry prefixes allowed when linting container directives. """
+    ci: dict[str, Any] | None = None
+    """ Configuration passed through to the centralised nf-core/actions CI workflows.
+    Deliberately a permissive dict rather than a typed model: nf-core/actions defines and
+    adds these keys independently (see src/actions/read-config/registry.ts in that repo). A
+    strict schema here would mean every new CI setting needs a tools release plus a template
+    sync before any pipeline could use it, reintroducing the coupling that centralising the
+    workflows removed. tools only needs to round-trip this block, not validate it. """
 
     def __getitem__(self, item: str) -> Any:
         return getattr(self, item)

tests/test_utils.py

@@ -272,3 +272,19 @@ def test_get_wf_files(self, tmpdir):
         files = nf_core.utils.get_wf_files(tmpdir)
         files = sorted(str(Path(f).relative_to(tmpdir)) for f in files)
         assert files == [".gitignore", "dir1/should-match-1", "should-match-2"]
+
+
+@pytest.mark.parametrize("repository_type", ["pipeline", "modules"])
+def test_nfcore_yml_ci_round_trip(repository_type):
+    """The `ci:` block (consumed by nf-core/actions) must survive a model_dump() rewrite."""
+    from nf_core.pydantic_models import NFCoreYamlConfig
+
+    ci = {
+        "nf_test_version": "0.9.0",
+        "nextflow_versions": ["24.04.2", "latest-stable"],
+        "profiles": ["docker", "singularity"],
+        "max_shards": 5,
+        "some_future_key": "value nf-core/actions may add independently",
+    }
+    config = NFCoreYamlConfig(repository_type=repository_type, ci=ci)
+    assert config.model_dump()["ci"] == ci