diff --git a/docs/api/_src/api/nf_core_yml.md b/docs/api/_src/api/nf_core_yml.md
new file mode 100644
index 0000000000..48d2fac750
--- /dev/null
+++ b/docs/api/_src/api/nf_core_yml.md
@@ -0,0 +1,67 @@
+# .nf-core.yml configuration
+
+The `.nf-core.yml` file at the root of any nf-core repository controls how nf-core
+tools behaves for that repository. It is read by `load_tools_config()` and validated
+against the `NFCoreYamlConfig` Pydantic model.
+
+## Minimal examples
+
+Pipeline repository:
+
+```yaml
+repository_type: pipeline
+nf_core_version: "3.2.0"
+```
+
+Modules repository:
+
+```yaml
+repository_type: modules
+nf_core_version: "3.2.0"
+container-registry:
+  - community.wave.seqera.io/library/
+```
+
+## Schema
+
+### Top-level `.nf-core.yml` schema (`NFCoreYamlConfig`)
+
+```{eval-rst}
+.. autopydantic_model:: nf_core.utils.NFCoreYamlConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :model-show-json: false
+    :model-show-config-summary: false
+    :model-show-validator-members: false
+    :model-show-field-summary: true
+    :field-show-alias: true
+```
+
+### `lint` block (`NFCoreYamlLintConfig`)
+
+```{eval-rst}
+.. autopydantic_model:: nf_core.utils.NFCoreYamlLintConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :model-show-json: false
+    :model-show-config-summary: false
+    :model-show-validator-members: false
+    :model-show-field-summary: true
+    :field-show-alias: true
+```
+
+### `template` block (`NFCoreTemplateConfig`)
+
+```{eval-rst}
+.. autopydantic_model:: nf_core.utils.NFCoreTemplateConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :model-show-json: false
+    :model-show-config-summary: false
+    :model-show-validator-members: false
+    :model-show-field-summary: true
+    :field-show-alias: true
+```
diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md
index e752b3b28b..8ebd988b1b 100644
--- a/docs/api/_src/index.md
+++ b/docs/api/_src/index.md
@@ -8,3 +8,4 @@ This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/t
 - [Module code lint tests](./module_lint_tests/environment_yml.md) (run by `nf-core modules lint`)
 - [Subworkflow code lint tests](./subworkflow_lint_tests/main_nf.md) (run by `nf-core subworkflows lint`)
 - [nf-core/tools Python package API reference](./api/utils.md)
+- [`.nf-core.yml` configuration reference](./api/nf_core_yml.md)
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index f115bf2bfa..7707a918fd 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1316,8 +1316,8 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
     "--registry",
     type=str,
     metavar="<registry>",
-    default=None,
-    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
+    default="quay.io,community.wave.seqera.io/library/",
+    help="Comma-separated list of allowed container registry prefixes.",
 )
 @click.option(
     "-k",
@@ -1608,8 +1608,8 @@ def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint:
     "--registry",
     type=str,
     metavar="<registry>",
-    default=None,
-    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
+    default="quay.io,community.wave.seqera.io/library/",
+    help="Comma-separated list of allowed container registry prefixes.",
 )
 @click.option(
     "-k",
diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index 7f5b991745..6f06b24550 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -262,7 +262,6 @@ def modules_lint(
         )
         module_lint.lint(
             module=tool,
-            registry=registry,
             key=key,
             all_modules=all_modules,
             print_results=True,
diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index 193e976401..79ce0f7523 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -130,7 +130,6 @@ def subworkflows_lint(
         )
         subworkflow_lint.lint(
             subworkflow=subworkflow,
-            registry=registry,
             key=key,
             all_subworkflows=all_subworkflows,
             print_results=True,
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index efcdc11d90..0cbe9decb9 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -62,7 +62,7 @@ def __init__(
         remote_url: str | None = None,
         branch: str | None = None,
         no_pull: bool = False,
-        registry: str | None = None,
+        registry: str = "quay.io,community.wave.seqera.io/library/",
         hide_progress: bool = False,
     ):
         super().__init__(
@@ -156,12 +156,11 @@ def __init__(
     def __repr__(self) -> str:
         return f"ComponentLint({self.component_type}, {self.directory})"
 
-    def _set_registry(self, registry) -> None:
-        if registry is None:
-            self.registry = self.config.get("docker.registry", "quay.io")
-        else:
-            self.registry = registry
-        log.debug(f"Registry set to {self.registry}")
+    def _set_registry(self, registry: str) -> None:
+        _, tools_config = nf_core.utils.load_tools_config(self.directory)
+        user_registries: list[str] = (tools_config.container_registry or []) if tools_config else []
+        self.registry: tuple[str, ...] = (*registry.split(","), *user_registries)
+        log.debug(f"Registries set to {self.registry}")
 
     @property
     def local_module_exclude_tests(self):
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index f2472db0d3..9821dc0c7d 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -69,7 +69,7 @@ def __init__(
         remote_url: str | None = None,
         branch: str | None = None,
         no_pull: bool = False,
-        registry: str | None = None,
+        registry: str = "quay.io,community.wave.seqera.io/library/",
         hide_progress: bool = False,
     ):
         super().__init__(
@@ -88,7 +88,6 @@ def __init__(
     def lint(
         self,
         module=None,
-        registry="quay.io",
         key=(),
         all_modules=False,
         print_results=True,
@@ -173,25 +172,22 @@ def lint(
 
         # Lint local modules
         if local and len(local_modules) > 0:
-            self.lint_modules(local_modules, registry=registry, local=True, fix_version=fix_version)
+            self.lint_modules(local_modules, local=True, fix_version=fix_version)
 
         # Lint nf-core modules
         if not local and len(remote_modules) > 0:
-            self.lint_modules(remote_modules, registry=registry, local=False, fix_version=fix_version)
+            self.lint_modules(remote_modules, local=False, fix_version=fix_version)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by, plain_text=plain_text)
             self.print_summary(plain_text=plain_text)
 
-    def lint_modules(
-        self, modules: list[NFCoreComponent], registry: str = "quay.io", local: bool = False, fix_version: bool = False
-    ) -> None:
+    def lint_modules(self, modules: list[NFCoreComponent], local: bool = False, fix_version: bool = False) -> None:
         """
         Lint a list of modules
 
         Args:
             modules ([NFCoreComponent]): A list of module objects
-            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core modules
             fix_version (boolean): Fix the module version if a newer version is available
         """
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index b589bc3f0c..0b8df9c046 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -20,7 +20,7 @@
 
 
 def main_nf(
-    module_lint_object, module: NFCoreComponent, fix_version: bool, registry: str, progress_bar: Progress
+    module_lint_object, module: NFCoreComponent, fix_version: bool, registry: tuple[str, ...], progress_bar: Progress
 ) -> tuple[list[str], list[str]]:
     """Lint a ``main.nf`` module file
 
@@ -359,15 +359,17 @@ def check_when_section(self, lines):
     self.passed.append(("main_nf", "when_condition", "when: condition is unchanged", self.main_nf))
 
 
-def check_process_section(self, lines, registry, fix_version, progress_bar):
+def check_process_section(
+    self, lines: list[str], registry: tuple[str, ...], fix_version: bool, progress_bar: Progress | None
+):
     """Lint the section of a module between the process definition
     and the 'input:' definition
     Specifically checks for correct software versions
     and containers
 
     Args:
-        lines (List[str]): Content of process.
-        registry (str): Base Docker registry for containers. Typically quay.io.
+        lines (list[str]): Content of process.
+        registry (tuple[str, ...]): Allowed container registry prefixes.
         fix_version (bool): Fix software version
         progress_bar (ProgressBar): Progress bar to update.
 
@@ -384,6 +386,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     singularity_tag = None
     docker_tag = None
     bioconda_packages = []
+    allowed_registries = registry
 
     # Process name should be all capital letters
     if all(x.upper() for x in self.process_name):
@@ -450,7 +453,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             else:
                 self.failed.append(("main_nf", "docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = None
-            if line.startswith((registry, "community.wave.seqera.io/library/")):
+            if line.startswith(allowed_registries):
                 l_stripped = re.sub(r"\W+$", "", line)
                 self.passed.append(
                     (
@@ -465,15 +468,11 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                     (
                         "main_nf",
                         "container_links",
-                        "Container prefix is not correct. Please add the registry prefix (e.g. 'quay.io/')",
+                        f"Container prefix is not correct. Please add one of the allowed registry prefixes: {', '.join(f'{r}' for r in allowed_registries)}",
                         self.main_nf,
                     )
                 )
 
-            # Guess if container name is simple one (e.g. nfcore/ubuntu:20.04)
-            # If so, add quay.io as default container prefix
-            if line.count("/") == 1 and line.count(":") == 1:
-                line = "/".join([registry, line]).replace("//", "/")
             url = urlparse(line.split("'")[0])
 
         if line.startswith("container") or _container_type(line) == "docker" or _container_type(line) == "singularity":
@@ -564,7 +563,10 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                         log.debug(f"Unable to update package {package} due to error: {e}")
                     else:
                         if fixed:
-                            progress_bar.print(f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}")
+                            if progress_bar is not None:
+                                progress_bar.print(
+                                    f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}"
+                                )
                             log.debug(f"Updating package {package} {ver} -> {last_ver}")
                             self.passed.append(
                                 (
@@ -575,9 +577,10 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                                 )
                             )
                         else:
-                            progress_bar.print(
-                                f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
-                            )
+                            if progress_bar is not None:
+                                progress_bar.print(
+                                    f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
+                                )
                             log.debug(f"Unable to update package {package} {ver} -> {last_ver}")
                             self.warned.append(
                                 (
diff --git a/nf_core/pipelines/lint/nfcore_yml.py b/nf_core/pipelines/lint/nfcore_yml.py
index f202adfd96..ff28a77129 100644
--- a/nf_core/pipelines/lint/nfcore_yml.py
+++ b/nf_core/pipelines/lint/nfcore_yml.py
@@ -12,11 +12,11 @@ def nfcore_yml(self) -> dict[str, list[str]]:
 
     The ``.nf-core.yml`` contains metadata for nf-core tools to correctly apply its features.
 
-    * repository type:
+    * ``repository_type``:
 
         Check that the repository type is set.
 
-    * nf core version:
+    * ``nf_core_version``:
 
         Check if the nf-core version is set to the latest version.
 
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index 7d5fbccdae..aad0b1b066 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -51,7 +51,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
-        registry=None,
+        registry: str = "quay.io,community.wave.seqera.io/library/",
         hide_progress=False,
     ):
         super().__init__(
@@ -69,7 +69,6 @@ def __init__(
     def lint(
         self,
         subworkflow=None,
-        registry="quay.io",
         key=(),
         all_subworkflows=False,
         print_results=True,
@@ -152,23 +151,22 @@ def lint(
 
         # Lint local subworkflows
         if local and len(local_subworkflows) > 0:
-            self.lint_subworkflows(local_subworkflows, registry=registry, local=True)
+            self.lint_subworkflows(local_subworkflows, local=True)
 
         # Lint nf-core subworkflows
         if not local and len(remote_subworkflows) > 0:
-            self.lint_subworkflows(remote_subworkflows, registry=registry, local=False)
+            self.lint_subworkflows(remote_subworkflows, local=False)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by, plain_text=plain_text)
             self.print_summary(plain_text=plain_text)
 
-    def lint_subworkflows(self, subworkflows, registry="quay.io", local=False):
+    def lint_subworkflows(self, subworkflows, local=False):
         """
         Lint a list of subworkflows
 
         Args:
             subworkflows ([NFCoreComponent]): A list of subworkflow objects
-            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core subworkflows
         """
         # TODO: consider unifying modules and subworkflows lint_subworkflows() function and add it to the ComponentLint class
@@ -189,9 +187,9 @@ def lint_subworkflows(self, subworkflows, registry="quay.io", local=False):
 
             for swf in subworkflows:
                 progress_bar.update(lint_progress, advance=1, test_name=swf.component_name)
-                self.lint_subworkflow(swf, progress_bar, registry=registry, local=local)
+                self.lint_subworkflow(swf, progress_bar, local=local)
 
-    def lint_subworkflow(self, swf, progress_bar, registry, local=False):
+    def lint_subworkflow(self, swf, progress_bar, local=False):
         """
         Perform linting on one subworkflow
 
diff --git a/nf_core/utils.py b/nf_core/utils.py
index d376559e53..d4aca9b0e6 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -33,7 +33,7 @@
 import rich.markup
 import yaml
 from packaging.version import Version
-from pydantic import BaseModel, ValidationError, field_validator
+from pydantic import BaseModel, ConfigDict, Field, ValidationError, field_validator
 from rich.live import Live
 from rich.spinner import Spinner
 
@@ -1388,6 +1388,8 @@ def __setitem__(self, item: str, value: Any) -> None:
 class NFCoreYamlConfig(BaseModel):
     """.nf-core.yml configuration file schema"""
 
+    model_config = ConfigDict(populate_by_name=True)
+
     repository_type: Literal["pipeline", "modules"] | None = None
     """ Type of repository """
     nf_core_version: str | None = None
@@ -1402,6 +1404,8 @@ class NFCoreYamlConfig(BaseModel):
     """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information. """
     update: dict[str, str | bool | dict[str, str | dict[str, str | bool]]] | None = None
     """ 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. """
 
     def __getitem__(self, item: str) -> Any:
         return getattr(self, item)
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index f6c3848f71..1eddede4d9 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -1,3 +1,6 @@
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
 import pytest
 
 import nf_core.modules.lint
@@ -6,6 +9,7 @@
     _parse_output_topics,
     check_container_link_line,
     check_process_labels,
+    check_process_section,
     check_script_section,
 )
 
@@ -101,6 +105,64 @@ def test_container_links(content, passed, warned, failed):
     assert len(mock_lint.failed) == failed
 
 
+@pytest.mark.parametrize(
+    "container_line,additional_registries,should_pass",
+    [
+        # Known additional registry passes when listed
+        (
+            "container 'community.wave.seqera.io/library/samtools:1.17--h87f3376_0'",
+            ["community.wave.seqera.io/library/"],
+            True,
+        ),
+        # Same registry fails when not in additional_registries
+        (
+            "container 'community.wave.seqera.io/library/samtools:1.17--h87f3376_0'",
+            [],
+            False,
+        ),
+        # Default registry still passes when additional_registries is populated
+        (
+            "container 'quay.io/biocontainers/samtools:1.17--h87f3376_0'",
+            ["community.wave.seqera.io/library/"],
+            True,
+        ),
+        # Multiple additional registries: second one matches
+        (
+            "container 'ghcr.io/org/tool:1.0--abc123'",
+            ["community.wave.seqera.io/library/", "ghcr.io/"],
+            True,
+        ),
+    ],
+)
+def test_check_process_section_additional_registries(container_line, additional_registries, should_pass, tmp_path):
+    """Test that container_links passes/fails based on additional_registries from .nf-core.yml."""
+    mock_lint = MockModuleLint()
+    mock_lint.process_name = "TOOL_SUBTOOL"
+    mock_lint.component_dir = tmp_path
+
+    with patch("requests.head") as mock_head:
+        mock_head.return_value = MagicMock(status_code=200)
+        check_process_section(
+            mock_lint,
+            [container_line],
+            ("quay.io", *additional_registries),
+            False,
+            None,
+        )
+
+    prefix_passed = any(r[1] == "container_links" and "Container prefix is correct" in r[2] for r in mock_lint.passed)
+    prefix_failed = any(
+        r[1] == "container_links" and "Container prefix is not correct" in r[2] for r in mock_lint.failed
+    )
+
+    if should_pass:
+        assert prefix_passed, f"Expected container prefix to pass; passed={mock_lint.passed}, failed={mock_lint.failed}"
+        assert not prefix_failed, f"Container prefix should not fail; failed={mock_lint.failed}"
+    else:
+        assert prefix_failed, f"Expected container prefix to fail; passed={mock_lint.passed}, failed={mock_lint.failed}"
+        assert not prefix_passed, f"Container prefix should not pass; passed={mock_lint.passed}"
+
+
 class TestMainNfLinting(TestModules):
     """
     Test main.nf linting functionality.
@@ -140,6 +202,68 @@ def test_main_nf_lint_with_alternative_registry(self):
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
 
+    def test_additional_registry_from_nf_core_yml_passes_container_link(self):
+        """Test that a container using a registry listed in .nf-core.yml container-registry passes linting.
+
+        Creates a local module whose container URL uses a custom registry (myreg.io/library/).
+        When that registry is listed under ``container-registry`` in ``.nf-core.yml``, the
+        ``container_links`` check must pass.  Without it, the same container must produce a
+        ``container_links`` warning (local-module failures are demoted to warnings).
+        """
+        local_mod_dir = Path(self.pipeline_dir) / "modules" / "local" / "mock_tool"
+        local_mod_dir.mkdir(parents=True, exist_ok=True)
+        (local_mod_dir / "main.nf").write_text(
+            "process MOCK_TOOL {\n"
+            "    container 'myreg.io/library/tool:1.0--abc123'\n"
+            "    input:\n"
+            "    val(x)\n"
+            "    output:\n"
+            "    path('out.txt'), emit: out\n"
+            "    script:\n"
+            "    'echo hello > out.txt'\n"
+            "}\n"
+        )
+
+        nf_core_yml_path = Path(self.pipeline_dir) / ".nf-core.yml"
+        from ruamel.yaml import YAML
+
+        yaml_parser = YAML()
+        nf_core_yml = yaml_parser.load(nf_core_yml_path)
+
+        # --- positive: registry listed in .nf-core.yml ---
+        nf_core_yml["container-registry"] = ["myreg.io/library/"]
+        yaml_parser.dump(nf_core_yml, nf_core_yml_path)
+
+        with patch("requests.head") as mock_head:
+            mock_head.return_value = MagicMock(status_code=200)
+            module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+            module_lint.lint(local=True, print_results=False)
+
+        container_link_warns = [
+            r for r in module_lint.warned if r.lint_test == "container_links" and "mock_tool" in r.component_name
+        ]
+        assert not any("Container prefix is not correct" in r.message for r in container_link_warns), (
+            f"Expected no container prefix failure for myreg.io when listed in .nf-core.yml; "
+            f"warned={[r.message for r in container_link_warns]}"
+        )
+
+        # --- negative: same container fails when registry is absent ---
+        del nf_core_yml["container-registry"]
+        yaml_parser.dump(nf_core_yml, nf_core_yml_path)
+
+        with patch("requests.head") as mock_head:
+            mock_head.return_value = MagicMock(status_code=200)
+            module_lint2 = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+            module_lint2.lint(local=True, print_results=False)
+
+        container_link_warns2 = [
+            r for r in module_lint2.warned if r.lint_test == "container_links" and "mock_tool" in r.component_name
+        ]
+        assert any("Container prefix is not correct" in r.message for r in container_link_warns2), (
+            f"Expected container prefix failure for myreg.io when not in .nf-core.yml; "
+            f"warned={[r.message for r in container_link_warns2]}"
+        )
+
     def test_topics_and_emits_version_check(self):
         """Test that main_nf version emit and topics check works correctly"""
 
diff --git a/tests/modules/lint/test_patch.py b/tests/modules/lint/test_patch.py
index e42b0b84a6..2c93f70b24 100644
--- a/tests/modules/lint/test_patch.py
+++ b/tests/modules/lint/test_patch.py
@@ -55,6 +55,6 @@ def test_modules_lint_patched_modules(self):
                 all_modules=True,
             )
 
-        assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py
index a77701b8ca..9f1e9bff71 100644
--- a/tests/modules/test_patch.py
+++ b/tests/modules/test_patch.py
@@ -6,6 +6,7 @@
 
 import nf_core.components.components_command
 import nf_core.components.patch
+import nf_core.modules.install
 import nf_core.modules.modules_json
 import nf_core.modules.patch
 import nf_core.modules.update
@@ -20,10 +21,10 @@
 testing if the update commands works correctly with patch files
 """
 
-ORG_SHA = "3dc7c14d29af40f1a0871a675364e437559d97a8"
-CORRECT_SHA = "63e780200600e340365b669f9c673b670764c569"
-SUCCEED_SHA = "0d0515c3f11266e1314e129bec3e308f804c8dc7"
-FAIL_SHA = "cb64a5c1ef85619b89ab99dec2e9097fe84e1dc8"
+ORG_SHA = "262178fbd015cd9be248630eec267f27e6048b03"
+CORRECT_SHA = "262178fbd015cd9be248630eec267f27e6048b03"
+SUCCEED_SHA = "b300b7e53f080a174a717d8e394cca1a82a5ba54"
+FAIL_SHA = "04d59325d44d309fb195f43d8b672674ee73d309"
 BISMARK_ALIGN = "bismark/align"
 REPO_NAME = "nf-core-test"
 PATCH_BRANCH = "patch-tester"
@@ -50,14 +51,16 @@ def modify_main_nf(path):
         lines = fh.readlines()
     # We want a patch file that looks something like:
     # -    tuple val(meta), path(reads)
-    # -    path index
+    # -    tuple val(meta3), path(index)
     # +    tuple val(meta), path(reads), path(index)
+    to_pop = None
     for line_index in range(len(lines)):
         if lines[line_index] == "    tuple val(meta), path(reads)\n":
             lines[line_index] = "    tuple val(meta), path(reads), path(index)\n"
-        elif lines[line_index] == "    path index\n":
+        elif lines[line_index] == "    tuple val(meta3), path(index)\n":
             to_pop = line_index
-    lines.pop(to_pop)
+    if to_pop:
+        lines.pop(to_pop)
     with open(path, "w") as fh:
         fh.writelines(lines)
 
@@ -108,7 +111,7 @@ def test_create_patch_change(self):
         assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf"
         assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
         assert "-    tuple val(meta), path(reads)\n" in patch_lines
-        assert "-    path index\n" in patch_lines
+        assert "-    tuple val(meta3), path(index)\n" in patch_lines
         assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
     def test_create_patch_try_apply_successful(self):
@@ -167,7 +170,7 @@ def test_create_patch_try_apply_successful(self):
         assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
         assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
         assert "-    tuple val(meta), path(reads)\n" in patch_lines
-        assert "-    path index\n" in patch_lines
+        assert "-    tuple val(meta3), path(index)\n" in patch_lines
         assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
         # Check that 'main.nf' is updated correctly
@@ -175,7 +178,7 @@ def test_create_patch_try_apply_successful(self):
             main_nf_lines = fh.readlines()
         # These lines should have been removed by the patch
         assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
-        assert "    path index\n" not in main_nf_lines
+        assert "    tuple val(meta3), path(index)\n" not in main_nf_lines
         # This line should have been added
         assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
 
@@ -268,7 +271,7 @@ def test_create_patch_update_success(self):
         assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
         assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
         assert "-    tuple val(meta), path(reads)\n" in patch_lines
-        assert "-    path index\n" in patch_lines
+        assert "-    tuple val(meta3), path(index)\n" in patch_lines
         assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
         # Check that 'main.nf' is updated correctly
@@ -276,7 +279,7 @@ def test_create_patch_update_success(self):
             main_nf_lines = fh.readlines()
         # These lines should have been removed by the patch
         assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
-        assert "    path index\n" not in main_nf_lines
+        assert "    tuple val(meta3), path(index)\n" not in main_nf_lines
         # This line should have been added
         assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
 
@@ -323,8 +326,8 @@ def test_create_patch_update_fail(self):
         ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir)
 
         temp_module_dir = temp_dir / BISMARK_ALIGN
-        temp_files = {f.name for f in temp_module_dir.iterdir()}
-        module_files = {f.name for f in module_path.iterdir()}
+        temp_files = {f.name for f in temp_module_dir.iterdir() if f.is_file()}
+        module_files = {f.name for f in module_path.iterdir() if f.is_file()}
         for file_name in temp_files:
             assert file_name in module_files
             with open(module_path / file_name) as fh:
diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py
index e888a1d6a1..a2c1babd6a 100644
--- a/tests/pipelines/lint/test_nfcore_yml.py
+++ b/tests/pipelines/lint/test_nfcore_yml.py
@@ -48,6 +48,15 @@ def test_nfcore_yml_fail_nfcore_version(self):
         assert len(results.get("passed", [])) >= 0
         assert len(results.get("ignored", [])) == 0
 
+    def test_nfcore_yml_container_registry_accepted(self):
+        """Lint test: nfcore_yml - PASS - container-registry field is accepted without errors"""
+        self.nf_core_yml["container-registry"] = ["community.wave.seqera.io/library/", "ghcr.io/"]
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
+
+        assert self.lint_obj._load()
+        results = self.lint_obj.nfcore_yml()
+        assert len(results.get("failed", [])) == 0
+
     def test_nfcore_yml_nested_lint_config(self) -> None:
         """Lint test: nfcore_yml with nested lint config - PASS"""
         valid_yaml = """