parse container registries from .nf-core.yml

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
+```

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)

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",

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,

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,

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):

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
         """

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(
                                 (

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.
 

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
 

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)