diff --git a/package-lock.json b/package-lock.json
index 9f60fc6ba9..7fb20a8c9f 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -16401,7 +16401,6 @@
             "integrity": "sha512-kgW13M54DUB7IsIRM5LvJkNlpH+WhMpooUcaWGFARkF1Tc82v9mIWkCbCYf+MBvpIUBSeSOTilpZjEPr2VYE6Q==",
             "license": "MIT",
             "optional": true,
-            "peer": true,
             "dependencies": {
                 "chokidar": "^4.0.0",
                 "immutable": "^5.1.5",
@@ -16471,7 +16470,6 @@
             ],
             "license": "MIT",
             "optional": true,
-            "peer": true,
             "dependencies": {
                 "sass": "1.99.0"
             }
@@ -16488,7 +16486,6 @@
             "os": [
                 "android"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16505,7 +16502,6 @@
             "os": [
                 "android"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16522,7 +16518,6 @@
             "os": [
                 "android"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16539,7 +16534,6 @@
             "os": [
                 "android"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16556,7 +16550,6 @@
             "os": [
                 "darwin"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16573,7 +16566,6 @@
             "os": [
                 "darwin"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16590,7 +16582,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16607,7 +16598,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16624,7 +16614,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16641,7 +16630,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16658,7 +16646,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16675,7 +16662,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16692,7 +16678,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16709,7 +16694,6 @@
             "os": [
                 "linux"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16726,7 +16710,6 @@
                 "!linux",
                 "!win32"
             ],
-            "peer": true,
             "dependencies": {
                 "sass": "1.99.0"
             }
@@ -16743,7 +16726,6 @@
             "os": [
                 "win32"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
@@ -16760,7 +16742,6 @@
             "os": [
                 "win32"
             ],
-            "peer": true,
             "engines": {
                 "node": ">=14.0.0"
             }
diff --git a/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md b/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md
new file mode 100644
index 0000000000..434c4f1766
--- /dev/null
+++ b/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md
@@ -0,0 +1,333 @@
+# .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: "4.0.2"
+```
+
+Modules repository:
+
+```yaml
+repository_type: modules
+nf_core_version: "4.0.2"
+container-registry:
+  - community.wave.seqera.io/library/
+```
+
+## Schema
+
+### `Top-level{:python}``.nf-core.yml``schema ({:python}``NFCoreYamlConfig``){:python}`
+
+### _`pydantic model{:python}`_`nf_core.utils.NFCoreYamlConfig{:python}`
+
+Bases: `BaseModel`
+
+.nf-core.yml configuration file schema
+
+- **Fields:**
+  - [`bump_version (dict[str, bool] | None)`](utils#nf_core.utils.NFCoreYamlConfig.bump_version)
+  - [`container_registry (list[str] | None)`](utils#nf_core.utils.NFCoreYamlConfig.container_registry)
+  - [`lint (nf_core.utils.NFCoreYamlLintConfig | None)`](utils#nf_core.utils.NFCoreYamlConfig.lint)
+  - [`nf_core_version (str | None)`](utils#nf_core.utils.NFCoreYamlConfig.nf_core_version)
+  - [`org_path (str | None)`](utils#nf_core.utils.NFCoreYamlConfig.org_path)
+  - [`repository_type (Literal['pipeline', 'modules'] | None)`](utils#nf_core.utils.NFCoreYamlConfig.repository_type)
+  - [`template (nf_core.utils.NFCoreTemplateConfig | None)`](utils#nf_core.utils.NFCoreYamlConfig.template)
+  - [`update (dict[str, str | bool | dict[str, str | dict[str, str | bool]]] | None)`](utils#nf_core.utils.NFCoreYamlConfig.update)
+
+#### _`field{:python}`_`bump_version{:python}`_: dict\[str, bool] | None_`{:python}`_= None_
+
+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.
+
+#### _`field{:python}`_`container_registry{:python}`_: list\[str] | None_`{:python}`_= None_`{:python}`_(alias 'container-registry')_
+
+Additional container registry prefixes allowed when linting container directives.
+
+#### _`field{:python}`_`lint{:python}`_: [NFCoreYamlLintConfig](utils#nf_core.utils.NFCoreYamlLintConfig) | None_`{:python}`_= None_
+
+Pipeline linting configuration, see <https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config> for examples and documentation
+
+#### _`field{:python}`_`nf_core_version{:python}`_: str | None_`{:python}`_= None_
+
+Version of nf-core/tools used to create/update the pipeline
+
+#### _`field{:python}`_`org_path{:python}`_: str | None_`{:python}`_= None_
+
+Path to the organisation’s modules repository (used for modules repo_type only)
+
+#### _`field{:python}`_`repository_type{:python}`_: Literal\['pipeline', 'modules'] | None_`{:python}`_= None_
+
+Type of repository
+
+#### _`field{:python}`_`template{:python}`_: [NFCoreTemplateConfig](utils#nf_core.utils.NFCoreTemplateConfig) | None_`{:python}`_= None_
+
+Pipeline template configuration
+
+#### _`field{:python}`_`update{:python}`_: dict\[str, str | bool | dict\[str, str | dict\[str, str | bool]]] | None_`{:python}`_= 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.
+
+### `lint``block ({:python}``NFCoreYamlLintConfig``){:python}`
+
+### _`pydantic model{:python}`_`nf_core.utils.NFCoreYamlLintConfig{:python}`
+
+Bases: `BaseModel`
+
+schema for linting config in .nf-core.yml should cover:
+
+```yaml
+files_unchanged:
+    - .github/workflows/branch.yml
+modules_config: False
+modules_config:
+        - fastqc
+# merge_markers: False
+merge_markers:
+        - docs/my_pdf.pdf
+nextflow_config: False
+nextflow_config:
+    - manifest.name
+    - config_defaults:
+        - params.annotation_db
+        - params.multiqc_comment_headers
+        - params.custom_table_headers
+# multiqc_config: False
+multiqc_config:
+    - report_section_order
+    - report_comment
+files_exist:
+    - CITATIONS.md
+template_strings: False
+template_strings:
+        - docs/my_pdf.pdf
+nfcore_components: False
+# nf_test_content: False
+nf_test_content:
+    - tests/<test_name>.nf.test
+    - tests/nextflow.config
+    - nf-test.config
+```
+
+- **Fields:**
+  - [`actions_awsfulltest (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.actions_awsfulltest)
+  - [`actions_awstest (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.actions_awstest)
+  - [`actions_nf_test (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.actions_nf_test)
+  - [`actions_schema_validation (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.actions_schema_validation)
+  - [`base_config (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.base_config)
+  - [`container_configs (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.container_configs)
+  - [`files_exist (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.files_exist)
+  - [`files_unchanged (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.files_unchanged)
+  - [`included_configs (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.included_configs)
+  - [`local_component_structure (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.local_component_structure)
+  - [`merge_markers (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.merge_markers)
+  - [`modules_config (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.modules_config)
+  - [`modules_json (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.modules_json)
+  - [`modules_structure (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.modules_structure)
+  - [`multiqc_config (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.multiqc_config)
+  - [`nextflow_config (bool | list[str | dict[str, list[str]]] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.nextflow_config)
+  - [`nf_test_content (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.nf_test_content)
+  - [`nfcore_components (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.nfcore_components)
+  - [`nfcore_yml (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.nfcore_yml)
+  - [`pipeline_if_empty_null (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.pipeline_if_empty_null)
+  - [`pipeline_name_conventions (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.pipeline_name_conventions)
+  - [`pipeline_todos (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.pipeline_todos)
+  - [`plugin_includes (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.plugin_includes)
+  - [`readme (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.readme)
+  - [`rocrate_readme_sync (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.rocrate_readme_sync)
+  - [`schema_description (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.schema_description)
+  - [`schema_lint (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.schema_lint)
+  - [`schema_params (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.schema_params)
+  - [`system_exit (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.system_exit)
+  - [`template_strings (bool | list[str] | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.template_strings)
+  - [`version_consistency (bool | None)`](utils#nf_core.utils.NFCoreYamlLintConfig.version_consistency)
+
+#### _`field{:python}`_`actions_awsfulltest{:python}`_: bool | None_`{:python}`_= None_
+
+Lint all required files to run full tests on AWS
+
+#### _`field{:python}`_`actions_awstest{:python}`_: bool | None_`{:python}`_= None_
+
+Lint all required files to run tests on AWS
+
+#### _`field{:python}`_`actions_nf_test{:python}`_: bool | None_`{:python}`_= None_
+
+Lint all required files to use GitHub Actions CI
+
+#### _`field{:python}`_`actions_schema_validation{:python}`_: bool | None_`{:python}`_= None_
+
+Lint GitHub Action workflow files with schema
+
+#### _`field{:python}`_`base_config{:python}`_: bool | None_`{:python}`_= None_
+
+Lint base.config file
+
+#### _`field{:python}`_`container_configs{:python}`_: bool | None_`{:python}`_= None_
+
+Lint that container configuration files in conf/ are up to date
+
+#### _`field{:python}`_`files_exist{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of files that can not exist
+
+#### _`field{:python}`_`files_unchanged{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of files that should not be changed
+
+#### _`field{:python}`_`included_configs{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for included configs
+
+#### _`field{:python}`_`local_component_structure{:python}`_: bool | None_`{:python}`_= None_
+
+Lint local components use correct structure mirroring remote
+
+#### _`field{:python}`_`merge_markers{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of files that should not contain merge markers
+
+#### _`field{:python}`_`modules_config{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of modules that should not be changed
+
+#### _`field{:python}`_`modules_json{:python}`_: bool | None_`{:python}`_= None_
+
+Lint modules.json file
+
+#### _`field{:python}`_`modules_structure{:python}`_: bool | None_`{:python}`_= None_
+
+Lint modules structure
+
+#### _`field{:python}`_`multiqc_config{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of MultiQC config options that be changed
+
+#### _`field{:python}`_`nextflow_config{:python}`_: bool | list\[str | dict\[str, list\[str]]] | None_`{:python}`_= None_
+
+List of Nextflow config files that should not be changed
+
+#### _`field{:python}`_`nf_test_content{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of nf-test content that should not be changed
+
+#### _`field{:python}`_`nfcore_components{:python}`_: bool | None_`{:python}`_= None_
+
+Lint all required files to use nf-core modules and subworkflows
+
+#### _`field{:python}`_`nfcore_yml{:python}`_: bool | None_`{:python}`_= None_
+
+Lint nf-core.yml
+
+#### _`field{:python}`_`pipeline_if_empty_null{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for ifEmpty(null) statements
+
+#### _`field{:python}`_`pipeline_name_conventions{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for pipeline name conventions
+
+#### _`field{:python}`_`pipeline_todos{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for TODOs statements
+
+#### _`field{:python}`_`plugin_includes{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for nextflow plugin
+
+#### _`field{:python}`_`readme{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+Lint the README.md file
+
+#### _`field{:python}`_`rocrate_readme_sync{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for README.md and rocrate.json sync
+
+#### _`field{:python}`_`schema_description{:python}`_: bool | None_`{:python}`_= None_
+
+Check that every parameter in the schema has a description.
+
+#### _`field{:python}`_`schema_lint{:python}`_: bool | None_`{:python}`_= None_
+
+Lint nextflow_schema.json file
+
+#### _`field{:python}`_`schema_params{:python}`_: bool | None_`{:python}`_= None_
+
+Lint schema for all params
+
+#### _`field{:python}`_`system_exit{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for System.exit calls in groovy/nextflow code
+
+#### _`field{:python}`_`template_strings{:python}`_: bool | list\[str] | None_`{:python}`_= None_
+
+List of files that can contain template strings
+
+#### _`field{:python}`_`version_consistency{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for version consistency
+
+### `template``block ({:python}``NFCoreTemplateConfig``){:python}`
+
+### _`pydantic model{:python}`_`nf_core.utils.NFCoreTemplateConfig{:python}`
+
+Bases: `BaseModel`
+
+Template configuration schema
+
+- **Fields:**
+  - [`author (str | None)`](utils#nf_core.utils.NFCoreTemplateConfig.author)
+  - [`description (str | None)`](utils#nf_core.utils.NFCoreTemplateConfig.description)
+  - [`force (bool | None)`](utils#nf_core.utils.NFCoreTemplateConfig.force)
+  - [`is_nfcore (bool | None)`](utils#nf_core.utils.NFCoreTemplateConfig.is_nfcore)
+  - [`name (str | None)`](utils#nf_core.utils.NFCoreTemplateConfig.name)
+  - [`org (str | None)`](utils#nf_core.utils.NFCoreTemplateConfig.org)
+  - [`outdir (str | pathlib.Path | None)`](utils#nf_core.utils.NFCoreTemplateConfig.outdir)
+  - [`skip_features (list | None)`](utils#nf_core.utils.NFCoreTemplateConfig.skip_features)
+  - [`version (str | None)`](utils#nf_core.utils.NFCoreTemplateConfig.version)
+- **Validators:**
+  - [`outdir_to_str`](utils#nf_core.utils.NFCoreTemplateConfig.outdir_to_str) » [`outdir`](utils#nf_core.utils.NFCoreTemplateConfig.outdir)
+
+#### _`field{:python}`_`author{:python}`_: str | None_`{:python}`_= None_
+
+Pipeline author
+
+#### _`field{:python}`_`description{:python}`_: str | None_`{:python}`_= None_
+
+Pipeline description
+
+#### _`field{:python}`_`force{:python}`_: bool | None_`{:python}`_= True_
+
+Force overwrite of existing files
+
+#### _`field{:python}`_`is_nfcore{:python}`_: bool | None_`{:python}`_= None_
+
+Whether the pipeline is an nf-core pipeline.
+
+#### _`field{:python}`_`name{:python}`_: str | None_`{:python}`_= None_
+
+Pipeline name
+
+#### _`field{:python}`_`org{:python}`_: str | None_`{:python}`_= None_
+
+Organisation name
+
+#### _`field{:python}`_`outdir{:python}`_: str | Path | None_`{:python}`_= None_
+
+Output directory
+
+- **Validated by:**
+  - [`outdir_to_str`](utils#nf_core.utils.NFCoreTemplateConfig.outdir_to_str)
+
+#### _`field{:python}`_`skip_features{:python}`_: list | None_`{:python}`_= None_
+
+Skip features. See <https://nf-co.re/docs/nf-core-tools/pipelines/create> for a list of features.
+
+#### _`field{:python}`_`version{:python}`_: str | None_`{:python}`_= None_
+
+Pipeline version
diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/index.md b/sites/docs/src/content/api_reference/dev/api/pipelines/index.md
index 207189bbcc..3cfe514e5b 100644
--- a/sites/docs/src/content/api_reference/dev/api/pipelines/index.md
+++ b/sites/docs/src/content/api_reference/dev/api/pipelines/index.md
@@ -5,8 +5,8 @@
 - [nf_core.pipelines.download](download)
 - [nf_core.pipelines.launch](launch)
 - [nf_core.pipelines.lint](lint)
+- [nf_core.pipelines.utils](lint_utils)
 - [nf_core.pipelines.list](list)
 - [nf_core.pipelines.params_file](params-file)
 - [nf_core.pipelines.schema](schema)
 - [nf_core.pipelines.sync](sync)
-- [nf_core.pipelines.utils](utils)
diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md b/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md
index 8010b15897..2324698dbc 100644
--- a/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md
+++ b/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md
@@ -11,18 +11,125 @@ Linting policy for nf-core pipeline projects.
 Tests Nextflow-based pipelines to check that they adhere to
 the nf-core community guidelines.
 
-### `nf_core.pipelines.lint.run_linting(pipeline_dir, release_mode: bool = False, fix=(), key=(), show_passed: bool = False, fail_ignored: bool = False, fail_warned: bool = False, sort_by: str = 'test', md_fn=None, json_fn=None, hide_progress: bool = False, plain_text: bool = False) → tuple[PipelineLint, ComponentLint | None, ComponentLint | None]{:python}`
+### `nf_core.pipelines.lint.run_linting(pipeline_dir, release_mode: bool = False, fix=(), key=(), show_passed: bool = False, fail_ignored: bool = False, fail_warned: bool = False, sort_by: str = 'test', md_fn=None, json_fn=None, hide_progress: bool = False, plain_text: bool = False) → tuple[{:python}`[`PipelineLint{:python}`](#nf_core.pipelines.lint.PipelineLint)`, ComponentLint | None, ComponentLint | None]{:python}`
 
 Runs all nf-core linting checks on a given Nextflow pipeline project
 in either release mode or normal mode (default). Returns an object
-of type `PipelineLint` after finished.
+of type [`PipelineLint`](#nf_core.pipelines.lint.PipelineLint) after finished.
 
 - **Parameters:**
   - **pipeline_dir** (_str_) – The path to the Nextflow pipeline root directory
   - **release_mode** (_bool_) – Set this to True, if the linting should be run in the release mode.
-    See `PipelineLint` for more information.
+    See [`PipelineLint`](#nf_core.pipelines.lint.PipelineLint) for more information.
   - **plain_text** (_bool_) – Print output in plain text without rich formatting
 - **Returns:**
-  An object of type `PipelineLint` that contains all the linting results.
+  An object of type [`PipelineLint`](#nf_core.pipelines.lint.PipelineLint) that contains all the linting results.
   An object of type `ComponentLint` that contains all the linting results for the modules.
   An object of type `ComponentLint` that contains all the linting results for the subworkflows.
+
+### _`class{:python}`_`nf_core.pipelines.lint.PipelineLint(wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False){:python}`
+
+Bases: [`Pipeline`](../utils#nf_core.utils.Pipeline)
+
+Object to hold linting information and results.
+
+Inherits [`nf_core.utils.Pipeline`](../utils#nf_core.utils.Pipeline) class.
+
+Use the [`PipelineLint._lint_pipeline()`](#nf_core.pipelines.lint.PipelineLint._lint_pipeline) function to run lint tests.
+
+- **Parameters:**
+  **path** (_str_) – The path to the nf-core pipeline directory.
+
+#### `failed{:python}`
+
+A list of tuples of the form: `(<test-name>, <reason>)`
+
+- **Type:**
+  list
+
+#### `ignored{:python}`
+
+A list of tuples of the form: `(<test-name>, <reason>)`
+
+- **Type:**
+  list
+
+#### `lint_config{:python}`
+
+The parsed nf-core linting config for this pipeline
+
+- **Type:**
+  dict
+
+#### `passed{:python}`
+
+A list of tuples of the form: `(<test-name>, <reason>)`
+
+- **Type:**
+  list
+
+#### `release_mode{:python}`
+
+True, if you the to linting was run in release mode, False else.
+
+- **Type:**
+  bool
+
+#### `warned{:python}`
+
+A list of tuples of the form: `(<warned no>, <reason>)`
+
+- **Type:**
+  list
+
+#### `_get_results_md(){:python}`
+
+Create a markdown file suitable for posting in a GitHub comment.
+
+- **Returns:**
+  Formatting markdown content
+- **Return type:**
+  markdown (str)
+
+#### `_lint_pipeline() → None{:python}`
+
+Main linting function.
+
+Takes the pipeline directory as the primary input and iterates through
+the different linting checks in order. Collects any warnings or errors
+into object attributes: `passed`, `ignored`, `warned` and `failed`.
+
+#### `_print_results(show_passed, plain_text=False){:python}`
+
+Print linting results to the command line.
+
+Uses the `rich` library to print a set of formatted tables to the command line
+summarising the linting results.
+
+#### `_save_json_results(json_fn){:python}`
+
+Function to dump lint results to a JSON file for downstream use
+
+- **Parameters:**
+  **json_fn** (_str_) – File path to write JSON to.
+
+#### `_wrap_quotes(files: list[str] | list[Path] | Path) → str{:python}`
+
+Helper function to take a list of filenames and format with markdown.
+
+- **Parameters:**
+  **files** (_list_) –
+
+  List of filenames, eg:
+
+  ```default
+  ['foo', 'bar', 'baz']
+  ```
+
+- **Returns:**
+  Formatted string of paths separated by word `or`, eg:
+  ```default
+  `foo` or bar` or `baz`
+  ```
+- **Return type:**
+  markdown (str)
diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md b/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md
new file mode 100644
index 0000000000..ba916db529
--- /dev/null
+++ b/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md
@@ -0,0 +1,60 @@
+# nf_core.pipelines.utils
+
+### `nf_core.pipelines.lint_utils.check_git_repo() → bool{:python}`
+
+Check if the current directory is a git repository.
+
+### `nf_core.pipelines.lint_utils.dump_json_with_prettier(file_name, file_content){:python}`
+
+Dump a JSON file and run prettier on it.
+:param file_name: A file identifier as a string or pathlib.Path.
+:type file_name: Path | str
+:param file_content: Content to dump into the JSON file
+:type file_content: dict
+
+### `nf_core.pipelines.lint_utils.dump_yaml_with_prettier(file_name: Path | str, file_content: dict) → None{:python}`
+
+Dump a YAML file and run prettier on it.
+
+- **Parameters:**
+  - **file_name** (_Path_ _|_ _str_) – A file identifier as a string or pathlib.Path.
+  - **file_content** (_dict_) – Content to dump into the YAML file
+
+### `nf_core.pipelines.lint_utils.ignore_file(lint_name: str, file_path: Path, dir_path: Path) → list[list[str]]{:python}`
+
+Ignore a file and add the result to the ignored list. Return the passed, failed, ignored and ignore_configs lists.
+
+### `nf_core.pipelines.lint_utils.print_fixes(lint_obj, plain_text=False){:python}`
+
+Prints available and applied fixes
+
+### `nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj, plain_text=False){:python}`
+
+Print a joint summary of the general pipe lint tests and the module and subworkflow lint tests
+
+### `nf_core.pipelines.lint_utils.print_results_plain_text(results_list, directory=None, component_type=None){:python}`
+
+Print lint results in plain text format.
+
+- **Parameters:**
+  - **results_list** – List of tuples (results, symbol, label, color, show_condition)
+  - **directory** – Base directory for relative paths (for component linting)
+  - **component_type** – “modules” or “subworkflows” (for component linting)
+
+### `nf_core.pipelines.lint_utils.print_summary(rows, plain_text=False, summary_colour=None){:python}`
+
+Print a summary table in plain text or rich format.
+
+- **Parameters:**
+  - **rows** – List of tuples (count, icon, label, color, always_show)
+  - **plain_text** – If True, print in plain text format
+  - **summary_colour** – Color for the rich table border (default: auto based on failures)
+
+### `nf_core.pipelines.lint_utils.run_prettier_on_file(file: Path | str | list[str]) → None{:python}`
+
+Run the pre-commit hook prettier on a file.
+
+- **Parameters:**
+  **file** (_Path_ _|_ _str_) – A file identifier as a string or pathlib.Path.
+- **Warns:**
+  **If Prettier is not installed, a warning is logged.**
diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/utils.md b/sites/docs/src/content/api_reference/dev/api/pipelines/utils.md
deleted file mode 100644
index 8ae937bff0..0000000000
--- a/sites/docs/src/content/api_reference/dev/api/pipelines/utils.md
+++ /dev/null
@@ -1 +0,0 @@
-# nf_core.pipelines.utils
diff --git a/sites/docs/src/content/api_reference/dev/api/utils.md b/sites/docs/src/content/api_reference/dev/api/utils.md
index 351a648399..541a61485c 100644
--- a/sites/docs/src/content/api_reference/dev/api/utils.md
+++ b/sites/docs/src/content/api_reference/dev/api/utils.md
@@ -65,7 +65,7 @@ Force overwrite of existing files
 
 Whether the pipeline is an nf-core pipeline.
 
-#### `model_config{:python}`_= {}_
+#### `model_config{:python}`_: ClassVar\[ConfigDict]_ _= {}_
 
 Configuration for the model, should be a dictionary conforming to \[ConfigDict]\[pydantic.config.ConfigDict].
 
@@ -94,7 +94,7 @@ Output directory
 
 Pipeline version
 
-### _`class{:python}`_`nf_core.utils.NFCoreYamlConfig(, repository_type: Literal['pipeline', 'modules'] | None = None, nf_core_version: str | None = None, org_path: str | None = None, lint:{:python}`[`NFCoreYamlLintConfig{:python}`](#nf_core.utils.NFCoreYamlLintConfig)`| None = None, template:{:python}`[`NFCoreTemplateConfig{:python}`](#nf_core.utils.NFCoreTemplateConfig)`| None = None, bump_version: dict[str, bool] | None = None, update: dict[str, str | bool | dict[str, str | dict[str, str | bool]]] | None = None){:python}`
+### _`class{:python}`_`nf_core.utils.NFCoreYamlConfig(, repository_type: Literal['pipeline', 'modules'] | None = None, nf_core_version: str | None = None, org_path: str | None = None, lint:{:python}`[`NFCoreYamlLintConfig{:python}`](#nf_core.utils.NFCoreYamlLintConfig)`| None = None, template:{:python}`[`NFCoreTemplateConfig{:python}`](#nf_core.utils.NFCoreTemplateConfig)`| None = None, bump_version: dict[str, bool] | None = None, update: dict[str, str | bool | dict[str, str | dict[str, str | bool]]] | None = None, container_registry: list[str] | None = None){:python}`
 
 Bases: `BaseModel`
 
@@ -109,6 +109,10 @@ Bases: `BaseModel`
 - **Type:**
   Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https
 
+#### `container_registry{:python}`_: list\[str] | None_
+
+Additional container registry prefixes allowed when linting container directives.
+
 #### `get(item: str, default: Any = None) → Any{:python}`
 
 #### `lint{:python}`_: [NFCoreYamlLintConfig](#nf_core.utils.NFCoreYamlLintConfig) | None_
@@ -118,7 +122,7 @@ Bases: `BaseModel`
 - **Type:**
   Pipeline linting configuration, see https
 
-#### `model_config{:python}`_= {}_
+#### `model_config{:python}`_: ClassVar\[ConfigDict]_ _= {'populate_by_name': True, 'validate_by_alias': True, 'validate_by_name': True}_
 
 Configuration for the model, should be a dictionary conforming to \[ConfigDict]\[pydantic.config.ConfigDict].
 
@@ -263,7 +267,7 @@ Lint local components use correct structure mirroring remote
 
 List of files that should not contain merge markers
 
-#### `model_config{:python}`_= {}_
+#### `model_config{:python}`_: ClassVar\[ConfigDict]_ _= {}_
 
 Configuration for the model, should be a dictionary conforming to \[ConfigDict]\[pydantic.config.ConfigDict].
 
diff --git a/sites/docs/src/content/api_reference/dev/index.md b/sites/docs/src/content/api_reference/dev/index.md
index 7f45b97c14..5b8f9e5fd2 100644
--- a/sites/docs/src/content/api_reference/dev/index.md
+++ b/sites/docs/src/content/api_reference/dev/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) (run by `nf-core modules lint`)
 - [Subworkflow code lint tests](subworkflow_lint_tests/main_nf) (run by `nf-core subworkflows lint`)
 - [nf-core/tools Python package API reference](api/utils)
+- [`.nf-core.yml` configuration reference](api/nf_core_yml)
diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md
index dbaaefaf80..75f17125f2 100644
--- a/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md
+++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md
@@ -1,6 +1,6 @@
 # main_nf
 
-#### `ModuleLint.main_nf(module: NFCoreComponent, fix_version: bool, registry: str, progress_bar: Progress) → tuple[list[str], list[str]]{:python}`
+#### `ModuleLint.main_nf(module: NFCoreComponent, fix_version: bool, registry: tuple[str, ...], progress_bar: Progress) → tuple[list[str], list[str]]{:python}`
 
 Lint a `main.nf` module file
 
diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md
deleted file mode 100644
index f6efdf6b91..0000000000
--- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md
+++ /dev/null
@@ -1,36 +0,0 @@
-# actions_ci
-
-#### `PipelineLint.actions_ci(){:python}`
-
-Checks that the GitHub Actions pipeline CI (Continuous Integration) workflow is valid.
-
-The `.github/workflows/ci.yml` GitHub Actions workflow runs the pipeline on a minimal test
-dataset using `-profile test` to check that no breaking changes have been introduced.
-Final result files are not checked, just that the pipeline exists successfully.
-
-This lint test checks this GitHub Actions workflow file for the following:
-
-- Workflow must be triggered on the following events:
-  ```yaml
-  on:
-    push:
-    branches:
-      - dev
-    pull_request:
-    release:
-    types: [published]
-  ```
-- The minimum Nextflow version specified in the pipeline’s `nextflow.config` matches that defined by `NXF_VER` in the test matrix:
-
-  ```yaml
-  strategy:
-    matrix:
-      # Nextflow versions: check pipeline minimum and current latest
-      NXF_VER: ["19.10.0", ""]
-  ```
-
-  :::note
-  These `matrix` variables run the test workflow twice, varying the `NXF_VER` variable each time.
-  This is used in the `nextflow run` commands to test the pipeline with both the latest available version
-  of the pipeline (`''`) and the stated minimum required version.
-  :::
diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md
index 5c740ae4e1..cc89afd887 100644
--- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md
+++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md
@@ -6,7 +6,7 @@ Repository `.nf-core.yml` tests
 
 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.