diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5b8483b01..b581f5c46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,8 @@
 
 ### Linting
 
+- allow mixed str and dict in lint config ([#3228](https://github.com/nf-core/tools/pull/3228))
+
 ### Modules
 
 ### Subworkflows
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index fcc3b414d..69740135a 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -22,7 +22,7 @@
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.pipelines.lint_utils import console
-from nf_core.utils import LintConfigType
+from nf_core.utils import NFCoreYamlLintConfig
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
@@ -80,7 +80,7 @@ def __init__(
         self.failed: List[LintResult] = []
         self.all_local_components: List[NFCoreComponent] = []
 
-        self.lint_config: Optional[LintConfigType] = None
+        self.lint_config: Optional[NFCoreYamlLintConfig] = None
         self.modules_json: Optional[ModulesJson] = None
 
         if self.component_type == "modules":
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 8ab547c1c..776fc8943 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -8,7 +8,7 @@
 import re
 import shutil
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union, cast
+from typing import Dict, List, Optional, Tuple, Union
 
 import git
 import git.config
@@ -21,7 +21,7 @@
 from nf_core.pipelines.create.utils import CreateConfig, features_yml_path, load_features_yaml
 from nf_core.pipelines.create_logo import create_logo
 from nf_core.pipelines.lint_utils import run_prettier_on_file
-from nf_core.utils import LintConfigType, NFCoreTemplateConfig
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig
 
 log = logging.getLogger(__name__)
 
@@ -67,7 +67,7 @@ def __init__(
                 _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else Path().cwd())
                 # Obtain a CreateConfig object from `.nf-core.yml` config file
                 if config_yml is not None and getattr(config_yml, "template", None) is not None:
-                    self.config = CreateConfig(**config_yml["template"].model_dump())
+                    self.config = CreateConfig(**config_yml["template"].model_dump(exclude_none=True))
                 else:
                     raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
                 # Update the output directory
@@ -205,7 +205,7 @@ def obtain_jinja_params_dict(
             config_yml = None
 
         # Set the parameters for the jinja template
-        jinja_params = self.config.model_dump()
+        jinja_params = self.config.model_dump(exclude_none=True)
 
         # Add template areas to jinja params and create list of areas with paths to skip
         skip_areas = []
@@ -363,8 +363,8 @@ def render_template(self) -> None:
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
             if config_fn is not None and config_yml is not None:
                 with open(str(config_fn), "w") as fh:
-                    config_yml.template = NFCoreTemplateConfig(**self.config.model_dump())
-                    yaml.safe_dump(config_yml.model_dump(), fh)
+                    config_yml.template = NFCoreTemplateConfig(**self.config.model_dump(exclude_none=True))
+                    yaml.safe_dump(config_yml.model_dump(exclude_none=True), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
         # Run prettier on files
@@ -395,9 +395,9 @@ def fix_linting(self):
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         if config_fn is not None and nf_core_yml is not None:
-            nf_core_yml.lint = cast(LintConfigType, lint_config)
+            nf_core_yml.lint = NFCoreYamlLintConfig(**lint_config)
             with open(self.outdir / config_fn, "w") as fh:
-                yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False)
+                yaml.dump(nf_core_yml.model_dump(exclude_none=True), fh, default_flow_style=False, sort_keys=False)
 
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 8cc7c37cb..f24374384 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -27,8 +27,8 @@
 from nf_core import __version__
 from nf_core.components.lint import ComponentLint
 from nf_core.pipelines.lint_utils import console
+from nf_core.utils import NFCoreYamlConfig, NFCoreYamlLintConfig, strip_ansi_codes
 from nf_core.utils import plural_s as _s
-from nf_core.utils import strip_ansi_codes
 
 from .actions_awsfulltest import actions_awsfulltest
 from .actions_awstest import actions_awstest
@@ -112,7 +112,7 @@ def __init__(
         # Initialise the parent object
         super().__init__(wf_path)
 
-        self.lint_config = {}
+        self.lint_config: Optional[NFCoreYamlLintConfig] = None
         self.release_mode = release_mode
         self.fail_ignored = fail_ignored
         self.fail_warned = fail_warned
@@ -173,13 +173,12 @@ def _load_lint_config(self) -> bool:
         Add parsed config to the `self.lint_config` class attribute.
         """
         _, tools_config = nf_core.utils.load_tools_config(self.wf_path)
-        self.lint_config = getattr(tools_config, "lint", {}) or {}
+        self.lint_config = getattr(tools_config, "lint", None) or None
         is_correct = True
-
         # Check if we have any keys that don't match lint test names
         if self.lint_config is not None:
-            for k in self.lint_config:
-                if k != "nfcore_components" and k not in self.lint_tests:
+            for k, v in self.lint_config:
+                if v is not None and k != "nfcore_components" and k not in self.lint_tests:
                     # nfcore_components is an exception to allow custom pipelines without nf-core components
                     log.warning(f"Found unrecognised test name '{k}' in pipeline lint config")
                     is_correct = False
@@ -594,7 +593,7 @@ def run_linting(
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
 
-    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config["nfcore_components"]:
+    if lint_obj.lint_config and lint_obj.lint_config["nfcore_components"] is False:
         module_lint_obj = None
         subworkflow_lint_obj = None
     else:
@@ -679,5 +678,4 @@ def run_linting(
     if len(lint_obj.failed) > 0:
         if release_mode:
             log.info("Reminder: Lint tests were run in --release mode.")
-
     return lint_obj, module_lint_obj, subworkflow_lint_obj
diff --git a/nf_core/pipelines/lint/multiqc_config.py b/nf_core/pipelines/lint/multiqc_config.py
index 2b0fc7902..fec5b518e 100644
--- a/nf_core/pipelines/lint/multiqc_config.py
+++ b/nf_core/pipelines/lint/multiqc_config.py
@@ -31,6 +31,15 @@ def multiqc_config(self) -> Dict[str, List[str]]:
             lint:
                 multiqc_config: False
 
+        To disable this test only for specific sections, you can specify a list of section names.
+        For example:
+
+        .. code-block:: yaml
+        lint:
+                multiqc_config:
+                    - report_section_order
+                    - report_comment
+
     """
 
     passed: List[str] = []
diff --git a/nf_core/pipelines/lint/nfcore_yml.py b/nf_core/pipelines/lint/nfcore_yml.py
index e0d5fb200..3395696d1 100644
--- a/nf_core/pipelines/lint/nfcore_yml.py
+++ b/nf_core/pipelines/lint/nfcore_yml.py
@@ -1,7 +1,8 @@
-import re
 from pathlib import Path
 from typing import Dict, List
 
+from ruamel.yaml import YAML
+
 from nf_core import __version__
 
 REPOSITORY_TYPES = ["pipeline", "modules"]
@@ -26,21 +27,23 @@ def nfcore_yml(self) -> Dict[str, List[str]]:
     failed: List[str] = []
     ignored: List[str] = []
 
+    yaml = YAML()
+
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get(".nf-core", []) if self.lint_config is not None else []
-    try:
-        with open(Path(self.wf_path, ".nf-core.yml")) as fh:
-            content = fh.read()
-    except FileNotFoundError:
-        with open(Path(self.wf_path, ".nf-core.yaml")) as fh:
-            content = fh.read()
+    for ext in (".yml", ".yaml"):
+        try:
+            nf_core_yml = yaml.load(Path(self.wf_path) / f".nf-core{ext}")
+            break
+        except FileNotFoundError:
+            continue
+    else:
+        raise FileNotFoundError("No `.nf-core.yml` file found.")
 
     if "repository_type" not in ignore_configs:
         # Check that the repository type is set in the .nf-core.yml
-        repo_type_re = r"repository_type: (.+)"
-        match = re.search(repo_type_re, content)
-        if match:
-            repo_type = match.group(1)
+        if "repository_type" in nf_core_yml:
+            repo_type = nf_core_yml["repository_type"]
             if repo_type not in REPOSITORY_TYPES:
                 failed.append(
                     f"Repository type in `.nf-core.yml` is not valid. "
@@ -55,10 +58,8 @@ def nfcore_yml(self) -> Dict[str, List[str]]:
 
     if "nf_core_version" not in ignore_configs:
         # Check that the nf-core version is set in the .nf-core.yml
-        nf_core_version_re = r"nf_core_version: (.+)"
-        match = re.search(nf_core_version_re, content)
-        if match:
-            nf_core_version = match.group(1).strip('"')
+        if "nf_core_version" in nf_core_yml:
+            nf_core_version = nf_core_yml["nf_core_version"]
             if nf_core_version != __version__ and "dev" not in nf_core_version:
                 warned.append(
                     f"nf-core version in `.nf-core.yml` is not set to the latest version. "
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index bdfad5200..5a10fbfce 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -23,6 +23,21 @@ def readme(self):
 
         * If pipeline is released but still contains a 'zenodo.XXXXXXX' tag, the test fails
 
+    To disable this test, add the following to the pipeline's ``.nf-core.yml`` file:
+
+    .. code-block:: yaml
+        lint:
+            readme: False
+
+    To disable subsets of these tests, add the following to the pipeline's ``.nf-core.yml`` file:
+
+    .. code-block:: yaml
+
+            lint:
+                readme:
+                    nextflow_badge
+                    zenodo_release
+
     """
     passed = []
     warned = []
diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py
index 11c5e8251..0cb669e55 100644
--- a/nf_core/pipelines/lint/template_strings.py
+++ b/nf_core/pipelines/lint/template_strings.py
@@ -39,8 +39,8 @@ def template_strings(self):
     ignored = []
     # Files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("template_strings", []) if self.lint_config is not None else []
-    files = self.list_files()
 
+    files = self.list_files()
     # Loop through files, searching for string
     num_matches = 0
     for fn in files:
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 12b29f15e..896adda94 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -105,7 +105,7 @@ def __init__(
                 with open(template_yaml_path) as f:
                     self.config_yml.template = yaml.safe_load(f)
                 with open(self.config_yml_path, "w") as fh:
-                    yaml.safe_dump(self.config_yml.model_dump(), fh)
+                    yaml.safe_dump(self.config_yml.model_dump(exclude_none=True), fh)
                 log.info(f"Saved pipeline creation settings to '{self.config_yml_path}'")
                 raise SystemExit(
                     f"Please commit your changes and delete the {template_yaml_path} file. Then run the sync command again."
@@ -271,7 +271,7 @@ def make_template_pipeline(self):
 
             self.config_yml.template.force = True
             with open(self.config_yml_path, "w") as config_path:
-                yaml.safe_dump(self.config_yml.model_dump(), config_path)
+                yaml.safe_dump(self.config_yml.model_dump(exclude_none=True), config_path)
 
         try:
             pipeline_create_obj = nf_core.pipelines.create.create.PipelineCreate(
@@ -291,7 +291,7 @@ def make_template_pipeline(self):
                 self.config_yml.template.outdir = "."
                 # Update nf-core version
                 self.config_yml.nf_core_version = nf_core.__version__
-                dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump())
+                dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump(exclude_none=True))
 
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 16125aed3..366985a95 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1088,7 +1088,102 @@ def get(self, item: str, default: Any = None) -> Any:
         return getattr(self, item, default)
 
 
-LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]]
+class NFCoreYamlLintConfig(BaseModel):
+    """
+    schema for linting config in `.nf-core.yml` should cover:
+
+    .. code-block:: 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:
+            - .github/CONTRIBUTING.md
+            - CITATIONS.md
+        template_strings: False
+        template_strings:
+                - docs/my_pdf.pdf
+        nfcore_components: False
+    """
+
+    files_unchanged: Optional[Union[bool, List[str]]] = None
+    """ List of files that should not be changed """
+    modules_config: Optional[Optional[Union[bool, List[str]]]] = None
+    """ List of modules that should not be changed """
+    merge_markers: Optional[Optional[Union[bool, List[str]]]] = None
+    """ List of files that should not contain merge markers """
+    nextflow_config: Optional[Optional[Union[bool, List[Union[str, Dict[str, List[str]]]]]]] = None
+    """ List of Nextflow config files that should not be changed """
+    multiqc_config: Optional[Union[bool, List[str]]] = None
+    """ List of MultiQC config options that be changed """
+    files_exist: Optional[Union[bool, List[str]]] = None
+    """ List of files that can not exist """
+    template_strings: Optional[Optional[Union[bool, List[str]]]] = None
+    """ List of files that can contain template strings """
+    readme: Optional[Union[bool, List[str]]] = None
+    """ Lint the README.md file """
+    nfcore_components: Optional[bool] = None
+    """ Lint all required files to use nf-core modules and subworkflows """
+    actions_ci: Optional[bool] = None
+    """ Lint all required files to use GitHub Actions CI """
+    actions_awstest: Optional[bool] = None
+    """ Lint all required files to run tests on AWS """
+    actions_awsfulltest: Optional[bool] = None
+    """ Lint all required files to run full tests on AWS """
+    pipeline_todos: Optional[bool] = None
+    """ Lint for TODOs statements"""
+    plugin_includes: Optional[bool] = None
+    """ Lint for nextflow plugin """
+    pipeline_name_conventions: Optional[bool] = None
+    """ Lint for pipeline name conventions """
+    schema_lint: Optional[bool] = None
+    """ Lint nextflow_schema.json file"""
+    schema_params: Optional[bool] = None
+    """ Lint schema for all params """
+    system_exit: Optional[bool] = None
+    """ Lint for System.exit calls in groovy/nextflow code """
+    schema_description: Optional[bool] = None
+    """ Check that every parameter in the schema has a description. """
+    actions_schema_validation: Optional[bool] = None
+    """ Lint GitHub Action workflow files with schema"""
+    modules_json: Optional[bool] = None
+    """ Lint modules.json file """
+    modules_structure: Optional[bool] = None
+    """ Lint modules structure """
+    base_config: Optional[bool] = None
+    """ Lint base.config file """
+    nfcore_yml: Optional[bool] = None
+    """ Lint nf-core.yml """
+    version_consistency: Optional[bool] = None
+    """ Lint for version consistency """
+    included_configs: Optional[bool] = None
+    """ Lint for included configs """
+
+    def __getitem__(self, item: str) -> Any:
+        return getattr(self, item)
+
+    def get(self, item: str, default: Any = None) -> Any:
+        if getattr(self, item, default) is None:
+            return default
+        return getattr(self, item, default)
+
+    def __setitem__(self, item: str, value: Any) -> None:
+        setattr(self, item, value)
 
 
 class NFCoreYamlConfig(BaseModel):
@@ -1100,7 +1195,7 @@ class NFCoreYamlConfig(BaseModel):
     """ Version of nf-core/tools used to create/update the pipeline """
     org_path: Optional[str] = None
     """ Path to the organisation's modules repository (used for modules repo_type only) """
-    lint: Optional[LintConfigType] = None
+    lint: Optional[NFCoreYamlLintConfig] = None
     """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """
     template: Optional[NFCoreTemplateConfig] = None
     """ Pipeline template configuration """
@@ -1115,6 +1210,9 @@ def __getitem__(self, item: str) -> Any:
     def get(self, item: str, default: Any = None) -> Any:
         return getattr(self, item, default)
 
+    def __setitem__(self, item: str, value: Any) -> None:
+        setattr(self, item, value)
+
     def model_dump(self, **kwargs) -> Dict[str, Any]:
         # Get the initial data
         config = super().model_dump(**kwargs)
@@ -1170,7 +1268,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path]
     except ValidationError as e:
         error_message = f"Config file '{config_fn}' is invalid"
         for error in e.errors():
-            error_message += f"\n{error['loc'][0]}: {error['msg']}"
+            error_message += f"\n{error['loc'][0]}: {error['msg']}\ninput: {error['input']}"
         raise AssertionError(error_message)
 
     wf_config = fetch_wf_config(Path(directory))
diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 97dd346cd..ebc529247 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -1,5 +1,7 @@
 from pathlib import Path
 
+from ruamel.yaml import YAML
+
 import nf_core.pipelines.lint
 
 from ..test_lint import TestLint
@@ -9,17 +11,17 @@ class TestLintFilesExist(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()
+        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
 
     def test_files_exist_missing_config(self):
         """Lint test: critical files missing FAIL"""
 
         Path(self.new_pipeline, "CHANGELOG.md").unlink()
 
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline"
+        assert self.lint_obj._load()
+        self.lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline"
 
-        results = lint_obj.files_exist()
+        results = self.lint_obj.files_exist()
         assert "File not found: `CHANGELOG.md`" in results["failed"]
 
     def test_files_exist_missing_main(self):
@@ -27,31 +29,27 @@ def test_files_exist_missing_main(self):
 
         Path(self.new_pipeline, "main.nf").unlink()
 
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
+        assert self.lint_obj._load()
 
-        results = lint_obj.files_exist()
+        results = self.lint_obj.files_exist()
         assert "File not found: `main.nf`" in results["warned"]
 
     def test_files_exist_deprecated_file(self):
         """Check whether deprecated file issues warning"""
 
-        nf = Path(self.new_pipeline, "parameters.settings.json")
-        nf.touch()
+        Path(self.new_pipeline, "parameters.settings.json").touch()
 
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
+        assert self.lint_obj._load()
 
-        results = lint_obj.files_exist()
+        results = self.lint_obj.files_exist()
         assert results["failed"] == ["File must be removed: `parameters.settings.json`"]
 
     def test_files_exist_pass(self):
         """Lint check should pass if all files are there"""
 
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
+        assert self.lint_obj._load()
 
-        results = lint_obj.files_exist()
+        results = self.lint_obj.files_exist()
         assert results["failed"] == []
 
     def test_files_exist_pass_conditional_nfschema(self):
@@ -62,9 +60,58 @@ def test_files_exist_pass_conditional_nfschema(self):
         with open(Path(self.new_pipeline, "nextflow.config"), "w") as f:
             f.write(config)
 
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lint_obj.nf_config["manifest.schema"] = "nf-core"
-        results = lint_obj.files_exist()
+        assert self.lint_obj._load()
+        self.lint_obj.nf_config["manifest.schema"] = "nf-core"
+        results = self.lint_obj.files_exist()
         assert results["failed"] == []
         assert results["ignored"] == []
+
+    def test_files_exists_pass_nf_core_yml_config(self):
+        """Check if linting passes with a valid nf-core.yml config"""
+        valid_yaml = """
+        files_exist:
+            - .github/CONTRIBUTING.md
+            - CITATIONS.md
+        """
+        yaml = YAML()
+        nf_core_yml_path = Path(self.new_pipeline, ".nf-core.yml")
+        nf_core_yml = yaml.load(nf_core_yml_path)
+
+        nf_core_yml["lint"] = yaml.load(valid_yaml)
+        yaml.dump(nf_core_yml, nf_core_yml_path)
+
+        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        assert self.lint_obj._load()
+
+        results = self.lint_obj.files_exist()
+        assert results["failed"] == []
+        assert "File is ignored: `.github/CONTRIBUTING.md`" in results["ignored"]
+        assert "File is ignored: `CITATIONS.md`" in results["ignored"]
+
+    def test_files_exists_fail_nf_core_yml_config(self):
+        """Check if linting fails with a valid nf-core.yml config"""
+        valid_yaml = """
+        files_exist:
+            - CITATIONS.md
+        """
+
+        # remove CITATIONS.md
+        Path(self.new_pipeline, "CITATIONS.md").unlink()
+        assert self.lint_obj._load()
+        # test first if linting fails correctly
+        results = self.lint_obj.files_exist()
+        assert "File not found: `CITATIONS.md`" in results["failed"]
+
+        yaml = YAML()
+        nf_core_yml_path = Path(self.new_pipeline, ".nf-core.yml")
+        nf_core_yml = yaml.load(nf_core_yml_path)
+
+        nf_core_yml["lint"] = yaml.load(valid_yaml)
+        yaml.dump(nf_core_yml, nf_core_yml_path)
+
+        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        assert self.lint_obj._load()
+
+        results = self.lint_obj.files_exist()
+        assert results["failed"] == []
+        assert "File is ignored: `CITATIONS.md`" in results["ignored"]
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index a655fb8ac..f8c3c1f31 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -6,7 +6,6 @@
 
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
-from nf_core.utils import NFCoreYamlConfig
 
 from ..test_lint import TestLint
 
@@ -125,23 +124,30 @@ def test_allow_params_reference_in_main_nf(self):
 
     def test_default_values_ignored(self):
         """Test ignoring linting of default values."""
+        valid_yaml = """
+        nextflow_config:
+            - manifest.name
+            - config_defaults:
+                - params.custom_config_version
+        """
         # Add custom_config_version to the ignore list
         nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
-        nf_core_yml = NFCoreYamlConfig(
-            repository_type="pipeline",
-            lint={"nextflow_config": [{"config_defaults": ["params.custom_config_version"]}]},
-        )
+
+        with open(nf_core_yml_path) as f:
+            nf_core_yml = yaml.safe_load(f)
+            nf_core_yml["lint"] = yaml.safe_load(valid_yaml)
         with open(nf_core_yml_path, "w") as f:
-            yaml.dump(nf_core_yml.model_dump(), f)
+            yaml.dump(nf_core_yml, f)
 
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj.load_pipeline_config()
         lint_obj._load_lint_config()
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) == 0
-        assert len(result["ignored"]) == 1
+        assert len(result["ignored"]) == 2
         assert "Config default value correct: params.custom_config_version" not in str(result["passed"])
         assert "Config default ignored: params.custom_config_version" in str(result["ignored"])
+        assert "Config variable ignored: `manifest.name`" in str(result["ignored"])
 
     def test_default_values_float(self):
         """Test comparing two float values."""
diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py
index b49b60436..2ac36ffe0 100644
--- a/tests/pipelines/lint/test_nfcore_yml.py
+++ b/tests/pipelines/lint/test_nfcore_yml.py
@@ -1,8 +1,9 @@
-import re
 from pathlib import Path
 
-import nf_core.pipelines.create
+from ruamel.yaml import YAML
+
 import nf_core.pipelines.lint
+from nf_core.utils import NFCoreYamlConfig
 
 from ..test_lint import TestLint
 
@@ -11,11 +12,14 @@ class TestLintNfCoreYml(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()
-        self.nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
+        self.nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
+        self.yaml = YAML()
+        self.nf_core_yml: NFCoreYamlConfig = self.yaml.load(self.nf_core_yml_path)
+        self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
 
     def test_nfcore_yml_pass(self):
         """Lint test: nfcore_yml - PASS"""
-        self.lint_obj._load()
+        assert self.lint_obj._load()
         results = self.lint_obj.nfcore_yml()
 
         assert "Repository type in `.nf-core.yml` is valid" in str(results["passed"])
@@ -27,33 +31,95 @@ def test_nfcore_yml_pass(self):
     def test_nfcore_yml_fail_repo_type(self):
         """Lint test: nfcore_yml - FAIL - repository type not set"""
 
-        with open(self.nf_core_yml) as fh:
-            content = fh.read()
-            new_content = content.replace("repository_type: pipeline", "repository_type: foo")
-        with open(self.nf_core_yml, "w") as fh:
-            fh.write(new_content)
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        # assert that it raises assertion error
+        self.nf_core_yml["repository_type"] = "foo"
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
         with self.assertRaises(AssertionError):
-            lint_obj._load()
-        results = lint_obj.nfcore_yml()
-        assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"])
-        assert len(results.get("warned", [])) == 0
-        assert len(results.get("passed", [])) >= 0
-        assert len(results.get("ignored", [])) == 0
+            self.lint_obj._load()
 
     def test_nfcore_yml_fail_nfcore_version(self):
         """Lint test: nfcore_yml - FAIL - nf-core version not set"""
 
-        with open(self.nf_core_yml) as fh:
-            content = fh.read()
-            new_content = re.sub(r"nf_core_version:.+", "nf_core_version: foo", content)
-        with open(self.nf_core_yml, "w") as fh:
-            fh.write(new_content)
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        results = lint_obj.nfcore_yml()
+        self.nf_core_yml["nf_core_version"] = "foo"
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
+        assert self.lint_obj._load()
+        results = self.lint_obj.nfcore_yml()
         assert "nf-core version in `.nf-core.yml` is not set to the latest version." in str(results["warned"])
         assert len(results.get("failed", [])) == 0
         assert len(results.get("passed", [])) >= 0
         assert len(results.get("ignored", [])) == 0
+
+    def test_nfcore_yml_nested_lint_config(self) -> None:
+        """Lint test: nfcore_yml with nested lint config - PASS"""
+        valid_yaml = """
+        lint:
+            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:
+                - report_section_order
+                - report_comment
+            files_exist:
+                - .github/CONTRIBUTING.md
+                - CITATIONS.md
+            # template_strings: False
+            template_strings:
+                    - docs/my_pdf.pdf
+        """
+        self.nf_core_yml["lint"] = self.yaml.load(valid_yaml)
+        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
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("ignored", [])) == 0
+
+    def test_nfcore_yml_nested_lint_config_bool(self) -> None:
+        """Lint test: nfcore_yml with nested lint config - PASS"""
+        valid_yaml = """
+        lint:
+            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:
+                - report_section_order
+                - report_comment
+            files_exist:
+                - .github/CONTRIBUTING.md
+                - CITATIONS.md
+            template_strings: False
+            # template_strings:
+            #         - docs/my_pdf.pdf
+        """
+        self.nf_core_yml["lint"] = self.yaml.load(valid_yaml)
+        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
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("ignored", [])) == 0
diff --git a/tests/pipelines/lint/test_template_strings.py b/tests/pipelines/lint/test_template_strings.py
index 406ba63e0..37b760480 100644
--- a/tests/pipelines/lint/test_template_strings.py
+++ b/tests/pipelines/lint/test_template_strings.py
@@ -1,6 +1,8 @@
 import subprocess
 from pathlib import Path
 
+import yaml
+
 import nf_core.pipelines.create
 import nf_core.pipelines.lint
 
@@ -11,6 +13,9 @@ class TestLintTemplateStrings(TestLint):
     def setUp(self) -> None:
         super().setUp()
         self.new_pipeline = self._make_pipeline_copy()
+        self.nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
+        with open(self.nf_core_yml_path) as f:
+            self.nf_core_yml = yaml.safe_load(f)
 
     def test_template_strings(self):
         """Tests finding a template string in a file fails linting."""
@@ -28,9 +33,12 @@ def test_template_strings(self):
     def test_template_strings_ignored(self):
         """Tests ignoring template_strings"""
         # Ignore template_strings test
-        nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
-        with open(nf_core_yml, "w") as f:
-            f.write("repository_type: pipeline\nlint:\n  template_strings: False")
+        valid_yaml = """
+        template_strings: false
+        """
+        self.nf_core_yml["lint"] = yaml.safe_load(valid_yaml)
+        with open(self.nf_core_yml_path, "w") as f:
+            yaml.safe_dump(self.nf_core_yml, f)
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj._load()
         lint_obj._lint_pipeline()
@@ -43,13 +51,21 @@ def test_template_strings_ignore_file(self):
         txt_file = Path(self.new_pipeline) / "docs" / "test.txt"
         with open(txt_file, "w") as f:
             f.write("my {{ template_string }}")
+
         subprocess.check_output(["git", "add", "docs"], cwd=self.new_pipeline)
+
         # Ignore template_strings test
-        nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml"
-        with open(nf_core_yml, "w") as f:
-            f.write("repository_type: pipeline\nlint:\n  template_strings:\n    - docs/test.txt")
+        valid_yaml = """
+        template_strings:
+            - docs/test.txt
+        """
+        self.nf_core_yml["lint"] = yaml.safe_load(valid_yaml)
+        with open(self.nf_core_yml_path, "w") as f:
+            yaml.safe_dump(self.nf_core_yml, f)
+
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj._load()
         result = lint_obj.template_strings()
+
         assert len(result["failed"]) == 0
         assert len(result["ignored"]) == 1
diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py
index 9ca29d249..ca7353d50 100644
--- a/tests/pipelines/test_lint.py
+++ b/tests/pipelines/test_lint.py
@@ -48,7 +48,8 @@ def test_init_pipeline_lint(self):
     def test_load_lint_config_not_found(self):
         """Try to load a linting config file that doesn't exist"""
         assert self.lint_obj._load_lint_config()
-        assert self.lint_obj.lint_config == {}
+        assert self.lint_obj.lint_config is not None
+        assert self.lint_obj.lint_config.model_dump(exclude_none=True) == {}
 
     def test_load_lint_config_ignore_all_tests(self):
         """Try to load a linting config file that ignores all tests"""
@@ -64,7 +65,8 @@ def test_load_lint_config_ignore_all_tests(self):
 
         # Load the new lint config file and check
         lint_obj._load_lint_config()
-        assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests)
+        assert lint_obj.lint_config is not None
+        assert sorted(list(lint_obj.lint_config.model_dump(exclude_none=True))) == sorted(lint_obj.lint_tests)
 
         # Try running linting and make sure that all tests are ignored
         lint_obj._lint_pipeline()