diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c2c755e55..c0fa29549e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@
 - Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(https://github.com/nf-core/tools/pull/2278/files)
 - Detect if container is 'simple name' and try to contact quay.io server by default ([#2281](https://github.com/nf-core/tools/pull/2281))
 - Warn about null/None/empty default values in `nextflow_schema.json` ([#3328](https://github.com/nf-core/tools/pull/2328))
+- Fix linting when creating a pipeline skipping some parts of the template and add CI test ([#2330](https://github.com/nf-core/tools/pull/2330))
 
 ### Modules
 
diff --git a/nf_core/create.py b/nf_core/create.py
index 9e3b38102f..7416bd8f74 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -352,6 +352,7 @@ def render_template(self):
         if self.template_yaml:
             with open(self.outdir / "pipeline_template.yml", "w") as fh:
                 yaml.safe_dump(self.template_yaml, fh)
+            run_prettier_on_file(self.outdir / "pipeline_template.yml")
 
     def update_nextflow_schema(self):
         """
@@ -403,6 +404,12 @@ def fix_linting(self):
                 ".github/workflows/awstest.yml",
                 ".github/workflows/awsfulltest.yml",
             ],
+            "files_unchanged": [
+                "CODE_OF_CONDUCT.md",
+                f"assets/nf-core-{short_name}_logo_light.png",
+                f"docs/images/nf-core-{short_name}_logo_light.png",
+                f"docs/images/nf-core-{short_name}_logo_dark.png",
+            ],
             "nextflow_config": [
                 "manifest.name",
                 "manifest.homePage",
@@ -415,9 +422,26 @@ def fix_linting(self):
             lint_config["files_exist"].extend(
                 [
                     ".github/ISSUE_TEMPLATE/bug_report.yml",
+                    ".github/ISSUE_TEMPLATE/feature_request.yml",
+                    ".github/PULL_REQUEST_TEMPLATE.md",
+                    ".github/CONTRIBUTING.md",
+                    ".github/.dockstore.yml",
+                    ".gitignore",
+                ]
+            )
+            lint_config["files_unchanged"].extend(
+                [
+                    ".github/ISSUE_TEMPLATE/bug_report.yml",
+                    ".github/ISSUE_TEMPLATE/config.yml",
+                    ".github/ISSUE_TEMPLATE/feature_request.yml",
+                    ".github/PULL_REQUEST_TEMPLATE.md",
+                    ".github/workflows/branch.yml",
+                    ".github/workflows/linting_comment.yml",
+                    ".github/workflows/linting.yml",
+                    ".github/CONTRIBUTING.md",
+                    ".github/.dockstore.yml",
                 ]
             )
-            lint_config["files_unchanged"] = [".github/ISSUE_TEMPLATE/bug_report.yml"]
 
         # Add CI specific configurations
         if not self.template_params["ci"]:
@@ -446,6 +470,10 @@ def fix_linting(self):
         if not self.template_params["github_badges"] or not self.template_params["github"]:
             lint_config["readme"] = ["nextflow_badge"]
 
+        # If the pipeline is unbranded
+        if not self.template_params["branded"]:
+            lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])
+
         # Add the lint content to the preexisting nf-core config
         config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
         nf_core_yml["lint"] = lint_config
diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
new file mode 100644
index 0000000000..b69175e0bb
--- /dev/null
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -0,0 +1,7 @@
+prefix: testprefix
+skip:
+  - github
+  - ci
+  - github_badges
+  - igenomes
+  - nf_core_configs
diff --git a/tests/test_create.py b/tests/test_create.py
index cc6bf8ba47..298eeecde5 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -13,6 +13,7 @@
 
 TEST_DATA_DIR = Path(__file__).parent / "data"
 PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
+PIPELINE_TEMPLATE_YML_SKIP = TEST_DATA_DIR / "pipeline_create_template_skip.yml"
 
 
 class NfcoreCreateTest(unittest.TestCase):
@@ -107,3 +108,31 @@ def test_pipeline_creation_initiation_customize_template(self, mock_questionary,
         assert os.path.exists(pipeline_template)
         with open(pipeline_template) as fh:
             assert fh.read() == PIPELINE_TEMPLATE_YML.read_text()
+
+    @with_temporary_folder
+    def test_pipeline_creation_with_yml_skip(self, tmp_path):
+        pipeline = nf_core.create.PipelineCreate(
+            name=self.pipeline_name,
+            description=self.pipeline_description,
+            author=self.pipeline_author,
+            version=self.pipeline_version,
+            no_git=False,
+            force=True,
+            outdir=tmp_path,
+            template_yaml_path=PIPELINE_TEMPLATE_YML_SKIP,
+            plain=True,
+            default_branch=self.default_branch,
+        )
+        pipeline.init_pipeline()
+        assert not os.path.isdir(os.path.join(pipeline.outdir, ".git"))
+
+        # Check pipeline yml has been dumped and matches input
+        pipeline_template = os.path.join(pipeline.outdir, "pipeline_template.yml")
+        assert os.path.exists(pipeline_template)
+        with open(pipeline_template) as fh:
+            assert fh.read() == PIPELINE_TEMPLATE_YML_SKIP.read_text()
+
+        # Check that some of the skipped files are not present
+        assert not os.path.exists(os.path.join(pipeline.outdir, "CODE_OF_CONDUCT.md"))
+        assert not os.path.exists(os.path.join(pipeline.outdir, ".github"))
+        assert not os.path.exists(os.path.join(pipeline.outdir, "conf", "igenomes.config"))