diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 3805c1a240..fb00471b90 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -38,6 +38,7 @@ jobs:
           - TEMPLATE: "template_skip_nf_core_configs.yml"
             runner: ubuntu-latest
             profile: "docker"
+      fail-fast: false
 
     steps:
       - name: go to working directory
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 9f117124a0..c58206158f 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -13,7 +13,7 @@ jobs:
     runs-on: self-hosted
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -31,11 +31,10 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
-          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,15 +46,15 @@ jobs:
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: ${{ steps.pre-commit.outcome }} == 'success'
+        if: steps.pre-commit.outcome == 'success'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: green_check_mark
+          reactions: "+1"
 
       - name: Commit & push changes
         id: commit-and-push
-        if: ${{ steps.pre-commit.outcome }} == 'failure'
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
@@ -66,17 +65,25 @@ jobs:
           git push
 
       - name: react if linting errors were fixed
-        if: ${{ steps.commit-and-push.outcome }} == 'success'
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: pencil2
+          reactions: hooray
 
       - name: react if linting errors were not fixed
-        if: ${{ steps.commit-and-push.outcome }} == 'failure'
+        if: steps.commit-and-push.outcome == 'failure'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: x
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-core/tools/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 56ebb5bfaa..d4eb6a721d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.13
+    rev: v0.1.14
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2222491165..09bb35c869 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,10 @@
 - switch to new image syntax in readme ([#2645](https://github.com/nf-core/tools/pull/2645))
 - Add conda channel order to nextflow.config ([#2094](https://github.com/nf-core/tools/pull/2094))
 - Fix tyop in pipeline nextflow.config ([#2664](https://github.com/nf-core/tools/pull/2664))
-- add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Remove `nfcore_external_java_deps.jar` from lib directory in pipeline template ([#2675](https://github.com/nf-core/tools/pull/2675))
+- Add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message ([#2680](https://github.com/nf-core/tools/pull/2680))
+- add 👀👍🏻🎉😕 reactions to fix-linting-bot action ([#2692](https://github.com/nf-core/tools/pull/2692))
 
 ### Download
 
@@ -19,6 +22,7 @@
 - Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
 - linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
+- lint `nextflow.config` default values match the ones specified in `nextflow_schema.json` ([#2684](https://github.com/nf-core/tools/pull/2684))
 
 ### Modules
 
@@ -39,7 +43,10 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.13 ([#2660](https://github.com/nf-core/tools/pull/2660))
 - Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([#2662](https://github.com/nf-core/tools/pull/2662))
 - Update actions/cache action to v4 ([#2666](https://github.com/nf-core/tools/pull/2666))
+- Handle api redirects from the old site ([#2672](https://github.com/nf-core/tools/pull/2672))
 - Remove redundanct v in pipeline version for emails ([#2667](https://github.com/nf-core/tools/pull/2667))
+- add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.14 ([#2674](https://github.com/nf-core/tools/pull/2674))
 - Update peter-evans/create-or-update-comment action to v4 ([#2683](https://github.com/nf-core/tools/pull/2683))
 
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
diff --git a/nf_core/create.py b/nf_core/create.py
index 76fc50e8fa..f9e9933ee3 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -505,10 +505,12 @@ def fix_linting(self):
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
         email_logo_path = Path(self.outdir) / "assets"
-        create_logo(text=self.template_params["short_name"], dir=email_logo_path, theme="light")
+        create_logo(text=self.template_params["short_name"], dir=email_logo_path, theme="light", force=self.force)
         for theme in ["dark", "light"]:
             readme_logo_path = Path(self.outdir) / "docs" / "images"
-            create_logo(text=self.template_params["short_name"], dir=readme_logo_path, width=600, theme=theme)
+            create_logo(
+                text=self.template_params["short_name"], dir=readme_logo_path, width=600, theme=theme, force=self.force
+            )
 
     def git_init_pipeline(self):
         """Initialises the new pipeline as a Git repository and submits first commit.
@@ -537,8 +539,24 @@ def git_init_pipeline(self):
         repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
         if default_branch:
             repo.active_branch.rename(default_branch)
-        repo.git.branch("TEMPLATE")
-        repo.git.branch("dev")
+        try:
+            repo.git.branch("TEMPLATE")
+            repo.git.branch("dev")
+
+        except git.GitCommandError as e:
+            if "already exists" in e.stderr:
+                log.debug("Branches 'TEMPLATE' and 'dev' already exist")
+                if self.force:
+                    log.debug("Force option set - deleting branches")
+                    repo.git.branch("-D", "TEMPLATE")
+                    repo.git.branch("-D", "dev")
+                    repo.git.branch("TEMPLATE")
+                    repo.git.branch("dev")
+                else:
+                    log.error(
+                        "Branches 'TEMPLATE' and 'dev' already exist. Use --force to overwrite existing branches."
+                    )
+                    sys.exit(1)
         log.info(
             "Done. Remember to add a remote and push to GitHub:\n"
             f"[white on grey23] cd {self.outdir} \n"
diff --git a/nf_core/create_logo.py b/nf_core/create_logo.py
index e40dd73452..4dfebd3712 100644
--- a/nf_core/create_logo.py
+++ b/nf_core/create_logo.py
@@ -5,6 +5,7 @@
 from PIL import Image, ImageDraw, ImageFont
 
 import nf_core
+from nf_core.utils import NFCORE_CACHE_DIR
 
 log = logging.getLogger(__name__)
 
@@ -26,7 +27,6 @@ def create_logo(
     if not dir.is_dir():
         log.debug(f"Creating directory {dir}")
         dir.mkdir(parents=True, exist_ok=True)
-
     assets = Path(nf_core.__file__).parent / "assets/logo"
 
     if format == "svg":
@@ -51,44 +51,56 @@ def create_logo(
     else:
         logo_filename = f"nf-core-{text}_logo_{theme}.png" if not filename else filename
         logo_filename = f"{logo_filename}.png" if not logo_filename.lower().endswith(".png") else logo_filename
+        cache_name = f"nf-core-{text}_logo_{theme}_{width}.png"
         logo_path = Path(dir, logo_filename)
 
         # Check if we haven't already created this logo
         if logo_path.is_file() and not force:
             log.info(f"Logo already exists at: {logo_path}. Use `--force` to overwrite.")
             return logo_path
-
-        log.debug(f"Creating logo for {text}")
-
-        # make sure the figure fits the text
-        font_path = assets / "MavenPro-Bold.ttf"
-        log.debug(f"Using font: {str(font_path)}")
-        font = ImageFont.truetype(str(font_path), 400)
-        text_length = font.getmask(text).getbbox()[2]  # get the width of the text based on the font
-
-        max_width = max(
-            2300, text_length + len(text) * 20
-        )  # need to add some more space to the text length to make sure it fits
-
-        template_fn = "nf-core-repo-logo-base-lightbg.png"
-        if theme == "dark":
-            template_fn = "nf-core-repo-logo-base-darkbg.png"
-
-        template_path = assets / template_fn
-        img = Image.open(str(template_path))
-        # get the height of the template image
-        height = img.size[1]
-
-        # Draw text
-        draw = ImageDraw.Draw(img)
-        color = theme == "dark" and (250, 250, 250) or (5, 5, 5)
-        draw.text((110, 465), text, color, font=font)
-
-        # Crop to max width
-        img = img.crop((0, 0, max_width, height))
-
-        # Resize
-        img = img.resize((width, int((width / max_width) * height)))
+        # cache file
+        cache_path = Path(NFCORE_CACHE_DIR, "logo", cache_name)
+        img = None
+        if cache_path.is_file():
+            log.debug(f"Logo already exists in cache at: {cache_path}. Reusing this file.")
+            img = Image.open(str(cache_path))
+        if not img:
+            log.debug(f"Creating logo for {text}")
+
+            # make sure the figure fits the text
+            font_path = assets / "MavenPro-Bold.ttf"
+            log.debug(f"Using font: {str(font_path)}")
+            font = ImageFont.truetype(str(font_path), 400)
+            text_length = font.getmask(text).getbbox()[2]  # get the width of the text based on the font
+
+            max_width = max(
+                2300, text_length + len(text) * 20
+            )  # need to add some more space to the text length to make sure it fits
+
+            template_fn = "nf-core-repo-logo-base-lightbg.png"
+            if theme == "dark":
+                template_fn = "nf-core-repo-logo-base-darkbg.png"
+
+            template_path = assets / template_fn
+            img = Image.open(str(template_path))
+            # get the height of the template image
+            height = img.size[1]
+
+            # Draw text
+            draw = ImageDraw.Draw(img)
+            color = theme == "dark" and (250, 250, 250) or (5, 5, 5)
+            draw.text((110, 465), text, color, font=font)
+
+            # Crop to max width
+            img = img.crop((0, 0, max_width, height))
+
+            # Resize
+            img = img.resize((width, int((width / max_width) * height)))
+
+            # Save to cache
+            Path(cache_path.parent).mkdir(parents=True, exist_ok=True)
+            log.debug(f"Saving logo to cache: {cache_path}")
+            img.save(cache_path, "PNG")
         # Save
         img.save(logo_path, "PNG")
 
diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index b4d0c10ff3..4f7657aec5 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -120,8 +120,10 @@ def run_linting(
     if subworkflow_lint_obj is not None:
         subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
 
-    # Set up files for modules linting test
+    # Set up files for component linting test
     module_lint_obj.set_up_pipeline_files()
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj.set_up_pipeline_files()
 
     # Run the pipeline linting tests
     try:
diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
index 117704d1f1..707f98a53a 100644
--- a/nf_core/lint/files_exist.py
+++ b/nf_core/lint/files_exist.py
@@ -1,5 +1,6 @@
 import logging
-import os
+from pathlib import Path
+from typing import Union
 
 log = logging.getLogger(__name__)
 
@@ -51,7 +52,6 @@ def files_exist(self):
         docs/output.md
         docs/README.md
         docs/usage.md
-        lib/nfcore_external_java_deps.jar
         lib/NfcoreTemplate.groovy
         lib/Utils.groovy
         lib/WorkflowMain.groovy
@@ -98,6 +98,12 @@ def files_exist(self):
 
         .travis.yml
 
+    Files that *must not* be present if a certain entry is present in ``nextflow.config``:
+
+    .. code-block:: bash
+
+        lib/nfcore_external_java_deps.jar # if "nf-validation" is in nextflow.config
+
     .. tip:: You can configure the ``nf-core lint`` tests to ignore any of these checks by setting
             the ``files_exist`` key as follows in your ``.nf-core.yml`` config file. For example:
 
@@ -132,48 +138,46 @@ def files_exist(self):
         ["CHANGELOG.md"],
         ["CITATIONS.md"],
         ["CODE_OF_CONDUCT.md"],
-        ["CODE_OF_CONDUCT.md"],
         ["LICENSE", "LICENSE.md", "LICENCE", "LICENCE.md"],  # NB: British / American spelling
         ["nextflow_schema.json"],
         ["nextflow.config"],
         ["README.md"],
-        [os.path.join(".github", ".dockstore.yml")],
-        [os.path.join(".github", "CONTRIBUTING.md")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "bug_report.yml")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "config.yml")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.yml")],
-        [os.path.join(".github", "PULL_REQUEST_TEMPLATE.md")],
-        [os.path.join(".github", "workflows", "branch.yml")],
-        [os.path.join(".github", "workflows", "ci.yml")],
-        [os.path.join(".github", "workflows", "linting_comment.yml")],
-        [os.path.join(".github", "workflows", "linting.yml")],
-        [os.path.join("assets", "email_template.html")],
-        [os.path.join("assets", "email_template.txt")],
-        [os.path.join("assets", "sendmail_template.txt")],
-        [os.path.join("assets", f"nf-core-{short_name}_logo_light.png")],
-        [os.path.join("conf", "modules.config")],
-        [os.path.join("conf", "test.config")],
-        [os.path.join("conf", "test_full.config")],
-        [os.path.join("docs", "images", f"nf-core-{short_name}_logo_light.png")],
-        [os.path.join("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
-        [os.path.join("docs", "output.md")],
-        [os.path.join("docs", "README.md")],
-        [os.path.join("docs", "README.md")],
-        [os.path.join("docs", "usage.md")],
-        [os.path.join("lib", "nfcore_external_java_deps.jar")],
-        [os.path.join("lib", "NfcoreTemplate.groovy")],
-        [os.path.join("lib", "Utils.groovy")],
-        [os.path.join("lib", "WorkflowMain.groovy")],
+        [Path(".github", ".dockstore.yml")],
+        [Path(".github", "CONTRIBUTING.md")],
+        [Path(".github", "ISSUE_TEMPLATE", "bug_report.yml")],
+        [Path(".github", "ISSUE_TEMPLATE", "config.yml")],
+        [Path(".github", "ISSUE_TEMPLATE", "feature_request.yml")],
+        [Path(".github", "PULL_REQUEST_TEMPLATE.md")],
+        [Path(".github", "workflows", "branch.yml")],
+        [Path(".github", "workflows", "ci.yml")],
+        [Path(".github", "workflows", "linting_comment.yml")],
+        [Path(".github", "workflows", "linting.yml")],
+        [Path("assets", "email_template.html")],
+        [Path("assets", "email_template.txt")],
+        [Path("assets", "sendmail_template.txt")],
+        [Path("assets", f"nf-core-{short_name}_logo_light.png")],
+        [Path("conf", "modules.config")],
+        [Path("conf", "test.config")],
+        [Path("conf", "test_full.config")],
+        [Path("docs", "images", f"nf-core-{short_name}_logo_light.png")],
+        [Path("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
+        [Path("docs", "output.md")],
+        [Path("docs", "README.md")],
+        [Path("docs", "README.md")],
+        [Path("docs", "usage.md")],
+        [Path("lib", "NfcoreTemplate.groovy")],
+        [Path("lib", "Utils.groovy")],
+        [Path("lib", "WorkflowMain.groovy")],
     ]
 
     files_warn = [
         ["main.nf"],
-        [os.path.join("assets", "multiqc_config.yml")],
-        [os.path.join("conf", "base.config")],
-        [os.path.join("conf", "igenomes.config")],
-        [os.path.join(".github", "workflows", "awstest.yml")],
-        [os.path.join(".github", "workflows", "awsfulltest.yml")],
-        [os.path.join("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy")],
+        [Path("assets", "multiqc_config.yml")],
+        [Path("conf", "base.config")],
+        [Path("conf", "igenomes.config")],
+        [Path(".github", "workflows", "awstest.yml")],
+        [Path(".github", "workflows", "awsfulltest.yml")],
+        [Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy")],
         ["modules.json"],
         ["pyproject.toml"],
     ]
@@ -184,45 +188,48 @@ def files_exist(self):
         "parameters.settings.json",
         "pipeline_template.yml",  # saving information in .nf-core.yml
         ".nf-core.yaml",  # yml not yaml
-        os.path.join("bin", "markdown_to_html.r"),
-        os.path.join("conf", "aws.config"),
-        os.path.join(".github", "workflows", "push_dockerhub.yml"),
-        os.path.join(".github", "ISSUE_TEMPLATE", "bug_report.md"),
-        os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.md"),
-        os.path.join("docs", "images", f"nf-core-{short_name}_logo.png"),
+        Path("bin", "markdown_to_html.r"),
+        Path("conf", "aws.config"),
+        Path(".github", "workflows", "push_dockerhub.yml"),
+        Path(".github", "ISSUE_TEMPLATE", "bug_report.md"),
+        Path(".github", "ISSUE_TEMPLATE", "feature_request.md"),
+        Path("docs", "images", f"nf-core-{short_name}_logo.png"),
         ".markdownlint.yml",
         ".yamllint.yml",
-        os.path.join("lib", "Checks.groovy"),
-        os.path.join("lib", "Completion.groovy"),
-        os.path.join("lib", "Workflow.groovy"),
+        Path("lib", "Checks.groovy"),
+        Path("lib", "Completion.groovy"),
+        Path("lib", "Workflow.groovy"),
     ]
     files_warn_ifexists = [".travis.yml"]
+    files_fail_ifinconfig = [[Path("lib", "nfcore_external_java_deps.jar"), "nf-validation"]]
 
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", [])
+    log.info(f"Files to ignore: {ignore_files}")
 
-    def pf(file_path):
-        return os.path.join(self.wf_path, file_path)
+    def pf(file_path: Union[str, Path]) -> Path:
+        return Path(self.wf_path, file_path)
 
     # First - critical files. Check that this is actually a Nextflow pipeline
-    if not os.path.isfile(pf("nextflow.config")) and not os.path.isfile(pf("main.nf")):
+    if not pf("nextflow.config").is_file() and not pf("main.nf").is_file():
         failed.append("File not found: nextflow.config or main.nf")
         raise AssertionError("Neither nextflow.config or main.nf found! Is this a Nextflow pipeline?")
 
     # Files that cause an error if they don't exist
     for files in files_fail:
-        if any([f in ignore_files for f in files]):
+        print(files)
+        if any([str(f) in ignore_files for f in files]):
             continue
-        if any([os.path.isfile(pf(f)) for f in files]):
+        if any([pf(f).is_file() for f in files]):
             passed.append(f"File found: {self._wrap_quotes(files)}")
         else:
             failed.append(f"File not found: {self._wrap_quotes(files)}")
 
     # Files that cause a warning if they don't exist
     for files in files_warn:
-        if any([f in ignore_files for f in files]):
+        if any([str(f) in ignore_files for f in files]):
             continue
-        if any([os.path.isfile(pf(f)) for f in files]):
+        if any([pf(f).is_file() for f in files]):
             passed.append(f"File found: {self._wrap_quotes(files)}")
         else:
             warned.append(f"File not found: {self._wrap_quotes(files)}")
@@ -231,16 +238,32 @@ def pf(file_path):
     for file in files_fail_ifexists:
         if file in ignore_files:
             continue
-        if os.path.isfile(pf(file)):
+        if pf(file).is_file():
             failed.append(f"File must be removed: {self._wrap_quotes(file)}")
         else:
             passed.append(f"File not found check: {self._wrap_quotes(file)}")
-
+    # Files that cause an error if they exists together with a certain entry in nextflow.config
+    for file in files_fail_ifinconfig:
+        if str(file[0]) in ignore_files:
+            continue
+        nextflow_config = pf("nextflow.config")
+        in_config = False
+        with open(nextflow_config) as f:
+            if file[1] in f.read():
+                in_config = True
+        if pf(file[0]).is_file() and in_config:
+            failed.append(f"File must be removed: {self._wrap_quotes(file[0])}")
+        elif pf(file[0]).is_file() and not in_config:
+            passed.append(f"File found check: {self._wrap_quotes(file[0])}")
+        elif not pf(file[0]).is_file() and not in_config:
+            failed.append(f"File not found check: {self._wrap_quotes(file[0])}")
+        elif not pf(file[0]).is_file() and in_config:
+            passed.append(f"File not found check: {self._wrap_quotes(file[0])}")
     # Files that cause a warning if they exist
     for file in files_warn_ifexists:
         if file in ignore_files:
             continue
-        if os.path.isfile(pf(file)):
+        if pf(file).is_file():
             warned.append(f"File should be removed: {self._wrap_quotes(file)}")
         else:
             passed.append(f"File not found check: {self._wrap_quotes(file)}")
diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
index 82b286fb44..176b0e9e65 100644
--- a/nf_core/lint/files_unchanged.py
+++ b/nf_core/lint/files_unchanged.py
@@ -1,8 +1,9 @@
 import filecmp
 import logging
-import os
 import shutil
 import tempfile
+from pathlib import Path
+from typing import Union
 
 import yaml
 
@@ -39,7 +40,6 @@ def files_unchanged(self):
         docs/images/nf-core-PIPELINE_logo_light.png
         docs/images/nf-core-PIPELINE_logo_dark.png
         docs/README.md'
-        lib/nfcore_external_java_deps.jar
         lib/NfcoreTemplate.groovy
         ['LICENSE', 'LICENSE.md', 'LICENCE', 'LICENCE.md'], # NB: British / American spelling
 
@@ -49,6 +49,10 @@ def files_unchanged(self):
         .prettierignore
         pyproject.toml
 
+    Files that need to be there or not based on a entry in nextflow config::
+
+        lib/nfcore_external_java_deps.jar # if config doesn't mention nf-validation
+
     .. tip:: You can configure the ``nf-core lint`` tests to ignore any of these checks by setting
              the ``files_unchanged`` key as follows in your ``.nf-core.yml`` config file. For example:
 
@@ -87,28 +91,30 @@ def files_unchanged(self):
         [".prettierrc.yml"],
         ["CODE_OF_CONDUCT.md"],
         ["LICENSE", "LICENSE.md", "LICENCE", "LICENCE.md"],  # NB: British / American spelling
-        [os.path.join(".github", ".dockstore.yml")],
-        [os.path.join(".github", "CONTRIBUTING.md")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "bug_report.yml")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "config.yml")],
-        [os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.yml")],
-        [os.path.join(".github", "PULL_REQUEST_TEMPLATE.md")],
-        [os.path.join(".github", "workflows", "branch.yml")],
-        [os.path.join(".github", "workflows", "linting_comment.yml")],
-        [os.path.join(".github", "workflows", "linting.yml")],
-        [os.path.join("assets", "email_template.html")],
-        [os.path.join("assets", "email_template.txt")],
-        [os.path.join("assets", "sendmail_template.txt")],
-        [os.path.join("assets", f"nf-core-{short_name}_logo_light.png")],
-        [os.path.join("docs", "images", f"nf-core-{short_name}_logo_light.png")],
-        [os.path.join("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
-        [os.path.join("docs", "README.md")],
-        [os.path.join("lib", "nfcore_external_java_deps.jar")],
-        [os.path.join("lib", "NfcoreTemplate.groovy")],
+        [Path(".github", ".dockstore.yml")],
+        [Path(".github", "CONTRIBUTING.md")],
+        [Path(".github", "ISSUE_TEMPLATE", "bug_report.yml")],
+        [Path(".github", "ISSUE_TEMPLATE", "config.yml")],
+        [Path(".github", "ISSUE_TEMPLATE", "feature_request.yml")],
+        [Path(".github", "PULL_REQUEST_TEMPLATE.md")],
+        [Path(".github", "workflows", "branch.yml")],
+        [Path(".github", "workflows", "linting_comment.yml")],
+        [Path(".github", "workflows", "linting.yml")],
+        [Path("assets", "email_template.html")],
+        [Path("assets", "email_template.txt")],
+        [Path("assets", "sendmail_template.txt")],
+        [Path("assets", f"nf-core-{short_name}_logo_light.png")],
+        [Path("docs", "images", f"nf-core-{short_name}_logo_light.png")],
+        [Path("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
+        [Path("docs", "README.md")],
+        [Path("lib", "NfcoreTemplate.groovy")],
     ]
     files_partial = [
         [".gitignore", ".prettierignore", "pyproject.toml"],
     ]
+    files_conditional = [
+        [Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf_validation"}],
+    ]
 
     # Only show error messages from pipeline creation
     logging.getLogger("nf_core.create").setLevel(logging.ERROR)
@@ -124,24 +130,24 @@ def files_unchanged(self):
         "prefix": prefix,
     }
 
-    template_yaml_path = os.path.join(tmp_dir, "template.yaml")
+    template_yaml_path = Path(tmp_dir, "template.yaml")
     with open(template_yaml_path, "w") as fh:
         yaml.dump(template_yaml, fh, default_flow_style=False)
 
-    test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")
+    test_pipeline_dir = Path(tmp_dir, f"{prefix}-{short_name}")
     create_obj = nf_core.create.PipelineCreate(
         None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path
     )
     create_obj.init_pipeline()
 
     # Helper functions for file paths
-    def _pf(file_path):
+    def _pf(file_path: Union[str, Path]) -> Path:
         """Helper function - get file path for pipeline file"""
-        return os.path.join(self.wf_path, file_path)
+        return Path(self.wf_path, file_path)
 
-    def _tf(file_path):
+    def _tf(file_path: Union[str, Path]) -> Path:
         """Helper function - get file path for template file"""
-        return os.path.join(test_pipeline_dir, file_path)
+        return Path(test_pipeline_dir, file_path)
 
     # Files that must be completely unchanged from template
     for files in files_exact:
@@ -151,7 +157,7 @@ def _tf(file_path):
             ignored.append(f"File ignored due to lint config: {self._wrap_quotes(files)}")
 
         # Ignore if we can't find the file
-        elif not any([os.path.isfile(_pf(f)) for f in files]):
+        elif not any([_pf(f).is_file() for f in files]):
             ignored.append(f"File does not exist: {self._wrap_quotes(files)}")
 
         # Check that the file has an identical match
@@ -180,7 +186,7 @@ def _tf(file_path):
             ignored.append(f"File ignored due to lint config: {self._wrap_quotes(files)}")
 
         # Ignore if we can't find the file
-        elif not any([os.path.isfile(_pf(f)) for f in files]):
+        elif not any([_pf(f).is_file() for f in files]):
             ignored.append(f"File does not exist: {self._wrap_quotes(files)}")
 
         # Check that the file contains the template file contents
@@ -208,6 +214,39 @@ def _tf(file_path):
                 except FileNotFoundError:
                     pass
 
+    # Files that should be there only if an entry in nextflow config is not set
+    for files in files_conditional:
+        # Ignore if file specified in linting config
+        ignore_files = self.lint_config.get("files_unchanged", [])
+        if files[0] in ignore_files:
+            ignored.append(f"File ignored due to lint config: {self._wrap_quotes(files)}")
+
+        # Ignore if we can't find the file
+        elif _pf(files[0]).is_file():
+            ignored.append(f"File does not exist: {self._wrap_quotes(files[0])}")
+
+        # Check that the file has an identical match
+        else:
+            config_key, config_value = list(files[1].items())[0]
+            if config_key in self.nf_config and self.nf_config[config_key] == config_value:
+                # Ignore if the config key is set to the expected value
+                ignored.append(f"File ignored due to config: {self._wrap_quotes(files)}")
+            else:
+                try:
+                    if filecmp.cmp(_pf(files[0]), _tf(files[0]), shallow=True):
+                        passed.append(f"`{files[0]}` matches the template")
+                    else:
+                        if "files_unchanged" in self.fix:
+                            # Try to fix the problem by overwriting the pipeline file
+                            shutil.copy(_tf(files[0]), _pf(files[0]))
+                            passed.append(f"`{files[0]}` matches the template")
+                            fixed.append(f"`{files[0]}` overwritten with template file")
+                        else:
+                            failed.append(f"`{files[0]}` does not match the template")
+                            could_fix = True
+                except FileNotFoundError:
+                    pass
+
     # cleaning up temporary dir
     shutil.rmtree(tmp_dir)
 
diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
index 328bc03759..1e0a6c4995 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -1,6 +1,9 @@
 import logging
 import os
 import re
+from pathlib import Path
+
+from nf_core.schema import PipelineSchema
 
 log = logging.getLogger(__name__)
 
@@ -113,6 +116,18 @@ def nextflow_config(self):
 
     * A ``test`` configuration profile should exist.
 
+    **The default values in ``nextflow.config`` should match the default values defined in the ``nextflow_schema.json``.**
+
+    .. tip:: You can choose to ignore tests for the default value of an specific parameter
+             by creating a file called ``.nf-core.yml`` in the root of your pipeline and creating
+             a list the config parameters that should be ignored. For example to ignore the default value for the input parameter:
+
+             .. code-block:: yaml
+
+                lint:
+                    nextflow_config:
+                        - config_defaults:
+                            - params.input
     """
     passed = []
     warned = []
@@ -347,4 +362,40 @@ def nextflow_config(self):
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
+    # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
+    ignore_defaults = []
+    for item in ignore_configs:
+        if isinstance(item, dict) and "config_defaults" in item:
+            ignore_defaults = item.get("config_defaults", [])
+    schema_path = Path(self.wf_path) / "nextflow_schema.json"
+    schema = PipelineSchema()
+    schema.schema_filename = schema_path
+    schema.no_prompts = True
+    schema.load_schema()
+    schema.get_schema_defaults()  # Get default values from schema
+    self.nf_config.keys()  # Params in nextflow.config
+    for param_name in schema.schema_defaults.keys():
+        param = "params." + param_name
+        # Convert booleans to strings if needed
+        schema_default = (
+            "true"
+            if str(schema.schema_defaults[param_name]) == "True"
+            else "false"
+            if str(schema.schema_defaults[param_name]) == "False"
+            else str(schema.schema_defaults[param_name])
+        )
+        if param in ignore_defaults:
+            ignored.append(f"Config default ignored: {param}")
+        elif param in self.nf_config.keys():
+            if str(self.nf_config[param]) == schema_default:
+                passed.append(f"Config default value correct: {param}")
+            else:
+                failed.append(
+                    f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
+                )
+        else:
+            failed.append(
+                f"Default value from the Nextflow schema '{param} = {self._wrap_quotes(schema_default)}' not found in `nextflow.config`."
+            )
+
     return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index d9986bd30f..71f235ef41 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -13,10 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
@@ -24,25 +31,59 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
-          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
 
       - name: Run pre-commit
-        run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
+
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.pre-commit.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
 
       - name: Commit & push changes
-        if: env.status == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with pre-commit"
-          git push {%- endraw %}
+          git commit -m "[automated] Fix code linting"
+          git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/{% endraw %}{{name}}{% raw %}/actions/runs/${{ github.run_id }}) for more details.{% endraw %}
diff --git a/nf_core/pipeline-template/lib/nfcore_external_java_deps.jar b/nf_core/pipeline-template/lib/nfcore_external_java_deps.jar
deleted file mode 100644
index 805c8bb5e4..0000000000
Binary files a/nf_core/pipeline-template/lib/nfcore_external_java_deps.jar and /dev/null differ
diff --git a/nf_core/pipeline-template/pyproject.toml b/nf_core/pipeline-template/pyproject.toml
index 984c091091..7d08e1c8ef 100644
--- a/nf_core/pipeline-template/pyproject.toml
+++ b/nf_core/pipeline-template/pyproject.toml
@@ -1,4 +1,4 @@
-# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Ruff.
+# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
 # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
 [tool.ruff]
 line-length = 120
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 558e9a1f9f..4583f2a9d6 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -127,6 +127,13 @@ workflow.onComplete {
     }
 }
 
+workflow.onError {
+    if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
+        println("🛑 Default resources exceed availability 🛑 ")
+        println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡")
+    }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 0b54056cfd..0c0590b0a3 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -420,11 +420,14 @@ def poll_nfcore_web_api(api_url, post_data=None):
         except requests.exceptions.ConnectionError:
             raise AssertionError(f"Could not connect to URL: {api_url}")
         else:
-            if response.status_code != 200:
+            if response.status_code != 200 and response.status_code != 301:
                 log.debug(f"Response content:\n{response.content}")
                 raise AssertionError(
                     f"Could not access remote API results: {api_url} (HTML {response.status_code} Error)"
                 )
+            # follow redirects
+            if response.status_code == 301:
+                return poll_nfcore_web_api(response.headers["Location"], post_data)
             try:
                 web_response = json.loads(response.content)
                 if "status" not in web_response:
diff --git a/tests/lint/files_exist.py b/tests/lint/files_exist.py
index 4e5e4d3c2b..5ba26d77a0 100644
--- a/tests/lint/files_exist.py
+++ b/tests/lint/files_exist.py
@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 
 import nf_core.lint
 
@@ -7,7 +8,7 @@ def test_files_exist_missing_config(self):
     """Lint test: critical files missing FAIL"""
     new_pipeline = self._make_pipeline_copy()
 
-    os.remove(os.path.join(new_pipeline, "CHANGELOG.md"))
+    Path(new_pipeline, "CHANGELOG.md").unlink()
 
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
@@ -21,7 +22,7 @@ def test_files_exist_missing_main(self):
     """Check if missing main issues warning"""
     new_pipeline = self._make_pipeline_copy()
 
-    os.remove(os.path.join(new_pipeline, "main.nf"))
+    Path(new_pipeline, "main.nf").unlink()
 
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
@@ -34,7 +35,7 @@ def test_files_exist_depreciated_file(self):
     """Check whether depreciated file issues warning"""
     new_pipeline = self._make_pipeline_copy()
 
-    nf = os.path.join(new_pipeline, "parameters.settings.json")
+    nf = Path(new_pipeline, "parameters.settings.json")
     os.system(f"touch {nf}")
 
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py
index 5d5f8e7345..60aaee5243 100644
--- a/tests/lint/nextflow_config.py
+++ b/tests/lint/nextflow_config.py
@@ -1,5 +1,6 @@
 import os
 import re
+from pathlib import Path
 
 import nf_core.create
 import nf_core.lint
@@ -53,3 +54,66 @@ def test_nextflow_config_missing_test_profile_failed(self):
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) > 0
     assert len(result["warned"]) == 0
+
+
+def test_default_values_match(self):
+    """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json."""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+    assert len(result["warned"]) == 0
+    assert "Config default value correct: params.max_cpus" in result["passed"]
+    assert "Config default value correct: params.validate_params" in result["passed"]
+
+
+def test_default_values_fail(self):
+    """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json."""
+    new_pipeline = self._make_pipeline_copy()
+    # Change the default value of max_cpus in nextflow.config
+    nf_conf_file = Path(new_pipeline) / "nextflow.config"
+    with open(nf_conf_file) as f:
+        content = f.read()
+        fail_content = re.sub(r"\bmax_cpus                   = 16\b", "max_cpus                   = 0", content)
+    with open(nf_conf_file, "w") as f:
+        f.write(fail_content)
+    # Change the default value of max_memory in nextflow_schema.json
+    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
+    with open(nf_schema_file) as f:
+        content = f.read()
+        fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content)
+        print(fail_content)
+    with open(nf_schema_file, "w") as f:
+        f.write(fail_content)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 2
+    assert (
+        "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`."
+        in result["failed"]
+    )
+    assert (
+        "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`."
+        in result["failed"]
+    )
+
+
+def test_default_values_ignored(self):
+    """Test ignoring linting of default values."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add max_cpus to the ignore list
+    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
+    with open(nf_core_yml, "w") as f:
+        f.write(
+            "repository_type: pipeline\nlint:\n  nextflow_config:\n    - config_defaults:\n      - params.max_cpus\n"
+        )
+    lint_obj = nf_core.lint.PipelineLint(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 "Config default value correct: params.max_cpus" not in result["passed"]
+    assert "Config default ignored: params.max_cpus" in result["ignored"]
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 32913bda0d..ff7e56744d 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -219,6 +219,9 @@ def test_sphinx_md_files(self):
         test_multiqc_incorrect_export_plots,
     )
     from .lint.nextflow_config import (  # type: ignore[misc]
+        test_default_values_fail,
+        test_default_values_ignored,
+        test_default_values_match,
         test_nextflow_config_bad_name_fail,
         test_nextflow_config_dev_in_release_mode_failed,
         test_nextflow_config_example_pass,