diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 7e90febb74..f07b31e9de 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -38,7 +38,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: go to subdirectory and change nextflow workdir
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 70125a10f3..1fb521b4bb 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -44,7 +44,7 @@ jobs:
       - name: Create Matrix
         id: create_matrix
         run: |
-          echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT
+          echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
     runs-on: ${{ matrix.runner }}
@@ -66,8 +66,6 @@ jobs:
             runner: ubuntu-latest
             profile: "docker"
         exclude:
-          - TEMPLATE: github
-          - TEMPLATE: is_nfcore
           - TEMPLATE: nf_core_configs
             profile: "self_hosted_runner"
       fail-fast: false
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index a95a477459..56c6c822a9 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -39,7 +39,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: go to working directory
diff --git a/.gitpod.yml b/.gitpod.yml
index b2fbb73133..efe193f35f 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,17 +6,14 @@ tasks:
       python -m pip install -r requirements-dev.txt
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
+  extensions:
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 815e980270..4f08d8419d 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: v0.5.6
+    rev: v0.6.0
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
index fff2a0bbb3..a98377e62c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,18 @@
 # nf-core/tools: Changelog
 
-## v2.14.2dev
+## v3.0.0dev
+
+**Highlights**
+
+- Pipeline commands are renamed from `nf-core <comand>` to `nf-core pipelines <command>` to follow the same command structure as modules and subworkflows commands.
+- More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it.
+- A new Text User Interface app when running `nf-core pipelines create` to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters)
+- We replaced nf-validation with nf-schema in the pipeline template
+- CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release.
+- New command `nf-core pipelines ro-crate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/) for a pipeline
+- `nf-core licences` command is deprecated.
+- The structure of nf-core/tools pytests has been updated
+- The structure of the API docs has been updated
 
 ### Template
 
@@ -9,66 +21,79 @@
 - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046))
 - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055))
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
+- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108), [#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
 - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
-- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108))
-- add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112))
+- add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
+- add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
+- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
+- add option to exclude nf-schema from the template ([#3116](https://github.com/nf-core/tools/pull/3116))
+- add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
+- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
+- add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
+- add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
+- run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
+- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
 
 ### Linting
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Remove defaults from conda `environment.yml` file. ([#3029](https://github.com/nf-core/tools/pull/3029))
 - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
+- Linting will now fail when an unpinned plugin is used ([#3116](https://github.com/nf-core/tools/pull/3116))
+- Linting will now check if the schema is correct for the used validation plugin ([#3116])(https://github.com/nf-core/tools/pull/3116)
+- Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(https://github.com/nf-core/tools/pull/3116)
+- Full linting for correct use of nf-schema and nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
+- Handle cases where the directory path contains the name of the component ([#3147](https://github.com/nf-core/tools/pull/3147))
+- Don't test conda `environment.yml` `name` attribute (which should no longer be there) ([#3161](https://github.com/nf-core/tools/pull/3161))
 
-### Download
+### Pipeline create command
+
+- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
+- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
+- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038))
+- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 
 ### Components
 
 - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005))
+- Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
+- Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 
 ### General
 
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))
-- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
 - move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983))
 - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
-- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
 - Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012))
 - README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017))
-- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020))
-- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031))
 - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036))
-- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
 - move pipeline commands to functions to avoid duplication ([#3039](https://github.com/nf-core/tools/pull/3039))
-- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038))
-- Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041))
-- Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048))
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
 - Add `--limit-output` argument for modules/subworkflow update ([#3047](https://github.com/nf-core/tools/pull/3047))
 - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
-- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061))
-- Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
-- Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
-- Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
-- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
-- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))
-- Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
+- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136))
+- fix syncing a pipeline from current directory ([#3143](https://github.com/nf-core/tools/pull/3143))
+- Patch gitpod conda setup to not use defaults channel ([#3159](https://github.com/nf-core/tools/pull/3159))
+
+## Version updates
+
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122))
+- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
+- Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124))
+- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
+- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058))
 - Update dependency prompt_toolkit to <=3.0.47 ([#3121](https://github.com/nf-core/tools/pull/3121))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
diff --git a/Dockerfile b/Dockerfile
index c88abcb1ce..fb1a867937 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:740d94a19218c8dd584b92f804b1158f85b0d241e5215ea26ed2dcade2b9d138
+FROM python:3.12-slim@sha256:59c7332a4a24373861c4a5f0eec2c92b87e3efeb8ddef011744ef9a751b1d11c
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 
diff --git a/MANIFEST.in b/MANIFEST.in
index 2bec403804..ce2e08c090 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -10,4 +10,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
 include nf_core/pipelines/create/create.tcss
-include nf_core/pipelines/create/templatefeatures.yml
+include nf_core/pipelines/create/template_features.yml
diff --git a/docs/api/_src/pipeline_lint_tests/plugin_includes.md b/docs/api/_src/pipeline_lint_tests/plugin_includes.md
new file mode 100644
index 0000000000..48bddadc80
--- /dev/null
+++ b/docs/api/_src/pipeline_lint_tests/plugin_includes.md
@@ -0,0 +1,5 @@
+# plugin_includes
+
+```{eval-rst}
+.. automethod:: nf_core.pipelines.lint.PipelineLint.plugin_includes
+```
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 153b8b7e75..0efea13ec9 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1136,6 +1136,13 @@ def command_modules_create(
 @modules.command("test")
 @click.pass_context
 @click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.option(
+    "-v",
+    "--verbose",
+    is_flag=True,
+    default=False,
+    help="Print verbose output to the console. Sets `--debug` inside the nf-test command.",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1171,10 +1178,12 @@ def command_modules_create(
     default=False,
     help="Migrate a module with pytest tests to nf-test",
 )
-def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest):
+def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose):
     """
     Run nf-test for a module.
     """
+    if verbose:
+        ctx.obj["verbose"] = verbose
     modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest)
 
 
diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index 4b6fa75f3e..23affb1d27 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -144,9 +144,12 @@ def pipelines_lint(
             ctx.obj["hide_progress"],
         )
         swf_failed = 0
+        module_failed = 0
         if subworkflow_lint_obj is not None:
             swf_failed = len(subworkflow_lint_obj.failed)
-        if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0:
+        if module_lint_obj is not None:
+            module_failed = len(module_lint_obj.failed)
+        if len(lint_obj.failed) + module_failed + swf_failed > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index d0f6685365..c1b1f24cb7 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -114,9 +114,7 @@ def __init__(
                         )
                     )
             if not self.all_remote_components:
-                raise LookupError(
-                    f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
-                )
+                log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
             local_component_dir = Path(self.directory, self.component_type, "local")
 
             if local_component_dir.exists():
@@ -146,7 +144,7 @@ def __init__(
             ]
             self.all_local_components = []
             if not self.all_remote_components:
-                raise LookupError(f"No {self.component_type} in '{self.component_type}' directory")
+                log.warning(f"No {self.component_type} in '{self.component_type}' directory")
 
             # This could be better, perhaps glob for all nextflow.config files in?
             self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True)
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index db3196be91..0f3cdcdfbd 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -64,7 +64,15 @@ def __init__(
             self.process_name = ""
             self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
-            repo_dir = self.component_dir.parts[: self.component_dir.parts.index(self.component_name.split("/")[0])][-1]
+            component_list = self.component_name.split("/")
+
+            name_index = len(self.component_dir.parts) - 1 - self.component_dir.parts[::-1].index(component_list[0])
+            if len(component_list) != 1 and component_list[0] == component_list[1]:
+                # Handle cases where the subtool has the same name as the tool
+                name_index -= 1
+
+            repo_dir = self.component_dir.parts[:name_index][-1]
+
             self.org = repo_dir
             self.nftest_testdir = Path(self.component_dir, "tests")
             self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")
diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index fd0e8bb799..c462c6a47e 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -1,6 +1,7 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
+# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
 FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c
 
 USER root
@@ -40,12 +41,11 @@ RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core
 
 # Change user to gitpod
 USER gitpod
-# Install nextflow, nf-core, Mamba, and pytest-workflow
-RUN conda config --add channels defaults && \
-    conda config --add channels bioconda && \
+# Install nextflow, nf-core, nf-test, and other useful tools
+RUN conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
-    conda install --quiet --yes --name base \
+    conda install --quiet --yes --update-all --name base \
     nextflow \
     nf-test \
     prettier \
@@ -63,3 +63,4 @@ RUN nextflow self-update && \
 # Setup pdiff for nf-test diffs
 ENV NFT_DIFF="pdiff"
 ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+ENV JAVA_TOOL_OPTIONS=
diff --git a/nf_core/module-template/environment.yml b/nf_core/module-template/environment.yml
index dcf510affb..a8a40a8e03 100644
--- a/nf_core/module-template/environment.yml
+++ b/nf_core/module-template/environment.yml
@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "{{ component_name_underscore }}"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index b75f7e7570..017b3965b4 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -110,7 +110,7 @@ def lint(
         """
         # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class
         # Prompt for module or all
-        if module is None and not all_modules:
+        if module is None and not all_modules and len(self.all_remote_components) > 0:
             questions = [
                 {
                     "type": "list",
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index 341b9cd730..4488b0befa 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -90,42 +90,3 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
                 env_yml["dependencies"].sort()
                 with open(Path(module.component_dir, "environment.yml"), "w") as fh:
                     yaml.dump(env_yml, fh, Dumper=custom_yaml_dumper())
-
-            # Check that the name in the environment.yml file matches the name in the meta.yml file
-            with open(Path(module.component_dir, "meta.yml")) as fh:
-                meta_yml = yaml.safe_load(fh)
-
-            if env_yml["name"] == meta_yml["name"]:
-                module.passed.append(
-                    (
-                        "environment_yml_name",
-                        "The module's `environment.yml` name matches module name",
-                        module.environment_yml,
-                    )
-                )
-            else:
-                module.failed.append(
-                    (
-                        "environment_yml_name",
-                        f"Conflicting process name between environment.yml (`{env_yml['name']}`) and meta.yml (`{module.component_name}`)",
-                        module.environment_yml,
-                    )
-                )
-
-            # Check that the name is lowercase
-            if env_yml["name"] == env_yml["name"].lower():
-                module.passed.append(
-                    (
-                        "environment_yml_name_lowercase",
-                        "The module's `environment.yml` name is lowercase",
-                        module.environment_yml,
-                    )
-                )
-            else:
-                module.failed.append(
-                    (
-                        "environment_yml_name_lowercase",
-                        "The module's `environment.yml` name is not lowercase",
-                        module.environment_yml,
-                    )
-                )
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index 72dda289a0..5145366e50 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -11,6 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
+{%- if modules %}
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -24,9 +25,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
+{%- endif %}
 
+{%- if email %}
 [/assets/email*]
 indent_size = unset
+{%- endif %}
 
 # ignore python and markdown
 [*.{py,md}]
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index 5a58501bb2..f331d38673 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -30,16 +30,18 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+{%- if test_config %}
 You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
 
 ```bash
 nf-test test --profile debug,test,docker --verbose
 ```
 
+{% endif %}
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
-There are typically two types of tests that run:
+{% if test_config %}There are typically two types of tests that run:{% endif %}
 
 ### Lint tests
 
@@ -48,12 +50,15 @@ To enforce these and ensure that all pipelines stay in sync, we have developed a
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
+{%- if test_config %}
+
 ### Pipeline tests
 
 Each `nf-core` pipeline should be set up with a minimal set of test-data.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
+{%- endif %}
 
 ## Patch
 
diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
index dee23ccab1..c96f2dd4c2 100644
--- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
+++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
@@ -20,8 +20,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
 - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
       {%- endif %}
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
+      {%- if test_config %}
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
+      {%- endif %}
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 6b2547765d..63fa99cec8 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 99a42d86d2..e7a28e5ac4 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -68,7 +68,7 @@ jobs:
           --download-configuration
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
@@ -83,4 +83,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}{% endif %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index ecd5e32f6c..dbba830ec1 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -53,12 +53,21 @@ jobs:
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
       - name: Save PR number
         if: ${{ always() }}
         run: echo ${{ github.event.pull_request.number }} > PR_number.txt
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
index 30e85ed977..5907fb59c9 100644
--- a/nf_core/pipeline-template/.gitpod.yml
+++ b/nf_core/pipeline-template/.gitpod.yml
@@ -4,9 +4,6 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
@@ -15,7 +12,7 @@ vscode:
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %}
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff
diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore
index 437d763d0c..c8e8ad9e11 100644
--- a/nf_core/pipeline-template/.prettierignore
+++ b/nf_core/pipeline-template/.prettierignore
@@ -1,6 +1,12 @@
+{%- if email %}
 email_template.html
+{%- endif %}
+{%- if adaptivecard %}
 adaptivecard.json
+{%- endif %}
+{%- if slackreport %}
 slackreport.json
+{%- endif %}
 .nextflow*
 work/
 data/
diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
index 7cf37e5018..2373f1de7f 100644
--- a/nf_core/pipeline-template/CITATIONS.md
+++ b/nf_core/pipeline-template/CITATIONS.md
@@ -12,11 +12,10 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+{% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
-
-{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> {% endif %} > {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 > {%- endif %}
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 7718d2e5f8..beb45ed511 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -7,6 +7,10 @@
   </picture>
 </h1>
 
+{%- else %}
+
+# {{ name }}
+
 {% endif -%}
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/ci.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/ci.yml)
@@ -16,7 +20,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -44,13 +48,13 @@
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-   {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
+{% if fastqc %}1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)){% endif %}
+{% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %}
 
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {% if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %}
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
diff --git a/nf_core/pipeline-template/assets/schema_input.json b/nf_core/pipeline-template/assets/schema_input.json
index e76b95fa99..28a468adaf 100644
--- a/nf_core/pipeline-template/assets/schema_input.json
+++ b/nf_core/pipeline-template/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/{{ name }}/master/assets/schema_input.json",
     "title": "{{ name }} pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
index 84972d8e24..35e861d9b1 100644
--- a/nf_core/pipeline-template/conf/modules.config
+++ b/nf_core/pipeline-template/conf/modules.config
@@ -18,9 +18,11 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    {% if fastqc -%}
     withName: FASTQC {
         ext.args = '--quiet'
     }
+    {%- endif %}
 
     {%- if multiqc %}
     withName: 'MULTIQC' {
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index edd48b83f4..5e42d50cc5 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -12,10 +12,13 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [FastQC](#fastqc) - Raw read QC
-  {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
+{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %}
+{% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %}
+
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
+{%- if fastqc %}
+
 ### FastQC
 
 <details markdown="1">
@@ -28,7 +31,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 </details>
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
-
+{%- endif %}
 {%- if multiqc %}
 
 ### MultiQC
@@ -55,7 +58,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 - `pipeline_info/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
+    {% if email %}- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %}
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
   - Parameters used by the pipeline run: `params.json`.
 
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index 1dc033eea5..ae2761797a 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -148,9 +148,12 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
 If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
 
+{%- if test_config %}
+
 - `test`
   - A profile with a complete configuration for automated testing
   - Includes links to test data so needs no other parameters
+    {%- endif %}
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
 - `singularity`
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index fddfc5489e..6516ebf90e 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -18,9 +18,10 @@
 */
 
 include { {{ short_name|upper }}  } from './workflows/{{ short_name }}'
+{%- if modules %}
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
-{% if igenomes %}
+{%- if igenomes %}
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 
 /*
@@ -33,7 +34,7 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ s
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
 params.fasta = getGenomeAttribute('fasta')
-{% endif %}
+{% endif %}{% endif %}
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -56,10 +57,10 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} {
     {{ short_name|upper }} (
         samplesheet
     )
-{%- if multiqc %}
+{%- if multiqc %}{%- if modules %}
     emit:
     multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html
-{%- endif %}
+{%- endif %}{%- endif %}
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -71,38 +72,46 @@ workflow {
 
     main:
 
+    {%- if modules %}
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
         params.outdir,
         params.input
     )
-
+    {% endif %}
     //
     // WORKFLOW: Run main workflow
     //
     {{ prefix_nodash|upper }}_{{ short_name|upper }} (
+        {%- if modules %}
         PIPELINE_INITIALISATION.out.samplesheet
+        {%- else %}
+        params.input
+        {%- endif %}
     )
 
+    {%- if modules %}
     //
     // SUBWORKFLOW: Run completion tasks
     //
     PIPELINE_COMPLETION (
+        {%- if email %}
         params.email,
         params.email_on_fail,
         params.plaintext_email,
+        {%- endif %}
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
-        {%- if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
+        {% if adaptivecard or slackreport %}params.hook_url,{% endif %}
+        {% if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %}
     )
+    {%- endif %}
 }
 
 /*
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index eb9391b29a..367202155a 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -5,11 +5,12 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    {%- if fastqc %}
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
-                    }{%- if multiqc %},
+                    }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
@@ -22,19 +23,19 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfvalidation_plugin": {
+                    }{% if nf_schema %},
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
-                    }
+                    }{% endif %}
                 }
             }
         }
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
index 1787b38a9a..0d5be45f26 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
@@ -2,6 +2,5 @@ name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
index ca39fb67e2..329ddb4870 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -2,6 +2,5 @@ name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::multiqc=1.21
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 0469d6cfec..8201916b3f 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -31,15 +31,19 @@ params {
 
     // Boilerplate options
     outdir                       = null
-    publish_dir_mode             = 'copy'
+    {% if modules %}publish_dir_mode             = 'copy'{% endif %}
+    {%- if email %}
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
-    monochrome_logs              = false
-    hook_url                     = null
-    help                         = false
+    {%- endif %}
+    {% if modules %}monochrome_logs              = false{% endif %}
+    {% if slackreport or adaptivecard %}hook_url                     = null{% endif %}
+    {% if nf_schema %}help                         = false
+    help_full                    = false
+    show_hidden                  = false{% endif %}
     version                      = false
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
     {%- if nf_core_configs %}
     // Config options
@@ -58,18 +62,26 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
+    {%- if nf_schema %}
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
+    validate_params            = true
+    {% endif %}
 }
-
+{% if modules %}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
+{%- else %}
+process {
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 1
+    maxErrors     = '-1'
+}
+{% endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
 try {
@@ -100,7 +112,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -187,8 +199,10 @@ profiles {
         executor.memory         = 8.GB
     }
     {%- endif %}
+    {%- if test_config %}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
+    {%- endif %}
 }
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
@@ -200,11 +214,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
-
 {% if igenomes -%}
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
@@ -262,14 +271,53 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=23.10.0'
     version         = '{{ version }}'
     doi             = ''
 }
 
+{% if nf_schema -%}
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+validation {
+    defaultIgnoreParams = ["genomes", "helpFull", "showHidden", "help-full", "show-hidden"] // The last 4 parameters are here because of a bug in nf-schema. This will be fixed in a later version
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        {%- if is_nfcore %}
+        beforeText = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+  https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""{% endif %}
+    }{% if is_nfcore %}
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
+    }{% endif %}
+}
+{% endif -%}
+{%- if modules %}
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-
+{% endif %}
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 4a1a22c3ee..446da25aed 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/{{ name }}/master/nextflow_schema.json",
     "title": "{{ name }} pipeline parameters",
     "description": "{{ description }}",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -28,20 +28,19 @@
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
-                },
+                }{% if email %},
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                }{% if multiqc %},
+                }{% endif %}{% if multiqc %},
                 "multiqc_title": {
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
-                }
-                {% endif %}
+                }{% endif %}
             }
         },
         {%- if igenomes %}
@@ -57,6 +56,7 @@
                     "fa_icon": "fas fa-book",
                     "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                 },
+                {%- if modules %}
                 "fasta": {
                     "type": "string",
                     "format": "file-path",
@@ -67,12 +67,21 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
+                {%- endif %}
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
                 }
             }
         },
@@ -169,18 +178,13 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
                 },
+                {%- if modules %}
                 "publish_dir_mode": {
                     "type": "string",
                     "default": "copy",
@@ -189,7 +193,7 @@
                     "fa_icon": "fas fa-copy",
                     "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
-                },
+                },{% endif %}{% if email %}
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -203,7 +207,7 @@
                     "description": "Send plain-text email instead of HTML.",
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
-                },
+                },{% endif %}
                 {%- if multiqc %}
                 "max_multiqc_email_size": {
                     "type": "string",
@@ -212,21 +216,22 @@
                     "default": "25.MB",
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
-                },
-                {% endif %}
+                },{% endif %}
+                {%- if modules %}
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
                     "hidden": true
-                },
+                },{% endif %}
+                {%- if slackreport or adaptivecard %}
                 "hook_url": {
                     "type": "string",
                     "description": "Incoming hook URL for messaging service",
                     "fa_icon": "fas fa-people-group",
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
-                },
+                },{% endif %}
                 {%- if multiqc %}
                 "multiqc_config": {
                     "type": "string",
@@ -252,53 +257,32 @@
                     "default": true,
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
-                },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
+                }{% if test_config %},
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
-                }
+                }{% endif %}
             }
         }
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {% if igenomes %}{
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/reference_genome_options"
         },{% endif %}
         {% if nf_core_configs %}{
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/institutional_config_options"
         },{% endif %}
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 72c9be85eb..ae66f3674c 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -8,17 +8,18 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+{% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'{% endif %}
+{%- if email %}
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+{%- if adaptivecard or slackreport %}
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+{%- endif %}
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ========================================================================================
@@ -30,7 +31,6 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -51,20 +51,16 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+    {% if nf_schema %}
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
+    {% endif %}
 
     //
     // Check config provided to the pipeline
@@ -83,8 +79,14 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
-    Channel
-        .fromSamplesheet("input")
+
+    Channel{% if nf_schema %}
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")){% else %}
+        .fromPath(params.input)
+        .splitCsv(header: true, strip: true)
+        .map { row ->
+            [[id:row.sample], row.fastq_1, row.fastq_2]
+        }{% endif %}
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -117,35 +119,48 @@ workflow PIPELINE_INITIALISATION {
 workflow PIPELINE_COMPLETION {
 
     take:
+    {%- if email %}
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
+    {% endif %}
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url        //  string: hook URL for notifications
+    {% if adaptivecard or slackreport %}hook_url        //  string: hook URL for notifications{% endif %}
     {% if multiqc %}multiqc_report  //  string: Path to MultiQC report{% endif %}
 
     main:
-
+    {%- if nf_schema %}
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    {%- else %}
+    summary_params = [:]
+    {%- endif %}
 
     //
     // Completion email and summary
     //
     workflow.onComplete {
+        {%- if email %}
         if (email || email_on_fail) {
-            {%- if multiqc %}
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
-            {%- else %}
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, [])
-            {%- endif %}
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                {% if multiqc %}multiqc_report.toList(){% else %}[]{% endif %}
+            )
         }
+        {%- endif %}
 
         completionSummary(monochrome_logs)
 
+        {%- if adaptivecard or slackreport %}
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
+        {%- endif %}
     }
 
     workflow.onError {
@@ -220,8 +235,8 @@ def toolCitationText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
             "Tools used in the workflow included:",
-            "FastQC (Andrews 2010),",
-            "MultiQC (Ewels et al. 2016)",
+            {% if fastqc %}"FastQC (Andrews 2010),",{% endif %}
+            {% if multiqc %}"MultiQC (Ewels et al. 2016)",{% endif %}
             "."
         ].join(' ').trim()
 
@@ -233,8 +248,8 @@ def toolBibliographyText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+            {% if fastqc %}"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",{% endif %}
+            {% if multiqc %}"<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"{% endif %}
         ].join(' ').trim()
 
     return reference_text
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f66..28e32b200e 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf6d..a09572e5bb 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3927..cbd8495bb6 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
     // Using a loop to handle multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
         temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 0000000000..4994303ea0
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 0000000000..f7d9f02885
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 0000000000..842dc432af
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 0000000000..0907ac58f0
--- /dev/null
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c93e..331e0d2f44 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65d1b..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
-    validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b04f5..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
deleted file mode 100644
index 5784a33f2f..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,200 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-                outdir          = 1
-            }
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-}
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff49..0000000000
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index d98c392f0c..5b7e0ff143 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -4,12 +4,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+{%- if modules %}
+{% if fastqc %}include { FASTQC                 } from '../modules/nf-core/fastqc/main'{% endif %}
 {% if multiqc %}include { MULTIQC                } from '../modules/nf-core/multiqc/main'{% endif %}
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+{% if nf_schema %}include { paramsSummaryMap       } from 'plugin/nf-schema'{% endif %}
 {% if multiqc %}include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %}
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %}
+{%- endif %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -22,11 +24,13 @@ workflow {{ short_name|upper }} {
     take:
     ch_samplesheet // channel: samplesheet read in from --input
 
+    {%- if modules %}
     main:
 
     ch_versions = Channel.empty()
     {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %}
 
+    {%- if fastqc %}
     //
     // MODULE: Run FastQC
     //
@@ -35,6 +39,7 @@ workflow {{ short_name|upper }} {
     )
     {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %}
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    {%- endif %}
 
     //
     // Collate and save software versions
@@ -42,7 +47,7 @@ workflow {{ short_name|upper }} {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
@@ -60,9 +65,13 @@ workflow {{ short_name|upper }} {
         Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
         Channel.empty()
 
+    {% if nf_schema %}
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    {% endif %}
 
     {%- if citations %}
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
@@ -72,8 +81,6 @@ workflow {{ short_name|upper }} {
         methodsDescriptionText(ch_multiqc_custom_methods_description))
     {%- endif %}
 
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     {%- if citations %}
     ch_multiqc_files = ch_multiqc_files.mix(
@@ -94,6 +101,7 @@ workflow {{ short_name|upper }} {
     emit:
     {%- if multiqc %}multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html{% endif %}
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
+{% endif %}
 }
 
 /*
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 05b04a5422..8e1d46c690 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -70,6 +70,8 @@ def __init__(
                     self.config = CreateConfig(**config_yml["template"].model_dump())
                 else:
                     raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
+                # Update the output directory
+                self.config.outdir = outdir if outdir else Path().cwd()
             except (FileNotFoundError, UserWarning):
                 log.debug("The '.nf-core.yml' configuration file was not found.")
         elif (name and description and author) or (
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/template_features.yml
similarity index 58%
rename from nf_core/pipelines/create/templatefeatures.yml
rename to nf_core/pipelines/create/template_features.yml
index b97bf347ab..b59a2e51a6 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -1,10 +1,18 @@
 github:
   skippable_paths:
-    - ".github/"
-    - ".gitignore"
-  short_description: "Skip the creation of a local Git repository."
-  description: ""
-  help_text: ""
+    - ".github"
+    - ".gitattributes"
+  short_description: "Use a GitHub repository."
+  description: "Create a GitHub repository for the pipeline."
+  help_text: |
+    This will create a GitHub repository for the pipeline.
+
+    The repository will include:
+    - Continuous Integration (CI) tests
+    - Issues and pull requests templates
+
+    The initialisation of a git repository is required to use the nf-core/tools.
+    This means that even if you unselect this option, your pipeline will still contain a `.git` directory and `.gitignore` file.
   linting:
     files_exist:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
@@ -12,7 +20,6 @@ github:
       - ".github/PULL_REQUEST_TEMPLATE.md"
       - ".github/CONTRIBUTING.md"
       - ".github/.dockstore.yml"
-      - ".gitignore"
     files_unchanged:
       - ".github/ISSUE_TEMPLATE/bug_report.yml"
       - ".github/ISSUE_TEMPLATE/config.yml"
@@ -26,7 +33,7 @@ github:
     readme:
       - "nextflow_badge"
   nfcore_pipelines: False
-  custom_pipelines: False
+  custom_pipelines: True
 ci:
   skippable_paths:
     - ".github/workflows/"
@@ -141,6 +148,10 @@ is_nfcore:
     nextflow_config:
       - "manifest.name"
       - "manifest.homePage"
+      - "validation.help.beforeText"
+      - "validation.help.afterText"
+      - "validation.summary.beforeText"
+      - "validation.summary.afterText"
     multiqc_config:
       - "report_comment"
   nfcore_pipelines: False
@@ -228,6 +239,39 @@ multiqc:
     multiqc_config: False
   nfcore_pipelines: True
   custom_pipelines: True
+fastqc:
+  skippable_paths:
+    - "modules/nf-core/fastqc/"
+  short_description: "Use fastqc"
+  description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files."
+  help_text: |
+    FastQC is a tool which provides quality control checks on raw sequencing data.
+    The pipeline will include the FastQC module.
+  nfcore_pipelines: True
+  custom_pipelines: True
+modules:
+  skippable_paths:
+    - "conf/base.config"
+    - "conf/modules.config"
+    - "modules.json"
+    - "modules"
+    - "subworkflows"
+  short_description: "Use nf-core components"
+  description: "Include all required files to use nf-core modules and subworkflows"
+  help_text: |
+    It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline.
+    This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands.
+  linting:
+    nfcore_components: False
+    modules_json: False
+    base_config: False
+    modules_config: False
+    files_exist:
+      - "conf/base.config"
+      - "conf/modules.config"
+      - "modules.json"
+  nfcore_pipelines: False
+  custom_pipelines: True
 changelog:
   skippable_paths:
     - "CHANGELOG.md"
@@ -242,3 +286,142 @@ changelog:
       - "CHANGELOG.md"
   nfcore_pipelines: False
   custom_pipelines: True
+nf_schema:
+  skippable_paths:
+    - "subworkflows/nf-core/utils_nfschema_plugin"
+    - "nextflow_schema.json"
+    - "assets/schema_input.json"
+    - "assets/samplesheet.csv"
+  short_description: "Use nf-schema"
+  description: "Use the nf-schema Nextflow plugin for this pipeline."
+  help_text: |
+    [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
+    It also provides helper functionality to create help messages, get a summary
+    of changed parameters and validate and convert a samplesheet to a channel.
+  linting:
+    files_exist:
+      - "nextflow_schema.json"
+    schema_params: False
+    schema_lint: False
+    schema_description: False
+    nextflow_config: False
+  nfcore_pipelines: True
+  custom_pipelines: True
+license:
+  skippable_paths:
+    - "LICENSE"
+  short_description: "Add a license File"
+  description: "Add the MIT license file."
+  help_text: |
+    To protect the copyright of the pipeline, you can add a LICENSE file.
+    This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT
+  linting:
+    files_exist:
+      - "LICENSE"
+    files_unchanged:
+      - "LICENSE"
+  nfcore_pipelines: False
+  custom_pipelines: True
+email:
+  skippable_paths:
+    - "assets/email_template.html"
+    - "assets/sendmail_template.txt"
+    - "assets/email_template.txt"
+  short_description: "Enable email updates"
+  description: "Enable sending emails on pipeline completion."
+  help_text: |
+    Enable the option of sending an email which will include pipeline execution reports on pipeline completion.
+  linting:
+    files_exist:
+      - "assets/email_template.html"
+      - "assets/sendmail_template.txt"
+      - "assets/email_template.txt"
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True
+adaptivecard:
+  skippable_paths:
+    - "assets/adaptivecard.json"
+  short_description: "Support Microsoft Teams notifications"
+  description: "Enable pipeline status update messages through Microsoft Teams"
+  help_text: |
+    This adds an Adaptive Card. A snippets of user interface.
+    This Adaptive Card is used as a template for pipeline update messages and it is compatible with Microsoft Teams.
+  linting:
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True
+slackreport:
+  skippable_paths:
+    - "assets/slackreport.json"
+  short_description: "Support Slack notifications"
+  description: "Enable pipeline status update messages through Slack"
+  help_text: |
+    This adds an JSON template used as a template for pipeline update messages in Slack.
+  linting:
+    files_unchanged:
+      - ".prettierignore"
+  nfcore_pipelines: False
+  custom_pipelines: True
+documentation:
+  skippable_paths:
+    - "docs"
+  short_description: "Add documentation"
+  description: "Add documentation to the pipeline"
+  help_text: |
+    This will add documentation markdown files where you can describe your pipeline.
+    It includes:
+    - docs/README.md: A README file where you can describe the structure of your documentation.
+    - docs/output.md: A file where you can explain the output generated by the pipeline
+    - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.
+
+    These files come with an exemplary documentation structure written.
+  linting:
+    files_exist:
+      - "docs/output.md"
+      - "docs/README.md"
+      - "docs/usage.md"
+  nfcore_pipelines: False
+  custom_pipelines: True
+test_config:
+  skippable_paths:
+    - "conf/test.config"
+    - "conf/test_full.config"
+    - ".github/workflows/awsfulltest.yml"
+    - ".github/workflows/awstest.yml"
+    - ".github/workflows/ci.yml"
+  short_description: "Add testing profiles"
+  description: "Add two default testing profiles"
+  help_text: |
+    This will add two default testing profiles to run the pipeline with different inputs.
+    You can customise them and add other test profiles.
+
+    These profiles can be used to run the pipeline with a minimal testing dataset with `nextflow run <your_pipeline> -profile test`.
+
+    The pipeline will include two profiles: `test` and `test_full`.
+    In nf-core, we typically use the `test` profile to run the pipeline with a minimal dataset and the `test_full` to run the pipeline with a larger dataset that simulates a real-world scenario.
+  linting:
+    files_exist:
+      - "conf/test.config"
+      - "conf/test_full.config"
+      - ".github/workflows/ci.yml"
+    nextflow_config: False
+    files_unchanged:
+      - ".github/CONTRIBUTING.md"
+      - ".github/PULL_REQUEST_TEMPLATE.md"
+  nfcore_pipelines: False
+  custom_pipelines: True
+seqera_platform:
+  skippable_paths:
+    - "tower.yml"
+  short_description: "Add Seqera Platform output"
+  description: "Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform"
+  help_text: |
+    When launching a pipeline with the Seqera Platform, a `tower.yml` file can be used to add configuration options.
+
+    In the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform.
+    You can extend this file adding any other desired configuration.
+  nfcore_pipelines: False
+  custom_pipelines: True
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 0b72c2bcf5..9b331c2a3b 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -37,7 +37,7 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]:
 NFCORE_PIPELINE_GLOBAL: bool = True
 
 # YAML file describing template features
-features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml"
+features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "template_features.yml"
 
 
 class CreateConfig(NFCoreTemplateConfig):
diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index e03982a25a..a80639ea94 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -263,15 +263,21 @@ def set_schema_inputs(self):
 
     def merge_nxf_flag_schema(self):
         """Take the Nextflow flag schema and merge it with the pipeline schema"""
+        if "allOf" not in self.schema_obj.schema:
+            self.schema_obj.schema["allOf"] = []
         # Add the coreNextflow subschema to the schema definitions
-        if "definitions" not in self.schema_obj.schema:
+        if "$defs" in self.schema_obj.schema or "definitions" not in self.schema_obj.schema:
+            if "$defs" not in self.schema_obj.schema:
+                self.schema_obj["$defs"] = {}
+            self.schema_obj.schema["$defs"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/$defs/coreNextflow"})
+
+        if "definitions" in self.schema_obj.schema:
             self.schema_obj.schema["definitions"] = {}
-        self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["definitions"].update(self.nxf_flag_schema)
+            self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
         # Add the new defintion to the allOf key so that it's included in validation
         # Put it at the start of the list so that it comes first
-        if "allOf" not in self.schema_obj.schema:
-            self.schema_obj.schema["allOf"] = []
-        self.schema_obj.schema["allOf"].insert(0, {"$ref": "#/definitions/coreNextflow"})
 
     def prompt_web_gui(self):
         """Ask whether to use the web-based or cli wizard to collect params"""
@@ -379,7 +385,8 @@ def sanitise_web_response(self):
         for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():
             questionary_objects[param_id] = self.single_param_to_questionary(param_id, param_obj, print_help=False)
 
-        for _, definition in self.schema_obj.schema.get("definitions", {}).items():
+        definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema.get("definitions", {})).items()
+        for _, definition in definitions_schemas:
             for param_id, param_obj in definition.get("properties", {}).items():
                 questionary_objects[param_id] = self.single_param_to_questionary(param_id, param_obj, print_help=False)
 
@@ -399,9 +406,10 @@ def prompt_schema(self):
         """Go through the pipeline schema and prompt user to change defaults"""
         answers = {}
         # Start with the subschema in the definitions - use order of allOf
+        definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema.get("definitions", {})).items()
         for allOf in self.schema_obj.schema.get("allOf", []):
             d_key = allOf["$ref"][14:]
-            answers.update(self.prompt_group(d_key, self.schema_obj.schema["definitions"][d_key]))
+            answers.update(self.prompt_group(d_key, definitions_schemas[d_key]))
 
         # Top level schema params
         for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index ed833d3219..6d27351b62 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -9,7 +9,7 @@
 import logging
 import os
 from pathlib import Path
-from typing import List, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import git
 import rich
@@ -45,6 +45,7 @@
 from .nfcore_yml import nfcore_yml
 from .pipeline_name_conventions import pipeline_name_conventions
 from .pipeline_todos import pipeline_todos
+from .plugin_includes import plugin_includes
 from .readme import readme
 from .schema_description import schema_description
 from .schema_lint import schema_lint
@@ -92,6 +93,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     nfcore_yml = nfcore_yml
     pipeline_name_conventions = pipeline_name_conventions
     pipeline_todos = pipeline_todos
+    plugin_includes = plugin_includes
     readme = readme
     schema_description = schema_description
     schema_lint = schema_lint
@@ -135,6 +137,7 @@ def _get_all_lint_tests(release_mode):
             "actions_awsfulltest",
             "readme",
             "pipeline_todos",
+            "plugin_includes",
             "pipeline_name_conventions",
             "template_strings",
             "schema_lint",
@@ -174,7 +177,8 @@ def _load_lint_config(self) -> bool:
         # 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 not in self.lint_tests:
+                if 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
 
@@ -543,7 +547,7 @@ def run_linting(
     md_fn=None,
     json_fn=None,
     hide_progress: bool = False,
-) -> Tuple[PipelineLint, ComponentLint, Union[ComponentLint, None]]:
+) -> Tuple[PipelineLint, Optional[ComponentLint], Optional[ComponentLint]]:
     """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 :class:`PipelineLint` after finished.
@@ -588,41 +592,45 @@ def run_linting(
     lint_obj._load_lint_config()
     lint_obj.load_pipeline_config()
 
-    # Create the modules lint object
-    module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
-    # Create the subworkflows lint object
-    try:
-        subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
-    except LookupError:
+    if "nfcore_components" in lint_obj.lint_config and not lint_obj.lint_config["nfcore_components"]:
+        module_lint_obj = None
         subworkflow_lint_obj = None
-
-    # Verify that the pipeline is correctly configured and has  a modules.json file
-    module_lint_obj.has_valid_directory()
-    module_lint_obj.has_modules_file()
-    # Run only the tests we want
-    if key:
-        # Select only the module lint tests
-        module_lint_tests = list(
-            set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
-        )
-        # Select only the subworkflow lint tests
-        subworkflow_lint_tests = list(
-            set(key).intersection(
-                set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
-            )
-        )
     else:
-        # If no key is supplied, run the default modules tests
-        module_lint_tests = list(("module_changes", "module_version"))
-        subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
-    module_lint_obj.filter_tests_by_key(module_lint_tests)
-    if subworkflow_lint_obj is not None:
-        subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
-
-    # 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()
+        # Create the modules lint object
+        module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
+        # Create the subworkflows lint object
+        try:
+            subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
+        except LookupError:
+            subworkflow_lint_obj = None
+
+        # Verify that the pipeline is correctly configured and has  a modules.json file
+        module_lint_obj.has_valid_directory()
+        module_lint_obj.has_modules_file()
+        # Run only the tests we want
+        if key:
+            # Select only the module lint tests
+            module_lint_tests = list(
+                set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
+            )
+            # Select only the subworkflow lint tests
+            subworkflow_lint_tests = list(
+                set(key).intersection(
+                    set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
+                )
+            )
+        else:
+            # If no key is supplied, run the default modules tests
+            module_lint_tests = list(("module_changes", "module_version"))
+            subworkflow_lint_tests = list(("subworkflow_changes", "subworkflow_version"))
+        module_lint_obj.filter_tests_by_key(module_lint_tests)
+        if subworkflow_lint_obj is not None:
+            subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
+
+        # 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:
@@ -632,13 +640,14 @@ def run_linting(
         log.info("Stopping tests...")
         return lint_obj, module_lint_obj, subworkflow_lint_obj
 
-    # Run the module lint tests
-    if len(module_lint_obj.all_local_components) > 0:
-        module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
-    if len(module_lint_obj.all_remote_components) > 0:
-        module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
-    # Run the subworkflows lint tests
+    if module_lint_obj is not None:
+        # Run the module lint tests
+        if len(module_lint_obj.all_local_components) > 0:
+            module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
+        if len(module_lint_obj.all_remote_components) > 0:
+            module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
     if subworkflow_lint_obj is not None:
+        # Run the subworkflows lint tests
         if len(subworkflow_lint_obj.all_local_components) > 0:
             subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
         if len(subworkflow_lint_obj.all_remote_components) > 0:
@@ -646,7 +655,8 @@ def run_linting(
 
     # Print the results
     lint_obj._print_results(show_passed)
-    module_lint_obj._print_results(show_passed, sort_by=sort_by)
+    if module_lint_obj is not None:
+        module_lint_obj._print_results(show_passed, sort_by=sort_by)
     if subworkflow_lint_obj is not None:
         subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
     nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index ad0605dcf7..bd25ff33d0 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Dict, List, Union
 
 log = logging.getLogger(__name__)
 
@@ -87,6 +87,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         lib/Workflow.groovy
         lib/WorkflowMain.groovy
         lib/WorkflowPIPELINE.groovy
+        lib/nfcore_external_java_deps.jar
         parameters.settings.json
         pipeline_template.yml # saving information in .nf-core.yml
         Singularity
@@ -98,12 +99,6 @@ def files_exist(self) -> Dict[str, List[str]]:
 
         .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 pipelines 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:
 
@@ -198,11 +193,9 @@ def files_exist(self) -> Dict[str, List[str]]:
         Path("parameters.settings.json"),
         Path("pipeline_template.yml"),  # saving information in .nf-core.yml
         Path("Singularity"),
+        Path("lib", "nfcore_external_java_deps.jar"),
     ]
     files_warn_ifexists = [Path(".travis.yml")]
-    files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = [
-        (Path("lib", "nfcore_external_java_deps.jar"), [{"plugins": "nf-validation"}, {"plugins": "nf-schema"}]),
-    ]
 
     # Remove files that should be ignored according to the linting config
     ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else []
@@ -241,24 +234,7 @@ def pf(file_path: Union[str, Path]) -> Path:
             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_cond in files_fail_ifinconfig:
-        if str(file_cond[0]) in ignore_files:
-            continue
-        in_config = False
-        for condition in file_cond[1]:
-            config_key, config_value = list(condition.items())[0]
-            if config_key in self.nf_config and config_value in self.nf_config[config_key]:
-                log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
-                in_config = True
-        if pf(file_cond[0]).is_file() and in_config:
-            failed.append(f"File must be removed: {self._wrap_quotes(file_cond[0])}")
-        elif pf(file_cond[0]).is_file() and not in_config:
-            passed.append(f"File found check: {self._wrap_quotes(file_cond[0])}")
-        elif not pf(file_cond[0]).is_file() and not in_config:
-            failed.append(f"File not found check: {self._wrap_quotes(file_cond[0])}")
-        elif not pf(file_cond[0]).is_file() and in_config:
-            passed.append(f"File not found check: {self._wrap_quotes(file_cond[0])}")
+
     # Files that cause a warning if they exist
     for file in files_warn_ifexists:
         if str(file) in ignore_files:
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index 96323af94d..790fc21797 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -1,3 +1,4 @@
+import ast
 import logging
 import re
 from pathlib import Path
@@ -65,14 +66,6 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         * Should always be set to default value:
         ``https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}``
 
-    * ``params.validationShowHiddenParams``
-
-        * Determines whether boilerplate params are showed by schema. Set to ``false`` by default
-
-    * ``params.validationSchemaIgnoreParams``
-
-        * A comma separated string of inputs the schema validation should ignore.
-
     **The following variables throw warnings if missing:**
 
     * ``manifest.mainScript``: The filename of the main pipeline script (should be ``main.nf``)
@@ -151,17 +144,9 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["process.time"],
         ["params.outdir"],
         ["params.input"],
-        ["params.validationShowHiddenParams"],
-        ["params.validationSchemaIgnoreParams"],
     ]
     # Throw a warning if these are missing
-    config_warn = [
-        ["manifest.mainScript"],
-        ["timeline.file"],
-        ["trace.file"],
-        ["report.file"],
-        ["dag.file"],
-    ]
+    config_warn = [["manifest.mainScript"], ["timeline.file"], ["trace.file"], ["report.file"], ["dag.file"]]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
         "params.nf_required_version",
@@ -172,6 +157,49 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         "params.enable_conda",
     ]
 
+    # Lint for plugins
+    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]"))
+    found_plugins = []
+    for plugin in config_plugins:
+        if "@" not in plugin:
+            failed.append(f"Plugin '{plugin}' does not have a pinned version")
+        found_plugins.append(plugin.split("@")[0])
+
+    if "nf-validation" in found_plugins or "nf-schema" in found_plugins:
+        if "nf-validation" in found_plugins and "nf-schema" in found_plugins:
+            failed.append("nextflow.config contains both nf-validation and nf-schema")
+
+        if "nf-schema" in found_plugins:
+            passed.append("Found nf-schema plugin")
+            if self.nf_config.get("validation.help.enabled", "false") == "false":
+                failed.append(
+                    "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages"
+                )
+            config_fail.extend([["validation.help.enabled"]])
+            config_warn.extend(
+                [
+                    ["validation.help.beforeText"],
+                    ["validation.help.afterText"],
+                    ["validation.help.command"],
+                    ["validation.summary.beforeText"],
+                    ["validation.summary.afterText"],
+                ]
+            )
+            config_fail_ifdefined.extend(
+                [
+                    "params.validationFailUnrecognisedParams",
+                    "params.validationLenientMode",
+                    "params.validationSchemaIgnoreParams",
+                    "params.validationShowHiddenParams",
+                ]
+            )
+
+        if "nf-validation" in found_plugins:
+            passed.append("Found nf-validation plugin")
+            warned.append(
+                "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/"
+            )
+
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
 
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
new file mode 100644
index 0000000000..4fc40ae26c
--- /dev/null
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -0,0 +1,44 @@
+import ast
+import glob
+import logging
+import re
+from typing import Dict, List
+
+log = logging.getLogger(__name__)
+
+
+def plugin_includes(self) -> Dict[str, List[str]]:
+    """Checks the include statements in the all *.nf files for plugin includes
+
+    When nf-schema is used in an nf-core pipeline, the include statements of the plugin
+    functions have to use nf-schema instead of nf-validation and vice versa
+    """
+    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
+    validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
+
+    passed: List[str] = []
+    warned: List[str] = []
+    failed: List[str] = []
+    ignored: List[str] = []
+
+    plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
+    workflow_files = [
+        file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")
+    ]
+    test_passed = True
+    for file in workflow_files:
+        with open(file) as of:
+            plugin_includes = re.findall(plugin_include_pattern, of.read())
+            for include in plugin_includes:
+                if include not in ["nf-validation", "nf-schema"]:
+                    continue
+                if include != validation_plugin:
+                    test_passed = False
+                    failed.append(
+                        f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`"
+                    )
+
+    if test_passed:
+        passed.append("No wrong validation plugin imports have been found")
+
+    return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}
diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py
index 4c16243690..1c09104258 100644
--- a/nf_core/pipelines/lint/readme.py
+++ b/nf_core/pipelines/lint/readme.py
@@ -36,7 +36,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)
diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py
index d617e40949..b586cc5242 100644
--- a/nf_core/pipelines/lint/schema_description.py
+++ b/nf_core/pipelines/lint/schema_description.py
@@ -36,8 +36,9 @@ def schema_description(self):
                 warned.append(f"Ungrouped param in schema: `{up}`")
 
     # Iterate over groups and add warning for parameters without a description
-    for group_key in self.schema_obj.schema["definitions"].keys():
-        group = self.schema_obj.schema["definitions"][group_key]
+    defs_notation = self.schema_obj.defs_notation
+    for group_key in self.schema_obj.schema[defs_notation].keys():
+        group = self.schema_obj.schema[defs_notation][group_key]
         for param_key, param in group["properties"].items():
             if param_key in ignore_params:
                 ignored.append(f"Ignoring description check for param in schema: `{param_key}`")
diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py
index 6786c5012d..4007bf8fe5 100644
--- a/nf_core/pipelines/lint/schema_lint.py
+++ b/nf_core/pipelines/lint/schema_lint.py
@@ -16,26 +16,26 @@ def schema_lint(self):
     The lint test checks the schema for the following:
 
     * Schema should be a valid JSON file
-    * Schema should adhere to `JSONSchema <https://json-schema.org/>`_, Draft 7.
+    * Schema should adhere to `JSONSchema <https://json-schema.org/>`_, Draft 7 or Draft 2020-12.
     * Parameters can be described in two places:
 
         * As ``properties`` in the top-level schema object
-        * As ``properties`` within subschemas listed in a top-level ``definitions`` objects
+        * As ``properties`` within subschemas listed in a top-level ``definitions``(draft 7) or ``$defs``(draft 2020-12) objects
 
     * The schema must describe at least one parameter
     * There must be no duplicate parameter IDs across the schema and definition subschema
-    * All subschema in ``definitions`` must be referenced in the top-level ``allOf`` key
+    * All subschema in ``definitions`` or ``$defs`` must be referenced in the top-level ``allOf`` key
     * The top-level ``allOf`` key must not describe any non-existent definitions
     * Default parameters in the schema must be valid
     * Core top-level schema attributes should exist and be set as follows:
 
-        * ``$schema``: ``https://json-schema.org/draft-07/schema``
+        * ``$schema``: ``https://json-schema.org/draft-07/schema`` or ``https://json-schema.org/draft/2020-12/schema``
         * ``$id``: URL to the raw schema file, eg. ``https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json``
         * ``title``: ``YOURPIPELINE pipeline parameters``
         * ``description``: The pipeline config ``manifest.description``
     * That the ``input`` property is defined and has a mimetype. A list of common mimetypes can be found `here <https://developer.mozilla.org/en-US/docs/Web/HTTP/Basics_of_HTTP/MIME_types/Common_types>`_.
 
-    For example, an *extremely* minimal schema could look like this:
+    For example, an *extremely* minimal schema could look like this (draft 7):
 
     .. code-block:: json
 
@@ -57,6 +57,28 @@ def schema_lint(self):
          "allOf": [{"$ref": "#/definitions/my_first_group"}]
        }
 
+    Or this (draft 2020-12):
+
+    .. code-block:: json
+
+       {
+         "$schema": "https://json-schema.org/draft/2020-12/schema",
+         "$id": "https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json",
+         "title": "YOURPIPELINE pipeline parameters",
+         "description": "This pipeline is for testing",
+         "properties": {
+           "first_param": { "type": "string" }
+         },
+         "$defs": {
+           "my_first_group": {
+             "properties": {
+               "second_param": { "type": "string" }
+             }
+           }
+         },
+         "allOf": [{"$ref": "#/$defs/my_first_group"}]
+       }
+
     .. tip:: You can check your pipeline schema without having to run the entire pipeline lint
              by running ``nf-core pipelines schema lint`` instead of ``nf-core pipelines lint``
     """
diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py
index ccab76295f..ff65fb0e56 100644
--- a/nf_core/pipelines/lint_utils.py
+++ b/nf_core/pipelines/lint_utils.py
@@ -22,15 +22,22 @@ def print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj):
     swf_passed = 0
     swf_warned = 0
     swf_failed = 0
+    module_passed = 0
+    module_warned = 0
+    module_failed = 0
     if subworkflow_lint_obj is not None:
         swf_passed = len(subworkflow_lint_obj.passed)
         swf_warned = len(subworkflow_lint_obj.warned)
         swf_failed = len(subworkflow_lint_obj.failed)
-    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + swf_passed
+    if module_lint_obj is not None:
+        module_passed = len(module_lint_obj.passed)
+        module_warned = len(module_lint_obj.warned)
+        module_failed = len(module_lint_obj.failed)
+    nbr_passed = len(lint_obj.passed) + module_passed + swf_passed
     nbr_ignored = len(lint_obj.ignored)
     nbr_fixed = len(lint_obj.fixed)
-    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + swf_warned
-    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed
+    nbr_warned = len(lint_obj.warned) + module_warned + swf_warned
+    nbr_failed = len(lint_obj.failed) + module_failed + swf_failed
 
     summary_colour = "red" if nbr_failed > 0 else "green"
     table = Table(box=rich.box.ROUNDED, style=summary_colour)
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 7f562bff38..95ed5e5b6e 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -32,7 +32,7 @@ def __init__(self):
 
         self.schema = {}
         self.pipeline_dir = ""
-        self.schema_filename = ""
+        self._schema_filename = ""
         self.schema_defaults = {}
         self.schema_types = {}
         self.schema_params = {}
@@ -46,6 +46,69 @@ def __init__(self):
         self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder"
         self.web_schema_build_web_url = None
         self.web_schema_build_api_url = None
+        self.validation_plugin = None
+        self.schema_draft = None
+        self.defs_notation = None
+        self.ignored_params = []
+
+    # Update the validation plugin code everytime the schema gets changed
+    def set_schema_filename(self, schema: str) -> None:
+        self._schema_filename = schema
+        self._update_validation_plugin_from_config()
+
+    def get_schema_filename(self) -> str:
+        return self._schema_filename
+
+    def del_schema_filename(self) -> None:
+        del self._schema_filename
+
+    schema_filename = property(get_schema_filename, set_schema_filename, del_schema_filename)
+
+    def _update_validation_plugin_from_config(self) -> None:
+        plugin = "nf-schema"
+        if self.schema_filename:
+            conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
+        else:
+            conf = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir))
+
+        plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",")
+        plugin_found = False
+        for plugin_instance in plugins:
+            if "nf-schema" in plugin_instance:
+                plugin = "nf-schema"
+                plugin_found = True
+                break
+            elif "nf-validation" in plugin_instance:
+                plugin = "nf-validation"
+                plugin_found = True
+                break
+
+        if not plugin_found:
+            log.info(
+                "Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema."
+            )
+
+        self.validation_plugin = plugin
+        # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
+        if plugin == "nf-schema":
+            self.defs_notation = "$defs"
+            ignored_params = [
+                conf.get("validation.help.shortParameter", "help"),
+                conf.get("validation.help.fullParameter", "helpFull"),
+                conf.get("validation.help.showHiddenParameter", "showHidden"),
+            ]  # Help parameter should be ignored by default
+            ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", [])
+            if len(ignored_params_config) > 0:
+                ignored_params.extend(ignored_params_config)
+            self.ignored_params = ignored_params
+            self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+
+        else:
+            self.defs_notation = "definitions"
+            self.schema_draft = "https://json-schema.org/draft-07/schema"
+            self.get_wf_params()
+            self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
+            self.ignored_params.append("validationSchemaIgnoreParams")
 
     def get_schema_path(
         self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None
@@ -116,6 +179,8 @@ def load_schema(self):
             self.schema = json.load(fh)
         self.schema_defaults = {}
         self.schema_params = {}
+        if "$schema" not in self.schema:
+            raise AssertionError("Schema missing top-level `$schema` attribute")
         log.debug(f"JSON file loaded: {self.schema_filename}")
 
     def sanitise_param_default(self, param):
@@ -168,10 +233,11 @@ def get_schema_defaults(self) -> None:
                 if param["default"] is not None:
                     self.schema_defaults[p_key] = param["default"]
 
+        # TODO add support for nested parameters
         # Grouped schema properties in subschema definitions
-        for defn_name, definition in self.schema.get("definitions", {}).items():
+        for defn_name, definition in self.schema.get(self.defs_notation, {}).items():
             for p_key, param in definition.get("properties", {}).items():
-                self.schema_params[p_key] = ("definitions", defn_name, "properties", p_key)
+                self.schema_params[p_key] = (self.defs_notation, defn_name, "properties", p_key)
                 if "default" in param:
                     param = self.sanitise_param_default(param)
                     if param["default"] is not None:
@@ -182,7 +248,7 @@ def get_schema_types(self) -> None:
         for name, param in self.schema.get("properties", {}).items():
             if "type" in param:
                 self.schema_types[name] = param["type"]
-        for _, definition in self.schema.get("definitions", {}).items():
+        for _, definition in self.schema.get(self.defs_notation, {}).items():
             for name, param in definition.get("properties", {}).items():
                 if "type" in param:
                     self.schema_types[name] = param["type"]
@@ -191,7 +257,7 @@ def save_schema(self, suppress_logging=False):
         """Save a pipeline schema to a file"""
         # Write results to a JSON file
         num_params = len(self.schema.get("properties", {}))
-        num_params += sum(len(d.get("properties", {})) for d in self.schema.get("definitions", {}).values())
+        num_params += sum(len(d.get("properties", {})) for d in self.schema.get(self.defs_notation, {}).values())
         if not suppress_logging:
             log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'")
         dump_json_with_prettier(self.schema_filename, self.schema)
@@ -248,13 +314,14 @@ def validate_default_params(self):
         if self.schema is None:
             log.error("[red][✗] Pipeline schema not found")
         try:
+            # TODO add support for nested parameters
             # Make copy of schema and remove required flags
             schema_no_required = copy.deepcopy(self.schema)
             if "required" in schema_no_required:
                 schema_no_required.pop("required")
-            for group_key, group in schema_no_required.get("definitions", {}).items():
+            for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
                 if "required" in group:
-                    schema_no_required["definitions"][group_key].pop("required")
+                    schema_no_required[self.defs_notation][group_key].pop("required")
             jsonschema.validate(self.schema_defaults, schema_no_required)
         except jsonschema.exceptions.ValidationError as e:
             raise AssertionError(f"Default parameters are invalid: {e.message}")
@@ -269,17 +336,11 @@ def validate_default_params(self):
         if self.pipeline_params == {}:
             self.get_wf_params()
 
-        # Collect parameters to ignore
-        if "validationSchemaIgnoreParams" in self.pipeline_params:
-            params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-        else:
-            params_ignore = []
-
         # Go over group keys
-        for group_key, group in schema_no_required.get("definitions", {}).items():
+        for group_key, group in schema_no_required.get(self.defs_notation, {}).items():
             group_properties = group.get("properties")
             for param in group_properties:
-                if param in params_ignore:
+                if param in self.ignored_params:
                     continue
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(param, group_properties[param], self.pipeline_params[param])
@@ -292,7 +353,7 @@ def validate_default_params(self):
         ungrouped_properties = self.schema.get("properties")
         if ungrouped_properties:
             for param in ungrouped_properties:
-                if param in params_ignore:
+                if param in self.ignored_params:
                     continue
                 if param in self.pipeline_params:
                     self.validate_config_default_parameter(
@@ -359,39 +420,66 @@ def validate_schema(self, schema=None):
         """
         if schema is None:
             schema = self.schema
-        try:
-            jsonschema.Draft7Validator.check_schema(schema)
-            log.debug("JSON Schema Draft7 validated")
-        except jsonschema.exceptions.SchemaError as e:
-            raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+
+        if "$schema" not in schema:
+            raise AssertionError("Schema missing top-level `$schema` attribute")
+        schema_draft = schema["$schema"]
+        if self.schema_draft != schema_draft:
+            raise AssertionError(f"Schema is using the wrong draft: {schema_draft}, should be {self.schema_draft}")
+        if self.schema_draft == "https://json-schema.org/draft-07/schema":
+            try:
+                jsonschema.Draft7Validator.check_schema(schema)
+                log.debug("JSON Schema Draft7 validated")
+            except jsonschema.exceptions.SchemaError as e:
+                raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}")
+        elif self.schema_draft == "https://json-schema.org/draft/2020-12/schema":
+            try:
+                jsonschema.Draft202012Validator.check_schema(schema)
+                log.debug("JSON Schema Draft2020-12 validated")
+            except jsonschema.exceptions.SchemaError as e:
+                raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}")
+        else:
+            raise AssertionError(
+                f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`"
+            )
 
         param_keys = list(schema.get("properties", {}).keys())
         num_params = len(param_keys)
-        for d_key, d_schema in schema.get("definitions", {}).items():
+
+        # Add a small check for older nf-schema JSON schemas
+        if "defs" in schema:
+            raise AssertionError(
+                f'Using "defs" for schema definitions is not supported. Please use "{self.defs_notation}" instead'
+            )
+
+        for d_key, d_schema in schema.get(self.defs_notation, {}).items():
             # Check that this definition is mentioned in allOf
             if "allOf" not in schema:
                 raise AssertionError("Schema has definitions, but no allOf key")
             in_allOf = False
             for allOf in schema.get("allOf", []):
-                if allOf["$ref"] == f"#/definitions/{d_key}":
+                if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}":
                     in_allOf = True
             if not in_allOf:
-                raise AssertionError(f"Definition subschema `{d_key}` not included in schema `allOf`")
+                raise AssertionError(
+                    f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`"
+                )
 
+            # TODO add support for nested parameters
             for d_param_id in d_schema.get("properties", {}):
                 # Check that we don't have any duplicate parameter IDs in different definitions
                 if d_param_id in param_keys:
-                    raise AssertionError(f"Duplicate parameter found in schema `definitions`: `{d_param_id}`")
+                    raise AssertionError(f"Duplicate parameter found in schema `{self.defs_notation}`: `{d_param_id}`")
                 param_keys.append(d_param_id)
                 num_params += 1
 
         # Check that everything in allOf exists
         for allOf in schema.get("allOf", []):
-            if "definitions" not in schema:
-                raise AssertionError("Schema has allOf, but no definitions")
-            def_key = allOf["$ref"][14:]
-            if def_key not in schema.get("definitions", {}):
-                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `definitions`")
+            _, allof_defs_notation, def_key = allOf["$ref"].split("/")  # "#/<defs_notation>/<def_name>"
+            if allof_defs_notation not in schema:
+                raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}")
+            if def_key not in schema.get(allof_defs_notation, {}):
+                raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allof_defs_notation}`")
 
         # Check that the schema describes at least one parameter
         if num_params == 0:
@@ -402,7 +490,7 @@ def validate_schema(self, schema=None):
     def validate_schema_title_description(self, schema=None):
         """
         Extra validation command for linting.
-        Checks that the schema "$id", "title" and "description" attributes match the piipeline config.
+        Checks that the schema "$id", "title" and "description" attributes match the pipeline config.
         """
         if schema is None:
             schema = self.schema
@@ -410,12 +498,6 @@ def validate_schema_title_description(self, schema=None):
             log.debug("Pipeline schema not set - skipping validation of top-level attributes")
             return None
 
-        if "$schema" not in self.schema:
-            raise AssertionError("Schema missing top-level `$schema` attribute")
-        schema_attr = "http://json-schema.org/draft-07/schema"
-        if self.schema["$schema"] != schema_attr:
-            raise AssertionError(f"Schema `$schema` should be `{schema_attr}`\n Found `{self.schema['$schema']}`")
-
         if self.pipeline_manifest == {}:
             self.get_wf_params()
 
@@ -465,9 +547,9 @@ def check_for_input_mimetype(self):
         if "input" not in self.schema_params:
             raise LookupError("Parameter `input` not found in schema")
         # Check that the input parameter is defined in the right place
-        if "input" not in self.schema.get("definitions", {}).get("input_output_options", {}).get("properties", {}):
+        if "input" not in self.schema.get(self.defs_notation, {}).get("input_output_options", {}).get("properties", {}):
             raise LookupError("Parameter `input` is not defined in the correct subschema (input_output_options)")
-        input_entry = self.schema["definitions"]["input_output_options"]["properties"]["input"]
+        input_entry = self.schema[self.defs_notation]["input_output_options"]["properties"]["input"]
         if "mimetype" not in input_entry:
             return None
         mimetype = input_entry["mimetype"]
@@ -519,7 +601,7 @@ def schema_to_markdown(self, columns):
         out = f"# {self.schema['title']}\n\n"
         out += f"{self.schema['description']}\n"
         # Grouped parameters
-        for definition in self.schema.get("definitions", {}).values():
+        for definition in self.schema.get(self.defs_notation, {}).values():
             out += f"\n## {definition.get('title', {})}\n\n"
             out += f"{definition.get('description', '')}\n\n"
             required = definition.get("required", [])
@@ -701,15 +783,15 @@ def remove_schema_empty_definitions(self):
         """
         # Identify and remove empty definitions from the schema
         empty_definitions = []
-        for d_key, d_schema in list(self.schema.get("definitions", {}).items()):
+        for d_key, d_schema in list(self.schema.get(self.defs_notation, {}).items()):
             if not d_schema.get("properties"):
-                del self.schema["definitions"][d_key]
+                del self.schema[self.defs_notation][d_key]
                 empty_definitions.append(d_key)
                 log.warning(f"Removing empty group: '{d_key}'")
 
         # Remove "allOf" group with empty definitions from the schema
         for d_key in empty_definitions:
-            allOf = {"$ref": f"#/definitions/{d_key}"}
+            allOf = {"$ref": f"#/{self.defs_notation}/{d_key}"}
             if allOf in self.schema.get("allOf", []):
                 self.schema["allOf"].remove(allOf)
 
@@ -718,8 +800,8 @@ def remove_schema_empty_definitions(self):
             del self.schema["allOf"]
 
         # If we don't have anything left in "definitions", remove it
-        if self.schema.get("definitions") == {}:
-            del self.schema["definitions"]
+        if self.schema.get(self.defs_notation) == {}:
+            del self.schema[self.defs_notation]
 
     def remove_schema_notfound_configs(self):
         """
@@ -729,9 +811,9 @@ def remove_schema_notfound_configs(self):
         # Top-level properties
         self.schema, params_removed = self.remove_schema_notfound_configs_single_schema(self.schema)
         # Sub-schemas in definitions
-        for d_key, definition in self.schema.get("definitions", {}).items():
+        for d_key, definition in self.schema.get(self.defs_notation, {}).items():
             cleaned_schema, p_removed = self.remove_schema_notfound_configs_single_schema(definition)
-            self.schema["definitions"][d_key] = cleaned_schema
+            self.schema[self.defs_notation][d_key] = cleaned_schema
             params_removed.extend(p_removed)
 
         return params_removed
@@ -783,13 +865,12 @@ def add_schema_found_configs(self):
         Update defaults if they have changed
         """
         params_added = []
-        params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
-        params_ignore.append("validationSchemaIgnoreParams")
+
         for p_key, p_val in self.pipeline_params.items():
             s_key = self.schema_params.get(p_key)
             # Check if key is in schema parameters
             # Key is in pipeline but not in schema or ignored from schema
-            if p_key not in self.schema_params and p_key not in params_ignore:
+            if p_key not in self.schema_params and p_key not in self.ignored_params:
                 if (
                     self.no_prompts
                     or self.schema_from_scratch
@@ -822,7 +903,7 @@ def add_schema_found_configs(self):
             elif (
                 s_key
                 and (p_key not in self.schema_defaults)
-                and (p_key not in params_ignore)
+                and (p_key not in self.ignored_params)
                 and (p_def := self.build_schema_param(p_val).get("default"))
             ):
                 if self.no_prompts or Confirm.ask(
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 96c16130ca..663efb6b46 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -654,7 +654,7 @@ def anaconda_package(dep, dep_channels=None):
     """
 
     if dep_channels is None:
-        dep_channels = ["conda-forge", "bioconda", "defaults"]
+        dep_channels = ["conda-forge", "bioconda"]
 
     # Check if each dependency is the latest available version
     if "=" in dep:
diff --git a/requirements.txt b/requirements.txt
index 46616510ab..e97e7d9360 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,7 +3,7 @@ filetype
 GitPython
 PyGithub
 jinja2
-jsonschema>=3.0
+jsonschema>=4.0
 markdown>=3.3
 packaging
 pillow
diff --git a/setup.py b/setup.py
index 8f32daa904..45df29b8bc 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "2.14.2dev"
+version = "3.0.0dev"
 
 with open("README.md") as f:
     readme = f.read()
diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index dfe288a6ee..51c814b88c 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -2,7 +2,6 @@
 from pathlib import Path
 from typing import Union
 
-import pytest
 import yaml
 from git.repo import Repo
 
@@ -187,12 +186,21 @@ def test_modules_lint_trimgalore(self):
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
+    def test_modules_lint_tabix_tabix(self):
+        """Test linting the tabix/tabix module"""
+        self.mods_install.install("tabix/tabix")
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        module_lint.lint(print_results=False, module="tabix/tabix")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
     def test_modules_lint_empty(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
-        with pytest.raises(LookupError):
-            nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+        assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text
 
     def test_modules_lint_new_modules(self):
         """lint a new module"""
@@ -206,8 +214,8 @@ def test_modules_lint_no_gitlab(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)
         self.mods_remove.remove("multiqc", force=True)
-        with pytest.raises(LookupError):
-            nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text
 
     def test_modules_lint_gitlab_modules(self):
         """Lint modules from a different remote"""
@@ -479,54 +487,6 @@ def test_modules_environment_yml_file_not_array(self):
         assert len(module_lint.warned) >= 0
         assert module_lint.failed[0].lint_test == "environment_yml_valid"
 
-    def test_modules_environment_yml_file_name_mismatch(self):
-        """Test linting a module with a different name in the environment.yml file"""
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            )
-        ) as fh:
-            yaml_content = yaml.safe_load(fh)
-        yaml_content["name"] = "bpipe-test"
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(yaml_content))
-        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
-        module_lint.lint(print_results=False, module="bpipe/test")
-        # reset changes
-        yaml_content["name"] = "bpipe_test"
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(yaml_content))
-
-        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.passed) > 0
-        assert len(module_lint.warned) >= 0
-        assert module_lint.failed[0].lint_test == "environment_yml_name"
-
     def test_modules_meta_yml_incorrect_licence_field(self):
         """Test linting a module with an incorrect Licence field in meta.yml"""
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
@@ -566,7 +526,7 @@ def test_modules_meta_yml_input_mismatch(self):
             fh.write(main_nf)
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) >= 0
-        assert len(module_lint.warned) == 2
+        assert len(module_lint.warned) == 2, f"Linting warning with {[x.__dict__ for x in module_lint.warned]}"
         lint_tests = [x.lint_test for x in module_lint.warned]
         # check that it is there twice:
         assert lint_tests.count("meta_input_meta_only") == 1
@@ -596,36 +556,11 @@ def test_modules_meta_yml_incorrect_name(self):
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
             meta_yml = yaml.safe_load(fh)
         meta_yml["name"] = "bpipe/test"
-        # need to make the same change to the environment.yml file
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            )
-        ) as fh:
-            environment_yml = yaml.safe_load(fh)
-        environment_yml["name"] = "bpipe/test"
         with open(
             Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"),
             "w",
         ) as fh:
             fh.write(yaml.dump(meta_yml))
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(environment_yml))
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
         module_lint.lint(print_results=False, module="bpipe/test")
 
@@ -636,19 +571,6 @@ def test_modules_meta_yml_incorrect_name(self):
             "w",
         ) as fh:
             fh.write(yaml.dump(meta_yml))
-        environment_yml["name"] = "bpipe_test"
-        with open(
-            Path(
-                self.nfcore_modules,
-                "modules",
-                "nf-core",
-                "bpipe",
-                "test",
-                "environment.yml",
-            ),
-            "w",
-        ) as fh:
-            fh.write(yaml.dump(environment_yml))
 
         assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) >= 0
diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr
index f4eb255087..6e3009e18e 100644
--- a/tests/pipelines/__snapshots__/test_create_app.ambr
+++ b/tests/pipelines/__snapshots__/test_create_app.ambr
@@ -851,257 +851,257 @@
           font-weight: 700;
       }
   
-      .terminal-3220763577-matrix {
+      .terminal-1208643741-matrix {
           font-family: Fira Code, monospace;
           font-size: 20px;
           line-height: 24.4px;
           font-variant-east-asian: full-width;
       }
   
-      .terminal-3220763577-title {
+      .terminal-1208643741-title {
           font-size: 18px;
           font-weight: bold;
           font-family: arial;
       }
   
-      .terminal-3220763577-r1 { fill: #c5c8c6 }
-  .terminal-3220763577-r2 { fill: #e3e3e3 }
-  .terminal-3220763577-r3 { fill: #989898 }
-  .terminal-3220763577-r4 { fill: #e1e1e1 }
-  .terminal-3220763577-r5 { fill: #4ebf71;font-weight: bold }
-  .terminal-3220763577-r6 { fill: #1e1e1e }
-  .terminal-3220763577-r7 { fill: #507bb3 }
-  .terminal-3220763577-r8 { fill: #e2e2e2 }
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diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 85ba817536..97dd346cdf 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -54,27 +54,6 @@ def test_files_exist_pass(self):
         results = lint_obj.files_exist()
         assert results["failed"] == []
 
-    def test_files_exist_pass_conditional(self):
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lint_obj.nf_config["plugins"] = []
-        lib_dir = Path(self.new_pipeline, "lib")
-        lib_dir.mkdir()
-        (lib_dir / "nfcore_external_java_deps.jar").touch()
-        results = lint_obj.files_exist()
-        assert results["failed"] == []
-        assert results["ignored"] == []
-
-    def test_files_exist_fail_conditional(self):
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
-        lint_obj._load()
-        lib_dir = Path(self.new_pipeline, "lib")
-        lib_dir.mkdir()
-        (lib_dir / "nfcore_external_java_deps.jar").touch()
-        results = lint_obj.files_exist()
-        assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"]
-        assert results["ignored"] == []
-
     def test_files_exist_pass_conditional_nfschema(self):
         # replace nf-validation with nf-schema in nextflow.config
         with open(Path(self.new_pipeline, "nextflow.config")) as f:
diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py
new file mode 100644
index 0000000000..8eb31e2671
--- /dev/null
+++ b/tests/pipelines/lint/test_plugin_includes.py
@@ -0,0 +1,24 @@
+import nf_core.pipelines.lint
+
+from ..test_lint import TestLint
+
+
+class TestLintPluginIncludes(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+
+    def test_default_values_match(self):
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        result = lint_obj.plugin_includes()
+        assert len(result["failed"]) == 0
+        assert len(result["warned"]) == 0
+
+    def test_wrong_include(self):
+        test_path = self.new_pipeline / "test.nf"
+        with open(test_path, "w") as of:
+            of.write("include { paramsSummary } from 'plugin/nf-validation'\n")
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        result = lint_obj.plugin_includes()
+        assert len(result["failed"]) == 1
+        assert len(result["warned"]) == 0
diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py
index 13fd3b24cd..f83cc274fc 100644
--- a/tests/pipelines/test_create.py
+++ b/tests/pipelines/test_create.py
@@ -15,6 +15,7 @@
 
 PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml"
 PIPELINE_TEMPLATE_YML_SKIP = TEST_DATA_DIR / "pipeline_create_template_skip.yml"
+PIPELINE_TEMPLATE = Path(nf_core.__file__).parent / "pipeline-template"
 
 
 class NfcoreCreateTest(unittest.TestCase):
@@ -134,3 +135,41 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         assert not (pipeline.outdir / ".github").exists()
         assert not (pipeline.outdir / "conf" / "igenomes.config").exists()
         assert not (pipeline.outdir / ".editorconfig").exists()
+
+    def test_template_customisation_all_files_grouping(self):
+        """Test that all pipeline template files are included in a pipeline customisation group."""
+        template_features_yml = load_features_yaml()
+        base_required_files = [
+            ".gitignore",
+            ".nf-core.yml",
+            "README.md",
+            "nextflow.config",
+            "CITATIONS.md",
+            "main.nf",
+            "workflows/pipeline.nf",
+        ]
+        all_skipped_files = []
+        for feature in template_features_yml.keys():
+            if template_features_yml[feature]["skippable_paths"]:
+                all_skipped_files.extend(template_features_yml[feature]["skippable_paths"])
+
+        for root, _, files in os.walk(PIPELINE_TEMPLATE):
+            for file in files:
+                str_path = str((Path(root) / file).relative_to(PIPELINE_TEMPLATE))
+                if str_path not in base_required_files:
+                    try:
+                        assert (
+                            str_path in all_skipped_files
+                        ), f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                    except AssertionError:
+                        if "/" in str_path:
+                            # Check if the parent directory is in the skipped files
+                            upper_dir_present = False
+                            for i in range(1, len(str_path.split("/"))):
+                                upper_dir = "/".join(str_path.split("/")[:i])
+                                if upper_dir in all_skipped_files:
+                                    upper_dir_present = True
+                                    break
+                            assert upper_dir_present, f"Template file `{str_path}` not present in a group for pipeline customisation in `template_features.yml`."
+                        else:
+                            raise
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index da7618d486..d63e7b6dc5 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -47,7 +47,7 @@ def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui,
     def test_get_pipeline_schema(self):
         """Test loading the params schema from a pipeline"""
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) > 2
 
     @with_temporary_folder
     def test_make_pipeline_schema(self, tmp_path):
@@ -60,8 +60,8 @@ def test_make_pipeline_schema(self, tmp_path):
         Path(test_pipeline_dir, "nextflow_schema.json").unlink()
         self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn)
         self.launcher.get_pipeline_schema()
-        assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2
-        assert self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]["outdir"] == {
+        assert len(self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]) >= 2
+        assert self.launcher.schema_obj.schema["$defs"]["input_output_options"]["properties"]["outdir"] == {
             "type": "string",
             "format": "directory-path",
             "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
@@ -91,8 +91,8 @@ def test_nf_merge_schema(self):
         self.launcher.get_pipeline_schema()
         self.launcher.set_schema_inputs()
         self.launcher.merge_nxf_flag_schema()
-        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/definitions/coreNextflow"}
-        assert "-resume" in self.launcher.schema_obj.schema["definitions"]["coreNextflow"]["properties"]
+        assert self.launcher.schema_obj.schema["allOf"][0] == {"$ref": "#/$defs/coreNextflow"}
+        assert "-resume" in self.launcher.schema_obj.schema["$defs"]["coreNextflow"]["properties"]
 
     def test_ob_to_questionary_string(self):
         """Check converting a python dict to a pyenquirer format - simple strings"""
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index 633de3db69..2abaf07bd2 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -24,6 +24,9 @@ class TestSchema(unittest.TestCase):
     def setUp(self):
         """Create a new PipelineSchema object"""
         self.schema_obj = nf_core.pipelines.schema.PipelineSchema()
+        self.schema_obj.schema_draft = "https://json-schema.org/draft/2020-12/schema"
+        self.schema_obj.defs_notation = "$defs"
+        self.schema_obj.validation_plugin = "nf-schema"
         self.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 
         # Create a test pipeline in temp directory
@@ -105,7 +108,7 @@ def test_schema_docs(self):
         docs = self.schema_obj.print_documentation()
         assert self.schema_obj.schema["title"] in docs
         assert self.schema_obj.schema["description"] in docs
-        for definition in self.schema_obj.schema.get("definitions", {}).values():
+        for definition in self.schema_obj.schema.get("$defs", {}).values():
             assert definition["title"] in docs
             assert definition["description"] in docs
 
@@ -175,40 +178,43 @@ def test_validate_schema_fail_duplicate_ids(self):
         Check that the schema validation fails when we have duplicate IDs in definition subschema
         """
         self.schema_obj.schema = {
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
-            "allOf": [{"$ref": "#/definitions/groupOne"}, {"$ref": "#/definitions/groupTwo"}],
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}},
+            "allOf": [{"$ref": "#/$defs/groupOne"}, {"$ref": "#/$defs/groupTwo"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Duplicate parameter found in schema `definitions`: `foo`"
+        assert exc_info.value.args[0] == "Duplicate parameter found in schema `$defs`: `foo`"
 
     def test_validate_schema_fail_missing_def(self):
         """
-        Check that the schema validation fails when we a definition in allOf is not in definitions
+        Check that the schema validation fails when we a definition in allOf is not in $defs
         """
         self.schema_obj.schema = {
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
-            "allOf": [{"$ref": "#/definitions/groupOne"}],
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
+            "allOf": [{"$ref": "#/$defs/groupOne"}],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Definition subschema `groupTwo` not included in schema `allOf`"
+        assert exc_info.value.args[0] == "Definition subschema `#/$defs/groupTwo` not included in schema `allOf`"
 
     def test_validate_schema_fail_unexpected_allof(self):
         """
         Check that the schema validation fails when we an unrecognised definition is in allOf
         """
         self.schema_obj.schema = {
-            "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
+            "$schema": "https://json-schema.org/draft/2020-12/schema",
+            "$defs": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}},
             "allOf": [
-                {"$ref": "#/definitions/groupOne"},
-                {"$ref": "#/definitions/groupTwo"},
-                {"$ref": "#/definitions/groupThree"},
+                {"$ref": "#/$defs/groupOne"},
+                {"$ref": "#/$defs/groupTwo"},
+                {"$ref": "#/$defs/groupThree"},
             ],
         }
         with pytest.raises(AssertionError) as exc_info:
             self.schema_obj.validate_schema(self.schema_obj.schema)
-        assert exc_info.value.args[0] == "Subschema `groupThree` found in `allOf` but not `definitions`"
+        assert exc_info.value.args[0] == "Subschema `groupThree` found in `allOf` but not `$defs`"
 
     def test_make_skeleton_schema(self):
         """Test making a new schema skeleton"""
@@ -264,7 +270,7 @@ def test_remove_schema_notfound_configs_childschema(self):
         even when they're in a group
         """
         self.schema_obj.schema = {
-            "definitions": {
+            "$defs": {
                 "subSchemaId": {
                     "properties": {"foo": {"type": "string"}, "bar": {"type": "string"}},
                     "required": ["foo"],
@@ -274,8 +280,8 @@ def test_remove_schema_notfound_configs_childschema(self):
         self.schema_obj.pipeline_params = {"bar": True}
         self.schema_obj.no_prompts = True
         params_removed = self.schema_obj.remove_schema_notfound_configs()
-        assert len(self.schema_obj.schema["definitions"]["subSchemaId"]["properties"]) == 1
-        assert "required" not in self.schema_obj.schema["definitions"]["subSchemaId"]
+        assert len(self.schema_obj.schema["$defs"]["subSchemaId"]["properties"]) == 1
+        assert "required" not in self.schema_obj.schema["$defs"]["subSchemaId"]
         assert len(params_removed) == 1
         assert "foo" in params_removed
 
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 2693008707..56574b865c 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -2,8 +2,6 @@
 import shutil
 from pathlib import Path
 
-import pytest
-
 import nf_core.subworkflows
 
 from ..test_subworkflows import TestSubworkflows
@@ -24,9 +22,9 @@ def test_subworkflows_lint_empty(self):
         """Test linting a pipeline with no subworkflows installed"""
         self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True)
         self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True)
-        self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True)
-        with pytest.raises(LookupError):
-            nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
+        self.subworkflow_remove.remove("utils_nfschema_plugin", force=True)
+        nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
+        assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text
 
     def test_subworkflows_lint_new_subworkflow(self):
         """lint a new subworkflow"""
@@ -39,8 +37,8 @@ def test_subworkflows_lint_new_subworkflow(self):
 
     def test_subworkflows_lint_no_gitlab(self):
         """Test linting a pipeline with no subworkflows installed"""
-        with pytest.raises(LookupError):
-            nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
+        assert f"No subworkflows from {GITLAB_URL} installed in pipeline" in self.caplog.text
 
     def test_subworkflows_lint_gitlab_subworkflows(self):
         """Lint subworkflows from a different remote"""
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 9ce74fd4e1..0e16497176 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -44,8 +44,8 @@ def create_modules_repo_dummy(tmp_dir):
         yaml.dump(nf_core_yml.model_dump(), fh)
     # mock biocontainers and anaconda response
     with responses.RequestsMock() as rsps:
-        mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0")
-        mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0")
+        mock_anaconda_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0")
+        mock_biocontainers_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0")
         # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
         module_create = nf_core.modules.create.ModuleCreate(
             root_dir, "bpipe/test", "@author", "process_single", False, False
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 0d012716a9..bde561d95e 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -81,7 +81,7 @@ def testload_pipeline_config(self):
     # def test_load_conda_env(self):
     #     """Load the pipeline Conda environment.yml file"""
     #     self.pipeline_obj._load_conda_environment()
-    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda", "defaults"]
+    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda"]
 
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0
deleted file mode 160000
index ee82f320cb..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
deleted file mode 160000
index f7fe48cf9d..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607
diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0
deleted file mode 160000
index dce3324acb..0000000000
--- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit dce3324acbbe32f905afae8553e042f39404b37e
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0
deleted file mode 160000
index e2638dca91..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_details0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
deleted file mode 160000
index 74cda800a8..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 74cda800a86fd07e93bbf8e00e4890516e3d838d
diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 b/tmp/pytest-of-gitpod/pytest-1/test_github_question0
deleted file mode 160000
index 444ebc5370..0000000000
--- a/tmp/pytest-of-gitpod/pytest-1/test_github_question0
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 444ebc5370bf91ea808f5d65c5788064f0480045