diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 71411be1b9..9dbd7a1f6b 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -6,7 +6,7 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a release.
 
-Learn more about contributing: https://github.com/nf-core/tools/tree/master/.github/CONTRIBUTING.md
+Learn more about contributing: https://github.com/nf-core/tools/tree/main/.github/CONTRIBUTING.md
 -->
 
 ## PR checklist
diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
index 9a1905c7a0..d64799382f 100644
--- a/.github/RELEASE_CHECKLIST.md
+++ b/.github/RELEASE_CHECKLIST.md
@@ -6,14 +6,13 @@
 4. Check that modules/subworkflows in template are up to date with the latest releases
 5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 6. Make sure all CI tests are passing!
-7. Create a PR from `dev` to `master`
-8. Make sure all CI tests are passing again (additional tests are run on PRs to `master`)
+7. Create a PR from `dev` to `main`
+8. Make sure all CI tests are passing again (additional tests are run on PRs to `main`)
 9. Request review (2 approvals required)
-10. Run `rich-codex` to regenerate docs screengrabs (actions `workflow_dispatch` button)
-11. Merge the PR into `master`
-12. Wait for CI tests on the commit to passed
-13. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
-14. Create a new release copying the `CHANGELOG` for that release into the description section.
+10. Merge the PR into `main`
+11. Wait for CI tests on the commit to passed
+12. (Optional but a good idea) Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR.
+13. Create a new release copying the `CHANGELOG` for that release into the description section.
 
 ## After release
 
@@ -21,3 +20,4 @@
 2. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 3. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
 4. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:dev`.
+5. Run `rich-codex` on the [tools/website repo](https://github.com/nf-core/website/actions/workflows/rich-codex.yml) to regenerate docs screengrabs (actions `workflow_dispatch` button)
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index bbac1cc6ff..9775c70e10 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/tools'
         run: |
@@ -21,7 +21,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -31,9 +31,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 09c5b01c37..782a08ac9f 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -71,10 +71,6 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
-          # echo current directory
-          pwd
-          # echo content of current directory
-          ls -la
           nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results
 
       - name: Upload log file artifact
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index dc88031886..ae2df47e61 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -49,7 +49,7 @@ jobs:
     steps:
       - name: Check conditions
         id: conditions
-        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
+        run: echo "run-tests=${{ github.ref == 'refs/heads/main' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
 
     outputs:
       python-version: ${{ matrix.python-version }}
@@ -142,18 +142,18 @@ jobs:
             exit 1
           fi
 
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
       - name: Store snapshot report
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         if: always()
         with:
-          name: Snapshot Report ${{ matrix.test }}
+          name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
 
-      - name: remove slashes from test name
-        run: |
-          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
-          echo "test=${test}" >> $GITHUB_ENV
-
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
deleted file mode 100644
index cd12b139d3..0000000000
--- a/.github/workflows/rich-codex.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: Generate images for docs
-on:
-  workflow_dispatch:
-jobs:
-  rich_codex:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out the repo
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-      - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
-        with:
-          python-version: 3.x
-          cache: pip
-          cache-dependency-path: setup.py
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-
-      - name: Install nf-core/tools
-        run: pip install git+https://github.com/nf-core/tools.git@dev
-
-      - name: Generate terminal images with rich-codex
-        uses: ewels/rich-codex@8ce988cc253c240a3027ba58e33e47640935dd8b # v1
-        env:
-          COLUMNS: 100
-          HIDE_PROGRESS: "true"
-        with:
-          commit_changes: "true"
-          clean_img_paths: docs/images/*.svg
-          terminal_width: 100
-          before_command: >
-            which nextflow &&
-            which nf-core &&
-            nextflow -version &&
-            nf-core --version
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 55880e8130..d453dc9305 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -19,6 +19,10 @@ on:
         description: "Force a PR to be created"
         type: boolean
         default: false
+      pipeline:
+        description: "Pipeline to sync"
+        type: string
+        default: "all"
 
 # Cancel if a newer run is started
 concurrency:
@@ -35,6 +39,14 @@ jobs:
         run: |
           if [ "${{ github.event.inputs.testpipeline }}" == "true" ]; then
             echo '{"pipeline":["testpipeline"]}' > pipeline_names.json
+          elif [ "${{ github.event.inputs.pipeline }}" != "all" ]; then
+            curl -O https://nf-co.re/pipeline_names.json
+            # check if the pipeline exists
+            if ! grep -q "\"${{ github.event.inputs.pipeline }}\"" pipeline_names.json; then
+              echo "Pipeline ${{ github.event.inputs.pipeline }} does not exist"
+              exit 1
+            fi
+            echo '{"pipeline":["${{ github.event.inputs.pipeline }}"]}' > pipeline_names.json
           else
             curl -O https://nf-co.re/pipeline_names.json
           fi
@@ -82,7 +94,7 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt sync -d nf-core/${{ matrix.pipeline }} \
+          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt pipelines sync -d nf-core/${{ matrix.pipeline }} \
             --from-branch dev \
             --pull-request \
             --username nf-core-bot \
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7cbde0c86b..67aa3204c4 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: v0.6.0
+    rev: v0.6.9
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 12a0c9911e..2b215214cd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,28 @@
 # nf-core/tools: Changelog
 
-## v3.0.0dev
+## 3.0.2dev
+
+### Template
+
+### Download
+
+### Linting
+
+### Modules
+
+### Subworkflows
+
+## [v3.0.1 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.1) - [2024-10-09]
+
+### Template
+
+- Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
+- Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
+- Fix too many empty lines added by jinja ([#3204](https://github.com/nf-core/tools/pull/3204) and [#3206](https://github.com/nf-core/tools/pull/3206))
+- Fix header blocks in local subworkflow including git merge marker-like strings ([#3201](https://github.com/nf-core/tools/pull/3201))
+- Update included subworkflows and modules ([#3208](https://github.com/nf-core/tools/pull/3208))
+
+## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 
 **Highlights**
 
@@ -9,10 +31,10 @@
 - 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
+- Changed default branch to `main`.
+- The structure of nf-core/tools pytests has been updated.
+- The structure of the API docs has been updated.
 
 ### Template
 
@@ -30,12 +52,12 @@
 - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104))
 - 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))
+- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116))
 - test pipeline with conda and singularity on PRs to master ([#3149](https://github.com/nf-core/tools/pull/3149))
 - 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))
@@ -43,6 +65,7 @@
 - Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168))
 - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176))
 - Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167))
+- Extend `download_pipeline.yml` to count pre-downloaded container images. ([#3182](https://github.com/nf-core/tools/pull/3182))
 
 ### Linting
 
@@ -60,16 +83,16 @@
 
 ### 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))
+- Allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
+- Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007))
+- Display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038))
+- 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))
+- Allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
 - Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077))
 
 ### Download
@@ -85,9 +108,10 @@
 
 ### General
 
+- Change default branch to `main` for the nf-core/tools repository
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
+- Remove `rich-codex.yml` action, images are now generated on the website repo ([#2989](https://github.com/nf-core/tools/pull/2989))
 - 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))
 - Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012))
@@ -111,6 +135,7 @@
 - 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 minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
 
 ## [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 fb1a867937..8269e95702 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:59c7332a4a24373861c4a5f0eec2c92b87e3efeb8ddef011744ef9a751b1d11c
+FROM python:3.12-slim@sha256:af4e85f1cac90dd3771e47292ea7c8a9830abfabbe4faa5c53f158854c2e819d
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 
diff --git a/README.md b/README.md
index 58fb708a0d..8a3e7d05e6 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,12 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nfcore-tools_logo_dark.png">
-    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nfcore-tools_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png">
+    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_light.png">
   </picture>
 </h1><!-- omit in toc -->
 
-[![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster)
-[![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
+[![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=main&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amain)
+[![codecov](https://codecov.io/gh/nf-core/tools/branch/main/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
 [![code style: prettier](https://img.shields.io/badge/code%20style-prettier-ff69b4.svg)](https://github.com/prettier/prettier)
 [![code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
 
@@ -21,7 +21,7 @@ For documentation of the internal Python functions, please refer to the [Tools P
 
 ## Installation
 
-For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/usage/tools).
+For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation).
 Below is a quick-start for those who know what they're doing:
 
 ### Bioconda
diff --git a/docs/api/_src/api/utils.md b/docs/api/_src/api/utils.md
new file mode 100644
index 0000000000..1353f97ef5
--- /dev/null
+++ b/docs/api/_src/api/utils.md
@@ -0,0 +1,9 @@
+# nf_core.utils
+
+```{eval-rst}
+.. automodule:: nf_core.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :private-members:
+```
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index bfdbd7888d..5a45483d9c 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -40,7 +40,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinxcontrib.autodoc_pydantic"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["./_templates"]
@@ -51,8 +51,8 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = ".rst"
 
-# The master toctree document.
-master_doc = "index"
+# The main toctree document.
+main_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -133,7 +133,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "nf-core.tex", "nf-core tools API documentation", "Phil Ewels, Sven Fillinger", "manual"),
+    (main_doc, "nf-core.tex", "nf-core tools API documentation", "Phil Ewels, Sven Fillinger", "manual"),
 ]
 
 
@@ -141,7 +141,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "nf-core", "nf-core tools API documentation", [author], 1)]
+man_pages = [(main_doc, "nf-core", "nf-core tools API documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -151,7 +151,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     (
-        master_doc,
+        main_doc,
         "nf-core",
         "nf-core tools API documentation",
         author,
diff --git a/docs/api/requirements.txt b/docs/api/requirements.txt
index abffe30740..1d23f0b27d 100644
--- a/docs/api/requirements.txt
+++ b/docs/api/requirements.txt
@@ -1,3 +1,4 @@
+autodoc_pydantic
 Sphinx>=3.3.1
 sphinxcontrib-napoleon
 sphinx-markdown-builder
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index c0095da234..c781905618 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -248,7 +248,7 @@ def _get_module_structure_components(self):
         if self.process_label is None:
             log.info(
                 "Provide an appropriate resource label for the process, taken from the "
-                "[link=https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config#L29]nf-core pipeline template[/link].\n"
+                "[link=https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config#L29]nf-core pipeline template[/link].\n"
                 "For example: {}".format(", ".join(process_label_defaults))
             )
         while self.process_label is None:
diff --git a/nf_core/components/list.py b/nf_core/components/list.py
index 05a8f71120..4c20e60864 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -25,7 +25,7 @@ def __init__(
         self.remote = remote
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
 
-    def _configure_repo_and_paths(self, nf_dir_req=True) -> None:
+    def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None:
         """
         Override the default with nf_dir_req set to False to allow
         info to be run from anywhere and still return remote info
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 9cce94acb5..37e43a536e 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -5,7 +5,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import Any, List, Optional, Tuple, Union
+from typing import Any, Dict, List, Optional, Tuple, Union
 
 log = logging.getLogger(__name__)
 
@@ -50,7 +50,7 @@ def __init__(
         self.passed: List[Tuple[str, str, Path]] = []
         self.warned: List[Tuple[str, str, Path]] = []
         self.failed: List[Tuple[str, str, Path]] = []
-        self.inputs: List[list[dict[str, dict[str, str]]]] = []
+        self.inputs: List[List[Dict[str, Dict[str, str]]]] = []
         self.outputs: List[str] = []
         self.has_meta: bool = False
         self.git_sha: Optional[str] = None
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index dbc1bed737..54a69b113e 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -342,6 +342,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             continue
         try:
             container_url = "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url)
+            log.debug(f"Trying to connect to URL: {container_url}")
             response = requests.head(
                 container_url,
                 stream=True,
diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py
index b6d7f0d0fa..f9ba9d30c7 100644
--- a/nf_core/modules/modules_differ.py
+++ b/nf_core/modules/modules_differ.py
@@ -391,8 +391,8 @@ def get_new_and_old_lines(patch):
     def try_apply_single_patch(file_lines, patch, reverse=False):
         """
         Tries to apply a patch to a modified file. Since the line numbers in
-        the patch does not agree if the file is modified, the old and new
-        lines inpatch are reconstructed and then we look for the old lines
+        the patch do not agree if the file is modified, the old and new
+        lines in the patch are reconstructed and then we look for the old lines
         in the modified file. If all hunk in the patch are found in the new file
         it is updated with the new lines from the patch file.
 
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 536589d81e..05c64b6dee 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -432,7 +432,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name
             to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}"
         shutil.move(str(current_path), local_dir / to_name)
 
-    def unsynced_components(self) -> Tuple[List[str], List[str], dict]:
+    def unsynced_components(self) -> Tuple[List[str], List[str], Dict]:
         """
         Compute the difference between the modules/subworkflows in the directory and the
         modules/subworkflows in the 'modules.json' file. This is done by looking at all
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index 5145366e50..c78ec8e960 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -11,7 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-{%- if modules %}
+{% if modules -%}
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -27,7 +27,7 @@ trim_trailing_whitespace = unset
 indent_style = unset
 {%- endif %}
 
-{%- if email %}
+{% if email -%}
 [/assets/email*]
 indent_size = unset
 {%- endif %}
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index f331d38673..0200ea26ce 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -30,14 +30,14 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-{%- if test_config %}
+{% 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 %}
+{% 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.
 
@@ -95,7 +95,7 @@ If you wish to contribute a new step, please use the following coding standards:
    {%- if multiqc %}
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
-    {% endif %}
+    {%- endif %}
 
 ### Default values
 
@@ -105,7 +105,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -139,4 +139,4 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-  {% endif %}
+  {%- endif %}
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index dc0450be43..d8987330d5 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,16 +14,18 @@ on:
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == '{{ name }}' && github.event.review.state == 'approved'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x
         id: check_approvals
         with:
-          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews
+          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index f704609ca8..29b9947549 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,33 +56,65 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
           nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}{% endif %}
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
+          {% endraw %}{% endif %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index dbba830ec1..0eee862f96 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -42,10 +42,10 @@ jobs:
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |
diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore
index c8e8ad9e11..7ecc9b61cb 100644
--- a/nf_core/pipeline-template/.prettierignore
+++ b/nf_core/pipeline-template/.prettierignore
@@ -1,4 +1,4 @@
-{%- if email %}
+{% if email -%}
 email_template.html
 {%- endif %}
 {%- if adaptivecard %}
diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md
index 2373f1de7f..01e97c1413 100644
--- a/nf_core/pipeline-template/CITATIONS.md
+++ b/nf_core/pipeline-template/CITATIONS.md
@@ -15,10 +15,12 @@
 {% 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].
-> {% endif %} > {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> {% 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 %}
+> {% endif %}
 
 ## Software packaging/containerisation tools
 
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 4331454288..a8f2e60546 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -7,7 +7,7 @@
   </picture>
 </h1>
 
-{%- else %}
+{% else %}
 
 # {{ name }}
 
@@ -128,7 +128,7 @@ An extensive list of references for the tools used by the pipeline can be found
 You can cite the `nf-core` publication as follows:
 
 {% else -%}
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
 
 {% endif -%}
 
diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index cd4e539b31..e6fd878986 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -3,11 +3,11 @@ report_comment: >
   This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
   analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
-  {%- else %}
+  {%- else -%}
   This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/{{ version }}" target="_blank">{{ name }}</a>
   analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/{{ version }}/docs/output" target="_blank">documentation</a>.{% endif %}
-  {% endif %}
+  {%- endif %}
 report_section_order:
   "{{ name_noslash }}-methods-description":
     order: -1000
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index 5e42d50cc5..1becf24b61 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -12,12 +12,16 @@ 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:
 
-{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %}
-{% 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 %}
+{% if fastqc -%}
 
 ### FastQC
 
@@ -32,7 +36,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [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 %}
+
+{% if multiqc -%}
 
 ### MultiQC
 
@@ -49,7 +54,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
-{% endif %}
+{%- endif %}
 
 ### Pipeline information
 
@@ -58,7 +63,8 @@ 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`.
-    {% 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 %}
+    {%- 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/modules.json b/nf_core/pipeline-template/modules.json
index 9bc344e7d1..fa4651ee13 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -13,7 +13,7 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
@@ -23,12 +23,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
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 f1cd99b079..6f5b867b76 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
index b9ccebdbbc..9724d2f34e 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
index b779e46924..2fcbb5ff7d 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 4c816a2a2c..f2bcda0977 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -13,14 +13,14 @@ params {
     // Input options
     input                      = null
 
-    {%- if igenomes %}
+    {% if igenomes -%}
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
     {%- endif %}
 
-    {%- if multiqc %}
+    {% if multiqc -%}
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -45,7 +45,7 @@ params {
     version                      = false
     {% if test_config %}pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'{% endif %}
 
-    {%- if nf_core_configs %}
+    {% if nf_core_configs -%}
     // Config options
     config_profile_name        = null
     config_profile_description = null
@@ -56,15 +56,17 @@ params {
     config_profile_url         = null
     {%- endif %}
 
-    {%- if nf_schema %}
+    {% if nf_schema -%}
     // Schema validation default options
     validate_params            = true
-    {% endif %}
+    {%- endif %}
 }
-{% if modules %}
+
+{% 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   = { 1    * task.attempt }
@@ -75,7 +77,7 @@ process {
     maxRetries    = 1
     maxErrors     = '-1'
 }
-{% endif %}
+{%- endif %}
 
 profiles {
     debug {
@@ -171,14 +173,14 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    {%- if gitpod %}
+    {% if gitpod -%}
     gitpod {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
     {%- endif %}
-    {%- if test_config %}
+    {% if test_config -%}
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
     {%- endif %}
@@ -191,7 +193,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 // Load {{ name }} custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
-{% endif -%}
+{%- endif %}
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -205,7 +207,7 @@ charliecloud.registry = 'quay.io'
 {% if igenomes -%}
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
-{% endif -%}
+{%- endif %}
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
@@ -273,7 +275,7 @@ validation {
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-        {%- if is_nfcore %}
+        {% if is_nfcore -%}
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -297,8 +299,9 @@ validation {
         afterText = validation.help.afterText
     }{% endif %}
 }
-{% endif -%}
-{%- if modules %}
+{%- endif %}
+
+{% if modules -%}
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
-{% endif %}
+{%- endif %}
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 9a58e489eb..bcf2f4a9a6 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
@@ -22,9 +22,9 @@ include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
@@ -111,9 +111,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -169,9 +169,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 {%- if igenomes %}
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 28e32b200e..2b0dc67a6a 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
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -72,11 +71,11 @@ def getWorkflowVersion() {
 // Dump pipeline parameters to a JSON file
 //
 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    = groovy.json.JsonOutput.toJson(params)
-    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
+    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   = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
     nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
@@ -91,9 +90,14 @@ def checkCondaChannels() {
     try {
         def config = parser.load("conda config --show channels".execute().text)
         channels = config.channels
-    } catch(NullPointerException | IOException e) {
-        log.warn "Could not verify conda channel configuration."
-        return
+    }
+    catch (NullPointerException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
@@ -106,19 +110,13 @@ def checkCondaChannels() {
 
     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]))
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
         }
     }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        log.warn(
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  There is a problem with your Conda configuration!\n\n" + "  You will need to set-up the conda-forge and bioconda channels correctly.\n" + "  Please refer to https://bioconda.github.io/\n" + "  The observed channel order is \n" + "  ${channels}\n" + "  but the following channel order is required:\n" + "  ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        )
     }
 }
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 cbd8495bb6..b78273ca4c 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
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE {
 def checkConfigProvided() {
     def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${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" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
+        )
         valid_config = false
     }
     return valid_config
@@ -49,12 +45,14 @@ def checkConfigProvided() {
 //
 def checkProfileProvided(nextflow_cli_args) {
     if (workflow.profile.endsWith(',')) {
-        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
     if (nextflow_cli_args[0]) {
-        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
 }
 
@@ -70,13 +68,7 @@ def workflowCitation() {
     manifest_doi.each { doi_ref ->
         temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
 //
@@ -102,7 +94,7 @@ def getWorkflowVersion() {
 //
 def processVersionsFromYAML(yaml_file) {
     def yaml = new org.yaml.snakeyaml.Yaml()
-    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -121,11 +113,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { version -> processVersionsFromYAML(version) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    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>$group</b></p>\n"
-            summary_section += "    <dl class=\"dl-horizontal\">\n"
-            group_params.keySet().sort().each { param ->
-                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                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"
             }
-            summary_section += "    </dl>\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/${workflow.manifest.name}'\n"
-    yaml_file_text        += "plot_type: 'html'\n"
-    yaml_file_text        += "data: |\n"
-    yaml_file_text        += "${summary_section}"
+    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/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
 
     return yaml_file_text
 }
@@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) {
     colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
@@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) {
 def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
     misc_fields['Date Started']              = workflow.start
     misc_fields['Date Completed']            = workflow.complete
     misc_fields['Pipeline script file path'] = workflow.scriptFile
     misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    if (workflow.repository) {
+        misc_fields['Pipeline repository Git URL']    = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    }
+    misc_fields['Nextflow Version']          = workflow.nextflow.version
+    misc_fields['Nextflow Build']            = workflow.nextflow.build
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
@@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // Render the sendmail template
     def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
@@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // 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 }
-    nextflow.extension.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 }
-    nextflow.extension.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()
 }
 
@@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) {
     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}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
+        }
+        else {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
         }
-    } else {
-        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+    misc_fields['start']          = workflow.start
+    misc_fields['complete']       = workflow.complete
+    misc_fields['scriptfile']     = workflow.scriptFile
+    misc_fields['scriptid']       = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['repository'] = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['commitid']   = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['revision']   = workflow.revision
+    }
+    misc_fields['nxf_version']    = workflow.nextflow.version
+    misc_fields['nxf_build']      = workflow.nextflow.build
+    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
 
     def msg_fields = [:]
     msg_fields['version']      = getWorkflowVersion()
@@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    def post = new URL(hook_url).openConnection()
     post.setRequestMethod("POST")
     post.setDoOutput(true)
     post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index dd45621bc6..6ae55501b2 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -465,6 +465,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
                     f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
                 )
         else:
+            schema_default = str(schema.schema_defaults[param_name])
             failed.append(
                 f"Default value from the Nextflow schema `{param} = {self._wrap_quotes(schema_default)}` not found in `nextflow.config`."
             )
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 3aec815c76..127aa123dc 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -97,10 +97,16 @@ def _update_validation_plugin_from_config(self) -> None:
                 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", [])
+            ignored_params_config_str = conf.get("validation.defaultIgnoreParams", "")
+            ignored_params_config = [
+                item.strip().strip("'") for item in ignored_params_config_str[1:-1].split(",")
+            ]  # Extract list elements and remove whitespace
+
             if len(ignored_params_config) > 0:
+                log.debug(f"Ignoring parameters from config: {ignored_params_config}")
                 ignored_params.extend(ignored_params_config)
             self.ignored_params = ignored_params
+            log.debug(f"Ignoring parameters: {self.ignored_params}")
             self.schema_draft = "https://json-schema.org/draft/2020-12/schema"
 
         else:
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 3f71de8d1e..068da22def 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -1050,15 +1050,26 @@ def get_repo_releases_branches(pipeline, wfs):
 
 
 class NFCoreTemplateConfig(BaseModel):
+    """Template configuration schema"""
+
     org: Optional[str] = None
+    """ Organisation name """
     name: Optional[str] = None
+    """ Pipeline name """
     description: Optional[str] = None
+    """ Pipeline description """
     author: Optional[str] = None
+    """ Pipeline author """
     version: Optional[str] = None
+    """ Pipeline version """
     force: Optional[bool] = True
+    """ Force overwrite of existing files """
     outdir: Optional[Union[str, Path]] = None
+    """ Output directory """
     skip_features: Optional[list] = None
+    """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """
     is_nfcore: Optional[bool] = None
+    """ Whether the pipeline is an nf-core pipeline. """
 
     # convert outdir to str
     @field_validator("outdir")
@@ -1081,13 +1092,22 @@ def get(self, item: str, default: Any = None) -> Any:
 
 
 class NFCoreYamlConfig(BaseModel):
+    """.nf-core.yml configuration file schema"""
+
     repository_type: str
+    """ Type of repository: pipeline or modules """
     nf_core_version: Optional[str] = None
+    """ Version of nf-core/tools used to create/update the pipeline"""
     org_path: Optional[str] = None
+    """ Path to the organisation's modules repository (used for modules repo_type only) """
     lint: Optional[LintConfigType] = None
+    """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """
     template: Optional[NFCoreTemplateConfig] = None
+    """ Pipeline template configuration """
     bump_version: Optional[Dict[str, bool]] = None
+    """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information."""
     update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None
+    """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information."""
 
     def __getitem__(self, item: str) -> Any:
         return getattr(self, item)
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 04c6372d72..aab9b1e5d7 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -6,7 +6,7 @@ responses
 ruff
 Sphinx
 sphinx-rtd-theme
-textual-dev==1.5.1
+textual-dev==1.6.1
 types-PyYAML
 types-requests
 types-jsonschema
diff --git a/setup.py b/setup.py
index 45df29b8bc..b45a52e4f4 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.0.0dev"
+version = "3.0.2dev"
 
 with open("README.md") as f:
     readme = f.read()