diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index d5f377a486..a3941f3ce1 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -27,7 +27,7 @@ jobs:
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
@@ -48,7 +48,9 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 5ce9b41118..4be3098629 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -33,7 +33,7 @@ jobs:
           - "template_skip_nf_core_configs.yml"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
@@ -52,7 +52,9 @@ jobs:
           version: latest-everything
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index d96518d7c6..4f66adae6b 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -26,7 +26,7 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 9b46f0731b..b847df9218 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index f56cb927fc..d846151205 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,9 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index a951230a6a..168fac653c 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -14,11 +14,13 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -28,11 +30,13 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -41,9 +45,9 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,10 +75,10 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
@@ -87,10 +91,10 @@ jobs:
           requirementsFiles: "requirements.txt requirements-dev.txt"
 
   static-type-check:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.12
           cache: "pip"
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index dea28cdd35..1230bfc9d3 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -13,7 +13,7 @@ concurrency:
 jobs:
   push_dockerhub:
     name: Push new Docker image to Docker Hub (dev)
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index 857b241022..49ce17dd84 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 03d5bc65e5..9f8172a3be 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -25,7 +25,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ${{ matrix.runner }}
+    runs-on: ["ubuntu-latest"]
     strategy:
       matrix:
         python-version: ["3.8", "3.12"]
@@ -55,6 +55,7 @@ jobs:
       run-tests: ${{ env.run-tests }}
 
   test:
+    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
     runs-on: ${{ needs.setup.outputs.runner }}
@@ -77,9 +78,9 @@ jobs:
         if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
         run: |
           sudo apt update
-          sudo apt remove git git-man
+          sudo apt remove -y git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
-          sudo apt install git
+          sudo apt install -y git
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
index 54aaf240df..8368255390 100644
--- a/.github/workflows/rich-codex.yml
+++ b/.github/workflows/rich-codex.yml
@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 5e7719973f..b8fb287944 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -36,10 +36,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 3a4725a944..f6106bd8b5 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -20,11 +20,11 @@ concurrency:
 jobs:
   api-docs:
     name: Build & push Sphinx API docs
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
index 8a6eda1318..412784c233 100644
--- a/.github/workflows/tools-api-docs-release.yml
+++ b/.github/workflows/tools-api-docs-release.yml
@@ -19,7 +19,7 @@ jobs:
           - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b7aeeb5bc9..578d17f769 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,3 +11,13 @@ repos:
     rev: "v2.7.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.7.1" # Use the sha / tag you want to point at
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - types-PyYAML
+          - types-requests
+          - types-jsonschema
+          - types-Markdown
+          - types-setuptools
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a68fcf810c..a467c75023 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,7 @@
 - Change testing framework for modules and subworkflows from pytest to nf-test ([#2490](https://github.com/nf-core/tools/pull/2490))
 - `bump_version` keeps now the indentation level of the updated version entries ([#2514](https://github.com/nf-core/tools/pull/2514))
 - Run tests with Python 3.12 ([#2522](https://github.com/nf-core/tools/pull/2522)).
+- Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545))
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index 4d8ae661d5..27eaf9bcb3 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -14,6 +14,7 @@
 #
 import os
 import sys
+from typing import Dict
 
 sys.path.insert(0, os.path.abspath("../../../nf_core"))
 import nf_core
@@ -58,7 +59,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language: str = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -113,7 +114,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
+latex_elements: Dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
diff --git a/mypy.ini b/mypy.ini
index f869fa7e47..c48aa5884b 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,2 +1,3 @@
 [mypy]
 warn_unused_configs = True
+ignore_missing_imports = true
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 6b8befb062..dfdd60f428 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -151,7 +151,7 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 
 
 # nf-core list
-@nf_core_cli.command()
+@nf_core_cli.command("list")
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option(
     "-s",
@@ -162,7 +162,7 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 )
 @click.option("--json", is_flag=True, default=False, help="Print full output as JSON")
 @click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows")
-def list(keywords, sort, json, show_archived):
+def list_pipelines(keywords, sort, json, show_archived):
     """
     List available nf-core pipelines with local info.
 
@@ -553,9 +553,9 @@ def subworkflows(ctx, git_remote, branch, no_pull):
 
 
 # nf-core modules list subcommands
-@modules.group()
+@modules.group("list")
 @click.pass_context
-def list(ctx):
+def modules_list(ctx):
     """
     List modules in a local pipeline or remote repository.
     """
@@ -563,11 +563,11 @@ def list(ctx):
 
 
 # nf-core modules list remote
-@list.command()
+@modules_list.command("remote")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
-def remote(ctx, keywords, json):
+def modules_list_remote(ctx, keywords, json):
     """
     List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
     """
@@ -588,7 +588,7 @@ def remote(ctx, keywords, json):
 
 
 # nf-core modules list local
-@list.command()
+@modules_list.command("local")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -599,7 +599,7 @@ def remote(ctx, keywords, json):
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     """
     List modules installed locally in a pipeline
     """
@@ -620,7 +620,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 
 
 # nf-core modules install
-@modules.command()
+@modules.command("install")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -633,7 +633,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
 @click.option("-f", "--force", is_flag=True, default=False, help="Force reinstallation of module if it already exists")
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
-def install(ctx, tool, dir, prompt, force, sha):
+def modules_install(ctx, tool, dir, prompt, force, sha):
     """
     Install DSL2 modules within a pipeline.
 
@@ -660,7 +660,7 @@ def install(ctx, tool, dir, prompt, force, sha):
 
 
 # nf-core modules update
-@modules.command()
+@modules.command("update")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -699,7 +699,7 @@ def install(ctx, tool, dir, prompt, force, sha):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps):
+def modules_update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 modules within a pipeline.
 
@@ -767,7 +767,7 @@ def patch(ctx, tool, dir, remove):
 
 
 # nf-core modules remove
-@modules.command()
+@modules.command("remove")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -777,7 +777,7 @@ def patch(ctx, tool, dir, remove):
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def remove(ctx, dir, tool):
+def modules_remove(ctx, dir, tool):
     """
     Remove a module from a pipeline.
     """
@@ -899,7 +899,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
 
 
 # nf-core modules lint
-@modules.command()
+@modules.command("lint")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
@@ -924,9 +924,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
     show_default=True,
 )
 @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
-def lint(
-    ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version
-):  # pylint: disable=redefined-outer-name
+def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
     """
     Lint one or more modules in a directory.
 
@@ -971,7 +969,7 @@ def lint(
 
 
 # nf-core modules info
-@modules.command()
+@modules.command("info")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -981,7 +979,7 @@ def lint(
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def info(ctx, tool, dir):
+def modules_info(ctx, tool, dir):
     """
     Show developer usage information about a given module.
 
@@ -1077,7 +1075,6 @@ def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest):
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<nf-core/modules directory>")
-@click.option("-t", "--run-tests", is_flag=True, default=False, help="Run the test workflows")
 @click.option("-p", "--no-prompts", is_flag=True, default=False, help="Use defaults without prompting")
 @click.option("-u", "--update", is_flag=True, default=False, help="Update existing snapshots")
 @click.option("-o", "--once", is_flag=True, default=False, help="Run tests only once. Don't check snapshot stability")
@@ -1108,9 +1105,9 @@ def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once):
 
 
 # nf-core subworkflows list subcommands
-@subworkflows.group()
+@subworkflows.group("list")
 @click.pass_context
-def list(ctx):
+def subworkflows_list(ctx):
     """
     List subworkflows in a local pipeline or remote repository.
     """
@@ -1118,11 +1115,11 @@ def list(ctx):
 
 
 # nf-core subworkflows list remote
-@list.command()
+@subworkflows_list.command("remote")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
-def remote(ctx, keywords, json):
+def subworkflows_list_remote(ctx, keywords, json):
     """
     List subworkflows in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
     """
@@ -1144,7 +1141,7 @@ def remote(ctx, keywords, json):
 
 
 # nf-core subworkflows list local
-@list.command()
+@subworkflows_list.command("local")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -1155,7 +1152,7 @@ def remote(ctx, keywords, json):
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     """
     List subworkflows installed locally in a pipeline
     """
@@ -1176,7 +1173,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 
 
 # nf-core subworkflows lint
-@subworkflows.command()
+@subworkflows.command("lint")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
@@ -1200,9 +1197,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     help="Sort lint output by subworkflow or test name.",
     show_default=True,
 )
-def lint(
-    ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by
-):  # pylint: disable=redefined-outer-name
+def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by):
     """
     Lint one or more subworkflows in a directory.
 
@@ -1246,7 +1241,7 @@ def lint(
 
 
 # nf-core subworkflows info
-@subworkflows.command()
+@subworkflows.command("info")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1256,7 +1251,7 @@ def lint(
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def info(ctx, tool, dir):
+def subworkflows_info(ctx, tool, dir):
     """
     Show developer usage information about a given subworkflow.
 
@@ -1285,7 +1280,7 @@ def info(ctx, tool, dir):
 
 
 # nf-core subworkflows install
-@subworkflows.command()
+@subworkflows.command("install")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1300,7 +1295,7 @@ def info(ctx, tool, dir):
     "-f", "--force", is_flag=True, default=False, help="Force reinstallation of subworkflow if it already exists"
 )
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install subworkflow at commit SHA")
-def install(ctx, subworkflow, dir, prompt, force, sha):
+def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
     """
     Install DSL2 subworkflow within a pipeline.
 
@@ -1327,7 +1322,7 @@ def install(ctx, subworkflow, dir, prompt, force, sha):
 
 
 # nf-core subworkflows remove
-@subworkflows.command()
+@subworkflows.command("remove")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1337,7 +1332,7 @@ def install(ctx, subworkflow, dir, prompt, force, sha):
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def remove(ctx, dir, subworkflow):
+def subworkflows_remove(ctx, dir, subworkflow):
     """
     Remove a subworkflow from a pipeline.
     """
@@ -1357,7 +1352,7 @@ def remove(ctx, dir, subworkflow):
 
 
 # nf-core subworkflows update
-@subworkflows.command()
+@subworkflows.command("update")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1395,7 +1390,7 @@ def remove(ctx, dir, subworkflow):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps):
+def subworkflows_update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 subworkflow within a pipeline.
 
@@ -1409,7 +1404,7 @@ def update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save
             force,
             prompt,
             sha,
-            all,
+            install_all,
             preview,
             save_diff,
             update_deps,
@@ -1509,11 +1504,11 @@ def build(dir, no_prompts, web_only, url):
 
 
 # nf-core schema lint
-@schema.command()
+@schema.command("lint")
 @click.argument(
     "schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>"
 )
-def lint(schema_path):
+def schema_lint(schema_path):
     """
     Check that a given pipeline schema is valid.
 
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index c46d68ff22..efffc28e85 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -10,7 +10,9 @@
 import os
 from pathlib import Path
 
-import rich
+import rich.box
+import rich.console
+import rich.panel
 from rich.markdown import Markdown
 from rich.table import Table
 
@@ -209,7 +211,7 @@ def _print_results(self, show_passed=False, sort_by="test"):
         self.failed.sort(key=operator.attrgetter(*sort_order))
 
         # Find maximum module name length
-        max_name_len = 40
+        max_name_len = len(self.component_type[:-1] + " name")
         for tests in [self.passed, self.warned, self.failed]:
             try:
                 for lint_result in tests:
@@ -264,7 +266,7 @@ def format_result(test_results, table):
             table = Table(style="yellow", box=rich.box.MINIMAL, pad_edge=False, border_style="dim")
             table.add_column(f"{self.component_type[:-1].title()} name", width=max_name_len)
             table.add_column("File path")
-            table.add_column("Test message")
+            table.add_column("Test message", overflow="fold")
             table = format_result(self.warned, table)
             console.print(
                 rich.panel.Panel(
@@ -278,10 +280,15 @@ def format_result(test_results, table):
 
         # Table of failing tests
         if len(self.failed) > 0:
-            table = Table(style="red", box=rich.box.MINIMAL, pad_edge=False, border_style="dim")
+            table = Table(
+                style="red",
+                box=rich.box.MINIMAL,
+                pad_edge=False,
+                border_style="dim",
+            )
             table.add_column(f"{self.component_type[:-1].title()} name", width=max_name_len)
             table.add_column("File path")
-            table.add_column("Test message")
+            table.add_column("Test message", overflow="fold")
             table = format_result(self.failed, table)
             console.print(
                 rich.panel.Panel(
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 190310faae..8d9b6840b0 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -4,6 +4,7 @@
 import logging
 import re
 from pathlib import Path
+from typing import Union
 
 log = logging.getLogger(__name__)
 
@@ -77,7 +78,7 @@ def __init__(
             self.test_yml = None
             self.test_main_nf = None
 
-    def _get_main_nf_tags(self, test_main_nf: str):
+    def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
         """Collect all tags from the main.nf.test file."""
         tags = []
         with open(test_main_nf, "r") as fh:
@@ -86,13 +87,19 @@ def _get_main_nf_tags(self, test_main_nf: str):
                     tags.append(line.strip().split()[1].strip('"'))
         return tags
 
-    def _get_included_components(self, main_nf: str):
+    def _get_included_components(self, main_nf: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
         with open(main_nf, "r") as fh:
             for line in fh:
                 if line.strip().startswith("include"):
-                    included_components.append(line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/"))
+                    # get tool/subtool or subworkflow name from include statement, can be in the form
+                    #'../../../modules/nf-core/hisat2/align/main'
+                    #'../bam_sort_stats_samtools/main'
+                    #'../subworkflows/nf-core/bam_sort_stats_samtools/main'
+                    component = line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/")
+                    component = component.replace("'../", "subworkflows/")
+                    included_components.append(component)
         return included_components
 
     def get_inputs_from_main_nf(self):
diff --git a/nf_core/params_file.py b/nf_core/params_file.py
index 39986b95c2..5c50c53fb9 100644
--- a/nf_core/params_file.py
+++ b/nf_core/params_file.py
@@ -89,7 +89,7 @@ def __init__(
         self,
         pipeline=None,
         revision=None,
-    ):
+    ) -> None:
         """Initialise the ParamFileBuilder class
 
         Args:
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 521f3e664a..3edd49f09d 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index f3dc3e50fe..31e8cd2b36 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index edce89065f..64d1851f2e 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 6a6bee6a83..31917a3e31 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -121,6 +121,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        runOptions             = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
diff --git a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test b/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
index b0a212f2a3..59c4fdb679 100644
--- a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
+++ b/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
@@ -8,7 +8,6 @@ nextflow_workflow {
 
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "{{ component_name }}"
     tag "subworkflows/{{ component_name }}"
     // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
     tag "samtools"
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index 44c7c21a37..ffba41f9da 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -29,12 +29,12 @@ class SubworkflowLint(ComponentLint):
     """
 
     # Import lint functions
-    from .main_nf import main_nf
-    from .meta_yml import meta_yml
-    from .subworkflow_changes import subworkflow_changes
-    from .subworkflow_tests import subworkflow_tests
-    from .subworkflow_todos import subworkflow_todos
-    from .subworkflow_version import subworkflow_version
+    from .main_nf import main_nf  # type: ignore[misc]
+    from .meta_yml import meta_yml  # type: ignore[misc]
+    from .subworkflow_changes import subworkflow_changes  # type: ignore[misc]
+    from .subworkflow_tests import subworkflow_tests  # type: ignore[misc]
+    from .subworkflow_todos import subworkflow_todos  # type: ignore[misc]
+    from .subworkflow_version import subworkflow_version  # type: ignore[misc]
 
     def __init__(
         self,
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index e82d00f636..a125be152f 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -102,11 +102,11 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                 "subworkflows",
                 f"subworkflows/{subworkflow.component_name}",
                 "subworkflows_nfcore",
-                subworkflow.component_name,
             ]
             included_components = []
             if subworkflow.main_nf.is_file():
                 included_components = subworkflow._get_included_components(subworkflow.main_nf)
+            log.debug(f"Required tags: {required_tags}")
             missing_tags = []
             for tag in required_tags + included_components:
                 if tag not in main_nf_tags:
diff --git a/pyproject.toml b/pyproject.toml
index f0702742fd..2380073107 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,8 +20,3 @@ norecursedirs = [ ".*", "build", "dist", "*.egg", "data", "__pycache__", ".githu
 profile = "black"
 known_first_party = ["nf_core"]
 multi_line_output = 3
-
-[tool.mypy]
-ignore_missing_imports = true
-follow_imports = "skip"
-disable_error_code = "no-redef"
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 12183eb98c..3ef0593085 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -11,3 +11,4 @@ types-PyYAML
 types-requests
 types-jsonschema
 types-Markdown
+types-setuptools
diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py
index 5bbe746f2e..1380db2260 100644
--- a/tests/subworkflows/lint.py
+++ b/tests/subworkflows/lint.py
@@ -28,9 +28,8 @@ def test_subworkflows_lint_new_subworkflow(self):
     """lint a new subworkflow"""
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=True, all_subworkflows=True)
-    assert (
-        len(subworkflow_lint.failed) == 1  # test snap missing after creating a subworkflow
-    ), f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+    assert len(subworkflow_lint.failed) == 0
+
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
 
@@ -68,7 +67,6 @@ def test_subworkflows_lint_multiple_remotes(self):
 
 def test_subworkflows_lint_snapshot_file(self):
     """Test linting a subworkflow with a snapshot file"""
-    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
     assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
@@ -78,8 +76,10 @@ def test_subworkflows_lint_snapshot_file(self):
 
 def test_subworkflows_lint_snapshot_file_missing_fail(self):
     """Test linting a subworkflow with a snapshot file missing, which should fail"""
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
@@ -96,8 +96,11 @@ def test_subworkflows_lint_snapshot_file_not_needed(self):
         Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test"), "w"
     ) as fh:
         fh.write(new_content)
+
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 67104e3ad0..69917b279d 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -178,44 +178,44 @@ def test_sphinx_md_files(self):
     #######################
     # SPECIFIC LINT TESTS #
     #######################
-    from .lint.actions_awsfulltest import (
+    from .lint.actions_awsfulltest import (  # type: ignore[misc]
         test_actions_awsfulltest_fail,
         test_actions_awsfulltest_pass,
         test_actions_awsfulltest_warn,
     )
-    from .lint.actions_awstest import (
+    from .lint.actions_awstest import (  # type: ignore[misc]
         test_actions_awstest_fail,
         test_actions_awstest_pass,
     )
-    from .lint.actions_ci import (
+    from .lint.actions_ci import (  # type: ignore[misc]
         test_actions_ci_fail_wrong_nf,
         test_actions_ci_fail_wrong_trigger,
         test_actions_ci_pass,
     )
-    from .lint.actions_schema_validation import (
+    from .lint.actions_schema_validation import (  # type: ignore[misc]
         test_actions_schema_validation_fails_for_additional_property,
         test_actions_schema_validation_missing_jobs,
         test_actions_schema_validation_missing_on,
     )
-    from .lint.files_exist import (
+    from .lint.files_exist import (  # type: ignore[misc]
         test_files_exist_depreciated_file,
         test_files_exist_missing_config,
         test_files_exist_missing_main,
         test_files_exist_pass,
     )
-    from .lint.files_unchanged import (
+    from .lint.files_unchanged import (  # type: ignore[misc]
         test_files_unchanged_fail,
         test_files_unchanged_pass,
     )
-    from .lint.merge_markers import test_merge_markers_found
-    from .lint.modules_json import test_modules_json_pass
-    from .lint.nextflow_config import (
+    from .lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
+    from .lint.modules_json import test_modules_json_pass  # type: ignore[misc]
+    from .lint.nextflow_config import (  # type: ignore[misc]
         test_nextflow_config_bad_name_fail,
         test_nextflow_config_dev_in_release_mode_failed,
         test_nextflow_config_example_pass,
         test_nextflow_config_missing_test_profile_failed,
     )
-    from .lint.version_consistency import test_version_consistency
+    from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
 
 
 # TODO nf-core: Assess and strip out if no longer required for DSL2
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 638a4bedb1..aaf4080a7b 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -4,6 +4,7 @@
 import os
 import shutil
 import unittest
+from pathlib import Path
 
 import nf_core.create
 import nf_core.modules
@@ -21,22 +22,18 @@
 def create_modules_repo_dummy(tmp_dir):
     """Create a dummy copy of the nf-core/modules repo"""
 
-    root_dir = os.path.join(tmp_dir, "modules")
-    os.makedirs(os.path.join(root_dir, "modules"))
-    os.makedirs(os.path.join(root_dir, "subworkflows"))
-    os.makedirs(os.path.join(root_dir, "subworkflows", "nf-core"))
-    os.makedirs(os.path.join(root_dir, "tests", "modules"))
-    os.makedirs(os.path.join(root_dir, "tests", "subworkflows"))
-    os.makedirs(os.path.join(root_dir, "tests", "config"))
-    with open(os.path.join(root_dir, "tests", "config", "pytest_modules.yml"), "w") as fh:
-        fh.writelines(["test:", "\n  - modules/test/**", "\n  - tests/modules/test/**"])
-    with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
+    root_dir = Path(tmp_dir, "modules")
+    Path(root_dir, "modules").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "subworkflows").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "subworkflows", "nf-core").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "tests", "config").mkdir(parents=True, exist_ok=True)
+    with open(Path(root_dir, ".nf-core.yml"), "w") as fh:
         fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"])
-
     # TODO Add a mock here
     subworkflow_create = nf_core.subworkflows.SubworkflowCreate(root_dir, "test_subworkflow", "@author", True)
     subworkflow_create.create()
 
+    Path(root_dir, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     return root_dir