diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index a90c06f9a9..75da414db6 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -92,7 +92,7 @@ pre-commit run --all
 ## API Documentation
 
 We aim to write function docstrings according to the [Google Python style-guide](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings). These are used to automatically generate package documentation on the nf-core website using Sphinx.
-You can find this documentation here: [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
+You can find this documentation here: [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/)
 
 If you would like to test the documentation, you can install Sphinx locally by following Sphinx's [installation instruction](https://www.sphinx-doc.org/en/master/usage/installation.html).
 Once done, you can run `make clean` and then `make html` in the `docs/api` directory of `nf-core tools`.
diff --git a/.github/renovate.json5 b/.github/renovate.json5
new file mode 100644
index 0000000000..f9b377c615
--- /dev/null
+++ b/.github/renovate.json5
@@ -0,0 +1,5 @@
+{
+    $schema: "https://docs.renovatebot.com/renovate-schema.json",
+    extends: ["github>nf-core/ops//.github/renovate/default.json5"],
+    baseBranches: ["dev"],
+}
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 8f6836f309..2a692da799 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:
@@ -27,14 +27,14 @@ 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
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -48,84 +48,101 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
-
-      - name: Install Prettier
-        run: npm install -g prettier
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
-      # Install the editorconfig linting tools
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
+      - name: Install Prettier and editorconfig-checker
+        run: npm install -g prettier editorconfig-checker
 
       # Build a pipeline from the template
       - name: nf-core create
-        run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+        run: |
+          mkdir create-lint-wf && cd create-lint-wf
+          export NXF_WORK=$(pwd)
+          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
 
       # Try syncing it before we change anything
       - name: nf-core sync
         run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
+        working-directory: create-lint-wf
 
       # Build a module from the template
       - name: nf-core modules create
         run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta
+        working-directory: create-lint-wf
 
       # Run code style linting
       - name: Run Prettier --check
-        run: prettier --check nf-core-testpipeline
+        run: prettier --check create-lint-wf/nf-core-testpipeline
 
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+        working-directory: create-lint-wf
 
       # Update modules to the latest version
       - name: nf-core modules update
         run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview
+        working-directory: create-lint-wf
 
       # Remove TODO statements
       - name: remove TODO
         run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+        working-directory: create-lint-wf
 
       # Replace zenodo.XXXXXX to pass readme linting
       - name: replace zenodo.XXXXXX
         run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+        working-directory: create-lint-wf
 
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+        working-directory: create-lint-wf
 
       # Run the other nf-core commands
       - name: nf-core list
         run: nf-core --log-file log.txt list
+        working-directory: create-lint-wf
 
       # - name: nf-core licences
       #   run: nf-core --log-file log.txt licences nf-core-testpipeline
 
       - name: nf-core schema
         run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
+        working-directory: create-lint-wf
 
       - name: nf-core bump-version
         run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
+        working-directory: create-lint-wf
 
       - name: nf-core lint in release mode
         run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+        working-directory: create-lint-wf
 
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
+        working-directory: create-lint-wf
 
       - name: nf-core modules install gitlab
         run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/
+        working-directory: create-lint-wf
 
       - name: nf-core modules list local
         run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+        working-directory: create-lint-wf
 
       - name: nf-core modules list remote
         run: nf-core --log-file log.txt modules list remote
+        working-directory: create-lint-wf
 
       - name: nf-core modules list remote gitlab
         run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
+        working-directory: create-lint-wf
 
       - name: Upload log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: log.txt
+          path: create-lint-wf/log.txt
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 2689805dd1..b4d8aead9f 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -33,13 +33,13 @@ 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 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -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
@@ -64,75 +66,86 @@ jobs:
       # Create template files
       - name: Create template skip all (except github)
         run: |
-          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > template_skip_all.yml
+          mkdir create-test-lint-wf
+          export NXF_WORK=$(pwd)
+          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
 
       - name: Create template skip github_badges
         run: |
-          printf "prefix: my-prefix\nskip: github_badges" > template_skip_github_badges.yml
+          printf "prefix: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
 
       - name: Create template skip igenomes
         run: |
-          printf "prefix: my-prefix\nskip: igenomes" > template_skip_igenomes.yml
+          printf "prefix: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
 
       - name: Create template skip ci
         run: |
-          printf "prefix: my-prefix\nskip: ci" > template_skip_ci.yml
+          printf "prefix: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
 
       - name: Create template skip nf_core_configs
         run: |
-          printf "prefix: my-prefix\nskip: nf_core_configs" > template_skip_nf_core_configs.yml
+          printf "prefix: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
+          cd create-test-lint-wf
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
       - name: run the pipeline
         run: |
+          cd create-test-lint-wf
           nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder
         run: |
-          rm -rf ./results
+          rm -rf create-test-lint-wf/results
 
       # Try syncing it before we change anything
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/
+        run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
       - name: Run Prettier --check
-        run: prettier --check my-prefix-testpipeline
+        run: prettier --check create-test-lint-wf/my-prefix-testpipeline
 
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+        working-directory: create-test-lint-wf
 
       # Remove TODO statements
       - name: remove TODO
         run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;
+        working-directory: create-test-lint-wf
 
       # Replace zenodo.XXXXXX to pass readme linting
       - name: replace zenodo.XXXXXX
         run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
+        working-directory: create-test-lint-wf
 
       # Run nf-core linting
       - name: nf-core lint
         run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned
+        working-directory: create-test-lint-wf
 
       # Run bump-version
       - name: nf-core bump-version
         run: nf-core --log-file log.txt bump-version --dir my-prefix-testpipeline/ 1.1
+        working-directory: create-test-lint-wf
 
       # Run nf-core linting in release mode
       - name: nf-core lint in release mode
         run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned --release
+        working-directory: create-test-lint-wf
 
       - name: Tar files
         run: tar -cvf artifact_files.tar log.txt template_skip*.yml
+        working-directory: create-test-lint-wf
 
       - name: Upload log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: artifact_files.tar
+          path: create-test-lint-wf/artifact_files.tar
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 5faa59772c..e4779d0684 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -26,13 +26,13 @@ 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 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -46,6 +46,8 @@ jobs:
 
       - name: Run nf-core/tools
         run: |
+          mkdir create-test-wf && cd create-test-wf
+          export NXF_WORK=$(pwd)
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
           nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
@@ -54,4 +56,4 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: log.txt
+          path: create-test-wf/log.txt
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 1f539fe09a..b847df9218 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index ed2314046a..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
@@ -38,10 +40,10 @@ jobs:
           # Override to remove the default --check flag so that we make changes
           options: "--color"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: python-isort
         uses: isort/isort-action@v1.0.0
         with:
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index edff9a8c82..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
@@ -71,15 +75,15 @@ 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 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: python-isort
         uses: isort/isort-action@v1.1.0
         with:
@@ -87,12 +91,12 @@ 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: 3.11
+          python-version: 3.12
           cache: "pip"
 
       - name: Install dependencies
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 4d9881d6bb..46ebe8e57d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -24,37 +24,53 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
-  pytest:
-    runs-on: ${{ matrix.runner }}
+  setup:
+    runs-on: ["ubuntu-latest"]
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
-          - runner: "ubuntu-20.04"
-            python-version: "3.8"
+          - python-version: "3.8"
+            runner: "ubuntu-20.04"
 
     steps:
-      - uses: actions/checkout@v3
+      - 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"
+
+    outputs:
+      python-version: ${{ matrix.python-version }}
+      runner: ${{ matrix.runner }}
+      run-tests: ${{ steps.conditions.outputs.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}}
+    runs-on: ${{ needs.setup.outputs.runner }}
+    steps:
+      - uses: actions/checkout@v2
         name: Check out source-code repository
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - name: Set up Python ${{ needs.setup.outputs.python-version }}
+        uses: actions/setup-python@v2
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
       - name: Downgrade git to the Ubuntu official repository's version
-        if: ${{ matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8' }}
+        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
@@ -71,7 +87,7 @@ jobs:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-nftest-${{ env.date }}
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'
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 fbbdacc8ab..a5cb451dc7 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -31,15 +31,15 @@ jobs:
 
   sync:
     needs: get-pipelines
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     strategy:
       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 }}
@@ -48,10 +48,10 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index add939aba1..f6106bd8b5 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -20,16 +20,16 @@ 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 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
index f049d74ca0..412784c233 100644
--- a/.github/workflows/tools-api-docs-release.yml
+++ b/.github/workflows/tools-api-docs-release.yml
@@ -19,12 +19,12 @@ 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 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
diff --git a/.gitpod.yml b/.gitpod.yml
index 1cc63b197f..3c8b6b5303 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,6 +6,9 @@ tasks:
       python -m pip install -r requirements-dev.txt
       pre-commit install --install-hooks
       nextflow self-update
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b7aeeb5bc9..ad23a3c895 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,3 +11,18 @@ repos:
     rev: "v2.7.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+  - 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/.prettierignore b/.prettierignore
index 778fb4fb2c..344cafca6e 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -3,6 +3,6 @@ adaptivecard.json
 slackreport.json
 docs/api/_build
 testing
-nf_core/module-template/modules/meta.yml
-nf_core/module-template/modules/tests/tags.yml
-nf_core/subworkflow-template/subworkflows/tests/tags.yml
+nf_core/module-template/meta.yml
+nf_core/module-template/tests/tags.yml
+nf_core/subworkflow-template/tests/tags.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b8fcce59fb..b7365fa3f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,28 +7,51 @@
 - Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465))
 - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503))
 - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509))
+- Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540))
+- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
+
+### Download
+
+- Add `docker://` prefix for absolute container URIs as well ([#2576](https://github.com/nf-core/tools/pull/2576)).
+- Bugfix for AttributeError: `ContainerError` object has no attribute `absoluteURI` ([#2543](https://github.com/nf-core/tools/pull/2543)).
 
 ### Linting
 
 - Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447))
 - Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([#2448](https://github.com/nf-core/tools/pull/2448))
+- Add pyupgrade to pre-commit config and dev requirements as mentioned in [#2200](https://github.com/nf-core/tools/issues/2200)
 - Check for spaces in modules container URLs ([#2452](https://github.com/nf-core/tools/issues/2452))
+- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables when linting a pipeline. ([#2507](https://github.com/nf-core/tools/pull/2507))
+- Lint nf-test main.nf.test tags include all used components in chained tests ([#2572](https://github.com/nf-core/tools/pull/2572))
+- Don't fail linting if md5sum for empty files are found in a stub test ([#2571](https://github.com/nf-core/tools/pull/2571))
 
 ### Modules
 
 - Added stub test creation to `create_test_yml` ([#2476](https://github.com/nf-core/tools/pull/2476))
 - Replace ModulePatch by ComponentPatch ([#2482](https://github.com/nf-core/tools/pull/2482))
 - Fixed `nf-core modules lint` to work with new module structure for nf-test ([#2494](https://github.com/nf-core/tools/pull/2494))
+- Add option `--migrate-pytest` to create a module with nf-test taking into account an existing module ([#2549](https://github.com/nf-core/tools/pull/2549))
+- When installing modules and subworkflows, automatically create the `./modules` directory if it doesn't exist ([#2563](https://github.com/nf-core/tools/issues/2563))
+- When `.nf-core.yml` is not found create it in the current directory instead of the root filesystem ([#2237](https://github.com/nf-core/tools/issues/2237))
+- Modules `--migrate-pytest` copies template scripts ([#2568](https://github.com/nf-core/tools/pull/2568))
 
 ### Subworkflows
 
 - Added stub test creation to `create_test_yml` ([#2476](https://github.com/nf-core/tools/pull/2476))
 - Fixed `nf-core subworkflows lint` to work with new module structure for nf-test ([#2494](https://github.com/nf-core/tools/pull/2494))
+- Add option `--migrate-pytest` to create a subworkflow with nf-test taking into account an existing subworkflow ([#2549](https://github.com/nf-core/tools/pull/2549))
 
 ### General
 
+- Update `schema build` functionality to automatically update defaults which have changed in the `nextflow.config`([#2479](https://github.com/nf-core/tools/pull/2479))
 - 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))
+- Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)).
+- GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)).
+- Sort the `installed_by` list in `modules.json` ([#2570](https://github.com/nf-core/tools/pull/2570)).
+- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 
diff --git a/README.md b/README.md
index 8e6b52d4c2..6a10e1f382 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,7 @@ A python package with helper tools for the nf-core community.
 - [Citation](#citation)
 
 The nf-core tools package is written in Python and can be imported and used within other packages.
-For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools-docs/).
+For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools/docs/).
 
 ## Installation
 
@@ -76,7 +76,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.11 nf-core nextflow
+conda create --name nf-core python=3.12 nf-core nextflow
 conda activate nf-core
 ```
 
@@ -186,7 +186,7 @@ for wf in wfs.remote_workflows:
     print(wf.full_name)
 ```
 
-Please see [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/) for the function documentation.
+Please see [https://nf-co.re/tools/docs/](https://nf-co.re/tools/docs/) for the function documentation.
 
 ### Automatic version check
 
@@ -433,7 +433,7 @@ If the download speeds are much slower than your internet connection is capable
 Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.
 
 :::tip
-Also without access to Tower, pipelines downloaded with the `--tower` flag can be run: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
+Also without access to Tower, pipelines downloaded with the `--tower` flag can be run if the _absolute_ path is specified: `nextflow run -r 2.5 file:/path/to/pipelinedownload.git`. Downloads in this format allow you to include multiple revisions of a pipeline in a single file, but require that the revision (e.g. `-r 2.5`) is always explicitly specified.
 :::
 
 ## Pipeline software licences
@@ -533,7 +533,7 @@ Each test result name on the left is a terminal hyperlink.
 In most terminals you can <kbd>ctrl</kbd> + <kbd>click</kbd> ( <kbd>cmd</kbd> + <kbd>click</kbd>) these
 links to open documentation specific to this test in your browser.
 
-Alternatively visit <https://nf-co.re/tools-docs/lint_tests/index.html> and find your test to read more.
+Alternatively visit <https://nf-co.re/tools/docs/latest/pipeline_lint_tests/index.html> and find your test to read more.
 
 ### Linting config
 
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
new file mode 100644
index 0000000000..c48aa5884b
--- /dev/null
+++ b/mypy.ini
@@ -0,0 +1,3 @@
+[mypy]
+warn_unused_configs = True
+ignore_missing_imports = true
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 232f1bf116..8cfacf7399 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.
 
@@ -448,7 +448,7 @@ def lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, ma
 
     Runs a large number of automated tests to ensure that the supplied pipeline
     meets the nf-core guidelines. Documentation of all lint tests can be found
-    on the nf-core website: [link=https://nf-co.re/tools-docs/]https://nf-co.re/tools-docs/[/]
+    on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/]
 
     You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/].
     See the documentation for details.
@@ -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.
     """
@@ -815,8 +815,20 @@ def remove(ctx, dir, tool):
     default=False,
     help="Create a module from the template without TODOs or examples",
 )
+@click.option("--migrate-pytest", is_flag=True, default=False, help="Migrate a module with pytest tests to nf-test")
 def create_module(
-    ctx, tool, dir, author, label, meta, no_meta, force, conda_name, conda_package_version, empty_template
+    ctx,
+    tool,
+    dir,
+    author,
+    label,
+    meta,
+    no_meta,
+    force,
+    conda_name,
+    conda_package_version,
+    empty_template,
+    migrate_pytest,
 ):
     """
     Create a new DSL2 module from the nf-core template.
@@ -841,7 +853,7 @@ def create_module(
     # Run function
     try:
         module_create = ModuleCreate(
-            dir, tool, author, label, has_meta, force, conda_name, conda_package_version, empty_template
+            dir, tool, author, label, has_meta, force, conda_name, conda_package_version, empty_template, migrate_pytest
         )
         module_create.create()
     except UserWarning as e:
@@ -887,7 +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>")
@@ -912,9 +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.
 
@@ -959,7 +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(
@@ -969,7 +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.
 
@@ -1035,7 +1045,8 @@ def bump_versions(ctx, tool, dir, all, show_all):
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<directory>")
 @click.option("-a", "--author", type=str, metavar="<author>", help="Module author's GitHub username prefixed with '@'")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
-def create_subworkflow(ctx, subworkflow, dir, author, force):
+@click.option("--migrate-pytest", is_flag=True, default=False, help="Migrate a module with pytest tests to nf-test")
+def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest):
     """
     Create a new subworkflow from the nf-core template.
 
@@ -1049,7 +1060,7 @@ def create_subworkflow(ctx, subworkflow, dir, author, force):
 
     # Run function
     try:
-        subworkflow_create = SubworkflowCreate(dir, subworkflow, author, force)
+        subworkflow_create = SubworkflowCreate(dir, subworkflow, author, force, migrate_pytest)
         subworkflow_create.create()
     except UserWarning as e:
         log.critical(e)
@@ -1064,7 +1075,6 @@ def create_subworkflow(ctx, subworkflow, dir, author, force):
 @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")
@@ -1095,9 +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.
     """
@@ -1105,11 +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[/])[/].
     """
@@ -1131,7 +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")
@@ -1142,7 +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
     """
@@ -1163,7 +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>")
@@ -1187,9 +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.
 
@@ -1233,7 +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(
@@ -1243,7 +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.
 
@@ -1272,7 +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(
@@ -1287,7 +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.
 
@@ -1314,7 +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(
@@ -1324,7 +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.
     """
@@ -1344,7 +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(
@@ -1382,7 +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.
 
@@ -1396,7 +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,
@@ -1496,11 +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/bump_version.py b/nf_core/bump_version.py
index 83979ed4e0..40c8f8984f 100644
--- a/nf_core/bump_version.py
+++ b/nf_core/bump_version.py
@@ -32,7 +32,8 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         new_version = new_version[1:]
     if not current_version:
         raise UserWarning("Could not find config variable 'manifest.version'")
-
+    if current_version == new_version:
+        raise UserWarning(f"Current version is already: {current_version}")
     log.info(f"Changing version number from '{current_version}' to '{new_version}'")
 
     # nextflow.config - workflow manifest version
@@ -48,17 +49,47 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
     )
     # multiqc_config.yaml
     multiqc_new_version = "dev" if "dev" in new_version else new_version
+    multiqc_current_version = "dev" if "dev" in current_version else current_version
+    if multiqc_current_version != "dev" and multiqc_new_version != "dev":
+        update_file_version(
+            Path("assets", "multiqc_config.yml"),
+            pipeline_obj,
+            [
+                (
+                    f"/releases/tag/{current_version}",
+                    f"/releases/tag/{new_version}",
+                )
+            ],
+        )
+    if multiqc_current_version != "dev" and multiqc_new_version == "dev":
+        update_file_version(
+            Path("assets", "multiqc_config.yml"),
+            pipeline_obj,
+            [
+                (
+                    f"/releases/tag/{current_version}",
+                    f"/tree/dev",
+                )
+            ],
+        )
+    if multiqc_current_version == "dev" and multiqc_new_version != "dev":
+        update_file_version(
+            Path("assets", "multiqc_config.yml"),
+            pipeline_obj,
+            [
+                (
+                    f"/tree/dev",
+                    f"/releases/tag/{multiqc_new_version}",
+                )
+            ],
+        )
     update_file_version(
         Path("assets", "multiqc_config.yml"),
         pipeline_obj,
         [
             (
-                "/dev",
-                f"/{multiqc_new_version}",
-            ),
-            (
-                rf"{re.escape(current_version)}",
-                f"{multiqc_new_version}",
+                f"/{multiqc_current_version}/",
+                f"/{multiqc_new_version}/",
             ),
         ],
     )
@@ -187,7 +218,7 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt
         if found_match:
             content = "\n".join(newcontent) + "\n"
         else:
-            log.error(f"Could not find version number in {filename}: '{pattern}'")
+            log.error(f"Could not find version number in {filename}: `{pattern}`")
 
     log.info(f"Updated version in '{filename}'")
     for replacement in replacements:
diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index 689a6819eb..3294c2878b 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -2,7 +2,6 @@
 The ComponentsTest class handles the generation and testing of nf-test snapshots.
 """
 
-from __future__ import print_function
 
 import logging
 import os
@@ -19,7 +18,6 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-from tests.utils import set_wd
 
 log = logging.getLogger(__name__)
 
@@ -92,7 +90,7 @@ def run(self) -> None:
         os.environ[
             "NFT_DIFF_ARGS"
         ] = "--line-numbers --expand-tabs=2"  # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences
-        with set_wd(Path(self.dir)):
+        with nf_core.utils.set_wd(Path(self.dir)):
             self.check_snapshot_stability()
         if len(self.errors) > 0:
             errors = "\n - ".join(self.errors)
@@ -191,10 +189,11 @@ def generate_snapshot(self) -> bool:
         verbose = "--verbose --debug" if self.verbose else ""
         update = "--update-snapshot" if self.update else ""
         self.update = False  # reset self.update to False to test if the new snapshot is stable
+        tag = f"subworkflows/{self.component_name}" if self.component_type == "subworkflows" else self.component_name
 
         result = nf_core.utils.run_cmd(
             "nf-test",
-            f"test --tag {self.component_name} --profile {os.environ['PROFILE']} {verbose} {update}",
+            f"test --tag {tag} --profile {os.environ['PROFILE']} {verbose} {update}",
         )
         if result is not None:
             nftest_out, nftest_err = result
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 54fade29a2..568ca22af5 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -7,8 +7,8 @@
 import glob
 import json
 import logging
-import os
 import re
+import shutil
 import subprocess
 from pathlib import Path
 from typing import Dict, Optional
@@ -16,11 +16,13 @@
 import jinja2
 import questionary
 import rich
+import yaml
 from packaging.version import parse as parse_version
 
 import nf_core
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
+from nf_core.lint_utils import run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -38,6 +40,7 @@ def __init__(
         conda_name: Optional[str] = None,
         conda_version: Optional[str] = None,
         empty_template: bool = False,
+        migrate_pytest: bool = False,
     ):
         super().__init__(component_type, directory)
         self.directory = directory
@@ -56,8 +59,9 @@ def __init__(
         self.bioconda = None
         self.singularity_container = None
         self.docker_container = None
-        self.file_paths: Dict[str, str] = {}
+        self.file_paths: Dict[str, Path] = {}
         self.not_empty_template = not empty_template
+        self.migrate_pytest = migrate_pytest
 
     def create(self):
         """
@@ -125,32 +129,47 @@ def create(self):
 
         # Determine the component name
         self.component_name = self.component
-        self.component_dir = self.component
+        self.component_dir = Path(self.component)
 
         if self.subtool:
             self.component_name = f"{self.component}/{self.subtool}"
-            self.component_dir = os.path.join(self.component, self.subtool)
+            self.component_dir = Path(self.component, self.subtool)
 
         self.component_name_underscore = self.component_name.replace("/", "_")
 
         # Check existence of directories early for fast-fail
         self.file_paths = self._get_component_dirs()
 
-        if self.component_type == "modules":
-            # Try to find a bioconda package for 'component'
-            self._get_bioconda_tool()
+        if self.migrate_pytest:
+            # Rename the component directory to old
+            component_old_dir = Path(str(self.component_dir) + "_old")
+            component_parent_path = Path(self.directory, self.component_type, self.org)
+            component_old_path = component_parent_path / component_old_dir
+            component_path = component_parent_path / self.component_dir
 
-        # Prompt for GitHub username
-        self._get_username()
+            component_path.rename(component_old_path)
+        else:
+            if self.component_type == "modules":
+                # Try to find a bioconda package for 'component'
+                self._get_bioconda_tool()
 
-        if self.component_type == "modules":
-            self._get_module_structure_components()
+            # Prompt for GitHub username
+            self._get_username()
+
+            if self.component_type == "modules":
+                self._get_module_structure_components()
 
         # Create component template with jinja2
         self._render_template()
         log.info(f"Created component template: '{self.component_name}'")
 
-        new_files = list(self.file_paths.values())
+        if self.migrate_pytest:
+            self._copy_old_files(component_old_path)
+            log.info("Migrate pytest tests: Copied original module files to new module")
+            shutil.rmtree(component_old_path)
+            self._print_and_delete_pytest_files()
+
+        new_files = [str(path) for path in self.file_paths.values()]
         log.info("Created following files:\n  " + "\n  ".join(new_files))
 
     def _get_bioconda_tool(self):
@@ -259,16 +278,16 @@ def _render_template(self):
 
             # Write output to the target file
             log.debug(f"Writing output to: '{dest_fn}'")
-            os.makedirs(os.path.dirname(dest_fn), exist_ok=True)
+            dest_fn.parent.mkdir(exist_ok=True, parents=True)
             with open(dest_fn, "w") as fh:
                 log.debug(f"Writing output to: '{dest_fn}'")
                 fh.write(rendered_output)
 
             # Mirror file permissions
-            template_stat = os.stat(
-                os.path.join(os.path.dirname(nf_core.__file__), f"{self.component_type[:-1]}-template", template_fn)
-            )
-            os.chmod(dest_fn, template_stat.st_mode)
+            template_stat = (
+                Path(nf_core.__file__).parent / f"{self.component_type[:-1]}-template" / template_fn
+            ).stat()
+            dest_fn.chmod(template_stat.st_mode)
 
     def _collect_name_prompt(self):
         """
@@ -319,17 +338,17 @@ def _get_component_dirs(self):
         """
         file_paths = {}
         if self.repo_type == "pipeline":
-            local_component_dir = os.path.join(self.directory, self.component_type, "local")
+            local_component_dir = Path(self.directory, self.component_type, "local")
             # Check whether component file already exists
-            component_file = os.path.join(local_component_dir, f"{self.component_name}.nf")
-            if os.path.exists(component_file) and not self.force_overwrite:
+            component_file = local_component_dir / f"{self.component_name}.nf"
+            if component_file.exists() and not self.force_overwrite:
                 raise UserWarning(
                     f"{self.component_type[:-1].title()} file exists already: '{component_file}'. Use '--force' to overwrite"
                 )
 
             if self.component_type == "modules":
                 # If a subtool, check if there is a module called the base tool name already
-                if self.subtool and os.path.exists(os.path.join(local_component_dir, f"{self.component}.nf")):
+                if self.subtool and (local_component_dir / f"{self.component}.nf").exists():
                     raise UserWarning(
                         f"Module '{self.component}' exists already, cannot make subtool '{self.component_name}'"
                     )
@@ -342,50 +361,42 @@ def _get_component_dirs(self):
                     )
 
             # Set file paths
-            file_paths[os.path.join(self.component_type, "main.nf")] = component_file
+            file_paths["main.nf"] = component_file
 
         if self.repo_type == "modules":
-            component_dir = os.path.join(self.directory, self.component_type, self.org, self.component_dir)
+            component_dir = Path(self.directory, self.component_type, self.org, self.component_dir)
 
             # Check if module/subworkflow directories exist already
-            if os.path.exists(component_dir) and not self.force_overwrite:
+            if component_dir.exists() and not self.force_overwrite and not self.migrate_pytest:
                 raise UserWarning(
                     f"{self.component_type[:-1]} directory exists: '{component_dir}'. Use '--force' to overwrite"
                 )
 
             if self.component_type == "modules":
                 # If a subtool, check if there is a module called the base tool name already
-                parent_tool_main_nf = os.path.join(
-                    self.directory, self.component_type, self.org, self.component, "main.nf"
-                )
-                if self.subtool and os.path.exists(parent_tool_main_nf):
+                parent_tool_main_nf = Path(self.directory, self.component_type, self.org, self.component, "main.nf")
+                if self.subtool and parent_tool_main_nf.exists() and not self.migrate_pytest:
                     raise UserWarning(
                         f"Module '{parent_tool_main_nf}' exists already, cannot make subtool '{self.component_name}'"
                     )
 
                 # If no subtool, check that there isn't already a tool/subtool
                 tool_glob = glob.glob(
-                    f"{os.path.join(self.directory, self.component_type, self.org, self.component)}/*/main.nf"
+                    f"{Path(self.directory, self.component_type, self.org, self.component)}/*/main.nf"
                 )
-                if not self.subtool and tool_glob:
+                if not self.subtool and tool_glob and not self.migrate_pytest:
                     raise UserWarning(
                         f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'"
                     )
 
             # Set file paths
             # For modules - can be tool/ or tool/subtool/ so can't do in template directory structure
-            file_paths[os.path.join(self.component_type, "main.nf")] = os.path.join(component_dir, "main.nf")
-            file_paths[os.path.join(self.component_type, "meta.yml")] = os.path.join(component_dir, "meta.yml")
+            file_paths["main.nf"] = component_dir / "main.nf"
+            file_paths["meta.yml"] = component_dir / "meta.yml"
             if self.component_type == "modules":
-                file_paths[os.path.join(self.component_type, "environment.yml")] = os.path.join(
-                    component_dir, "environment.yml"
-                )
-            file_paths[os.path.join(self.component_type, "tests", "tags.yml")] = os.path.join(
-                component_dir, "tests", "tags.yml"
-            )
-            file_paths[os.path.join(self.component_type, "tests", "main.nf.test")] = os.path.join(
-                component_dir, "tests", "main.nf.test"
-            )
+                file_paths["environment.yml"] = component_dir / "environment.yml"
+            file_paths["tests/tags.yml"] = component_dir / "tests" / "tags.yml"
+            file_paths["tests/main.nf.test"] = component_dir / "tests" / "main.nf.test"
 
         return file_paths
 
@@ -396,8 +407,7 @@ def _get_username(self):
         # Try to guess the current user if `gh` is installed
         author_default = None
         try:
-            with open(os.devnull, "w") as devnull:
-                gh_auth_user = json.loads(subprocess.check_output(["gh", "api", "/user"], stderr=devnull))
+            gh_auth_user = json.loads(subprocess.check_output(["gh", "api", "/user"], stderr=subprocess.DEVNULL))
             author_default = f"@{gh_auth_user['login']}"
         except Exception as e:
             log.debug(f"Could not find GitHub username using 'gh' cli command: [red]{e}")
@@ -411,3 +421,65 @@ def _get_username(self):
                 f"[violet]GitHub Username:[/]{' (@author)' if author_default is None else ''}",
                 default=author_default,
             )
+
+    def _copy_old_files(self, component_old_path):
+        """Copy files from old module to new module"""
+        log.debug("Copying original main.nf file")
+        shutil.copyfile(component_old_path / "main.nf", self.file_paths["main.nf"])
+        log.debug("Copying original meta.yml file")
+        shutil.copyfile(component_old_path / "meta.yml", self.file_paths["meta.yml"])
+        if self.component_type == "modules":
+            log.debug("Copying original environment.yml file")
+            shutil.copyfile(component_old_path / "environment.yml", self.file_paths["environment.yml"])
+            if (component_old_path / "templates").is_dir():
+                log.debug("Copying original templates directory")
+                shutil.copytree(
+                    component_old_path / "templates", self.file_paths["environment.yml"].parent / "templates"
+                )
+        # Create a nextflow.config file if it contains information other than publishDir
+        pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
+        nextflow_config = pytest_dir / "nextflow.config"
+        if nextflow_config.is_file():
+            with open(nextflow_config, "r") as fh:
+                config_lines = ""
+                for line in fh:
+                    if "publishDir" not in line:
+                        config_lines += line
+            if len(config_lines) > 0:
+                log.debug("Copying nextflow.config file from pytest tests")
+                with open(
+                    Path(self.directory, self.component_type, self.org, self.component_dir, "tests", "nextflow.config"),
+                    "w+",
+                ) as ofh:
+                    ofh.write(config_lines)
+
+    def _print_and_delete_pytest_files(self):
+        """Prompt if pytest files should be deleted and printed to stdout"""
+        pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
+        if rich.prompt.Confirm.ask(
+            "[violet]Do you want to delete the pytest files?[/]\nPytest file 'main.nf' will be printed to standard output to allow migrating the tests manually to 'main.nf.test'.",
+            default=False,
+        ):
+            with open(pytest_dir / "main.nf", "r") as fh:
+                log.info(fh.read())
+            shutil.rmtree(pytest_dir)
+            log.info(
+                "[yellow]Please convert the pytest tests to nf-test in 'main.nf.test'.[/]\n"
+                "You can find more information about nf-test [link=https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test]at the nf-core web[/link]. "
+            )
+        else:
+            log.info(
+                "[yellow]Please migrate the pytest tests to nf-test in 'main.nf.test'.[/]\n"
+                "You can find more information about nf-test [link=https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test]at the nf-core web[/link].\n"
+                f"Once done, make sure to delete the module pytest files to avoid linting errors: {pytest_dir}"
+            )
+        # Delete tags from pytest_modules.yml
+        modules_yml = Path(self.directory, "tests", "config", "pytest_modules.yml")
+        with open(modules_yml, "r") as fh:
+            yml_file = yaml.safe_load(fh)
+        yml_key = str(self.component_dir) if self.component_type == "modules" else f"subworkflows/{self.component_dir}"
+        if yml_key in yml_file:
+            del yml_file[yml_key]
+        with open(modules_yml, "w") as fh:
+            yaml.dump(yml_file, fh)
+        run_prettier_on_file(modules_yml)
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index f7a5fe6680..6385ee4092 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -127,6 +127,8 @@ def install(self, component, silent=False):
             self.install_included_components(component_dir)
 
         if not silent:
+            modules_json.load()
+            modules_json.dump(run_prettier=True)
             # Print include statement
             component_name = "_".join(component.upper().split("/"))
             log.info(f"Use the following statement to include this {self.component_type[:-1]}:")
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/list.py b/nf_core/components/list.py
index d05c6d84a5..47c0eaad62 100644
--- a/nf_core/components/list.py
+++ b/nf_core/components/list.py
@@ -2,7 +2,7 @@
 import logging
 from typing import Dict, List, Optional, Tuple, Union, cast
 
-import rich
+import rich.table
 
 from nf_core.components.components_command import ComponentCommand
 from nf_core.modules.modules_json import ModulesJson
@@ -24,7 +24,7 @@ def __init__(
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.remote = remote
 
-    def list_components(self, keywords: Optional[List[str]] = None, print_json=False) -> rich.table.Table:
+    def list_components(self, keywords: Optional[List[str]] = None, print_json=False) -> Union[rich.table.Table, str]:
         keywords = keywords or []
         """
         Get available modules/subworkflows names from GitHub tree for repo
@@ -38,7 +38,7 @@ def list_components(self, keywords: Optional[List[str]] = None, print_json=False
         table.add_column(f"{self.component_type[:-1].capitalize()} Name")
         components: List[str] = []
 
-        def pattern_msg(keywords: List[str]):
+        def pattern_msg(keywords: List[str]) -> str:
             if len(keywords) == 0:
                 return ""
             if len(keywords) == 1:
@@ -107,37 +107,40 @@ def pattern_msg(keywords: List[str]):
             table.add_column("Date")
 
             # Load 'modules.json'
-            modules_json = modules_json.modules_json
+            modules_json_file = modules_json.modules_json
 
             for repo_url, component_with_dir in sorted(repos_with_comps.items()):
                 repo_entry: Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]
-
-                repo_entry = modules_json["repos"].get(repo_url, {})
-                for install_dir, component in sorted(component_with_dir):
-                    # Use cast() to predict the return type of recursive get():s
-                    repo_modules = cast(dict, repo_entry.get(self.component_type))
-                    component_entry = cast(dict, cast(dict, repo_modules.get(install_dir)).get(component))
-
-                    if component_entry:
-                        version_sha = component_entry["git_sha"]
-                        try:
-                            # pass repo_name to get info on modules even outside nf-core/modules
-                            message, date = ModulesRepo(
-                                remote_url=repo_url,
-                                branch=component_entry["branch"],
-                            ).get_commit_info(version_sha)
-                        except LookupError as e:
-                            log.warning(e)
+                if modules_json_file is None:
+                    log.warning(f"Modules JSON file '{modules_json.modules_json_path}' is missing. ")
+                    continue
+                else:
+                    repo_entry = modules_json_file["repos"].get(repo_url, {})
+                    for install_dir, component in sorted(component_with_dir):
+                        # Use cast() to predict the return type of recursive get():s
+                        repo_modules = cast(dict, repo_entry.get(self.component_type))
+                        component_entry = cast(dict, cast(dict, repo_modules.get(install_dir)).get(component))
+
+                        if component_entry:
+                            version_sha = component_entry["git_sha"]
+                            try:
+                                # pass repo_name to get info on modules even outside nf-core/modules
+                                message, date = ModulesRepo(
+                                    remote_url=repo_url,
+                                    branch=component_entry["branch"],
+                                ).get_commit_info(version_sha)
+                            except LookupError as e:
+                                log.warning(e)
+                                date = "[red]Not Available"
+                                message = "[red]Not Available"
+                        else:
+                            log.warning(
+                                f"Commit SHA for {self.component_type[:-1]} '{install_dir}/{self.component_type}' is missing from 'modules.json'"
+                            )
+                            version_sha = "[red]Not Available"
                             date = "[red]Not Available"
                             message = "[red]Not Available"
-                    else:
-                        log.warning(
-                            f"Commit SHA for {self.component_type[:-1]} '{install_dir}/{self.component_type}' is missing from 'modules.json'"
-                        )
-                        version_sha = "[red]Not Available"
-                        date = "[red]Not Available"
-                        message = "[red]Not Available"
-                    table.add_row(component, repo_url, version_sha, message, date)
+                        table.add_row(component, repo_url, version_sha, message, date)
 
         if print_json:
             return json.dumps(components, sort_keys=True, indent=4)
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 94e7584a9b..874fa570bc 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -1,7 +1,12 @@
 """
 The NFCoreComponent class holds information and utility functions for a single module or subworkflow
 """
+import logging
+import re
 from pathlib import Path
+from typing import Union
+
+log = logging.getLogger(__name__)
 
 
 class NFCoreComponent:
@@ -44,16 +49,16 @@ def __init__(
 
         if remote_component:
             # Initialize the important files
-            self.main_nf = self.component_dir / "main.nf"
-            self.meta_yml = self.component_dir / "meta.yml"
+            self.main_nf = Path(self.component_dir, "main.nf")
+            self.meta_yml = Path(self.component_dir, "meta.yml")
             self.process_name = ""
-            self.environment_yml = self.component_dir / "environment.yml"
+            self.environment_yml = Path(self.component_dir, "environment.yml")
 
             repo_dir = self.component_dir.parts[: self.component_dir.parts.index(self.component_name.split("/")[0])][-1]
             self.org = repo_dir
-            self.nftest_testdir = self.component_dir / "tests"
-            self.nftest_main_nf = self.nftest_testdir / "main.nf.test"
-            self.tags_yml = self.nftest_testdir / "tags.yml"
+            self.nftest_testdir = Path(self.component_dir, "tests")
+            self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")
+            self.tags_yml = Path(self.nftest_testdir, "tags.yml")
 
             if self.repo_type == "pipeline":
                 patch_fn = f"{self.component_name.replace('/', '-')}.diff"
@@ -73,7 +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:
@@ -82,11 +87,107 @@ 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'
+                    #'plugin/nf-validation'
+                    component = line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/")
+                    component = component.replace("'../", "subworkflows/")
+                    component = component.replace("'", "")
+                    included_components.append(component)
+        return included_components
+
+    def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, str]):
+        """Collect all included components from the main.nf file."""
+        included_components = []
+        with open(main_nf_test, "r") as fh:
+            for line in fh:
+                if line.strip().startswith("script"):
+                    # get tool/subtool or subworkflow name from script statement, can be:
+                    # if the component is a module TOOL/SUBTOOL:
+                    # '../../SUBTOOL/main.nf'
+                    # '../../../TOOL/SUBTOOL/main.nf'
+                    # '../../../TOOL/main.nf'
+                    # if the component is a module TOOL:
+                    # '../../TOOL/main.nf'
+                    # '../../TOOL/SUBTOOL/main.nf'
+                    # if the component uses full paths or is a subworkflow:
+                    # '(../../)modules/nf-core/TOOL/(SUBTOOL/)main.nf'
+                    # '(../../)subworkflows/nf-core/TOOL/(SUBTOOL/)main.nf'
+                    # the line which uses the current component script:
+                    # '../main.nf'
+                    component = (
+                        line.strip()
+                        .split("../")[-1]
+                        .split(self.org)[-1]
+                        .split("main.nf")[0]
+                        .strip("'")
+                        .strip('"')
+                        .strip("/")
+                    )
+                    if (
+                        "/" in self.component_name
+                        and "/" not in component
+                        and line.count("../") == 2
+                        and self.org not in line
+                        and component != ""
+                    ):
+                        # Add the current component name "TOOL" to the tag
+                        component = f"{self.component_name.split('/')[0]}/{component}"
+                    if "subworkflows" in line:
+                        # Add the subworkflows prefix to the tag
+                        component = f"subworkflows/{component}"
+                    if component != "":
+                        included_components.append(component)
         return included_components
+
+    def get_inputs_from_main_nf(self):
+        """Collect all inputs from the main.nf file."""
+        inputs = []
+        with open(self.main_nf, "r") as f:
+            data = f.read()
+        # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
+        # regex matches:
+        # val(foo)
+        # path(bar)
+        # val foo
+        # val bar
+        # path bar
+        # path foo
+        # don't match anything inside comments or after "output:"
+        if "input:" not in data:
+            log.info(f"Could not find any inputs in {self.main_nf}")
+            return inputs
+        input_data = data.split("input:")[1].split("output:")[0]
+        regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
+        matches = re.finditer(regex, input_data, re.MULTILINE)
+        for matchNum, match in enumerate(matches, start=1):
+            if match.group(3):
+                inputs.append(match.group(3))
+            elif match.group(4):
+                inputs.append(match.group(4))
+        log.info(f"Found {len(inputs)} inputs in {self.main_nf}")
+        self.inputs = inputs
+
+    def get_outputs_from_main_nf(self):
+        outputs = []
+        with open(self.main_nf, "r") as f:
+            data = f.read()
+        # get output values from main.nf after "output:". the names are always after "emit:"
+        if "output:" not in data:
+            log.info(f"Could not find any outputs in {self.main_nf}")
+            return outputs
+        output_data = data.split("output:")[1].split("when:")[0]
+        regex = r"emit:\s*([^)\s,]+)"
+        matches = re.finditer(regex, output_data, re.MULTILINE)
+        for matchNum, match in enumerate(matches, start=1):
+            outputs.append(match.group(1))
+        log.info(f"Found {len(outputs)} outputs in {self.main_nf}")
+        self.outputs = outputs
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index 6fc6e03544..077cb2b840 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -288,20 +288,21 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 updated.append(component)
                 recursive_update = True
                 modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
-                if not silent and not self.update_all and len(modules_to_update + subworkflows_to_update) > 0:
-                    log.warning(
-                        f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
-                        "It is advised to keep all your modules and subworkflows up to date.\n"
-                        "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
-                    )
-                    if self.update_deps:
-                        recursive_update = True
-                    else:
-                        recursive_update = questionary.confirm(
-                            "Would you like to continue updating all modules and subworkflows?",
-                            default=True,
-                            style=nf_core.utils.nfcore_question_style,
-                        ).unsafe_ask()
+                if not silent and len(modules_to_update + subworkflows_to_update) > 0:
+                    if not self.update_all:
+                        log.warning(
+                            f"All modules and subworkflows linked to the updated {self.component_type[:-1]} will be {'asked for update' if self.show_diff else 'automatically updated'}.\n"
+                            "It is advised to keep all your modules and subworkflows up to date.\n"
+                            "It is not guaranteed that a subworkflow will continue working as expected if all modules/subworkflows used in it are not up to date.\n"
+                        )
+                        if self.update_deps:
+                            recursive_update = True
+                        else:
+                            recursive_update = questionary.confirm(
+                                "Would you like to continue updating all modules and subworkflows?",
+                                default=True,
+                                style=nf_core.utils.nfcore_question_style,
+                            ).unsafe_ask()
                 if recursive_update and len(modules_to_update + subworkflows_to_update) > 0:
                     # Update linked components
                     self.update_linked_components(modules_to_update, subworkflows_to_update, updated)
@@ -323,8 +324,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 )
         elif not all_patches_successful and not silent:
             log.info(f"Updates complete. Please apply failed patch{plural_es(components_info)} manually.")
+            self.modules_json.load()
+            self.modules_json.dump(run_prettier=True)
         elif not silent:
             log.info("Updates complete :sparkles:")
+            self.modules_json.load()
+            self.modules_json.dump(run_prettier=True)
 
         return exit_value
 
diff --git a/nf_core/create.py b/nf_core/create.py
index 470623f551..56d0912a07 100644
--- a/nf_core/create.py
+++ b/nf_core/create.py
@@ -11,7 +11,7 @@
 import time
 from pathlib import Path
 
-import filetype
+import filetype  # type: ignore
 import git
 import jinja2
 import questionary
diff --git a/nf_core/download.py b/nf_core/download.py
index 9ca786b5e3..08bef935ba 100644
--- a/nf_core/download.py
+++ b/nf_core/download.py
@@ -493,7 +493,7 @@ def prompt_singularity_cachedir_utilization(self):
         ):
             stderr.print(
                 "\nIf you are working on the same system where you will run Nextflow, you can amend the downloaded images to the ones in the"
-                "[blue not bold]$NXF_SINGULARITY_CACHEDIR[/] folder, Nextflow will automatically find them."
+                "[blue not bold]$NXF_SINGULARITY_CACHEDIR[/] folder, Nextflow will automatically find them. "
                 "However if you will transfer the downloaded files to a different system then they should be copied to the target folder."
             )
             self.container_cache_utilisation = questionary.select(
@@ -1081,7 +1081,7 @@ def get_singularity_images(self, current_revision=""):
                                     continue
                             except ContainerError.ImageNotFound as e:
                                 # Try other registries
-                                if e.error_log.absoluteURI:
+                                if e.error_log.absolute_URI:
                                     break  # there no point in trying other registries if absolute URI was specified.
                                 else:
                                     continue
@@ -1092,7 +1092,7 @@ def get_singularity_images(self, current_revision=""):
                                 # Try other registries
                                 log.error(e.message)
                                 log.error(e.helpmessage)
-                                if e.error_log.absoluteURI:
+                                if e.error_log.absolute_URI:
                                     break  # there no point in trying other registries if absolute URI was specified.
                                 else:
                                     continue
@@ -1247,7 +1247,7 @@ def singularity_pull_image(self, container, out_path, cache_path, library, progr
         # Thus, if an explicit registry is specified, the provided -l value is ignored.
         container_parts = container.split("/")
         if len(container_parts) > 2:
-            address = container
+            address = f"docker://{container}"
             absolute_URI = True
         else:
             address = f"docker://{library}/{container.replace('docker://', '')}"
diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
index 47b27bb514..e721f210d0 100644
--- a/nf_core/gitpod/gitpod.Dockerfile
+++ b/nf_core/gitpod/gitpod.Dockerfile
@@ -1,3 +1,6 @@
+# Test build locally before making a PR
+#   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
+
 FROM gitpod/workspace-base
 
 USER root
@@ -43,16 +46,17 @@ RUN conda config --add channels defaults && \
     conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
-    conda install --quiet --yes --name base mamba && \
-    mamba install --quiet --yes --name base \
+    conda install --quiet --yes --name base \
+        mamba \
         nextflow \
         nf-core \
         nf-test \
         black \
         prettier \
         pre-commit \
+        openjdk \
         pytest-workflow && \
-    mamba clean --all -f -y
+    conda clean --all --force-pkgs-dirs --yes
 
 # Update Nextflow
 RUN nextflow self-update
diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index 70f7ea925f..797ebbcc91 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -164,26 +164,30 @@ class PipelineLint(nf_core.utils.Pipeline):
         warned (list): A list of tuples of the form: ``(<warned no>, <reason>)``
     """
 
-    from .actions_awsfulltest import actions_awsfulltest
-    from .actions_awstest import actions_awstest
-    from .actions_ci import actions_ci
-    from .actions_schema_validation import actions_schema_validation
-    from .files_exist import files_exist
-    from .files_unchanged import files_unchanged
-    from .merge_markers import merge_markers
-    from .modules_json import modules_json
-    from .modules_structure import modules_structure
-    from .multiqc_config import multiqc_config
-    from .nextflow_config import nextflow_config
-    from .pipeline_name_conventions import pipeline_name_conventions
-    from .pipeline_todos import pipeline_todos
-    from .readme import readme
-    from .schema_description import schema_description
-    from .schema_lint import schema_lint
-    from .schema_params import schema_params
-    from .system_exit import system_exit
-    from .template_strings import template_strings
-    from .version_consistency import version_consistency
+    from .actions_awsfulltest import actions_awsfulltest  # type: ignore[misc]
+    from .actions_awstest import actions_awstest  # type: ignore[misc]
+    from .actions_ci import actions_ci  # type: ignore[misc]
+    from .actions_schema_validation import (  # type: ignore[misc]
+        actions_schema_validation,
+    )
+    from .files_exist import files_exist  # type: ignore[misc]
+    from .files_unchanged import files_unchanged  # type: ignore[misc]
+    from .merge_markers import merge_markers  # type: ignore[misc]
+    from .modules_json import modules_json  # type: ignore[misc]
+    from .modules_structure import modules_structure  # type: ignore[misc]
+    from .multiqc_config import multiqc_config  # type: ignore[misc]
+    from .nextflow_config import nextflow_config  # type: ignore[misc]
+    from .pipeline_name_conventions import (  # type: ignore[misc]
+        pipeline_name_conventions,
+    )
+    from .pipeline_todos import pipeline_todos  # type: ignore[misc]
+    from .readme import readme  # type: ignore[misc]
+    from .schema_description import schema_description  # type: ignore[misc]
+    from .schema_lint import schema_lint  # type: ignore[misc]
+    from .schema_params import schema_params  # type: ignore[misc]
+    from .system_exit import system_exit  # type: ignore[misc]
+    from .template_strings import template_strings  # type: ignore[misc]
+    from .version_consistency import version_consistency  # type: ignore[misc]
 
     def __init__(
         self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False
@@ -367,10 +371,10 @@ def format_result(test_results):
             Given an list of error message IDs and the message texts, return a nicely formatted
             string for the terminal with appropriate ASCII colours.
             """
+            tools_version = __version__
+            if "dev" in __version__:
+                tools_version = "latest"
             for eid, msg in test_results:
-                tools_version = __version__
-                if "dev" in __version__:
-                    tools_version = "latest"
                 yield Markdown(
                     f"[{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html): {msg}"
                 )
@@ -462,6 +466,10 @@ def _get_results_md(self):
         if len(self.failed) > 0:
             overall_result = "Failed :x:"
 
+        tools_version = __version__
+        if "dev" in __version__:
+            tools_version = "latest"
+
         # List of tests for details
         test_failure_count = ""
         test_failures = ""
@@ -470,7 +478,7 @@ def _get_results_md(self):
             test_failures = "### :x: Test failures:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.failed
                     ]
@@ -484,7 +492,7 @@ def _get_results_md(self):
             test_ignored = "### :grey_question: Tests ignored:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.ignored
                     ]
@@ -498,7 +506,7 @@ def _get_results_md(self):
             test_fixed = "### :grey_question: Tests fixed:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.fixed
                     ]
@@ -512,7 +520,7 @@ def _get_results_md(self):
             test_warnings = "### :heavy_exclamation_mark: Test warnings:\n\n{}\n\n".format(
                 "\n".join(
                     [
-                        f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html) - "
+                        f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.warned
                     ]
@@ -527,7 +535,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         (
-                            f"* [{eid}](https://nf-co.re/tools-docs/lint_tests/{eid}.html)"
+                            f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}.html)"
                             f" - {strip_ansi_codes(msg, '`')}"
                         )
                         for eid, msg in self.passed
diff --git a/nf_core/lint/multiqc_config.py b/nf_core/lint/multiqc_config.py
index a1b831ae2d..cbbeae07a8 100644
--- a/nf_core/lint/multiqc_config.py
+++ b/nf_core/lint/multiqc_config.py
@@ -1,9 +1,10 @@
 import os
+from typing import Dict, List
 
 import yaml
 
 
-def multiqc_config(self):
+def multiqc_config(self) -> Dict[str, List[str]]:
     """Make sure basic multiQC plugins are installed and plots are exported
     Basic template:
 
@@ -20,8 +21,8 @@ def multiqc_config(self):
 
         export_plots: true
     """
-    passed = []
-    failed = []
+    passed: List[str] = []
+    failed: List[str] = []
 
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("multiqc_config", [])
@@ -38,10 +39,16 @@ def multiqc_config(self):
     except Exception as e:
         return {"failed": [f"Could not parse yaml file: {fn}, {e}"]}
 
-    # Check that the report_comment exists and matches
+    # check if requried sections are present
+    required_sections = ["report_section_order", "export_plots", "report_comment"]
+    for section in required_sections:
+        if section not in mqc_yml and section not in ignore_configs:
+            failed.append(f"'assets/multiqc_config.yml' does not contain `{section}`")
+            return {"passed": passed, "failed": failed}
+        else:
+            passed.append(f"'assets/multiqc_config.yml' contains `{section}`")
+
     try:
-        if "report_section_order" not in mqc_yml:
-            raise AssertionError()
         orders = {}
         summary_plugin_name = f"{self.pipeline_prefix}-{self.pipeline_name}-summary"
         min_plugins = ["software_versions", summary_plugin_name]
@@ -70,27 +77,37 @@ def multiqc_config(self):
 
     if "report_comment" not in ignore_configs:
         # Check that the minimum plugins exist and are coming first in the summary
-        try:
-            version = self.nf_config.get("manifest.version", "").strip(" '\"")
-            version = "dev" if "dev" in version else version
-            if "report_comment" not in mqc_yml:
-                raise AssertionError()
-            if mqc_yml["report_comment"].strip() != (
-                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/releases/tag/{version}" '
-                f'target="_blank">nf-core/{self.pipeline_name}</a> analysis pipeline. For information about how to '
-                f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}/{version}/docs/output" '
-                'target="_blank">documentation</a>.'
-            ):
-                raise AssertionError()
-        except (AssertionError, KeyError, TypeError):
-            failed.append("'assets/multiqc_config.yml' does not contain a matching 'report_comment'.")
+        version = self.nf_config.get("manifest.version", "").strip(" '\"")
+        if "dev" in version:
+            version = "dev"
+            report_comments = (
+                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/tree/dev" target="_blank">nf-core/{self.pipeline_name}</a>'
+                f" analysis pipeline. For information about how to interpret these results, please see the "
+                f'<a href="https://nf-co.re/{self.pipeline_name}/dev/docs/output" target="_blank">documentation</a>.'
+            )
+
+        else:
+            report_comments = (
+                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/releases/tag/{version}" target="_blank">nf-core/{self.pipeline_name}</a>'
+                f" analysis pipeline. For information about how to interpret these results, please see the "
+                f'<a href="https://nf-co.re/{self.pipeline_name}/{version}/docs/output" target="_blank">documentation</a>.'
+            )
+
+        if mqc_yml["report_comment"].strip() != report_comments:
+            # find where the report_comment is wrong and give it as a hint
+            hint = report_comments
+            failed.append(
+                f"'assets/multiqc_config.yml' does not contain a matching 'report_comment'.  \n"
+                f"The expected comment is:  \n"
+                f"```{hint}```  \n"
+                f"The current comment is:  \n"
+                f"```{ mqc_yml['report_comment'].strip()}```"
+            )
         else:
             passed.append("'assets/multiqc_config.yml' contains a matching 'report_comment'.")
 
     # Check that export_plots is activated
     try:
-        if "export_plots" not in mqc_yml:
-            raise AssertionError()
         if not mqc_yml["export_plots"]:
             raise AssertionError()
     except (AssertionError, KeyError, TypeError):
diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
index 71c908b7b5..24f1e5c12f 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -203,6 +203,8 @@ def nextflow_config(self):
 
     # Check the variables that should be set to 'true'
     for k in ["timeline.enabled", "report.enabled", "trace.enabled", "dag.enabled"]:
+        if k in ignore_configs:
+            continue
         if self.nf_config.get(k) == "true":
             passed.append(f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``")
         else:
diff --git a/nf_core/module-template/modules/environment.yml b/nf_core/module-template/environment.yml
similarity index 100%
rename from nf_core/module-template/modules/environment.yml
rename to nf_core/module-template/environment.yml
diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/main.nf
similarity index 96%
rename from nf_core/module-template/modules/main.nf
rename to nf_core/module-template/main.nf
index a2cabfd2f4..5258403e8f 100644
--- a/nf_core/module-template/modules/main.nf
+++ b/nf_core/module-template/main.nf
@@ -27,7 +27,7 @@ process {{ component_name_underscore|upper }} {
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     {% endif -%}
-    conda '${modulesDir}/environment.yml'
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'biocontainers/YOUR-TOOL-HERE' }}' }"
@@ -91,7 +91,7 @@ process {{ component_name_underscore|upper }} {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        {{ component }}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        {{ component }}: \$(samtools --version |& sed '1!d ; s/samtools //')
     END_VERSIONS
     """
 
@@ -113,7 +113,7 @@ process {{ component_name_underscore|upper }} {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        {{ component }}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        {{ component }}: \$(samtools --version |& sed '1!d ; s/samtools //')
     END_VERSIONS
     """
 }
diff --git a/nf_core/module-template/modules/meta.yml b/nf_core/module-template/meta.yml
similarity index 100%
rename from nf_core/module-template/modules/meta.yml
rename to nf_core/module-template/meta.yml
diff --git a/nf_core/module-template/modules/tests/main.nf.test b/nf_core/module-template/tests/main.nf.test
similarity index 95%
rename from nf_core/module-template/modules/tests/main.nf.test
rename to nf_core/module-template/tests/main.nf.test
index 883a3ffa40..105c70eb96 100644
--- a/nf_core/module-template/modules/tests/main.nf.test
+++ b/nf_core/module-template/tests/main.nf.test
@@ -40,7 +40,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out).match() }
                 //TODO nf-core: Add all required assertions to verify the test output.
             )
         }
diff --git a/nf_core/module-template/modules/tests/tags.yml b/nf_core/module-template/tests/tags.yml
similarity index 100%
rename from nf_core/module-template/modules/tests/tags.yml
rename to nf_core/module-template/tests/tags.yml
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index cb77d4c043..25259f1a16 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -49,7 +49,7 @@ def __init__(
         self.tools_config: Dict[str, Any] = {}
 
     def bump_versions(
-        self, module: Union[NFCoreComponent, None] = None, all_modules: bool = False, show_uptodate: bool = False
+        self, module: Union[str, None] = None, all_modules: bool = False, show_uptodate: bool = False
     ) -> None:
         """
         Bump the container and conda version of single module or all modules
diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py
index b5368130ce..a5e0795a9f 100644
--- a/nf_core/modules/create.py
+++ b/nf_core/modules/create.py
@@ -17,6 +17,7 @@ def __init__(
         conda_name=None,
         conda_version=None,
         empty_template=False,
+        migrate_pytest=False,
     ):
         super().__init__(
             "modules",
@@ -29,4 +30,5 @@ def __init__(
             conda_name,
             conda_version,
             empty_template,
+            migrate_pytest,
         )
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index d9c0cbf7f9..a052425539 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -32,7 +32,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
         # check if the module's main.nf requires a conda environment
         with open(Path(module.component_dir, "main.nf"), "r") as fh:
             main_nf = fh.read()
-            if "conda '${modulesDir}/environment.yml'" in main_nf:
+            if 'conda "${moduleDir}/environment.yml"' in main_nf:
                 module.failed.append(
                     ("environment_yml_exists", "Module's `environment.yml` does not exist", module.environment_yml)
                 )
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 6bdc4ed223..7552c1ceae 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -22,7 +22,24 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
     and module input is consistent between the
     ``meta.yml`` and the ``main.nf``.
 
+    If the module has inputs or outputs, they are expected to be
+    formatted as:
+
+    ..code-block::
+        tuple val(foo) path(bar)
+        val foo
+        path foo
+
+    or permutations of the above.
+
+    Args:
+        module_lint_object (ComponentLint): The lint object for the module
+        module (NFCoreComponent): The module to lint
+
     """
+
+    module.get_inputs_from_main_nf()
+    module.get_outputs_from_main_nf()
     # Check if we have a patch file, get original file in that case
     meta_yaml = None
     if module.is_patched:
@@ -45,14 +62,14 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
             return
 
     # Confirm that the meta.yml file is valid according to the JSON schema
-    valid_meta_yml = True
+    valid_meta_yml = False
     try:
         with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/meta-schema.json"), "r") as fh:
             schema = json.load(fh)
         validators.validate(instance=meta_yaml, schema=schema)
         module.passed.append(("meta_yml_valid", "Module `meta.yml` is valid", module.meta_yml))
+        valid_meta_yml = True
     except exceptions.ValidationError as e:
-        valid_meta_yml = False
         hint = ""
         if len(e.path) > 0:
             hint = f"\nCheck the entry for `{e.path[0]}`."
@@ -79,26 +96,87 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
             meta_input = [list(x.keys())[0] for x in meta_yaml["input"]]
             for input in module.inputs:
                 if input in meta_input:
-                    module.passed.append(("meta_input", f"`{input}` specified", module.meta_yml))
+                    module.passed.append(("meta_input_main_only", f"`{input}` specified", module.meta_yml))
+                else:
+                    module.warned.append(
+                        (
+                            "meta_input_main_only",
+                            f"`{input}` is present as an input in the `main.nf`, but missing in `meta.yml`",
+                            module.meta_yml,
+                        )
+                    )
+            # check if there are any inputs in meta.yml that are not in main.nf
+            for input in meta_input:
+                if input in module.inputs:
+                    module.passed.append(
+                        (
+                            "meta_input_meta_only",
+                            f"`{input}` is present as an input in `meta.yml` and `main.nf`",
+                            module.meta_yml,
+                        )
+                    )
                 else:
-                    module.failed.append(("meta_input", f"`{input}` missing in `meta.yml`", module.meta_yml))
+                    module.warned.append(
+                        (
+                            "meta_input_meta_only",
+                            f"`{input}` is present as an input in `meta.yml` but not in `main.nf`",
+                            module.meta_yml,
+                        )
+                    )
 
-        if "output" in meta_yaml:
+        if "output" in meta_yaml and meta_yaml["output"] is not None:
             meta_output = [list(x.keys())[0] for x in meta_yaml["output"]]
             for output in module.outputs:
                 if output in meta_output:
-                    module.passed.append(("meta_output", f"`{output}` specified", module.meta_yml))
+                    module.passed.append(("meta_output_main_only", f"`{output}` specified", module.meta_yml))
                 else:
-                    module.failed.append(("meta_output", f"`{output}` missing in `meta.yml`", module.meta_yml))
-
+                    module.warned.append(
+                        (
+                            "meta_output_main_only",
+                            f"`{output}`  is present as an output in the `main.nf`, but missing in `meta.yml`",
+                            module.meta_yml,
+                        )
+                    )
+            # check if there are any outputs in meta.yml that are not in main.nf
+            for output in meta_output:
+                if output in module.outputs:
+                    module.passed.append(
+                        (
+                            "meta_output_meta_only",
+                            f"`{output}` is present as an output in `meta.yml` and `main.nf`",
+                            module.meta_yml,
+                        )
+                    )
+                elif output == "meta":
+                    module.passed.append(
+                        (
+                            "meta_output_meta_only",
+                            f"`{output}` is skipped for `meta.yml` outputs",
+                            module.meta_yml,
+                        )
+                    )
+                else:
+                    module.warned.append(
+                        (
+                            "meta_output_meta_only",
+                            f"`{output}` is present as an output in `meta.yml` but not in `main.nf`",
+                            module.meta_yml,
+                        )
+                    )
         # confirm that the name matches the process name in main.nf
         if meta_yaml["name"].upper() == module.process_name:
-            module.passed.append(("meta_name", "Correct name specified in `meta.yml`", module.meta_yml))
+            module.passed.append(
+                (
+                    "meta_name",
+                    "Correct name specified in `meta.yml`.",
+                    module.meta_yml,
+                )
+            )
         else:
             module.failed.append(
                 (
                     "meta_name",
-                    f"Conflicting process name between meta.yml (`{meta_yaml['name']}`) and main.nf (`{module.process_name}`)",
+                    f"Conflicting `process` name between meta.yml (`{meta_yaml['name']}`) and main.nf (`{module.process_name}`)",
                     module.meta_yml,
                 )
             )
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 8188787f90..87033e3f49 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -1,6 +1,7 @@
 """
 Lint the tests of a module in nf-core/modules
 """
+import json
 import logging
 from pathlib import Path
 
@@ -34,12 +35,12 @@ def module_tests(_, module: NFCoreComponent):
 
     # Lint the test main.nf file
     if module.nftest_main_nf.is_file():
-        module.passed.append(("test_main_exists", "test `main.nf.test` exists", module.nftest_main_nf))
+        module.passed.append(("test_main_nf_exists", "test `main.nf.test` exists", module.nftest_main_nf))
     else:
         if is_pytest:
-            module.warned.append(("test_main_exists", "test `main.nf.test` does not exist", module.nftest_main_nf))
+            module.warned.append(("test_main_nf_exists", "test `main.nf.test` does not exist", module.nftest_main_nf))
         else:
-            module.failed.append(("test_main_exists", "test `main.nf.test` does not exist", module.nftest_main_nf))
+            module.failed.append(("test_main_nf_exists", "test `main.nf.test` does not exist", module.nftest_main_nf))
 
     if module.nftest_main_nf.is_file():
         # Check if main.nf.test.snap file exists, if 'snap(' is inside main.nf.test
@@ -52,36 +53,64 @@ def module_tests(_, module: NFCoreComponent):
                     )
                     # Validate no empty files
                     with open(snap_file, "r") as snap_fh:
-                        snap_content = snap_fh.read()
-                        if "d41d8cd98f00b204e9800998ecf8427e" in snap_content:
+                        try:
+                            snap_content = json.load(snap_fh)
+                            for test_name in snap_content.keys():
+                                if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
+                                    if "stub" not in test_name:
+                                        module.failed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
+                                                snap_file,
+                                            )
+                                        )
+                                    else:
+                                        module.passed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for empty file found, but it is a stub test",
+                                                snap_file,
+                                            )
+                                        )
+                                else:
+                                    module.passed.append(
+                                        (
+                                            "test_snap_md5sum",
+                                            "no md5sum for empty file found",
+                                            snap_file,
+                                        )
+                                    )
+                                if "7029066c27ac6f5ef18d660d5741979a" in str(snap_content[test_name]):
+                                    if "stub" not in test_name:
+                                        module.failed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
+                                                snap_file,
+                                            )
+                                        )
+                                    else:
+                                        module.passed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for compressed empty file found, but it is a stub test",
+                                                snap_file,
+                                            )
+                                        )
+                                else:
+                                    module.passed.append(
+                                        (
+                                            "test_snap_md5sum",
+                                            "no md5sum for compressed empty file found",
+                                            snap_file,
+                                        )
+                                    )
+                        except json.decoder.JSONDecodeError as e:
                             module.failed.append(
                                 (
-                                    "test_snap_md5sum",
-                                    "md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
-                                    snap_file,
-                                )
-                            )
-                        else:
-                            module.passed.append(
-                                (
-                                    "test_snap_md5sum",
-                                    "no md5sum for empty file found",
-                                    snap_file,
-                                )
-                            )
-                        if "7029066c27ac6f5ef18d660d5741979a" in snap_content:
-                            module.failed.append(
-                                (
-                                    "test_snap_md5sum",
-                                    "md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
-                                    snap_file,
-                                )
-                            )
-                        else:
-                            module.passed.append(
-                                (
-                                    "test_snap_md5sum",
-                                    "no md5sum for compressed empty file found",
+                                    "test_snapshot_exists",
+                                    f"snapshot file `main.nf.test.snap` can't be read: {e}",
                                     snap_file,
                                 )
                             )
@@ -94,8 +123,11 @@ def module_tests(_, module: NFCoreComponent):
             required_tags = ["modules", "modules_nfcore", module.component_name]
             if module.component_name.count("/") == 1:
                 required_tags.append(module.component_name.split("/")[0])
+            chained_components_tags = module._get_included_components_in_chained_tests(module.nftest_main_nf)
             missing_tags = []
-            for tag in required_tags:
+            log.debug(f"Required tags: {required_tags}")
+            log.debug(f"Included components for chained nf-tests: {chained_components_tags}")
+            for tag in set(required_tags + chained_components_tags):
                 if tag not in main_nf_tags:
                     missing_tags.append(tag)
             if len(missing_tags) == 0:
@@ -104,7 +136,7 @@ def module_tests(_, module: NFCoreComponent):
                 module.failed.append(
                     (
                         "test_main_tags",
-                        f"Tags do not adhere to guidelines. Tags missing in `main.nf.test`: {missing_tags}",
+                        f"Tags do not adhere to guidelines. Tags missing in `main.nf.test`: `{','.join(missing_tags)}`",
                         module.nftest_main_nf,
                     )
                 )
@@ -140,12 +172,18 @@ def module_tests(_, module: NFCoreComponent):
                 if f"modules/{module.org}/{module.component_name}/**" in tags_yml[module.component_name]:
                     module.passed.append(("test_tags_yml", "correct path in tags.yml", module.tags_yml))
                 else:
-                    module.failed.append(("test_tags_yml", "incorrect path in tags.yml", module.tags_yml))
+                    module.failed.append(
+                        (
+                            "test_tags_yml",
+                            f"incorrect path in tags.yml, expected `modules/{module.org}/{module.component_name}/**`, got `{tags_yml[module.component_name][0]}`",
+                            module.tags_yml,
+                        )
+                    )
             else:
                 module.failed.append(
                     (
                         "test_tags_yml",
-                        "incorrect entry in tags.yml, should be '<TOOL>' or '<TOOL>/<SUBTOOL>'",
+                        f"incorrect key in tags.yml, should be `{module.component_name}`, got `{list(tags_yml.keys())[0]}`.",
                         module.tags_yml,
                     )
                 )
@@ -154,3 +192,17 @@ def module_tests(_, module: NFCoreComponent):
             module.warned.append(("test_tags_yml_exists", "file `tags.yml` does not exist", module.tags_yml))
         else:
             module.failed.append(("test_tags_yml_exists", "file `tags.yml` does not exist", module.tags_yml))
+
+    # Check that the old test directory does not exist
+    if not is_pytest:
+        old_test_dir = Path(module.base_dir, "tests", "modules", module.component_name)
+        if old_test_dir.is_dir():
+            module.failed.append(
+                (
+                    "test_old_test_dir",
+                    f"Pytest files are still present at `{Path('tests', 'modules', module.component_name)}`. Please remove this directory and its contents.",
+                    old_test_dir,
+                )
+            )
+        else:
+            module.passed.append(("test_old_test_dir", "Old pytests don't exist for this module", old_test_dir))
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 9c3d1ae9b1..ee912843b6 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -6,9 +6,11 @@
 import shutil
 import tempfile
 from pathlib import Path
+from typing import Union
 
 import git
 import questionary
+import rich.prompt
 from git.exc import GitCommandError
 
 import nf_core.utils
@@ -41,7 +43,7 @@ def __init__(self, pipeline_dir):
         self.modules_dir = Path(self.dir, "modules")
         self.subworkflows_dir = Path(self.dir, "subworkflows")
         self.modules_json_path = Path(self.dir, "modules.json")
-        self.modules_json = None
+        self.modules_json: Union(dict, None) = None
         self.pipeline_modules = None
         self.pipeline_subworkflows = None
         self.pipeline_components = None
@@ -67,7 +69,13 @@ def create(self):
         new_modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}}
 
         if not self.modules_dir.exists():
-            raise UserWarning("Can't find a ./modules directory. Is this a DSL2 pipeline?")
+            if rich.prompt.Confirm.ask(
+                "[bold][blue]?[/] Can't find a ./modules directory. Would you like me to create one?", default=True
+            ):
+                log.info(f"Creating ./modules directory in '{self.dir}'")
+                self.modules_dir.mkdir()
+            else:
+                raise UserWarning("Cannot proceed without a ./modules directory.")
 
         # Get repositories
         repos, _ = self.get_pipeline_module_repositories("modules", self.modules_dir)
@@ -678,7 +686,7 @@ def update(
             repo_component_entry[component_name]["installed_by"] = [installed_by]
         finally:
             new_installed_by = repo_component_entry[component_name]["installed_by"] + list(installed_by_log)
-            repo_component_entry[component_name]["installed_by"] = [*set(new_installed_by)]
+            repo_component_entry[component_name]["installed_by"] = sorted([*set(new_installed_by)])
 
         # Sort the 'modules.json' repo entries
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
@@ -1035,13 +1043,17 @@ def get_component_branch(self, component_type, component, repo_url, install_dir)
             )
         return branch
 
-    def dump(self):
+    def dump(self, run_prettier: bool = False):
         """
         Sort the modules.json, and write it to file
         """
         # Sort the modules.json
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
-        dump_json_with_prettier(self.modules_json_path, self.modules_json)
+        if run_prettier:
+            dump_json_with_prettier(self.modules_json_path, self.modules_json)
+        else:
+            with open(self.modules_json_path, "w") as fh:
+                json.dump(self.modules_json, fh, indent=4)
 
     def resolve_missing_installation(self, missing_installation, component_type):
         missing_but_in_mod_json = [
diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
index 504cb1095d..3ae01e9eef 100644
--- a/nf_core/modules/modules_utils.py
+++ b/nf_core/modules/modules_utils.py
@@ -37,7 +37,7 @@ def repo_full_name_from_remote(remote_url: str) -> str:
     return path
 
 
-def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], List[str]]:
+def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], List[NFCoreComponent]]:
     """
     Make a list of all modules installed in this repository
 
@@ -52,7 +52,7 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
     """
     # initialize lists
     local_modules: List[str] = []
-    nfcore_modules: List[str] = []
+    nfcore_modules_names: List[str] = []
     local_modules_dir: Optional[str] = None
     nfcore_modules_dir = os.path.join(dir, "modules", "nf-core")
 
@@ -76,9 +76,9 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
             # Not a module, but contains sub-modules
             if not "main.nf" in m_content:
                 for tool in m_content:
-                    nfcore_modules.append(os.path.join(m, tool))
+                    nfcore_modules_names.append(os.path.join(m, tool))
             else:
-                nfcore_modules.append(m)
+                nfcore_modules_names.append(m)
 
     # Make full (relative) file paths and create NFCoreComponent objects
     if local_modules_dir:
@@ -93,7 +93,7 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis
             base_dir=Path(dir),
             component_type="modules",
         )
-        for m in nfcore_modules
+        for m in nfcore_modules_names
     ]
 
     return local_modules, nfcore_modules
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 29fc466ed6..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
@@ -71,14 +71,14 @@ 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
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
index 25488dcc08..acf7269536 100644
--- a/nf_core/pipeline-template/.gitpod.yml
+++ b/nf_core/pipeline-template/.gitpod.yml
@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files
diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index 9ab59067a1..39943ffe49 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -1,6 +1,6 @@
 report_comment: >
   {% if 'dev' in version -%}
-  This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/dev" target="_blank">{{ name }}</a>
+  This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
   analysis pipeline.{% if branded %} 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 %}
diff --git a/nf_core/pipeline-template/assets/slackreport.json b/nf_core/pipeline-template/assets/slackreport.json
index ec03b3968a..96d2cb8afc 100644
--- a/nf_core/pipeline-template/assets/slackreport.json
+++ b/nf_core/pipeline-template/assets/slackreport.json
@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "{{ name }} v${version} - ${runName}",
+            "author_name": "{{ name }} ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 20ec78b5fc..20423a5f2e 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/schema.py b/nf_core/schema.py
index b00697334b..7e4726f189 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -35,7 +35,7 @@ def __init__(self):
         self.pipeline_dir = None
         self.schema_filename = None
         self.schema_defaults = {}
-        self.schema_params = []
+        self.schema_params = {}
         self.input_params = {}
         self.pipeline_params = {}
         self.invalid_nextflow_config_default_parameters = {}
@@ -110,7 +110,7 @@ def load_schema(self):
         with open(self.schema_filename, "r") as fh:
             self.schema = json.load(fh)
         self.schema_defaults = {}
-        self.schema_params = []
+        self.schema_params = {}
         log.debug(f"JSON file loaded: {self.schema_filename}")
 
     def sanitise_param_default(self, param):
@@ -141,6 +141,9 @@ def sanitise_param_default(self, param):
             param["default"] = float(param["default"])
             return param
 
+        if param["default"] is None:
+            return param
+
         # Strings
         param["default"] = str(param["default"])
         return param
@@ -154,18 +157,20 @@ def get_schema_defaults(self):
         """
         # Top level schema-properties (ungrouped)
         for p_key, param in self.schema.get("properties", {}).items():
-            self.schema_params.append(p_key)
+            self.schema_params[p_key] = ("properties", p_key)
             if "default" in param:
                 param = self.sanitise_param_default(param)
-                self.schema_defaults[p_key] = param["default"]
+                if param["default"] is not None:
+                    self.schema_defaults[p_key] = param["default"]
 
         # Grouped schema properties in subschema definitions
-        for _, definition in self.schema.get("definitions", {}).items():
+        for defn_name, definition in self.schema.get("definitions", {}).items():
             for p_key, param in definition.get("properties", {}).items():
-                self.schema_params.append(p_key)
+                self.schema_params[p_key] = ("definitions", defn_name, "properties", p_key)
                 if "default" in param:
                     param = self.sanitise_param_default(param)
-                    self.schema_defaults[p_key] = param["default"]
+                    if param["default"] is not None:
+                        self.schema_defaults[p_key] = param["default"]
 
     def save_schema(self, suppress_logging=False):
         """Save a pipeline schema to a file"""
@@ -239,9 +244,9 @@ def validate_default_params(self):
         except jsonschema.exceptions.ValidationError as e:
             raise AssertionError(f"Default parameters are invalid: {e.message}")
         for param, default in self.schema_defaults.items():
-            if default in ("null", "", None, "None"):
+            if default in ("null", "", None, "None") or default is False:
                 log.warning(
-                    f"[yellow][!] Default parameter '{param}' is empty or null. It is advisable to remove the default from the schema"
+                    f"[yellow][!] Default parameter '{param}' is empty, null, or False. It is advisable to remove the default from the schema"
                 )
         log.info("[green][✓] Default parameters match schema validation")
 
@@ -762,12 +767,15 @@ def prompt_remove_schema_notfound_config(self, p_key):
     def add_schema_found_configs(self):
         """
         Add anything that's found in the Nextflow params that's missing in the pipeline schema
+        Update defaults if they have changed
         """
         params_added = []
         params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",")
         params_ignore.append("validationSchemaIgnoreParams")
         for p_key, p_val in self.pipeline_params.items():
+            s_key = self.schema_params.get(p_key)
             # Check if key is in schema parameters
+            # Key is in pipeline but not in schema or ignored from schema
             if p_key not in self.schema_params and p_key not in params_ignore:
                 if (
                     self.no_prompts
@@ -782,7 +790,35 @@ def add_schema_found_configs(self):
                     self.schema["properties"][p_key] = self.build_schema_param(p_val)
                     log.debug(f"Adding '{p_key}' to pipeline schema")
                     params_added.append(p_key)
-
+            # Param has a default that does not match the schema
+            elif p_key in self.schema_defaults and (s_def := self.schema_defaults[p_key]) != (
+                p_def := self.build_schema_param(p_val).get("default")
+            ):
+                if self.no_prompts or Confirm.ask(
+                    f":sparkles: Default for [bold]'params.{p_key}'[/] in the pipeline config does not match schema. (schema: '{s_def}' | config: '{p_def}'). "
+                    "[blue]Update pipeline schema?"
+                ):
+                    s_key_def = s_key + ("default",)
+                    if p_def is None:
+                        nf_core.utils.nested_delitem(self.schema, s_key_def)
+                        log.debug(f"Removed '{p_key}' default from pipeline schema")
+                    else:
+                        nf_core.utils.nested_setitem(self.schema, s_key_def, p_def)
+                        log.debug(f"Updating '{p_key}' default to '{p_def}' in pipeline schema")
+            # There is no default in schema but now there is a default to write
+            elif (
+                s_key
+                and (p_key not in self.schema_defaults)
+                and (p_key not in params_ignore)
+                and (p_def := self.build_schema_param(p_val).get("default"))
+            ):
+                if self.no_prompts or Confirm.ask(
+                    f":sparkles: Default for [bold]'params.{p_key}'[/] is not in schema (def='{p_def}'). "
+                    "[blue]Update pipeline schema?"
+                ):
+                    s_key_def = s_key + ("default",)
+                    nf_core.utils.nested_setitem(self.schema, s_key_def, p_def)
+                    log.debug(f"Updating '{p_key}' default to '{p_def}' in pipeline schema")
         return params_added
 
     def build_schema_param(self, p_val):
@@ -806,13 +842,15 @@ def build_schema_param(self, p_val):
             p_val = None
 
         # Booleans
-        if p_val in ["True", "False"]:
-            p_val = p_val == "True"  # Convert to bool
+        if p_val in ["true", "false", "True", "False"]:
+            p_val = p_val in ["true", "True"]  # Convert to bool
             p_type = "boolean"
 
-        p_schema = {"type": p_type, "default": p_val}
+        # Don't return a default for anything false-y except 0
+        if not p_val and not (p_val == 0 and p_val is not False):
+            return {"type": p_type}
 
-        return p_schema
+        return {"type": p_type, "default": p_val}
 
     def launch_web_builder(self):
         """
diff --git a/nf_core/subworkflow-template/subworkflows/main.nf b/nf_core/subworkflow-template/main.nf
similarity index 100%
rename from nf_core/subworkflow-template/subworkflows/main.nf
rename to nf_core/subworkflow-template/main.nf
diff --git a/nf_core/subworkflow-template/subworkflows/meta.yml b/nf_core/subworkflow-template/meta.yml
similarity index 100%
rename from nf_core/subworkflow-template/subworkflows/meta.yml
rename to nf_core/subworkflow-template/meta.yml
diff --git a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test b/nf_core/subworkflow-template/tests/main.nf.test
similarity index 98%
rename from nf_core/subworkflow-template/subworkflows/tests/main.nf.test
rename to nf_core/subworkflow-template/tests/main.nf.test
index b0a212f2a3..59c4fdb679 100644
--- a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
+++ b/nf_core/subworkflow-template/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/subworkflow-template/subworkflows/tests/tags.yml b/nf_core/subworkflow-template/tests/tags.yml
similarity index 100%
rename from nf_core/subworkflow-template/subworkflows/tests/tags.yml
rename to nf_core/subworkflow-template/tests/tags.yml
diff --git a/nf_core/subworkflows/create.py b/nf_core/subworkflows/create.py
index 963076455e..93e9f271be 100644
--- a/nf_core/subworkflows/create.py
+++ b/nf_core/subworkflows/create.py
@@ -12,6 +12,7 @@ def __init__(
         component="",
         author=None,
         force=False,
+        migrate_pytest=False,
     ):
         super().__init__(
             "subworkflows",
@@ -19,4 +20,5 @@ def __init__(
             component,
             author,
             force=force,
+            migrate_pytest=migrate_pytest,
         )
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 8e76c03ceb..1ebced6d42 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -1,6 +1,7 @@
 """
 Lint the tests of a subworkflow in nf-core/modules
 """
+import json
 import logging
 from pathlib import Path
 
@@ -24,10 +25,10 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
     repo_dir = subworkflow.component_dir.parts[
         : subworkflow.component_dir.parts.index(subworkflow.component_name.split("/")[0])
     ][-1]
-    test_dir = Path(subworkflow.base_dir, "tests", "subworfklows", repo_dir, subworkflow.component_name)
+    test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", repo_dir, subworkflow.component_name)
     pytest_main_nf = Path(test_dir, "main.nf")
     is_pytest = pytest_main_nf.is_file()
-
+    log.debug(f"{pytest_main_nf} is pytest: {is_pytest}")
     if subworkflow.nftest_testdir.is_dir():
         subworkflow.passed.append(("test_dir_exists", "nf-test test directory exists", subworkflow.nftest_testdir))
     else:
@@ -39,15 +40,15 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
 
     # Lint the test main.nf file
     if subworkflow.nftest_main_nf.is_file():
-        subworkflow.passed.append(("test_main_exists", "test `main.nf.test` exists", subworkflow.nftest_main_nf))
+        subworkflow.passed.append(("test_main_nf_exists", "test `main.nf.test` exists", subworkflow.nftest_main_nf))
     else:
         if is_pytest:
             subworkflow.warned.append(
-                ("test_main_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf)
+                ("test_main_nf_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf)
             )
         else:
             subworkflow.failed.append(
-                ("test_main_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf)
+                ("test_main_nf_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf)
             )
 
     if subworkflow.nftest_main_nf.is_file():
@@ -59,36 +60,64 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                     subworkflow.passed.append(("test_snapshot_exists", "test `main.nf.test.snap` exists", snap_file))
                     # Validate no empty files
                     with open(snap_file, "r") as snap_fh:
-                        snap_content = snap_fh.read()
-                        if "d41d8cd98f00b204e9800998ecf8427e" in snap_content:
-                            subworkflow.failed.append(
-                                (
-                                    "test_snap_md5sum",
-                                    "md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
-                                    snap_file,
-                                )
-                            )
-                        else:
-                            subworkflow.passed.append(
-                                (
-                                    "test_snap_md5sum",
-                                    "no md5sum for empty file found",
-                                    snap_file,
-                                )
-                            )
-                        if "7029066c27ac6f5ef18d660d5741979a" in snap_content:
+                        try:
+                            snap_content = json.load(snap_fh)
+                            for test_name in snap_content.keys():
+                                if "d41d8cd98f00b204e9800998ecf8427e" in str(snap_content[test_name]):
+                                    if "stub" not in test_name:
+                                        subworkflow.failed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
+                                                snap_file,
+                                            )
+                                        )
+                                    else:
+                                        subworkflow.passed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for empty file found, but it is a stub test",
+                                                snap_file,
+                                            )
+                                        )
+                                else:
+                                    subworkflow.passed.append(
+                                        (
+                                            "test_snap_md5sum",
+                                            "no md5sum for empty file found",
+                                            snap_file,
+                                        )
+                                    )
+                                if "7029066c27ac6f5ef18d660d5741979a" in str(snap_content[test_name]):
+                                    if "stub" not in test_name:
+                                        subworkflow.failed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
+                                                snap_file,
+                                            )
+                                        )
+                                    else:
+                                        subworkflow.failed.append(
+                                            (
+                                                "test_snap_md5sum",
+                                                "md5sum for compressed empty file found, but it is a stub test",
+                                                snap_file,
+                                            )
+                                        )
+                                else:
+                                    subworkflow.passed.append(
+                                        (
+                                            "test_snap_md5sum",
+                                            "no md5sum for compressed empty file found",
+                                            snap_file,
+                                        )
+                                    )
+                        except json.decoder.JSONDecodeError as e:
                             subworkflow.failed.append(
                                 (
-                                    "test_snap_md5sum",
-                                    "md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
-                                    snap_file,
-                                )
-                            )
-                        else:
-                            subworkflow.passed.append(
-                                (
-                                    "test_snap_md5sum",
-                                    "no md5sum for compressed empty file found",
+                                    "test_snapshot_exists",
+                                    f"snapshot file `main.nf.test.snap` can't be read: {e}",
                                     snap_file,
                                 )
                             )
@@ -102,13 +131,16 @@ 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)
+            chained_components_tags = subworkflow._get_included_components_in_chained_tests(subworkflow.nftest_main_nf)
+            log.debug(f"Included components: {included_components}")
+            log.debug(f"Required tags: {required_tags}")
+            log.debug(f"Included components for chained nf-tests: {chained_components_tags}")
             missing_tags = []
-            for tag in required_tags + included_components:
+            for tag in set(required_tags + included_components + chained_components_tags):
                 if tag not in main_nf_tags:
                     missing_tags.append(tag)
             if len(missing_tags) == 0:
@@ -170,3 +202,11 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
             subworkflow.warned.append(("test_tags_yml_exists", "file `tags.yml` does not exist", subworkflow.tags_yml))
         else:
             subworkflow.failed.append(("test_tags_yml_exists", "file `tags.yml` does not exist", subworkflow.tags_yml))
+
+    # Check that the old test directory does not exist
+    if not is_pytest:
+        old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name)
+        if old_test_dir.is_dir():
+            subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir))
+        else:
+            subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir))
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 41e0853f2e..a2107f633c 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -3,9 +3,9 @@
 import os
 import shutil
 from pathlib import Path
+from typing import Dict
 
 import git
-import rich
 import rich.progress
 from git.exc import GitCommandError
 
@@ -61,7 +61,7 @@ class SyncedRepo:
     An object to store details about a locally cached code repository.
     """
 
-    local_repo_statuses = {}
+    local_repo_statuses: Dict[str, bool] = {}
     no_pull_global = False
 
     @staticmethod
diff --git a/nf_core/utils.py b/nf_core/utils.py
index c57990a9d3..bcc8faa3fd 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -16,8 +16,9 @@
 import subprocess
 import sys
 import time
+from contextlib import contextmanager
 from pathlib import Path
-from typing import Tuple, Union
+from typing import Generator, Tuple, Union
 
 import git
 import prompt_toolkit
@@ -1036,12 +1037,12 @@ def load_tools_config(directory: Union[str, Path] = "."):
 
 def determine_base_dir(directory="."):
     base_dir = start_dir = Path(directory).absolute()
-    while not get_first_available_path(base_dir, CONFIG_PATHS) and base_dir != base_dir.parent:
+    while base_dir != base_dir.parent:
         base_dir = base_dir.parent
         config_fn = get_first_available_path(base_dir, CONFIG_PATHS)
         if config_fn:
-            break
-    return directory if base_dir == start_dir else base_dir
+            return directory if base_dir == start_dir else base_dir
+    return directory
 
 
 def get_first_available_path(directory, paths):
@@ -1147,3 +1148,48 @@ def validate_file_md5(file_name, expected_md5hex):
         raise IOError(f"{file_name} md5 does not match remote: {expected_md5hex} - {file_md5hex}")
 
     return True
+
+
+def nested_setitem(d, keys, value):
+    """Sets the value in a nested dict using a list of keys to traverse
+
+    Args:
+        d (dict): the nested dictionary to traverse
+        keys (list[Any]): A list of keys to iteratively traverse
+        value (Any): The value to be set for the last key in the chain
+    """
+    current = d
+    for k in keys[:-1]:
+        current = current[k]
+    current[keys[-1]] = value
+
+
+def nested_delitem(d, keys):
+    """Deletes a key from a nested dictionary
+
+    Args:
+        d (dict): the nested dictionary to traverse
+        keys (list[Any]): A list of keys to iteratively traverse, deleting the final one
+    """
+    current = d
+    for k in keys[:-1]:
+        current = current[k]
+    del current[keys[-1]]
+
+
+@contextmanager
+def set_wd(path: Path) -> Generator[None, None, None]:
+    """Sets the working directory for this context.
+
+    Arguments
+    ---------
+
+    path : Path
+        Path to the working directory to be used inside this context.
+    """
+    start_wd = Path().absolute()
+    os.chdir(Path(path).resolve())
+    try:
+        yield
+    finally:
+        os.chdir(start_wd)
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 c94874b193..13dba6f30d 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -8,4 +8,8 @@ Sphinx
 sphinx-rtd-theme
 mypy
 types-PyYAML
+pyupgrade
 types-requests
+types-jsonschema
+types-Markdown
+types-setuptools
diff --git a/tests/components/generate_snapshot.py b/tests/components/generate_snapshot.py
index c7eb696722..46fd63fe3f 100644
--- a/tests/components/generate_snapshot.py
+++ b/tests/components/generate_snapshot.py
@@ -6,8 +6,9 @@
 import pytest
 
 from nf_core.components.components_test import ComponentsTest
+from nf_core.utils import set_wd
 
-from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL, set_wd
+from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL
 
 
 def test_generate_snapshot_module(self):
diff --git a/tests/components/snapshot_test.py b/tests/components/snapshot_test.py
index 371f0d6fbe..d774618476 100644
--- a/tests/components/snapshot_test.py
+++ b/tests/components/snapshot_test.py
@@ -5,8 +5,7 @@
 import pytest
 
 from nf_core.components.components_test import ComponentsTest
-
-from ..utils import set_wd
+from nf_core.utils import set_wd
 
 
 def test_components_test_check_inputs(self):
diff --git a/tests/lint/multiqc_config.py b/tests/lint/multiqc_config.py
new file mode 100644
index 0000000000..446b4378b0
--- /dev/null
+++ b/tests/lint/multiqc_config.py
@@ -0,0 +1,106 @@
+from pathlib import Path
+
+import yaml
+
+import nf_core.lint
+
+
+def test_multiqc_config_exists_ignore(self):
+    """Test that linting fails if the multiqc_config.yml file is missing"""
+    # Delete the file
+    new_pipeline = self._make_pipeline_copy()
+    Path(Path(new_pipeline, "assets", "multiqc_config.yml")).unlink()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    result = lint_obj.multiqc_config()
+    assert result["ignored"] == ["'assets/multiqc_config.yml' not found"]
+
+
+def test_multiqc_config_missing_report_section_order(self):
+    """Test that linting fails if the multiqc_config.yml file is missing the report_section_order"""
+    new_pipeline = self._make_pipeline_copy()
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+        mqc_yml = yaml.safe_load(fh)
+    mqc_yml_tmp = mqc_yml
+    mqc_yml.pop("report_section_order")
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml, fh)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    result = lint_obj.multiqc_config()
+    # Reset the file
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml_tmp, fh)
+    assert result["failed"] == ["'assets/multiqc_config.yml' does not contain `report_section_order`"]
+
+
+def test_multiqc_incorrect_export_plots(self):
+    """Test that linting fails if the multiqc_config.yml file has an incorrect value for export_plots"""
+    new_pipeline = self._make_pipeline_copy()
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+        mqc_yml = yaml.safe_load(fh)
+    mqc_yml_tmp = mqc_yml
+    mqc_yml["export_plots"] = False
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml, fh)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    result = lint_obj.multiqc_config()
+    # Reset the file
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml_tmp, fh)
+    assert result["failed"] == ["'assets/multiqc_config.yml' does not contain 'export_plots: true'."]
+
+
+def test_multiqc_config_report_comment_fail(self):
+    """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment"""
+    new_pipeline = self._make_pipeline_copy()
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+        mqc_yml = yaml.safe_load(fh)
+    mqc_yml_tmp = mqc_yml
+    mqc_yml["report_comment"] = "This is a test"
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml, fh)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    result = lint_obj.multiqc_config()
+    # Reset the file
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml_tmp, fh)
+    assert len(result["failed"]) == 1
+    assert result["failed"][0].startswith("'assets/multiqc_config.yml' does not contain a matching 'report_comment'.")
+
+
+def test_multiqc_config_report_comment_release_fail(self):
+    """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment for a release version"""
+    new_pipeline = self._make_pipeline_copy()
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "r") as fh:
+        mqc_yml = yaml.safe_load(fh)
+    mqc_yml_tmp = mqc_yml
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml, fh)
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    # bump version
+    lint_obj.nf_config["manifest.version"] = "1.0"
+    result = lint_obj.multiqc_config()
+    # Reset the file
+    with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh:
+        yaml.safe_dump(mqc_yml_tmp, fh)
+    assert len(result["failed"]) == 1
+    assert result["failed"][0].startswith("'assets/multiqc_config.yml' does not contain a matching 'report_comment'.")
+
+
+def test_multiqc_config_report_comment_release_succeed(self):
+    """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version"""
+
+    import nf_core.bump_version
+
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+    # bump version using the bump_version function
+    nf_core.bump_version.bump_pipeline_version(lint_obj, "1.0")
+    # lint again
+    lint_obj._load()
+    result = lint_obj.multiqc_config()
+    assert "'assets/multiqc_config.yml' contains a matching 'report_comment'." in result["passed"]
diff --git a/tests/modules/create.py b/tests/modules/create.py
index 7cfba484a1..74e5ec3896 100644
--- a/tests/modules/create.py
+++ b/tests/modules/create.py
@@ -1,11 +1,22 @@
+import filecmp
 import os
+import shutil
+from pathlib import Path
+from unittest import mock
 
 import pytest
 import requests_cache
 import responses
+import yaml
+from git.repo import Repo
 
 import nf_core.modules
-from tests.utils import mock_anaconda_api_calls, mock_biocontainers_api_calls
+from tests.utils import (
+    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
+    GITLAB_URL,
+    mock_anaconda_api_calls,
+    mock_biocontainers_api_calls,
+)
 
 
 def test_modules_create_succeed(self):
@@ -65,3 +76,66 @@ def test_modules_create_nfcore_modules_subtool(self):
     assert os.path.exists(
         os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test")
     )
+
+
+@mock.patch("rich.prompt.Confirm.ask")
+def test_modules_migrate(self, mock_rich_ask):
+    """Create a module with the --migrate-pytest option to convert pytest to nf-test"""
+    pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
+    module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort")
+
+    # Clone modules repo with pytests
+    shutil.rmtree(self.nfcore_modules)
+    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+    with open(module_dir / "main.nf", "r") as fh:
+        old_main_nf = fh.read()
+    with open(module_dir / "meta.yml", "r") as fh:
+        old_meta_yml = fh.read()
+
+    # Create a module with --migrate-pytest
+    mock_rich_ask.return_value = True
+    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+    module_create.create()
+
+    with open(module_dir / "main.nf", "r") as fh:
+        new_main_nf = fh.read()
+    with open(module_dir / "meta.yml", "r") as fh:
+        new_meta_yml = fh.read()
+    nextflow_config = module_dir / "tests" / "nextflow.config"
+
+    # Check that old files have been copied to the new module
+    assert old_main_nf == new_main_nf
+    assert old_meta_yml == new_meta_yml
+    assert nextflow_config.is_file()
+
+    # Check that pytest folder is deleted
+    assert not pytest_dir.is_dir()
+
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "samtools/sort" not in modules_yml.keys()
+
+
+@mock.patch("rich.prompt.Confirm.ask")
+def test_modules_migrate_no_delete(self, mock_rich_ask):
+    """Create a module with the --migrate-pytest option to convert pytest to nf-test.
+    Test that pytest directory is not deleted."""
+    pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort")
+
+    # Clone modules repo with pytests
+    shutil.rmtree(self.nfcore_modules)
+    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+
+    # Create a module with --migrate-pytest
+    mock_rich_ask.return_value = False
+    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True)
+    module_create.create()
+
+    # Check that pytest folder is not deleted
+    assert pytest_dir.is_dir()
+
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "samtools/sort" not in modules_yml.keys()
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index a3a7a80b71..a8a775e6f6 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -2,11 +2,13 @@
 
 import pytest
 import yaml
+from git.repo import Repo
 
 import nf_core.modules
 from nf_core.modules.lint import main_nf
+from nf_core.utils import set_wd
 
-from ..utils import GITLAB_URL, set_wd
+from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL
 from .patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf
 
 
@@ -419,3 +421,226 @@ def test_modules_environment_yml_file_name_mismatch(self):
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
     assert module_lint.failed[0].lint_test == "environment_yml_name"
+
+
+def test_modules_meta_yml_incorrect_licence_field(self):
+    """Test linting a module with an incorrect Licence field in meta.yml"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
+        meta_yml = yaml.safe_load(fh)
+    meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]"
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh:
+        fh.write(yaml.dump(meta_yml))
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+
+    # reset changes
+    meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"]
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh:
+        fh.write(yaml.dump(meta_yml))
+
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "meta_yml_valid"
+
+
+def test_modules_meta_yml_input_mismatch(self):
+    """Test linting a module with an extra entry in input fields in meta.yml compared to module.input"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
+        main_nf = fh.read()
+    main_nf_new = main_nf.replace("path bam", "path bai")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+        fh.write(main_nf_new)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+        fh.write(main_nf)
+    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) == 2
+    lint_tests = [x.lint_test for x in module_lint.warned]
+    # check that it is there twice:
+    assert lint_tests.count("meta_input_meta_only") == 1
+    assert lint_tests.count("meta_input_main_only") == 1
+
+
+def test_modules_meta_yml_output_mismatch(self):
+    """Test linting a module with an extra entry in output fields in meta.yml compared to module.output"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
+        main_nf = fh.read()
+    main_nf_new = main_nf.replace("emit: bam", "emit: bai")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+        fh.write(main_nf_new)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
+        fh.write(main_nf)
+    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) == 2
+    lint_tests = [x.lint_test for x in module_lint.warned]
+    # check that it is there twice:
+    assert lint_tests.count("meta_output_meta_only") == 1
+    assert lint_tests.count("meta_output_main_only") == 1
+
+
+def test_modules_meta_yml_incorrect_name(self):
+    """Test linting a module with an incorrect name in meta.yml"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh:
+        meta_yml = yaml.safe_load(fh)
+    meta_yml["name"] = "bpipe/test"
+    # need to make the same change to the environment.yml file
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")) as fh:
+        environment_yml = yaml.safe_load(fh)
+    environment_yml["name"] = "bpipe/test"
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh:
+        fh.write(yaml.dump(meta_yml))
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh:
+        fh.write(yaml.dump(environment_yml))
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+
+    # reset changes
+    meta_yml["name"] = "bpipe_test"
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh:
+        fh.write(yaml.dump(meta_yml))
+    environment_yml["name"] = "bpipe_test"
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh:
+        fh.write(yaml.dump(environment_yml))
+
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "meta_name"
+
+
+def test_modules_missing_test_dir(self):
+    """Test linting a module with a missing test directory"""
+    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak")
+    )
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests")
+    )
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_dir_exists"
+
+
+def test_modules_missing_test_main_nf(self):
+    """Test linting a module with a missing test/main.nf file"""
+    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test").rename(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.bak")
+    )
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.bak").rename(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")
+    )
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_main_nf_exists"
+
+
+def test_modules_missing_required_tag(self):
+    """Test linting a module with a missing required tag"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "r") as fh:
+        content = fh.read()
+        new_content = content.replace("modules_nfcore", "foo")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh:
+        fh.write(new_content)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh:
+        fh.write(content)
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_main_tags"
+
+
+def test_modules_missing_tags_yml(self):
+    """Test linting a module with a missing tags.yml file"""
+    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml").rename(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml.bak")
+    )
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml.bak").rename(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml")
+    )
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_tags_yml_exists"
+
+
+def test_modules_incorrect_tags_yml_key(self):
+    """Test linting a module with an incorrect key in tags.yml file"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "r") as fh:
+        content = fh.read()
+        new_content = content.replace("bpipe/test:", "bpipe_test:")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "w") as fh:
+        fh.write(new_content)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=True, module="bpipe/test")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "w") as fh:
+        fh.write(content)
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_tags_yml"
+
+
+def test_modules_incorrect_tags_yml_values(self):
+    """Test linting a module with an incorrect path in tags.yml file"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "r") as fh:
+        content = fh.read()
+        new_content = content.replace("modules/nf-core/bpipe/test/**", "foo")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "w") as fh:
+        fh.write(new_content)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml"), "w") as fh:
+        fh.write(content)
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_tags_yml"
+
+
+def test_modules_unused_pytest_files(self):
+    """Test linting a nf-test module with files still present in `tests/modules/`"""
+    Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir()
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_old_test_dir"
+
+
+def test_nftest_failing_linting(self):
+    """Test linting a module which includes other modules in nf-test tests.
+    Linting tests"""
+    # Clone modules repo with testing modules
+    tmp_dir = self.nfcore_modules.parent
+    self.nfcore_modules = Path(tmp_dir, "modules-test")
+    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH)
+
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="kallisto/quant")
+
+    assert len(module_lint.failed) == 4, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "environment_yml_valid"
+    assert module_lint.failed[1].lint_test == "meta_yml_valid"
+    assert module_lint.failed[2].lint_test == "test_main_tags"
+    assert "kallisto/index" in module_lint.failed[2].message
+    assert module_lint.failed[3].lint_test == "test_tags_yml"
diff --git a/tests/subworkflows/create.py b/tests/subworkflows/create.py
index 94c2a66331..fc628df34f 100644
--- a/tests/subworkflows/create.py
+++ b/tests/subworkflows/create.py
@@ -1,8 +1,15 @@
+import filecmp
 import os
+import shutil
+from pathlib import Path
+from unittest import mock
 
 import pytest
+import yaml
+from git.repo import Repo
 
 import nf_core.subworkflows
+from tests.utils import GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, GITLAB_URL
 
 
 def test_subworkflows_create_succeed(self):
@@ -35,3 +42,70 @@ def test_subworkflows_create_nfcore_modules(self):
     assert os.path.exists(
         os.path.join(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test")
     )
+
+
+@mock.patch("rich.prompt.Confirm.ask")
+def test_subworkflows_migrate(self, mock_rich_ask):
+    """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test"""
+    pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools")
+    subworkflow_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "bam_stats_samtools")
+
+    # Clone modules repo with pytests
+    shutil.rmtree(self.nfcore_modules)
+    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+    with open(subworkflow_dir / "main.nf", "r") as fh:
+        old_main_nf = fh.read()
+    with open(subworkflow_dir / "meta.yml", "r") as fh:
+        old_meta_yml = fh.read()
+
+    # Create a subworkflow with --migrate-pytest
+    mock_rich_ask.return_value = True
+    subworkflow_create = nf_core.subworkflows.SubworkflowCreate(
+        self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True
+    )
+    subworkflow_create.create()
+
+    with open(subworkflow_dir / "main.nf", "r") as fh:
+        new_main_nf = fh.read()
+    with open(subworkflow_dir / "meta.yml", "r") as fh:
+        new_meta_yml = fh.read()
+    nextflow_config = subworkflow_dir / "tests" / "nextflow.config"
+
+    # Check that old files have been copied to the new module
+    assert old_main_nf == new_main_nf
+    assert old_meta_yml == new_meta_yml
+    assert nextflow_config.is_file()
+
+    # Check that pytest folder is deleted
+    assert not pytest_dir.is_dir()
+
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
+
+
+@mock.patch("rich.prompt.Confirm.ask")
+def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
+    """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test.
+    Test that pytest directory is not deleted."""
+    pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools")
+
+    # Clone modules repo with pytests
+    shutil.rmtree(self.nfcore_modules)
+    Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH)
+
+    # Create a module with --migrate-pytest
+    mock_rich_ask.return_value = False
+    module_create = nf_core.subworkflows.SubworkflowCreate(
+        self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True
+    )
+    module_create.create()
+
+    # Check that pytest folder is not deleted
+    assert pytest_dir.is_dir()
+
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
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_download.py b/tests/test_download.py
index feb2090b27..7c9532e977 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -264,6 +264,11 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
                 "hello-world", f"{tmp_dir}/hello-world.sif", None, "docker.io", mock_rich_progress
             )
 
+        # Test successful pull with absolute URI (use tiny 3.5MB test container from the "Kogia" project: https://github.com/bschiffthaler/kogia)
+        download_obj.singularity_pull_image(
+            "docker.io/bschiffthaler/sed", f"{tmp_dir}/sed.sif", None, "docker.io", mock_rich_progress
+        )
+
         # try to pull from non-existing registry (Name change hello-world_new.sif is needed, otherwise ImageExists is raised before attempting to pull.)
         with pytest.raises(ContainerError.RegistryNotFound):
             download_obj.singularity_pull_image(
@@ -290,6 +295,16 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_rich_p
                 "a-container", f"{tmp_dir}/acontainer.sif", None, "ghcr.io", mock_rich_progress
             )
 
+        # test Image not found for absolute URI.
+        with pytest.raises(ContainerError.ImageNotFound):
+            download_obj.singularity_pull_image(
+                "docker.io/bschiffthaler/nothingtopullhere",
+                f"{tmp_dir}/nothingtopullhere.sif",
+                None,
+                "docker.io",
+                mock_rich_progress,
+            )
+
         # Traffic from Github Actions to GitHub's Container Registry is unlimited, so no harm should be done here.
         with pytest.raises(ContainerError.InvalidTag):
             download_obj.singularity_pull_image(
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 67104e3ad0..b2e7f3b574 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -30,6 +30,7 @@ def setUp(self):
             "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=self.test_pipeline_dir, plain=True
         )
         self.create_obj.init_pipeline()
+
         # Base lint object on this directory
         self.lint_obj = nf_core.lint.PipelineLint(self.test_pipeline_dir)
 
@@ -178,44 +179,52 @@ 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.multiqc_config import (  # type: ignore[misc]
+        test_multiqc_config_exists_ignore,
+        test_multiqc_config_missing_report_section_order,
+        test_multiqc_config_report_comment_fail,
+        test_multiqc_config_report_comment_release_fail,
+        test_multiqc_config_report_comment_release_succeed,
+        test_multiqc_incorrect_export_plots,
+    )
+    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_modules.py b/tests/test_modules.py
index 39c600b986..92c8dfda3f 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -3,12 +3,12 @@
 
 import os
 import shutil
-import tempfile
 import unittest
 from pathlib import Path
 
 import requests_cache
 import responses
+import yaml
 
 import nf_core.create
 import nf_core.modules
@@ -45,16 +45,34 @@ def create_modules_repo_dummy(tmp_dir):
             module_create.create()
 
     # Remove doi from meta.yml which makes lint fail
-    meta_yml = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml")
-    Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap").touch()
-    with open(meta_yml, "r") as fh:
-        lines = fh.readlines()
-    for line_index in range(len(lines)):
-        if "doi" in lines[line_index]:
-            to_pop = line_index
-    lines.pop(to_pop)
-    with open(meta_yml, "w") as fh:
-        fh.writelines(lines)
+    meta_yml_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml")
+
+    with open(meta_yml_path, "r") as fh:
+        meta_yml = yaml.safe_load(fh)
+    del meta_yml["tools"][0]["bpipe"]["doi"]
+    with open(meta_yml_path, "w") as fh:
+        yaml.dump(meta_yml, fh)
+    # Add dummy content to main.nf.test.snap
+    test_snap_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap")
+    test_snap_path.touch()
+    with open(test_snap_path, "w") as fh:
+        fh.write('{\n    "my test": {}\n}')
+
+    # remove "TODO" statements from main.nf
+    main_nf_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "main.nf")
+    with open(main_nf_path, "r") as fh:
+        main_nf = fh.read()
+    main_nf = main_nf.replace("TODO", "")
+    with open(main_nf_path, "w") as fh:
+        fh.write(main_nf)
+
+    # remove "TODO" statements from main.nf.test
+    main_nf_test_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")
+    with open(main_nf_test_path, "r") as fh:
+        main_nf_test = fh.read()
+    main_nf_test = main_nf_test.replace("TODO", "")
+    with open(main_nf_test_path, "w") as fh:
+        fh.write(main_nf_test)
 
     return root_dir
 
@@ -139,6 +157,8 @@ def test_modulesrepo_class(self):
         test_modules_create_nfcore_modules,
         test_modules_create_nfcore_modules_subtool,
         test_modules_create_succeed,
+        test_modules_migrate,
+        test_modules_migrate_no_delete,
     )
     from .modules.info import (  # type: ignore[misc]
         test_modules_info_in_modules_repo,
@@ -164,6 +184,8 @@ def test_modulesrepo_class(self):
         test_modules_environment_yml_file_not_array,
         test_modules_environment_yml_file_sorted_correctly,
         test_modules_environment_yml_file_sorted_incorrectly,
+        test_modules_incorrect_tags_yml_key,
+        test_modules_incorrect_tags_yml_values,
         test_modules_lint_check_process_labels,
         test_modules_lint_check_url,
         test_modules_lint_empty,
@@ -176,6 +198,16 @@ def test_modulesrepo_class(self):
         test_modules_lint_snapshot_file_missing_fail,
         test_modules_lint_snapshot_file_not_needed,
         test_modules_lint_trimgalore,
+        test_modules_meta_yml_incorrect_licence_field,
+        test_modules_meta_yml_incorrect_name,
+        test_modules_meta_yml_input_mismatch,
+        test_modules_meta_yml_output_mismatch,
+        test_modules_missing_required_tag,
+        test_modules_missing_tags_yml,
+        test_modules_missing_test_dir,
+        test_modules_missing_test_main_nf,
+        test_modules_unused_pytest_files,
+        test_nftest_failing_linting,
     )
     from .modules.list import (  # type: ignore[misc]
         test_modules_install_and_list_pipeline,
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 33cad81e3d..19872ee168 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 +22,23 @@
 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()
 
+    # Add dummy content to main.nf.test.snap
+    test_snap_path = Path(root_dir, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap")
+    test_snap_path.touch()
+    with open(test_snap_path, "w") as fh:
+        fh.write('{\n    "my test": {}\n}')
+
     return root_dir
 
 
@@ -95,6 +97,8 @@ def tearDown(self):
         test_subworkflows_create_fail_exists,
         test_subworkflows_create_nfcore_modules,
         test_subworkflows_create_succeed,
+        test_subworkflows_migrate,
+        test_subworkflows_migrate_no_delete,
     )
     from .subworkflows.info import (  # type: ignore[misc]
         test_subworkflows_info_in_modules_repo,
diff --git a/tests/test_test_utils.py b/tests/test_test_utils.py
index c4e3d49ae0..154a31fca6 100644
--- a/tests/test_test_utils.py
+++ b/tests/test_test_utils.py
@@ -3,7 +3,7 @@
 
 import pytest
 
-from .utils import set_wd, with_temporary_file, with_temporary_folder
+from .utils import with_temporary_file, with_temporary_folder
 
 
 def test_with_temporary_file():
@@ -30,20 +30,3 @@ def tmp_folder_exists(tmp_folder):
 def test_tmp_folder_does_not_exist_after():
     tmp_folder = with_temporary_folder(lambda x: x)()
     assert not Path(tmp_folder).exists()
-
-
-def test_set_wd():
-    with tempfile.TemporaryDirectory() as tmpdirname:
-        with set_wd(tmpdirname):
-            context_wd = Path().resolve()
-        assert context_wd == Path(tmpdirname).resolve()
-        assert context_wd != Path().resolve()
-
-
-def test_set_wd_revert_on_raise():
-    wd_before_context = Path().resolve()
-    with tempfile.TemporaryDirectory() as tmpdirname:
-        with pytest.raises(Exception):
-            with set_wd(tmpdirname):
-                raise Exception
-    assert wd_before_context == Path().resolve()
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 2ab5b64bfc..90d1886dbd 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -175,13 +175,13 @@ def test_get_repo_releases_branches_nf_core(self):
     def test_get_repo_releases_branches_not_nf_core(self):
         wfs = nf_core.list.Workflows()
         wfs.get_remote_workflows()
-        pipeline, wf_releases, wf_branches = nf_core.utils.get_repo_releases_branches("ewels/MultiQC", wfs)
+        pipeline, wf_releases, wf_branches = nf_core.utils.get_repo_releases_branches("MultiQC/MultiQC", wfs)
         for r in wf_releases:
             if r.get("tag_name") == "v1.10":
                 break
         else:
             raise AssertionError("MultiQC release v1.10 not found")
-        assert "master" in wf_branches.keys()
+        assert "main" in wf_branches.keys()
 
     def test_get_repo_releases_branches_not_exists(self):
         wfs = nf_core.list.Workflows()
@@ -207,3 +207,34 @@ def test_validate_file_md5():
         nf_core.utils.validate_file_md5(test_file, different_md5)
     with pytest.raises(ValueError):
         nf_core.utils.validate_file_md5(test_file, non_hex_string)
+
+
+def test_nested_setitem():
+    d = {"a": {"b": {"c": "value"}}}
+    nf_core.utils.nested_setitem(d, ["a", "b", "c"], "value new")
+    assert d["a"]["b"]["c"] == "value new"
+    assert d == {"a": {"b": {"c": "value new"}}}
+
+
+def test_nested_delitem():
+    d = {"a": {"b": {"c": "value"}}}
+    nf_core.utils.nested_delitem(d, ["a", "b", "c"])
+    assert "c" not in d["a"]["b"]
+    assert d == {"a": {"b": {}}}
+
+
+def test_set_wd():
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        with nf_core.utils.set_wd(tmpdirname):
+            context_wd = Path().resolve()
+        assert context_wd == Path(tmpdirname).resolve()
+        assert context_wd != Path().resolve()
+
+
+def test_set_wd_revert_on_raise():
+    wd_before_context = Path().resolve()
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        with pytest.raises(Exception):
+            with nf_core.utils.set_wd(tmpdirname):
+                raise Exception
+    assert wd_before_context == Path().resolve()
diff --git a/tests/utils.py b/tests/utils.py
index 307129b5b2..198ac3d583 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -59,24 +59,6 @@ def wrapper(*args: Any, **kwargs: Any) -> Any:
     return wrapper
 
 
-@contextmanager
-def set_wd(path: Path) -> Generator[None, None, None]:
-    """Sets the working directory for this context.
-
-    Arguments
-    ---------
-
-    path : Path
-        Path to the working directory to be used iside this context.
-    """
-    start_wd = Path().absolute()
-    os.chdir(Path(path).resolve())
-    try:
-        yield
-    finally:
-        os.chdir(start_wd)
-
-
 def mock_anaconda_api_calls(rsps: responses.RequestsMock, module: str, version: str) -> None:
     """Mock anaconda api calls for module"""
     anaconda_api_url = f"https://api.anaconda.org/package/bioconda/{module}"