diff --git a/.devcontainer/build-devcontainer/Dockerfile b/.devcontainer/build-devcontainer/Dockerfile
index 8e843ab1bf..355041eb35 100644
--- a/.devcontainer/build-devcontainer/Dockerfile
+++ b/.devcontainer/build-devcontainer/Dockerfile
@@ -1,6 +1,6 @@
 # devcontainers/miniconda image based on debian (bookworm)
 # see tags and images: https://mcr.microsoft.com/en-us/artifact/mar/devcontainers/miniconda/tags
-FROM mcr.microsoft.com/devcontainers/miniconda@sha256:1a85cf3e3da9d999f994f74cf501b1d02c9aa73ebfa3552f806dbe4570d7d5b5 AS build
+FROM mcr.microsoft.com/devcontainers/miniconda@sha256:617c7e42311066ac0bac3b7f0a3647daa9eec70fb8e3aeb8a5b083337a8a8687 AS build
 
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
@@ -27,7 +27,7 @@ RUN rm -f /etc/apt/sources.list.d/yarn.list && \
     rm -rf /var/lib/apt/lists/*
 
 # Final stage to copy only the required files after installation
-FROM mcr.microsoft.com/devcontainers/base:2.1.8-debian12@sha256:17e6cc517b483d1108b333d4c34352b0a21617f0117052e9b259d47113a9dc37 AS final
+FROM mcr.microsoft.com/devcontainers/base:2.1.11-debian12@sha256:bb7b81b6e5be17b5267f92f4ffda534fea37dab1df97b5e86c1f9b91da5c0b5d AS final
 
 # Copy only the conda environment and site-packages from build stage
 COPY --from=build /opt/conda /opt/conda
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
index e19a29c74a..2ffcd8cbc5 100755
--- a/.devcontainer/setup.sh
+++ b/.devcontainer/setup.sh
@@ -10,7 +10,7 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 nextflow self-update
 
 # Install specifically the version of tools from the workspace
-uv sync --all-extras
+uv sync
 
 # Activate the virtual environment automatically on login
 echo "source $(pwd)/.venv/bin/activate" >> $HOME/.bashrc
diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
index 97a6b95cd9..69d42c5d07 100644
--- a/.github/actions/create-lint-wf/action.yml
+++ b/.github/actions/create-lint-wf/action.yml
@@ -16,7 +16,7 @@ runs:
         export NXF_WORK=$(pwd)
 
     - name: Install Nextflow
-      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
       with:
         version: ${{ matrix.NXF_VER }}
 
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index d2ce28df65..dd5ff6e347 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -3,27 +3,46 @@ on:
   issue_comment:
     types: [created] # Add "@nf-core-bot changelog" as a PR comment to trigger this workflow.
 
+permissions: {}
+
 jobs:
   update_changelog:
     runs-on: ubuntu-latest
-    if: contains(github.event.comment.body, '@nf-core-bot changelog')
+    if: >
+      github.event.issue.pull_request &&
+      contains(github.event.comment.body, '@nf-core-bot changelog')
 
     steps:
-      - name: branch-deploy
-        id: branch-deploy
-        if: github.event_name == 'issue_comment'
-        uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2
-        with:
-          trigger: "@nf-core-bot changelog"
-          reaction: "eyes"
-          stable_branch: "dev"
+      - name: Verify commenter is on the nf-core/infrastructure team
+        env:
+          GH_TOKEN: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          ACTOR: ${{ github.event.comment.user.login }}
+        run: |
+          state=$(gh api "orgs/nf-core/teams/infrastructure/memberships/${ACTOR}" --jq '.state' 2>/dev/null || true)
+          if [ "$state" != "active" ]; then
+            echo "::error::@${ACTOR} is not an active member of nf-core/infrastructure; refusing to run."
+            exit 1
+          fi
+          echo "@${ACTOR} is on nf-core/infrastructure — proceeding."
+
+      - name: React to the triggering comment
+        env:
+          GH_TOKEN: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+        run: |
+          gh api --method POST \
+            "repos/${{ github.repository }}/issues/comments/${{ github.event.comment.id }}/reactions" \
+            -f content=eyes
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      # Checks out the base ref (the trusted version of the repo) first.
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
 
-      # Action runs on the issue comment, so we don't get the PR by default.
-      # Use the GitHub CLI to check out the PR:
+      - name: Save trusted scripts
+        run: |
+          cp "${GITHUB_WORKSPACE}/.github/workflows/changelog.py" "${RUNNER_TEMP}/changelog.py"
+          cp "${GITHUB_WORKSPACE}/.pre-commit-config.yaml" "${RUNNER_TEMP}/pre-commit-config.yaml"
+
       - name: Checkout Pull Request
         env:
           GH_TOKEN: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
@@ -31,7 +50,7 @@ jobs:
           PR_NUMBER="${{ github.event.issue.number }}"
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
@@ -45,30 +64,31 @@ jobs:
           PR_NUMBER: ${{ github.event.issue.number || github.event.pull_request.number }}
           PR_TITLE: ${{ github.event.issue.title || github.event.pull_request.title }}
         run: |
-          python ${GITHUB_WORKSPACE}/.github/workflows/changelog.py
+          python "${RUNNER_TEMP}/changelog.py"
 
       - name: Check if CHANGELOG.md actually changed
         id: file_changed
         run: |
           # Show the diff for debugging
-          git diff -- ${GITHUB_WORKSPACE}/CHANGELOG.md
+          git diff -- "${GITHUB_WORKSPACE}/CHANGELOG.md"
 
           # Check if file has unstaged changes
-          [ -n "$(git diff -- ${GITHUB_WORKSPACE}/CHANGELOG.md)" ] && file_changed="TRUE" || file_changed="FALSE"
+          [ -n "$(git diff -- "${GITHUB_WORKSPACE}/CHANGELOG.md")" ] && file_changed="TRUE" || file_changed="FALSE"
 
           echo "File changed: $file_changed"
-          echo "changed=$file_changed" >> $GITHUB_OUTPUT
+          echo "changed=$file_changed" >> "$GITHUB_OUTPUT"
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        if: steps.file_changed.outputs.changed == 'TRUE'
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         continue-on-error: true
         with:
-          extra-args: --config .pre-commit-config.yaml --all-files
+          extra-args: --config ${{ runner.temp }}/pre-commit-config.yaml --files CHANGELOG.md
 
       - name: Commit and push changes
         if: steps.file_changed.outputs.changed == 'TRUE'
@@ -77,7 +97,7 @@ jobs:
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
-          git add ${GITHUB_WORKSPACE}/CHANGELOG.md
+          git add "${GITHUB_WORKSPACE}/CHANGELOG.md"
           git status
           git commit -m "[automated] Update CHANGELOG.md [skip ci]"
           git push
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index db2903eb28..866b79f14b 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml
new file mode 100644
index 0000000000..0667bcd659
--- /dev/null
+++ b/.github/workflows/codspeed.yml
@@ -0,0 +1,66 @@
+name: CodSpeed benchmarks
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+    paths:
+      - codspeed.yml
+      - nf_core/**/*.py
+  pull_request:
+    paths:
+      - codspeed.yml
+      - nf_core/**/*.py
+  workflow_dispatch:
+
+# Cancel if a newer run with the same workflow name is queued
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  id-token: write # for OpenID Connect authentication with CodSpeed
+
+jobs:
+  startup-benchmarks:
+    name: Run start-up benchmarks
+    runs-on: codspeed-macro
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        name: Check out source-code repository
+
+      - name: Set up Python
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+        with:
+          python-version: "3.14"
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+        with:
+          version: ${{ github.event.inputs.nextflow-version || matrix.nextflow-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      # Clone nf-core/modules into the local cache here, while network is
+      # available. The modules-install benchmark then runs entirely offline
+      # (no per-round fetch), so it stays deterministic even if the CodSpeed
+      # step sandboxes network during measurement.
+      - name: Warm nf-core/modules cache
+        run: uv run python -c "from nf_core.modules.modules_repo import ModulesRepo; ModulesRepo()"
+
+      # These benchmarks spawn a fresh interpreter per round to measure
+      # import/start-up cost, which CodSpeed's instruction-counting
+      # "simulation" instrument can't see. Use "walltime" mode instead.
+      - name: Run start-up benchmarks
+        uses: CodSpeedHQ/action@88472375d0a4572cf70a9f1fe3a4e0ab8da1b924 # v5.0.1
+        with:
+          mode: walltime
+          run: uv run pytest benchmarks/test_startup_benchmarks.py --codspeed
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 56033d8eaa..c078ac4068 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -42,22 +42,22 @@ jobs:
           export NXF_WORK=$(pwd)
 
       # Get the repo code
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out source-code repository
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
       - name: Install python dependencies
-        run: uv sync --all-extras
+        run: uv sync
 
       - name: run create-lint-wf
         uses: ./.github/actions/create-lint-wf
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 9bb608e97f..9c101fbdd5 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -32,7 +32,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: checkout
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
       - name: Create Matrix
         id: create_matrix
         run: |
@@ -56,23 +56,23 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
       - name: Install python dependencies
-        run: uv sync --all-extras
+        run: uv sync
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
         with:
           version: latest-everything
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 879bd68849..9a3774ac2b 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -41,16 +41,16 @@ jobs:
           cd create-test-wf
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
@@ -58,7 +58,7 @@ jobs:
         run: uv sync
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
         with:
           version: ${{ matrix.NXF_VER }}
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index cd2c7c78d8..8786b5a084 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -13,16 +13,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
@@ -34,6 +34,6 @@ jobs:
 
       - name: Publish dist to PyPI
         if: github.repository == 'nf-core/tools'
-        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # release/v1
+        uses: pypa/gh-action-pypi-publish@ba38be9e461d3875417946c167d0b5f3d385a247 # release/v1
         with:
           password: ${{ secrets.pypi_password }}
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 46d6d10a29..4415e97907 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -12,14 +12,14 @@ jobs:
     steps:
       - name: branch-deploy
         id: branch-deploy
-        uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2
+        uses: github/branch-deploy@f0984057ffe1aa340aa017b6eafb894310aed88e # v12.0.0
         with:
           trigger: "@nf-core-bot fix linting"
           reaction: "eyes"
           stable_branch: "dev"
 
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -33,7 +33,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
         continue-on-error: true
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 11d2c5fd6e..681c5563a5 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -19,9 +19,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml
index 92dd32a763..649fdc42dc 100644
--- a/.github/workflows/nextflow-source-test.yml
+++ b/.github/workflows/nextflow-source-test.yml
@@ -14,13 +14,13 @@ jobs:
 
     steps:
       - name: Check out Nextflow
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           repository: nextflow-io/nextflow
           path: nextflow
 
       - name: Set up Java
-        uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
+        uses: actions/setup-java@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 # v5
         with:
           distribution: "temurin"
           architecture: x64
@@ -38,19 +38,19 @@ jobs:
           chmod +x $HOME/.local/bin/nextflow
           nextflow -version
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out nf-core/tools
         with:
           ref: dev
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
diff --git a/.github/workflows/push_dockerhub.yml b/.github/workflows/push_dockerhub.yml
index 23411d275c..98f4085aa9 100644
--- a/.github/workflows/push_dockerhub.yml
+++ b/.github/workflows/push_dockerhub.yml
@@ -34,16 +34,16 @@ jobs:
           swap-storage: true
 
       - name: Check out code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Set up QEMU for multi-architecture build
-        uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4
+        uses: docker/setup-qemu-action@96fe6ef7f33517b61c61be40b68a1882f3264fb8 # v4
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4
+        uses: docker/setup-buildx-action@bb05f3f5519dd87d3ba754cc423b652a5edd6d2c # v4
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@4907a6ddec9925e35a0a9e82d7399ccc52663121 # v4
+        uses: docker/login-action@dbcb813823bdd20940b903addbd779551569679f # v4
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASS }}
@@ -74,7 +74,7 @@ jobs:
               --push --no-cache .
 
       - name: Build and push nfcore/devcontainer image
-        uses: devcontainers/ci@b63b30de439b47a52267f241112c5b453b673db5 # v0.3
+        uses: devcontainers/ci@513af61f4de4f75d37e4438f184ba4358f0fc1ca # v0.3
         with:
           configFile: .devcontainer/build-devcontainer/devcontainer.json
           imageName: nfcore/devcontainer
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 85cbd02188..fd2f04dd2d 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -40,7 +40,7 @@ jobs:
     name: Get test file matrix
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out source-code repository
 
       - name: List tests
@@ -58,10 +58,12 @@ jobs:
       - runner=4cpu-linux-x64
     strategy:
       matrix:
-        # On main branch test with 3.10 and 3.14, otherwise just 3.10
-        python-version: ${{ (github.base_ref == 'main' || github.event_name == 'push') && fromJson('["3.10", "3.14"]') || fromJson('["3.10"]') }}
+        # On PRs to main test with 3.10 and 3.14, otherwise just 3.10
+        python-version: ${{ github.base_ref == 'main' && fromJson('["3.10", "3.14"]') || fromJson('["3.10"]') }}
         test: ${{ fromJson(needs.list_tests.outputs.tests).test }}
-        nextflow-version: ${{ (github.base_ref == 'main' || github.event_name == 'push') && fromJson('["25.10.4", "latest-stable"]') || fromJson('["25.10.4"]') }}
+        # On push/release test both NF versions, otherwise just 25.10.4
+        # Note: python×nextflow must stay ≤2 with 88 tests to stay under GitHub's 256-config limit
+        nextflow-version: ${{ (github.event_name == 'push' || github.event_name == 'release') && fromJson('["25.10.4", "latest-stable"]') || fromJson('["25.10.4"]') }}
       fail-fast: false # run all tests even if one fails
     steps:
       - name: go to subdirectory and change nextflow workdir
@@ -70,29 +72,29 @@ jobs:
           cd pytest
           export NXF_WORK=$(pwd)
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: ${{ matrix.python-version }}
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
       - name: Install dependencies
-        run: uv sync --all-extras
+        run: uv sync
 
       - name: Set up Apptainer
         if: ${{ startsWith(matrix.test, 'pipelines/download/') }}
         uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
         with:
           version: ${{ github.event.inputs.nextflow-version || matrix.nextflow-version }}
 
@@ -126,7 +128,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: always()
-        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
         with:
           files: ./coverage.xml
           flags: python-${{ matrix.python-version }}
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index f239c2eafd..7d9cf05901 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -62,12 +62,12 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
@@ -77,12 +77,12 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
@@ -90,7 +90,7 @@ jobs:
         run: uv sync
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
         with:
           version: "25.10.4"
 
@@ -108,7 +108,31 @@ jobs:
           git config --global init.defaultBranch $defaultBranch
 
       - name: Run synchronisation
+        id: sync
         if: github.repository == 'nf-core/tools'
+        continue-on-error: true
+        env:
+          GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+        run: |
+          git config --global user.email "core@nf-co.re"
+          git config --global user.name "nf-core-bot"
+          uv run nf-core --log-file sync_log_${{ matrix.pipeline }}.txt \
+            ${{ github.event.inputs.debug == 'true' && '--verbose' || '' }} \
+            pipelines sync -d nf-core/${{ matrix.pipeline }} \
+            --from-branch dev \
+            --pull-request \
+            --username nf-core-bot \
+            --github-repository nf-core/${{ matrix.pipeline }} \
+            --blog-post ${{inputs.blog_post}}
+
+      - name: Install newer Nextflow (retry fallback)
+        if: github.repository == 'nf-core/tools' && steps.sync.outcome == 'failure'
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+        with:
+          version: "26.04.6"
+
+      - name: Retry synchronisation with newer Nextflow
+        if: github.repository == 'nf-core/tools' && steps.sync.outcome == 'failure'
         env:
           GITHUB_AUTH_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
         run: |
diff --git a/.github/workflows/test_offline_configs.yml b/.github/workflows/test_offline_configs.yml
index 12f069fcfd..1e11f802db 100644
--- a/.github/workflows/test_offline_configs.yml
+++ b/.github/workflows/test_offline_configs.yml
@@ -53,11 +53,11 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out nf-core/tools
         with:
           ref: ${{ github.ref_name }}
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
index 05eaa2d3b2..8adbcda40e 100644
--- a/.github/workflows/update-template-snapshots.yml
+++ b/.github/workflows/update-template-snapshots.yml
@@ -15,14 +15,14 @@ jobs:
     steps:
       - name: branch-deploy
         id: branch-deploy
-        uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2
+        uses: github/branch-deploy@f0984057ffe1aa340aa017b6eafb894310aed88e # v12.0.0
         with:
           trigger: "@nf-core-bot update template snapshots"
           reaction: "eyes"
           stable_branch: "dev"
 
       - name: checkout
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Create Matrix
         id: create_matrix
@@ -43,7 +43,7 @@ jobs:
       fail-fast: false
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -56,20 +56,20 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
       - name: Install dependencies
-        run: uv sync --all-extras
+        run: uv sync
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
         with:
           version: latest-everything
 
@@ -145,7 +145,7 @@ jobs:
     runs-on: ubuntu-latest
     if: always() && needs.update-snapshots.result != 'skipped'
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index 6b185c314f..fe029d48b9 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -10,14 +10,14 @@ jobs:
     steps:
       - name: branch-deploy
         id: branch-deploy
-        uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2
+        uses: github/branch-deploy@f0984057ffe1aa340aa017b6eafb894310aed88e # v12.0.0
         with:
           trigger: "@nf-core-bot update textual snapshots"
           reaction: "eyes"
           stable_branch: "dev"
 
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -37,22 +37,22 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
 
       - name: Install dependencies
-        run: uv sync --all-extras
+        run: uv sync
 
       - name: Run pytest to update snapshots
         id: pytest
         run: |
-          uv run python -m pytest tests/pipelines/test_create_app.py --snapshot-update --color=yes --durations=0 -n auto
+          uv run python -m pytest tests/pipelines/test_create_app.py --snapshot-update --color=yes --durations=0 -n logical
         continue-on-error: true
 
       # indication that the run has finished
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 59c29157bb..9e70f640c2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,9 +1,10 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.16.0
     hooks:
       - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
+        priority: 10
       - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"
@@ -11,12 +12,13 @@ repos:
       - id: prettier
         entry: prettier --experimental-cli --write --ignore-unknown --no-cache
         additional_dependencies:
-          - prettier@3.8.3
+          - prettier@3.9.6
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
+        priority: 10
         exclude: |
           (?x)^(
               .*\.snap$|
@@ -25,6 +27,7 @@ repos:
               tests/pipelines/__snapshots__/.*
           )$
       - id: end-of-file-fixer
+        priority: 10
         exclude: |
           (?x)^(
               .*\.snap$|
@@ -33,9 +36,11 @@ repos:
               tests/pipelines/__snapshots__/.*
           )$
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.20.2"
+    rev: "v2.3.0"
     hooks:
       - id: mypy
+        args: [--ignore-missing-imports, --scripts-are-modules, -n4]
+        priority: 20
         additional_dependencies:
           - types-PyYAML
           - types-requests
@@ -44,13 +49,15 @@ repos:
           - types-setuptools
           - pydantic
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.11.8
+    rev: 0.12.0
     hooks:
       - id: uv-lock
+        priority: 20
   - repo: local
     hooks:
       - id: lint-test-docstrings
         name: Check lint test names are documented in docstrings
         language: system
         entry: python3 docs/api/check_lint_docstrings.py
+        priority: 20
         files: ^nf_core/(modules|subworkflows)/lint/.*\.py$
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c6e077cc56..61ba31f6f7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,50 @@
 # nf-core/tools: Changelog
 
+## [v4.1.0 - Marshalled Mamba](https://github.com/nf-core/tools/releases/tag/4.1.0) - [2026-07-29]
+
+### General
+
+- container configs: use correct key for conda configs ([#4269](https://github.com/nf-core/tools/pull/4269))
+- Coerce launch params_out to Path to fix AttributeError (#4299) ([#4317](https://github.com/nf-core/tools/pull/4317))
+- generate valid Markdown when piping schema docs to file ([#4319](https://github.com/nf-core/tools/pull/4319))
+- fix API docs bug in pydantic autodoc ([#4320](https://github.com/nf-core/tools/pull/4320))
+- Improve CLI startup speed ([#4383](https://github.com/nf-core/tools/pull/4383))
+
+### Linting
+
+- accept `process_low_memory` as a standard module label ([#4264](https://github.com/nf-core/tools/pull/4264))
+- improve linting for `modules.json` to add support for only installing subworkflows from a repository and provide more explicit error messages ([#4287](https://github.com/nf-core/tools/pull/4287))
+- improve singularity_tag linting check (add skip, handle exceptions correctly, check against oras) ([#4358](https://github.com/nf-core/tools/pull/4358))
+- make regex for meta keys more specific to avoid false positives ([#4280](https://github.com/nf-core/tools/pull/4280))
+
+### Modules
+
+- `modules info`: handle one element channels correctly ([#4268](https://github.com/nf-core/tools/pull/4268))
+- `module` lint for module name matching against nf-core module naming specifications ([#4325](https://github.com/nf-core/tools/pull/4325))
+- Clarify execution context of nf-core modules test command ([#4346](https://github.com/nf-core/tools/pull/4346))
+- Add `nf-core modules containers create` to build module containers via Seqera Wave and record them in the `containers:` section of `meta.yml` ([#3954](https://github.com/nf-core/tools/pull/3954))
+- Add a log hint in `modules create` for `create containers` and switch `modules bump-versions` to use Seqera containers ([#4374](https://github.com/nf-core/tools/pull/4374))
+
+### Template
+
+- New pre-commit hooks blocking large files and merge markers in pipeline template ([#3935](https://github.com/nf-core/tools/pull/3935))
+- add `process_low_memory` resource label to `base.config` ([#4264](https://github.com/nf-core/tools/pull/4264))
+- Simpler test data path in `tests/nextflow.config` ([#4285](https://github.com/nf-core/tools/pull/4285))
+- fix dead link ([#4307](https://github.com/nf-core/tools/pull/4307))
+- remove date placeholder from changelog title ([#4333](https://github.com/nf-core/tools/pull/4333))
+- correct always-true `nf-core pipelines lint` condition in the linting workflow and fix doc typos (broken `#lint-tests` anchor, duplicate word, stray code-span space) ([#4324](https://github.com/nf-core/tools/pull/4324))
+- Fix publishDir configuration in modules.config for multiqc ([#4347](https://github.com/nf-core/tools/pull/4347))
+- Switch to a more secure approach for PR comments by splitting the GitHub Actions workflow ([#4342](https://github.com/nf-core/tools/pull/4342))
+
+### Download
+
+- Included support for Apptainer in `nf-core pipelines download --container-system apptainer` ([#4352](https://github.com/nf-core/tools/pull/4352))
+
+#### Version updates
+
+- Update pre-commit hook pre-commit/mirrors-mypy to v2 ([#4270](https://github.com/nf-core/tools/pull/4270))
+- Update pre-commit npm dependencies to v3.8.4 ([#4335](https://github.com/nf-core/tools/pull/4335))
+
 ## [v4.0.3 - Bold Boa Patch 3](https://github.com/nf-core/tools/releases/tag/4.0.3) - [2026-07-23]
 
 This is a security patch to prohibit write access to the repository through certain GitHub Action workflows.
@@ -34,6 +79,10 @@ This is a security patch to prohibit write access to the repository through cert
 - switch changelog bot trigger only on comments ([#4241](https://github.com/nf-core/tools/pull/4241))
 - fix indentation in generated api docs ([#4245](https://github.com/nf-core/tools/pull/4245))
 
+### Linting
+
+- Store `EDAM.tsv` in `NFCORE_CACHE_DIR` and fix yaml comment loss when running `lint --fix` ([#4242](https://github.com/nf-core/tools/pull/4242))
+
 ### Modules
 
 - Allow task.ext.prefix2 in modules linting ([#4234](https://github.com/nf-core/tools/pull/4234))
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 12f2a469ff..5b06df0b14 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -24,7 +24,7 @@ If you want to work with developing the nf-core/tools code, you'll need a couple
 Install using `uv`:
 
 ```bash
-uv sync --all-extras
+uv sync
 ```
 
 This will install all dependencies (listed in `pyproject.toml`) and install your local fork of nf-core/tools in editable mode. The virtual environment is automatically created in `.venv/` in the project directory.
@@ -90,7 +90,7 @@ Note: The `--config` flag is important in this repository to ensure prek uses th
 ## 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: [nf-core tools Python API docs](https://nf-co.re/docs/nf-core-tools/api_reference/latest/).
 
 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/Dockerfile b/Dockerfile
index d3ac94f7dc..6a7090ebce 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.14-slim@sha256:5b3879b6f3cb77e712644d50262d05a7c146b7312d784a18eff7ff5462e77033
+FROM python:3.14-slim@sha256:cea0e6040540fb2b965b6e7fb5ffa00871e632eef63719f0ea54bca189ce14a6
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 
diff --git a/README.md b/README.md
index 88542d2176..5a8ecc1c23 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@
 A python package with helper tools for the nf-core community.
 
 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 [nf-core tools Python API docs](https://nf-co.re/docs/nf-core-tools/api_reference/latest/).
 
 ## Installation
 
@@ -56,7 +56,7 @@ pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
 If editing, fork and clone the repo, then install as follows:
 
 ```bash
-uv sync --all-extras
+uv sync
 
 # Activate the virtual environment
 source .venv/bin/activate
diff --git a/benchmarks/test_startup_benchmarks.py b/benchmarks/test_startup_benchmarks.py
new file mode 100644
index 0000000000..52322c5433
--- /dev/null
+++ b/benchmarks/test_startup_benchmarks.py
@@ -0,0 +1,136 @@
+"""CodSpeed wall-time benchmarks for nf-core CLI start-up cost.
+
+These spawn a fresh interpreter per round so that heavy, lazily-imported
+dependencies (pydantic, requests, questionary, PyGithub, trogon, ...) are not
+cached in sys.modules from a previous round. Run them under CodSpeed's
+"walltime" instrument: the "simulation" instrument only profiles the parent
+test process and never sees the child interpreter's import cost.
+
+Rounds are kept low because each one pays for a full interpreter boot.
+"""
+
+import os
+import shutil
+import subprocess
+import sys
+
+import pytest
+
+IMPORT_CMD = [sys.executable, "-c", "import nf_core.__main__"]
+HELP_CMD = [sys.executable, "-m", "nf_core", "--help"]
+COMMAND_GROUPS = ["pipelines", "modules", "subworkflows", "test-datasets"]
+
+# Keep the help invocation offline and deterministic.
+_ENV = {**os.environ, "NFCORE_NO_VERSION_CHECK": "1"}
+
+
+def _benchmark_command(benchmark, command):
+    def run():
+        subprocess.run(command, check=True, capture_output=True, env=_ENV)
+
+    benchmark.pedantic(run, rounds=10, warmup_rounds=2)
+
+
+def _cli_script(setup, args):
+    return f"{setup}\nimport sys\nsys.argv = {args!r}\nfrom nf_core.__main__ import run_nf_core\nrun_nf_core()"
+
+
+@pytest.fixture(scope="session")
+def generated_pipeline(tmp_path_factory):
+    """Render a real pipeline scaffold once, reused by the realistic benchmarks.
+
+    Generation is expensive and identical for every consumer, so it happens a
+    single time per session and outside any measured rounds. Consumers that
+    mutate the pipeline (e.g. installing a module) must work on a copy so the
+    shared scaffold stays pristine and the suite is order-independent.
+    """
+    from nf_core.pipelines.create.create import PipelineCreate
+
+    pipeline_dir = tmp_path_factory.mktemp("pipeline_fixture") / "pipeline"
+    PipelineCreate("benchmark", "benchmark pipeline", "nf-core", outdir=pipeline_dir, no_git=True).init_pipeline()
+    return pipeline_dir
+
+
+@pytest.fixture(scope="session")
+def modules_cache():
+    """Ensure a local nf-core/modules clone exists, without ever fetching.
+
+    Constructing ``ModulesRepo`` clones the remote into ``NFCORE_DIR`` only if it
+    is not already present; ``no_pull_global`` suppresses the ``git fetch`` on an
+    existing clone. In CI the clone is warmed by an earlier, network-enabled
+    workflow step, so this fixture (and every measured round) runs offline. When
+    run locally against a cold cache it performs the one-off clone here, outside
+    the measured rounds.
+    """
+    from nf_core.modules.modules_repo import ModulesRepo
+
+    ModulesRepo.no_pull_global = True
+    ModulesRepo()
+
+
+def test_import_main_startup(benchmark):
+    """Wall-time cost of importing the CLI entry point in a fresh interpreter."""
+    _benchmark_command(benchmark, IMPORT_CMD)
+
+
+def test_cli_help_startup(benchmark):
+    """Wall-time cost of a full `nf-core --help` invocation."""
+    _benchmark_command(benchmark, HELP_CMD)
+
+
+@pytest.mark.parametrize("command_group", COMMAND_GROUPS)
+def test_cli_command_group_help_startup(benchmark, command_group):
+    """Wall-time cost of loading each top-level command tree and rendering its help."""
+    _benchmark_command(benchmark, [sys.executable, "-m", "nf_core", command_group, "--help"])
+
+
+def test_pipelines_create_startup(benchmark, tmp_path):
+    """Start the create command, stubbing only template generation and other writes."""
+    args = [
+        "nf-core",
+        "pipelines",
+        "create",
+        "--name",
+        "benchmark",
+        "--description",
+        "benchmark pipeline",
+        "--author",
+        "nf-core",
+        "--outdir",
+        str(tmp_path / "pipeline"),
+    ]
+    setup = (
+        "from nf_core.pipelines.create.create import PipelineCreate\nPipelineCreate.init_pipeline = lambda self: None"
+    )
+    _benchmark_command(benchmark, [sys.executable, "-c", _cli_script(setup, args)])
+
+
+def test_modules_install_startup(benchmark, generated_pipeline, modules_cache, tmp_path):
+    """Install a real module into a real pipeline, offline.
+
+    The pipeline scaffold (``generated_pipeline``) and the nf-core/modules clone
+    (``modules_cache``) are both prepared once, outside the measured rounds. The
+    rounds then run the real install (git checkout + file copy + modules.json
+    write) against a private copy of the scaffold. ``no_pull_global`` suppresses
+    the per-round ``git fetch`` and ``--force`` avoids the re-install prompt, so
+    every round is deterministic and network-free.
+    """
+    target = tmp_path / "pipeline"
+    shutil.copytree(generated_pipeline, target)
+    args = ["nf-core", "modules", "install", "fastp", "-d", str(target), "--force"]
+    setup = "from nf_core.modules.modules_repo import ModulesRepo\nModulesRepo.no_pull_global = True"
+    _benchmark_command(benchmark, [sys.executable, "-c", _cli_script(setup, args)])
+
+
+def test_pipelines_schema_lint_startup(benchmark, generated_pipeline):
+    """Lint a real, freshly generated pipeline schema.
+
+    The schema fixture is rendered once by ``generated_pipeline`` (outside the
+    measured rounds); the benchmark then runs the real lint (JSON parse +
+    JSON-Schema validation + default-param checks). Only ``fetch_wf_config`` is
+    stubbed to skip the ``nextflow config`` JVM subprocess, which would
+    otherwise dominate wall time and require Nextflow on the runner.
+    """
+    args = ["nf-core", "pipelines", "schema", "lint", str(generated_pipeline)]
+    setup = "import nf_core.utils\nnf_core.utils.fetch_wf_config = lambda *args, **kwargs: {}"
+    _benchmark_command(benchmark, [sys.executable, "-c", _cli_script(setup, args)])
diff --git a/docs/api/_src/api/nf_core_yml.md b/docs/api/_src/api/nf_core_yml.md
new file mode 100644
index 0000000000..ab03b23304
--- /dev/null
+++ b/docs/api/_src/api/nf_core_yml.md
@@ -0,0 +1,68 @@
+# .nf-core.yml configuration
+
+The `.nf-core.yml` file at the root of any nf-core repository controls how nf-core
+tools behaves for that repository. It is read by `load_tools_config()` and validated
+against the `NFCoreYamlConfig` Pydantic model.
+
+## Minimal examples
+
+Pipeline repository:
+
+```yaml
+repository_type: pipeline
+nf_core_version: "4.0.2"
+```
+
+Modules repository:
+
+```yaml
+repository_type: modules
+nf_core_version: "4.0.2"
+container-registry:
+  - community.wave.seqera.io/library/
+```
+
+## Schema
+
+### Top-level `.nf-core.yml` schema (`NFCoreYamlConfig`)
+
+```{eval-rst}
+.. autopydantic_model:: nf_core.utils.NFCoreYamlConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :model-show-json: false
+    :model-show-config-summary: false
+    :model-show-validator-members: false
+    :model-show-field-summary: true
+    :field-show-alias: true
+```
+
+### `lint` block (`NFCoreYamlLintConfig`)
+
+```{eval-rst}
+.. autopydantic_model:: nf_core.utils.NFCoreYamlLintConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :model-show-json: false
+    :model-show-config-summary: false
+    :model-show-validator-members: false
+    :model-show-field-summary: true
+    :field-show-alias: true
+```
+
+### `template` block (`NFCoreTemplateConfig`)
+
+```{eval-rst}
+.. autopydantic_model:: nf_core.utils.NFCoreTemplateConfig
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :model-show-json: false
+    :model-show-config-summary: false
+    :model-show-validator-members: false
+    :model-show-field-summary: true
+    :field-show-alias: true
+    :no-index:
+```
diff --git a/docs/api/_src/api/pipelines/lint.md b/docs/api/_src/api/pipelines/lint.md
index 91b37c26f6..9fdfba0812 100644
--- a/docs/api/_src/api/pipelines/lint.md
+++ b/docs/api/_src/api/pipelines/lint.md
@@ -12,7 +12,7 @@ See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests)
 ```
 
 ```{eval-rst}
-.. autoclass:: nf_core.lint.PipelineLint
+.. autoclass:: nf_core.pipelines.lint.PipelineLint
     :members: _lint_pipeline
     :private-members: _print_results, _get_results_md, _save_json_results, _wrap_quotes
     :show-inheritance:
diff --git a/docs/api/_src/api/pipelines/utils.md b/docs/api/_src/api/pipelines/lint_utils.md
similarity index 73%
rename from docs/api/_src/api/pipelines/utils.md
rename to docs/api/_src/api/pipelines/lint_utils.md
index 36c2ecca4d..f74c103ad3 100644
--- a/docs/api/_src/api/pipelines/utils.md
+++ b/docs/api/_src/api/pipelines/lint_utils.md
@@ -1,7 +1,7 @@
 # nf_core.pipelines.utils
 
 ```{eval-rst}
-.. automodule:: nf_core.pipelines.utils
+.. automodule:: nf_core.pipelines.lint_utils
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md
index e752b3b28b..8ebd988b1b 100644
--- a/docs/api/_src/index.md
+++ b/docs/api/_src/index.md
@@ -8,3 +8,4 @@ This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/t
 - [Module code lint tests](./module_lint_tests/environment_yml.md) (run by `nf-core modules lint`)
 - [Subworkflow code lint tests](./subworkflow_lint_tests/main_nf.md) (run by `nf-core subworkflows lint`)
 - [nf-core/tools Python package API reference](./api/utils.md)
+- [`.nf-core.yml` configuration reference](./api/nf_core_yml.md)
diff --git a/docs/api/check_lint_docstrings.py b/docs/api/check_lint_docstrings.py
index b9f27548f4..f7edda9f73 100644
--- a/docs/api/check_lint_docstrings.py
+++ b/docs/api/check_lint_docstrings.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 """
 Pre-commit hook: verify that every lint test name used in a result tuple is
-mentioned in the docstring of its enclosing function.
+documented as a section heading in the docstring of its enclosing function.
 
 Applies to nf-core component lint files where results are accumulated as:
 
@@ -9,6 +9,14 @@
     component.warned.append(("category", "test_name", "message", path))
     component.failed.append(("category", "test_name", "message", path))
 
+The heading requirement (rather than a plain substring match) exists because
+the linter links each result to ``.../<parent_lint_test>#<test_name>``. That
+anchor only resolves on the docs site if ``test_name`` is rendered as a
+heading, i.e. the docstring must contain an RST section of the form::
+
+    test_name
+    ^^^^^^^^^
+
 Usage (called by pre-commit with the changed files as arguments):
 
     python scripts/check_lint_docstrings.py nf_core/modules/lint/module_tests.py ...
@@ -18,6 +26,33 @@
 import sys
 from pathlib import Path
 
+# Punctuation characters reStructuredText accepts as section-title adornments.
+_RST_ADORNMENTS = set("=-`:.'\"~^_*+#<>!$%&(),/;?@[\\]{|}")
+
+
+def collect_doc_headings(docstring: str) -> set[str]:
+    """Return the set of RST section-heading titles found in a docstring.
+
+    A heading is a non-empty title line immediately followed by an underline
+    line built from a single, repeated adornment character that is at least as
+    long as the title (matching reStructuredText section syntax). ``docstring``
+    is assumed to be dedented (as returned by ``ast.get_docstring``).
+    """
+    headings: set[str] = set()
+    lines = docstring.splitlines()
+    for title_line, underline_line in zip(lines, lines[1:], strict=False):
+        title = title_line.strip()
+        underline = underline_line.strip()
+        if (
+            title
+            and underline
+            and len(underline) >= len(title)
+            and len(set(underline)) == 1
+            and underline[0] in _RST_ADORNMENTS
+        ):
+            headings.add(title)
+    return headings
+
 
 def collect_test_names(func_node: ast.FunctionDef | ast.AsyncFunctionDef) -> dict[str, list[int]]:
     """Return {test_name: [line_numbers]} for all result-tuple appends in the function."""
@@ -66,11 +101,14 @@ def check_file(path: Path) -> list[str]:
         if node.name != module_stem:
             continue
         docstring = ast.get_docstring(node) or ""
+        headings = collect_doc_headings(docstring)
         test_names = collect_test_names(node)
         for test_name, lines in sorted(test_names.items()):
-            if test_name not in docstring:
+            if test_name not in headings:
                 errors.append(
-                    f"{path}:{lines[0]}: '{test_name}' used in {node.name}() but not documented in its docstring"
+                    f"{path}:{lines[0]}: '{test_name}' is emitted by {node.name}() but is not "
+                    f"documented as a section heading in its docstring (required for the docs "
+                    f"anchor #{test_name})"
                 )
         break  # only one function per file can match the stem
     return errors
diff --git a/nf_core/.pre-commit-prettier-config.yaml b/nf_core/.pre-commit-prettier-config.yaml
index d7235f440d..5178d5a205 100644
--- a/nf_core/.pre-commit-prettier-config.yaml
+++ b/nf_core/.pre-commit-prettier-config.yaml
@@ -4,4 +4,4 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.8.3
+          - prettier@3.9.6
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index f115bf2bfa..bdf60b8cda 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -6,92 +6,55 @@
 import sys
 from pathlib import Path
 
-import requests
-import rich.console
-import rich.logging
-import rich.traceback
 import rich_click as click
 import rich_click.rich_click as rc
-from trogon import tui
 
 from nf_core import __version__
-from nf_core.commands_modules import (
-    modules_bump_versions,
-    modules_create,
-    modules_info,
-    modules_install,
-    modules_lint,
-    modules_list_local,
-    modules_list_remote,
-    modules_patch,
-    modules_remove,
-    modules_test,
-    modules_update,
-)
-from nf_core.commands_pipelines import (
-    pipelines_bump_version,
-    pipelines_create,
-    pipelines_create_logo,
-    pipelines_create_params_file,
-    pipelines_download,
-    pipelines_launch,
-    pipelines_lint,
-    pipelines_list,
-    pipelines_rocrate,
-    pipelines_schema_build,
-    pipelines_schema_docs,
-    pipelines_schema_lint,
-    pipelines_schema_validate,
-    pipelines_sync,
-)
-from nf_core.commands_subworkflows import (
-    subworkflows_create,
-    subworkflows_info,
-    subworkflows_install,
-    subworkflows_lint,
-    subworkflows_list_local,
-    subworkflows_list_remote,
-    subworkflows_remove,
-    subworkflows_test,
-    subworkflows_update,
-)
-from nf_core.commands_test_datasets import test_datasets_list_branches, test_datasets_list_remote, test_datasets_search
-from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows
 from nf_core.components.constants import NF_CORE_MODULES_REMOTE
-from nf_core.pipelines.download.download import DownloadError
-from nf_core.pipelines.list import autocomplete_pipelines
-from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
+from nf_core.utils import check_if_outdated, nfcore_logo, stderr
+
+
+def autocomplete_pipelines(ctx, param, incomplete):
+    from nf_core.pipelines.list import autocomplete_pipelines as complete
+
+    return complete(ctx, param, incomplete)
+
+
+def autocomplete_modules(ctx, param, incomplete):
+    from nf_core.components.components_completion import autocomplete_modules as complete
+
+    return complete(ctx, param, incomplete)
+
+
+def autocomplete_subworkflows(ctx, param, incomplete):
+    from nf_core.components.components_completion import autocomplete_subworkflows as complete
+
+    return complete(ctx, param, incomplete)
+
 
 # Set up logging as the root logger
 # Submodules should all traverse back to this
 log = logging.getLogger()
 
-# Set up .nfcore directory for storing files between sessions
-setup_nfcore_dir()
-
 # Set up nicer formatting of click cli help messages
 rc.MAX_WIDTH = 100
 rc.USE_RICH_MARKUP = True
 rc.COMMANDS_BEFORE_OPTIONS = True
 
 
-# Set up rich stderr console
-stderr = rich.console.Console(stderr=True, force_terminal=rich_force_colors())
-stdout = rich.console.Console(force_terminal=rich_force_colors())
-
-# Set up the rich traceback
-rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1)
-
-
 # Define exceptions for which no traceback should be printed,
 # because they are actually preliminary, but intended program terminations.
 # (Custom exceptions are cleaner than `sys.exit(1)`, which we used before)
 def selective_traceback_hook(exctype, value, traceback):
+    from nf_core.pipelines.download.download import DownloadError
+
     if exctype in {DownloadError, UserWarning, ValueError}:  # extend set as needed
         log.error(value)
     else:
+        from rich.traceback import Traceback
+
         # print the colored traceback for all other exceptions with rich as usual
-        stderr.print(rich.traceback.Traceback.from_exception(exctype, value, traceback))
+        stderr.print(Traceback.from_exception(exctype, value, traceback, width=200, extra_lines=1))
 
 
 sys.excepthook = selective_traceback_hook
@@ -116,21 +79,17 @@ def run_nf_core():
             f"\n[grey39]    nf-core/tools version {__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
             highlight=False,
         )
-        try:
-            is_outdated, _, remote_vers = check_if_outdated()
-            if is_outdated:
-                stderr.print(
-                    f"[bold bright_yellow]    There is a new version of nf-core/tools available! ({remote_vers})",
-                    highlight=False,
-                )
-        except requests.exceptions.RequestException as e:
-            log.debug(f"Could not check latest version: {e}")
+        is_outdated, _, remote_vers = check_if_outdated()
+        if is_outdated:
+            stderr.print(
+                f"[bold bright_yellow]    There is a new version of nf-core/tools available! ({remote_vers})",
+                highlight=False,
+            )
         stderr.print("\n")
     # Launch the click cli
     nf_core_cli(auto_envvar_prefix="NFCORE")
 
 
-@tui(command="interface", help="Launch the nf-core interface")
 @click.group(context_settings={"help_option_names": ["-h", "--help"]})
 @click.version_option(__version__)
 @click.option(
@@ -158,11 +117,16 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
     # Set the base logger to output DEBUG
     log.setLevel(logging.DEBUG)
 
-    # Set up logs to the console
+    # Set up logs to the console - use the shared console so log output
+    # coordinates with progress spinners (avoids output on the same line)
+    from rich.logging import RichHandler
+
+    from nf_core.utils import stdout as shared_console
+
     log.addHandler(
-        rich.logging.RichHandler(
+        RichHandler(
             level=logging.DEBUG if verbose else logging.INFO,
-            console=rich.console.Console(stderr=True, force_terminal=rich_force_colors()),
+            console=shared_console,
             show_time=False,
             show_path=verbose,  # True if verbose, false otherwise
             markup=True,
@@ -190,6 +154,15 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
     }
 
 
+# nf-core interface (registered by hand so trogon is only imported when run)
+@nf_core_cli.command("interface", help="Launch the nf-core interface")
+@click.pass_context
+def interface(ctx):
+    from trogon import Trogon
+
+    Trogon(nf_core_cli, app_name=None, command_name="interface", click_context=ctx).run()
+
+
 # nf-core pipelines subcommands
 @nf_core_cli.group(aliases=["p", "pipeline"])
 @click.command_panel("For users", commands=["download", "create-params-file", "launch", "list"])
@@ -231,6 +204,8 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
     """
     Create a new pipeline using the nf-core template.
     """
+    from nf_core.commands_pipelines import pipelines_create
+
     pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
 
 
@@ -314,6 +289,8 @@ def command_pipelines_lint(
     """
     Check pipeline code against nf-core guidelines.
     """
+    from nf_core.commands_pipelines import pipelines_lint
+
     pipelines_lint(
         ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by, plain_text
     )
@@ -365,7 +342,7 @@ def command_pipelines_lint(
 @click.option(
     "-s",
     "--container-system",
-    type=click.Choice(["none", "singularity", "docker"]),
+    type=click.Choice(["none", "singularity", "docker", "apptainer"]),
     help="Download container images of required software.",
 )
 @click.option(
@@ -413,6 +390,8 @@ def command_pipelines_download(
     """
     Download a pipeline, nf-core/configs and pipeline singularity images.
     """
+    from nf_core.commands_pipelines import pipelines_download
+
     pipelines_download(
         ctx,
         pipeline,
@@ -462,6 +441,8 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force,
     """
     Build a parameter file for a pipeline.
     """
+    from nf_core.commands_pipelines import pipelines_create_params_file
+
     pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden, no_prompts)
 
 
@@ -485,7 +466,7 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force,
 @click.option(
     "-o",
     "--params-out",
-    type=click.Path(),
+    type=click.Path(path_type=Path),
     default=str(Path.cwd() / "nf-params.json"),
     help="Path to save run parameters file",
 )
@@ -534,6 +515,8 @@ def command_pipelines_launch(
     """
     Launch a pipeline using a web GUI or command line prompts.
     """
+    from nf_core.commands_pipelines import pipelines_launch
+
     pipelines_launch(
         ctx, pipeline, launch_id, revision, command_only, params_in, params_out, save_all, show_hidden, url, no_prompts
     )
@@ -556,6 +539,8 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
     """
     List available nf-core pipelines with local info.
     """
+    from nf_core.commands_pipelines import pipelines_list
+
     pipelines_list(ctx, keywords, sort, json, show_archived)
 
 
@@ -594,6 +579,8 @@ def rocrate(
     """
     Make an Research Object Crate
     """
+    from nf_core.commands_pipelines import pipelines_rocrate
+
     pipelines_rocrate(ctx, pipeline_dir, json_path, zip_path, pipeline_version)
 
 
@@ -630,7 +617,7 @@ def rocrate(
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-@click.option("-b", "--blog-post", type=str, help="Link to the blog post")
+@click.option("--blog-post", type=str, help="Link to the blog post")
 @click.option("-n", "--no-prompts", is_flag=True, default=False, help="Run without prompting for user input")
 def command_pipelines_sync(
     ctx,
@@ -647,6 +634,8 @@ def command_pipelines_sync(
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
     """
+    from nf_core.commands_pipelines import pipelines_sync
+
     pipelines_sync(
         ctx,
         directory,
@@ -684,6 +673,8 @@ def command_pipelines_bump_version(ctx, new_version, directory, nextflow):
     """
     Update nf-core pipeline version number with `nf-core pipelines bump-version`.
     """
+    from nf_core.commands_pipelines import pipelines_bump_version
+
     pipelines_bump_version(ctx, new_version, directory, nextflow)
 
 
@@ -730,6 +721,8 @@ def command_pipelines_create_logo(logo_text, directory, name, theme, width, img_
     """
     Generate a logo with the nf-core logo template.
     """
+    from nf_core.commands_pipelines import pipelines_create_logo
+
     pipelines_create_logo(logo_text, directory, name, theme, width, img_format, force)
 
 
@@ -770,6 +763,8 @@ def command_pipelines_schema_validate(directory, pipeline, params):
         # this is a local pipeline
         pipeline = Path(directory, pipeline)
 
+    from nf_core.commands_pipelines import pipelines_schema_validate
+
     pipelines_schema_validate(pipeline, params)
 
 
@@ -803,6 +798,8 @@ def command_pipelines_schema_build(directory, no_prompts, web_only, url):
     """
     Interactively build a pipeline schema from Nextflow params.
     """
+    from nf_core.commands_pipelines import pipelines_schema_build
+
     pipelines_schema_build(directory, no_prompts, web_only, url)
 
 
@@ -826,6 +823,8 @@ def command_pipelines_schema_lint(directory, schema_file):
     """
     Check that a given pipeline schema is valid.
     """
+    from nf_core.commands_pipelines import pipelines_schema_lint
+
     pipelines_schema_lint(Path(directory, schema_file))
 
 
@@ -874,6 +873,8 @@ def command_pipelines_schema_docs(directory, schema_file, output, output_format,
     """
     Outputs parameter documentation for a pipeline schema.
     """
+    from nf_core.commands_pipelines import pipelines_schema_docs
+
     pipelines_schema_docs(Path(directory, schema_file), output, output_format, force, columns)
 
 
@@ -901,7 +902,7 @@ def command_pipelines_schema_docs(directory, schema_file, output, output_format,
     help="Do not pull in latest changes to local clone of modules repository.",
 )
 @click.command_panel("For pipeline development", commands=["list", "info", "install", "update", "remove", "patch"])
-@click.command_panel("For module development", commands=["create", "lint", "test", "bump-versions"])
+@click.command_panel("For module development", commands=["create", "lint", "test", "bump-versions", "containers"])
 @click.pass_context
 def modules(ctx, git_remote, branch, no_pull):
     """
@@ -936,6 +937,8 @@ def command_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[/])[/].
     """
+    from nf_core.commands_modules import modules_list_remote
+
     modules_list_remote(ctx, keywords, json)
 
 
@@ -956,6 +959,8 @@ def command_modules_list_local(ctx, keywords, json, directory):  # pylint: disab
     """
     List modules installed locally in a pipeline
     """
+    from nf_core.commands_modules import modules_list_local
+
     modules_list_local(ctx, keywords, json, directory)
 
 
@@ -997,6 +1002,8 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha):
     """
     Install DSL2 modules within a pipeline.
     """
+    from nf_core.commands_modules import modules_install
+
     modules_install(ctx, tool, directory, prompt, force, sha)
 
 
@@ -1065,6 +1072,12 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
+@click.option(
+    "--skip-deps",
+    is_flag=True,
+    default=False,
+    help="Skip the cascade to linked components. Conflicts with --update-deps and --all.",
+)
 def command_modules_update(
     ctx,
     tool,
@@ -1077,11 +1090,16 @@ def command_modules_update(
     save_diff,
     update_deps,
     limit_output,
+    skip_deps,
 ):
     """
     Update DSL2 modules within a pipeline.
     """
-    modules_update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output)
+    from nf_core.commands_modules import modules_update
+
+    modules_update(
+        ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output, skip_deps
+    )
 
 
 # nf-core modules patch
@@ -1108,6 +1126,8 @@ def command_modules_patch(ctx, tool, directory, remove):
     """
     Create a patch file for minor changes in a module
     """
+    from nf_core.commands_modules import modules_patch
+
     modules_patch(ctx, tool, directory, remove)
 
 
@@ -1141,6 +1161,8 @@ def command_modules_remove(ctx, directory, tool, force):
     """
     Remove a module from a pipeline.
     """
+    from nf_core.commands_modules import modules_remove
+
     modules_remove(ctx, directory, tool, force)
 
 
@@ -1221,6 +1243,8 @@ def command_modules_create(
     """
     Create a new DSL2 module from the nf-core template.
     """
+    from nf_core.commands_modules import modules_create
+
     modules_create(
         ctx,
         tool,
@@ -1285,10 +1309,12 @@ def command_modules_create(
 )
 def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, verbose):
     """
-    Run nf-test for a module.
+    Run nf-test for a module. Only works on module repositories, not pipeline repositories.
     """
     if verbose:
         ctx.obj["verbose"] = verbose
+    from nf_core.commands_modules import modules_test
+
     modules_test(ctx, tool, directory, no_prompts, update, once, profile)
 
 
@@ -1316,8 +1342,8 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
     "--registry",
     type=str,
     metavar="<registry>",
-    default=None,
-    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
+    default="quay.io,community.wave.seqera.io/library",
+    help="Comma-separated list of allowed container registry prefixes.",
 )
 @click.option(
     "-k",
@@ -1356,11 +1382,13 @@ def command_modules_lint(
     """
     Lint one or more modules in a directory.
     """
+    from nf_core.commands_modules import modules_lint
+
     modules_lint(
         ctx,
         tool,
         directory,
-        registry,
+        tuple(registry.split(",")),
         key,
         all_modules,
         fail_warned,
@@ -1396,6 +1424,8 @@ def command_modules_info(ctx, tool, directory):
     """
     Show developer usage information about a given module.
     """
+    from nf_core.commands_modules import modules_info
+
     modules_info(ctx, tool, directory)
 
 
@@ -1426,9 +1456,111 @@ def command_modules_bump_versions(ctx, tool, directory, all_modules, show_all, d
     Bump versions for one or more modules in a clone of
     the nf-core/modules repo.
     """
+    from nf_core.commands_modules import modules_bump_versions
+
     modules_bump_versions(ctx, tool, directory, all_modules, show_all, dry_run)
 
 
+@modules.group("containers", aliases=["container", "con"])
+@click.pass_context
+def modules_containers(ctx):
+    """Manage module container builds and metadata [yellow](beta)[/]."""
+    from rich.panel import Panel
+
+    stderr.print(
+        Panel(
+            "The [bold]nf-core modules containers[/] commands are still in beta.\n"
+            "Their behaviour and output may change in future releases.\n"
+            "Best to always use the latest dev version.",
+            title="[bold][!] Beta feature",
+            title_align="left",
+            style="yellow",
+        )
+    )
+
+
+# nf-core modules containers create
+@modules_containers.command("create", aliases=["c"])
+@click.pass_context
+@click.argument(
+    "module",
+    type=str,
+    required=False,
+    callback=normalize_case,
+    metavar="<module> or <module/submodule>",
+    shell_complete=autocomplete_modules,
+)
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True, path_type=Path),
+    default=".",
+    metavar="<nf-core/modules directory>",
+)
+@click.option(
+    "-f",
+    "--force",
+    "force",
+    is_flag=True,
+    default=False,
+    help="Force container creation even if the container already exists.",
+)
+def command_modules_containers_create(ctx, module: str, directory: Path, force: bool) -> None:
+    """
+    Build docker and singularity container files for linux/arm64 and linux/amd64 with wave from environment.yml and create container config file.
+    """
+    from nf_core.commands_modules import modules_containers_create
+
+    modules_containers_create(ctx, module, directory, force)
+
+
+@modules_containers.command("conda-lock")
+@click.pass_context
+@click.argument(
+    "module",
+    type=str,
+    required=False,
+    callback=normalize_case,
+    metavar="<module> or <module/submodule>",
+    shell_complete=autocomplete_modules,
+)
+def command_modules_containers_conda_lock(ctx, module: str) -> None:
+    """
+    Build a Docker linux/arm64 container and fetch the conda lock file for a module.
+    """
+    from nf_core.commands_modules import modules_containers_conda_lock
+
+    modules_containers_conda_lock(ctx, module)
+
+
+# nf-core modules containers list
+@modules_containers.command("list", aliases=["ls"])
+@click.pass_context
+@click.argument(
+    "module",
+    type=str,
+    required=False,
+    callback=normalize_case,
+    metavar="<module> or <module/submodule>",
+    shell_complete=autocomplete_modules,
+)
+@click.option(
+    "-p",
+    "--plain-text",
+    is_flag=True,
+    default=False,
+    help="Output in plain text format",
+)
+def command_modules_containers_list(ctx, module, plain_text):
+    """
+    Print containers defined in a module meta.yml.
+    """
+    from nf_core.commands_modules import modules_containers_list
+
+    modules_containers_list(ctx, module, plain_text)
+
+
 # nf-core subworkflows click command
 @nf_core_cli.group(aliases=["s", "swf", "subworkflow"])
 @click.option(
@@ -1492,6 +1624,8 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force):
     """
     Create a new subworkflow from the nf-core template.
     """
+    from nf_core.commands_subworkflows import subworkflows_create
+
     subworkflows_create(ctx, subworkflow, directory, author, force)
 
 
@@ -1539,6 +1673,8 @@ def command_subworkflows_test(ctx, subworkflow, directory, no_prompts, update, o
     """
     Run nf-test for a subworkflow.
     """
+    from nf_core.commands_subworkflows import subworkflows_test
+
     subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile)
 
 
@@ -1561,6 +1697,8 @@ def command_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[/])[/].
     """
+    from nf_core.commands_subworkflows import subworkflows_list_remote
+
     subworkflows_list_remote(ctx, keywords, json)
 
 
@@ -1581,6 +1719,8 @@ def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint:
     """
     List subworkflows installed locally in a pipeline
     """
+    from nf_core.commands_subworkflows import subworkflows_list_local
+
     subworkflows_list_local(ctx, keywords, json, directory)
 
 
@@ -1608,8 +1748,8 @@ def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint:
     "--registry",
     type=str,
     metavar="<registry>",
-    default=None,
-    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
+    default="quay.io,community.wave.seqera.io/library",
+    help="Comma-separated list of allowed container registry prefixes.",
 )
 @click.option(
     "-k",
@@ -1643,11 +1783,13 @@ def command_subworkflows_lint(
     """
     Lint one or more subworkflows in a directory.
     """
+    from nf_core.commands_subworkflows import subworkflows_lint
+
     subworkflows_lint(
         ctx,
         subworkflow,
         directory,
-        registry,
+        tuple(registry.split(",")),
         key,
         all_subworkflows,
         fail_warned,
@@ -1682,6 +1824,8 @@ def command_subworkflows_info(ctx, subworkflow, directory):
     """
     Show developer usage information about a given subworkflow.
     """
+    from nf_core.commands_subworkflows import subworkflows_info
+
     subworkflows_info(ctx, subworkflow, directory)
 
 
@@ -1725,11 +1869,19 @@ def command_subworkflows_info(ctx, subworkflow, directory):
     metavar="<commit sha>",
     help="Install subworkflow at commit SHA",
 )
-def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha):
+@click.option(
+    "--skip-deps",
+    is_flag=True,
+    default=False,
+    help="With --force, refresh only the named subworkflow; leave transitive deps' files and SHAs pinned.",
+)
+def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha, skip_deps):
     """
     Install DSL2 subworkflow within a pipeline.
     """
-    subworkflows_install(ctx, subworkflow, directory, prompt, force, sha)
+    from nf_core.commands_subworkflows import subworkflows_install
+
+    subworkflows_install(ctx, subworkflow, directory, prompt, force, sha, skip_deps)
 
 
 # nf-core subworkflows patch
@@ -1807,6 +1959,8 @@ def command_subworkflows_remove(ctx, directory, subworkflow, force):
     """
     Remove a subworkflow from a pipeline.
     """
+    from nf_core.commands_subworkflows import subworkflows_remove
+
     subworkflows_remove(ctx, directory, subworkflow, force)
 
 
@@ -1882,6 +2036,12 @@ def command_subworkflows_remove(ctx, directory, subworkflow, force):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
+@click.option(
+    "--skip-deps",
+    is_flag=True,
+    default=False,
+    help="Skip the cascade to linked components. Conflicts with --update-deps and --all.",
+)
 def command_subworkflows_update(
     ctx,
     subworkflow,
@@ -1894,12 +2054,26 @@ def command_subworkflows_update(
     save_diff,
     update_deps,
     limit_output,
+    skip_deps,
 ):
     """
     Update DSL2 subworkflow within a pipeline.
     """
+    from nf_core.commands_subworkflows import subworkflows_update
+
     subworkflows_update(
-        ctx, subworkflow, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output
+        ctx,
+        subworkflow,
+        directory,
+        force,
+        prompt,
+        sha,
+        install_all,
+        preview,
+        save_diff,
+        update_deps,
+        limit_output,
+        skip_deps,
     )
 
 
@@ -1939,6 +2113,8 @@ def command_test_dataset_search(ctx, branch, generate_nf_path, generate_dl_url,
     Search files filtered by QUERY on a specified branch in the nf-core/test-datasets repository.
     If no QUERY is given or QUERY is ambiguous, an auto-completion form is shown.
     """
+    from nf_core.commands_test_datasets import test_datasets_search
+
     test_datasets_search(ctx, branch, generate_nf_path, generate_dl_url, query)
 
 
@@ -1964,6 +2140,8 @@ def command_test_dataset_list_remote(ctx, branch, generate_nf_path, generate_dl_
     """
     List files on a specified branch in the nf-core/test-datasets repository.
     """
+    from nf_core.commands_test_datasets import test_datasets_list_remote
+
     test_datasets_list_remote(ctx, branch, generate_nf_path, generate_dl_url)
 
 
@@ -1974,6 +2152,8 @@ def command_test_datasets_list_branches(ctx):
     """
     List remote branches with test data in the nf-core/test-dataset repository.
     """
+    from nf_core.commands_test_datasets import test_datasets_list_branches
+
     test_datasets_list_branches(ctx)
 
 
diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index 7f5b991745..21c5791c73 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -1,9 +1,10 @@
 import logging
 import sys
+from pathlib import Path
 
 import rich
 
-from nf_core.utils import rich_force_colors
+from nf_core.utils import CONTAINER_PLATFORMS, rich_force_colors
 
 log = logging.getLogger(__name__)
 stdout = rich.console.Console(force_terminal=rich_force_colors())
@@ -87,6 +88,7 @@ def modules_update(
     save_diff,
     update_deps,
     limit_output,
+    skip_deps,
 ):
     """
     Update DSL2 modules within a pipeline.
@@ -109,6 +111,7 @@ def modules_update(
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
             limit_output,
+            skip_deps,
         )
         exit_status = module_install.update(tool)
         if not exit_status and install_all:
@@ -254,7 +257,7 @@ def modules_lint(
             directory,
             fail_warned=fail_warned,
             fix=fix,
-            registry=ctx.params["registry"],
+            registry=registry,
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
             no_pull=ctx.obj["modules_repo_no_pull"],
@@ -262,7 +265,6 @@ def modules_lint(
         )
         module_lint.lint(
             module=tool,
-            registry=registry,
             key=key,
             all_modules=all_modules,
             print_results=True,
@@ -325,10 +327,91 @@ def modules_bump_versions(ctx, tool, directory, all_modules, show_all, dry_run):
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
         )
-        version_bumper.bump_versions(module=tool, all_modules=all_modules, show_up_to_date=show_all, dry_run=dry_run)
+        version_bumper.bump_versions(
+            module=tool,
+            all_modules=all_modules,
+            show_up_to_date=show_all,
+            dry_run=dry_run,
+            hide_progress=ctx.obj["hide_progress"],
+        )
     except ModuleExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
         log.critical(e)
         sys.exit(1)
+
+
+def modules_containers_create(ctx, module: str, directory: Path, force: bool) -> None:
+    """
+    Build docker and singularity containers for linux/arm64 and linux/amd64 using wave.
+    """
+    from nf_core.modules.containers import ModuleContainers
+
+    try:
+        module_containers = ModuleContainers(module=module, directory=directory, verbose=ctx.obj["verbose"])
+        ModuleContainers.check_tower_token()
+
+        if module_containers.all_modules:
+            if not module_containers.available_modules:
+                log.error("No modules found to build containers for")
+                sys.exit(1)
+            log.info(f"Building containers for {len(module_containers.available_modules)} module(s)")
+
+        failed_modules = module_containers.build_containers_with_progress(
+            force=force, hide_progress=ctx.obj["hide_progress"]
+        )
+
+        if failed_modules:
+            if module_containers.all_modules:
+                log.warning(
+                    f"Failed to build containers for {len(failed_modules)} module(s): {', '.join(failed_modules)}"
+                )
+            else:
+                log.error(f"✗ Some container builds failed for {module_containers.module}")
+                sys.exit(1)
+        elif module_containers.all_modules:
+            log.info("Successfully built containers for all modules")
+
+    except (UserWarning, LookupError, FileNotFoundError, ValueError, RuntimeError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
+def modules_containers_conda_lock(ctx, module, platform=CONTAINER_PLATFORMS[0]):
+    """
+    Build a Docker linux/arm64 container and fetch the conda lock file using wave.
+    """
+    from nf_core.modules.containers import ModuleContainers
+
+    try:
+        module_containers = ModuleContainers(module, ".", verbose=ctx.obj["verbose"])
+        lock_file = module_containers.get_conda_lock_file(platform)
+        stdout.print(lock_file)
+    except (UserWarning, LookupError, FileNotFoundError, ValueError, RuntimeError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
+def modules_containers_list(ctx, module, plain_text=False):
+    """
+    Print containers defined in a module meta.yml.
+    """
+    from nf_core.modules.containers import ModuleContainers
+
+    try:
+        module_containers = ModuleContainers(module, ".", verbose=ctx.obj["verbose"])
+        containers = module_containers.list_containers()
+
+        if plain_text:
+            for cs, p, img in containers:
+                stdout.print(f"{cs} {p} {img}")
+        else:
+            t = rich.table.Table("Container System", "Platform")
+            t.add_column("Image", overflow="fold")
+            for cs, p, img in containers:
+                t.add_row(cs, p, img)
+            stdout.print(t)
+    except (UserWarning, LookupError, FileNotFoundError, ValueError) as e:
+        log.error(e)
+        sys.exit(1)
diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
index 273097c474..1384540f6d 100644
--- a/nf_core/commands_pipelines.py
+++ b/nf_core/commands_pipelines.py
@@ -5,7 +5,6 @@
 import rich
 
 import nf_core.utils
-from nf_core.pipelines.params_file import ParamsFileBuilder
 from nf_core.utils import rich_force_colors
 
 log = logging.getLogger(__name__)
@@ -95,7 +94,7 @@ def pipelines_bump_version(ctx, new_version, directory, nextflow):
             bump_pipeline_version(pipeline_obj, new_version)
         else:
             bump_nextflow_version(pipeline_obj, new_version)
-    except UserWarning as e:
+    except (UserWarning, ValueError) as e:
         log.error(e)
         sys.exit(1)
 
@@ -120,7 +119,7 @@ def pipelines_lint(
 
     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/docs/nf-core-tools/api_reference/latest/]https://nf-co.re/docs/nf-core-tools/api_reference/latest/[/]
 
     You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/].
     See the documentation for details.
@@ -162,8 +161,10 @@ def pipelines_lint(
     except AssertionError as e:
         log.critical(e)
         sys.exit(1)
-    except UserWarning as e:
-        log.error(e)
+    except (UserWarning, RuntimeError) as e:
+        from rich.text import Text
+
+        log.error(Text.from_ansi(str(e)))
         sys.exit(1)
 
 
@@ -224,6 +225,8 @@ def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hi
     Run using a remote pipeline name (such as GitHub `user/repo` or a URL),
     a local pipeline directory.
     """
+    from nf_core.pipelines.params_file import ParamsFileBuilder
+
     builder = ParamsFileBuilder(pipeline, revision, no_prompts)
 
     if not builder.write_params_file(Path(output), show_hidden=show_hidden, force=force):
@@ -359,7 +362,7 @@ def pipelines_sync(
             no_prompts,
         )
         sync_obj.sync()
-    except (SyncExceptionError, PullRequestExceptionError) as e:
+    except (UserWarning, SyncExceptionError, PullRequestExceptionError) as e:
         log.error(e)
         sys.exit(1)
 
diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index 193e976401..f87fc9b5c2 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -122,7 +122,7 @@ def subworkflows_lint(
             directory,
             fail_warned=fail_warned,
             fix=fix,
-            registry=ctx.params["registry"],
+            registry=registry,
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
             no_pull=ctx.obj["modules_repo_no_pull"],
@@ -130,7 +130,6 @@ def subworkflows_lint(
         )
         subworkflow_lint.lint(
             subworkflow=subworkflow,
-            registry=registry,
             key=key,
             all_subworkflows=all_subworkflows,
             print_results=True,
@@ -177,7 +176,7 @@ def subworkflows_info(ctx, subworkflow, directory):
         sys.exit(1)
 
 
-def subworkflows_install(ctx, subworkflow, directory, prompt, force, sha):
+def subworkflows_install(ctx, subworkflow, directory, prompt, force, sha, skip_deps=False):
     """
     Install DSL2 subworkflow within a pipeline.
 
@@ -194,6 +193,7 @@ def subworkflows_install(ctx, subworkflow, directory, prompt, force, sha):
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
+            skip_deps=skip_deps,
         )
         exit_status = subworkflow_install.install(subworkflow)
         if not exit_status:
@@ -234,6 +234,7 @@ def subworkflows_update(
     save_diff,
     update_deps,
     limit_output,
+    skip_deps,
 ):
     """
     Update DSL2 subworkflow within a pipeline.
@@ -256,6 +257,7 @@ def subworkflows_update(
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
             limit_output,
+            skip_deps,
         )
         exit_status = subworkflow_install.update(subworkflow)
         if not exit_status and install_all:
diff --git a/nf_core/commands_test_datasets.py b/nf_core/commands_test_datasets.py
index b9a2688cd3..a6b94ae7d1 100644
--- a/nf_core/commands_test_datasets.py
+++ b/nf_core/commands_test_datasets.py
@@ -3,8 +3,6 @@
 import click
 import rich
 
-from nf_core.test_datasets.list import list_dataset_branches, list_datasets
-from nf_core.test_datasets.search import search_datasets
 from nf_core.utils import rich_force_colors
 
 log = logging.getLogger(__name__)
@@ -17,6 +15,8 @@ def test_datasets_list_branches(ctx: click.Context) -> None:
     Only lists test data and module test data based on the curated list
     of pipeline names [on the website](https://raw.githubusercontent.com/nf-core/website/refs/heads/main/public/pipeline_names.json).
     """
+    from nf_core.test_datasets.list import list_dataset_branches
+
     list_dataset_branches()
 
 
@@ -25,6 +25,8 @@ def test_datasets_list_remote(ctx: click.Context, branch: str, generate_nf_path:
     List all files on a given branch in the remote nf-core/testdatasets repository on github.
     The resulting files can be parsed as a nextflow path or a url for downloading.
     """
+    from nf_core.test_datasets.list import list_datasets
+
     list_datasets(branch, generate_nf_path, generate_dl_url)
 
 
@@ -37,4 +39,6 @@ def test_datasets_search(
     Specifying a branch is required.
     The resulting file can optionally be parsed as a nextflow path or a url for downloading
     """
+    from nf_core.test_datasets.search import search_datasets
+
     search_datasets(branch, generate_nf_path=generate_nf_path, generate_dl_url=generate_dl_url, query=query)
diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py
index 2e01c245d3..7fffbf8e44 100644
--- a/nf_core/components/components_command.py
+++ b/nf_core/components/components_command.py
@@ -7,6 +7,7 @@
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
+from nf_core.modules.modules_utils import scan_modules_dir
 
 from .components_utils import get_repo_info
 
@@ -74,12 +75,7 @@ def get_local_components(self) -> list[str]:
         Get the local modules/subworkflows in a pipeline
         """
         local_component_dir = Path(self.directory, self.component_type, "local")
-        # TODO: Return list of Path objects instead of strings to avoid unnecessary conversion
-        return [
-            str(Path(directory).relative_to(local_component_dir))
-            for directory, _, files in os.walk(local_component_dir)
-            if "main.nf" in files
-        ] + [
+        return scan_modules_dir(local_component_dir) + [
             str(path.relative_to(local_component_dir)) for path in local_component_dir.iterdir() if path.suffix == ".nf"
         ]
 
@@ -91,12 +87,7 @@ def get_components_clone_modules(self) -> list[str]:
             component_base_path = Path(self.directory, self.default_modules_path)
         elif self.component_type == "subworkflows":
             component_base_path = Path(self.directory, self.default_subworkflows_path)
-        # TODO: Return list of Path objects instead of strings to avoid unnecessary conversion
-        return [
-            str(Path(directory).relative_to(component_base_path))
-            for directory, _, files in os.walk(component_base_path)
-            if "main.nf" in files
-        ]
+        return scan_modules_dir(component_base_path)
 
     def has_valid_directory(self) -> bool:
         """Check that we were given a pipeline or clone of nf-core/modules"""
@@ -162,10 +153,7 @@ def components_from_repo(self, install_dir: str) -> list[str]:
         if not repo_dir.exists():
             raise LookupError(f"Nothing installed from {install_dir} in pipeline")
 
-        # TODO: Return list of Path objects instead of strings to avoid unnecessary conversion
-        return [
-            str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files
-        ]
+        return scan_modules_dir(repo_dir)
 
     def install_component_files(
         self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: str | Path
diff --git a/nf_core/components/components_completion.py b/nf_core/components/components_completion.py
index 8abecb4649..4f2179c837 100644
--- a/nf_core/components/components_completion.py
+++ b/nf_core/components/components_completion.py
@@ -1,13 +1,11 @@
 import sys
 
-import git
 from click.shell_completion import CompletionItem
 
-from nf_core.modules.list import ModuleList
-from nf_core.subworkflows.list import SubworkflowList
-
 
 def autocomplete_components(ctx, param, incomplete: str, component_type: str, list_class):
+    import git
+
     # Defaults
     modules_repo_url = "https://github.com/nf-core/modules"
     modules_repo_branch = "master"
@@ -31,8 +29,12 @@ def autocomplete_components(ctx, param, incomplete: str, component_type: str, li
 
 
 def autocomplete_modules(ctx, param, incomplete: str):
+    from nf_core.modules.list import ModuleList
+
     return autocomplete_components(ctx, param, incomplete, "modules", ModuleList)
 
 
 def autocomplete_subworkflows(ctx, param, incomplete: str):
+    from nf_core.subworkflows.list import SubworkflowList
+
     return autocomplete_components(ctx, param, incomplete, "subworkflows", SubworkflowList)
diff --git a/nf_core/components/components_differ.py b/nf_core/components/components_differ.py
index b028b55626..5024478d48 100644
--- a/nf_core/components/components_differ.py
+++ b/nf_core/components/components_differ.py
@@ -235,16 +235,16 @@ def append_modules_json_diff(diff_path, old_modules_json, new_modules_json, modu
 
     @staticmethod
     def print_diff(
-        component,
-        repo_path,
-        from_dir,
-        to_dir,
-        current_version=None,
-        new_version=None,
-        dsp_from_dir=None,
-        dsp_to_dir=None,
-        limit_output=False,
-    ):
+        component: str,
+        repo_path: str,
+        from_dir: str | Path,
+        to_dir: str | Path,
+        current_version: str | None = None,
+        new_version: str | None = None,
+        dsp_from_dir: str | Path | None = None,
+        dsp_to_dir: str | Path | None = None,
+        limit_output: bool = False,
+    ) -> None:
         """
         Prints the diffs between two component versions to the terminal
 
diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
index db33ad8b80..b4cc7bea18 100644
--- a/nf_core/components/components_utils.py
+++ b/nf_core/components/components_utils.py
@@ -19,6 +19,9 @@
 yaml = ruamel.yaml.YAML()
 yaml.preserve_quotes = True
 yaml.indent(mapping=2, sequence=2, offset=0)
+# Disable line wrapping: long plain-scalar keys (e.g. version `eval` expressions)
+# become invalid YAML if ruamel folds them onto a second line.
+yaml.width = 4096
 
 
 def get_repo_info(directory: Path, use_prompt: bool | None = True) -> tuple[Path, str | None, str]:
@@ -204,6 +207,27 @@ def get_components_to_install(
     return list(modules.values()), list(subworkflows.values())
 
 
+def read_meta_yml(meta_yml_path: Path) -> dict:
+    """
+    Read and parse a meta.yml file.
+
+    Args:
+        meta_yml_path: Path to the meta.yml file
+
+    Returns:
+        dict: Parsed YAML content
+
+    Raises:
+        FileNotFoundError: If meta.yml doesn't exist
+    """
+    if not meta_yml_path.exists():
+        raise FileNotFoundError(f"meta.yml not found at {meta_yml_path}")
+
+    with open(meta_yml_path) as f:
+        meta = yaml.load(f)
+    return meta
+
+
 def get_biotools_response(tool_name: str) -> dict | None:
     """
     Try to get bio.tools information for 'tool'
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 334278efbc..5ce3194c48 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -177,6 +177,13 @@ def create(self) -> bool:
         run_prettier_on_file(new_files)
 
         log.info("Created following files:\n  " + "\n  ".join(new_files))
+
+        if self.component_type == "modules":
+            log.info(
+                f"Build Docker & Singularity images (Seqera/Wave) and update [magenta]main.nf[/] with the container URLs:\n"
+                f"  [blue]nf-core modules containers create {self.component_name}[/]"
+            )
+
         return True
 
     def _get_bioconda_tool(self):
@@ -249,6 +256,7 @@ def _get_module_structure_components(self):
             "process_medium",
             "process_high",
             "process_long",
+            "process_low_memory",
             "process_high_memory",
         ]
         if self.process_label is None:
@@ -424,11 +432,11 @@ def _get_username(self):
         except (subprocess.CalledProcessError, FileNotFoundError) as e:
             log.debug(f"Could not find GitHub username using 'gh' cli command: [red]{e}")
 
-        # Regex to valid GitHub username: https://github.com/shinnn/github-username-regex
-        github_username_regex = re.compile(r"^@[a-zA-Z\d](?:[a-zA-Z\d]|-(?=[a-zA-Z\d])){0,38}$")
-        while self.author is None or not github_username_regex.match(self.author):
-            if self.author is not None and not github_username_regex.match(self.author):
-                log.warning("Does not look like a valid GitHub username (must start with an '@')!")
+        # Regex to validate username (GitHub, GitLab, and other git-based code hosting services)
+        username_regex = re.compile(r"^@[a-zA-Z\d](?:[a-zA-Z\d\.]|-(?=[a-zA-Z\d\.])){0,38}$")
+        while self.author is None or not username_regex.match(self.author):
+            if self.author is not None:
+                log.warning("Does not look like a valid username (must start with an '@')!")
             self.require_prompts("GitHub username not provided.\nPlease provide the `--author` option")
             self.author = rich.prompt.Prompt.ask(
                 f"[violet]GitHub Username:[/]{' (@author)' if author_default is None else ''}",
@@ -440,8 +448,9 @@ def generate_meta_yml_file(self) -> None:
         Generate the meta.yml file.
         """
         # TODO: The meta.yml could be handled with a Pydantic model. The reason it is not implemented is because we want to maintain comments in the meta.yml file.
-        with open(self.file_paths["meta.yml"]) as fh:
-            meta_yml: ruamel.yaml.comments.CommentedMap = yaml.load(fh)
+        from nf_core.components.components_utils import read_meta_yml
+
+        meta_yml: ruamel.yaml.comments.CommentedMap = read_meta_yml(self.file_paths["meta.yml"])
 
         versions: dict[str, list | dict] = {
             f"versions_{self.component}": [
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index cc30f8dec9..57f0a3858e 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -299,9 +299,12 @@ def generate_component_info_help(self):
         # Inputs
         if self.meta.get("input"):
             inputs_table = self.generate_params_table("Inputs")
+            log.debug(f"Input channels: {self.meta['input']}")
             for i, input_channel in enumerate(self.meta["input"]):
                 inputs_table.add_row(f"[italic]input[{i}][/]", "", "")
                 if self.component_type == "modules":
+                    if not isinstance(input_channel, list):
+                        input_channel = [input_channel]
                     for element in input_channel:
                         for key, info in element.items():
                             inputs_table.add_row(
diff --git a/nf_core/components/install.py b/nf_core/components/install.py
index 8350159320..fc6c790dd3 100644
--- a/nf_core/components/install.py
+++ b/nf_core/components/install.py
@@ -37,6 +37,7 @@ def __init__(
         branch: str | None = None,
         no_pull: bool = False,
         installed_by: list[str] | None = None,
+        skip_deps: bool = False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.current_remote = ModulesRepo(remote_url, branch)
@@ -45,6 +46,7 @@ def __init__(
         self.prompt = prompt
         self.sha = sha
         self.current_sha = sha
+        self.skip_deps = skip_deps
         if installed_by is not None:
             self.installed_by = installed_by
         else:
@@ -166,12 +168,23 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool
         )
 
         if self.component_type == "subworkflows":
-            # Install included modules and subworkflows
-            self.install_included_components(component_dir)
+            # Under --skip-deps, don't propagate --force to transitive deps so
+            # already-installed ones keep their pinned SHAs and just have
+            # installed_by tracking refreshed.
+            if self.skip_deps:
+                original_force = self.force
+                self.force = False
+                try:
+                    self.install_included_components(component_dir)
+                finally:
+                    self.force = original_force
+            else:
+                self.install_included_components(component_dir)
 
-        # Regenerate container configuration files for the pipeline when modules are installed
+        # Update container configs for the installed module. Subworkflows have no container entries of their
+        # own; their included modules each trigger this when installed above.
         if self.component_type == "modules":
-            try_generate_container_configs(self.directory, component_dir, component)
+            try_generate_container_configs(self.directory, component_dir)
 
         if not silent:
             modules_json.load()
diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index efcdc11d90..9b603fe461 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -62,7 +62,7 @@ def __init__(
         remote_url: str | None = None,
         branch: str | None = None,
         no_pull: bool = False,
-        registry: str | None = None,
+        registry: tuple[str, ...] = ("quay.io", "community.wave.seqera.io/library"),
         hide_progress: bool = False,
     ):
         super().__init__(
@@ -156,12 +156,11 @@ def __init__(
     def __repr__(self) -> str:
         return f"ComponentLint({self.component_type}, {self.directory})"
 
-    def _set_registry(self, registry) -> None:
-        if registry is None:
-            self.registry = self.config.get("docker.registry", "quay.io")
-        else:
-            self.registry = registry
-        log.debug(f"Registry set to {self.registry}")
+    def _set_registry(self, registry: tuple[str, ...]) -> None:
+        _, tools_config = nf_core.utils.load_tools_config(self.directory)
+        user_registries: list[str] = (tools_config.container_registry or []) if tools_config else []
+        self.registry: tuple[str, ...] = (*registry, *user_registries)
+        log.debug(f"Registries set to {self.registry}")
 
     @property
     def local_module_exclude_tests(self):
@@ -293,7 +292,7 @@ def format_result(test_results: list[LintResult], table: Table) -> Table:
                 tools_version = __version__
                 if "dev" in __version__:
                     tools_version = "dev"
-                test_link_message = f"[{lint_result.lint_test}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/{self.component_type[:-1]}_lint_tests/{lint_result.parent_lint_test}): {lint_result.message}"
+                test_link_message = f"[{lint_result.lint_test}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/{self.component_type[:-1]}_lint_tests/{lint_result.parent_lint_test}#{lint_result.lint_test}): {lint_result.message}"
 
                 table.add_row(
                     module_name,
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 37744bf291..e620881aad 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -2,11 +2,14 @@
 The NFCoreComponent class holds information and utility functions for a single module or subworkflow
 """
 
+import json
 import logging
 import re
 from pathlib import Path
 from typing import Any
 
+from nf_core.utils import NF_INSPECT_MIN_NF_VERSION, check_nextflow_version, run_cmd, set_wd_tempdir
+
 log = logging.getLogger(__name__)
 
 
@@ -58,6 +61,9 @@ def __init__(
         self.is_patched: bool = False
         self.branch: str | None = None
         self.workflow_name: str | None = None
+        self.container: dict = {}
+        self.container_from_main_nf: str | None = None
+        self._meta_yml_content: dict | None = None
 
         if remote_component:
             # Initialize the important files
@@ -109,6 +115,21 @@ def __init__(
     def __repr__(self) -> str:
         return f"<NFCoreComponent {self.component_name} {self.component_dir} {self.repo_url}>"
 
+    def load_meta_yml(self, reload: bool = False) -> dict | None:
+        """
+        Return the parsed content of the component's ``meta.yml``, cached after the first read.
+
+        Pass ``reload=True`` after writing to ``meta.yml`` to refresh the cache.
+        Returns ``None`` if the component has no ``meta.yml``.
+        """
+        if reload or self._meta_yml_content is None:
+            if self.meta_yml is None or not Path(self.meta_yml).exists():
+                return None
+            from nf_core.components.components_utils import read_meta_yml
+
+            self._meta_yml_content = read_meta_yml(Path(self.meta_yml))
+        return self._meta_yml_content
+
     def _get_main_nf_tags(self, test_main_nf: Path | str):
         """Collect all tags from the main.nf.test file."""
         tags = []
@@ -131,7 +152,8 @@ def _get_included_components(self, main_nf: Path | str):
                     #'plugin/nf-validation'
                     component = line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/")
                     component = component.replace("'../", "subworkflows/")
-                    component = component.replace("'", "")
+                    # Replace trailing quotes
+                    component = component.replace("'", "").replace('"', "")
                     included_components.append(component)
         return included_components
 
@@ -377,3 +399,77 @@ def get_topics_from_main_nf(self) -> None:
             log.debug(f"Found {len(list(topics.keys()))} topics in {self.main_nf}")
             log.debug(f"Topics: {topics}")
             self.topics = topics
+
+    def get_container_from_main_nf(self) -> str | None:
+        """Cached accessor for the (profile-agnostic) container resolved from ``main.nf``."""
+        if self.container_from_main_nf is not None:
+            return self.container_from_main_nf
+
+        self.container_from_main_nf = self.get_container_with_inspect()
+
+        if not self.container_from_main_nf:
+            log.warning(f"No container was extracted for {self.component_name} from {self.main_nf}")
+
+        return self.container_from_main_nf
+
+    def get_container_with_inspect(self, profile: str | None = None) -> str | None:
+        """Resolve the container declared in the module's ``main.nf`` using ``nextflow inspect``.
+
+        Running inspect lets Nextflow evaluate the container selection logic in the module
+        (and return the fully resolved container in its JSON output) instead of parsing it
+        with brittle regexes. Pass ``profile`` (e.g. ``"docker"`` or ``"singularity"``) to
+        resolve the container for a specific profile.
+
+        Returns:
+            str | None: The resolved container, or ``None`` if it could not be resolved
+            (not a module, Nextflow too old to support ``nextflow inspect``, or inspect
+            failed).
+        """
+        if self.component_type != "modules":
+            return None
+
+        if not check_nextflow_version(NF_INSPECT_MIN_NF_VERSION, silent=True):
+            log.debug("Nextflow version too old to resolve containers with `nextflow inspect`")
+            return None
+
+        main_nf_abs = self.main_nf.absolute()
+
+        with set_wd_tempdir():
+            # Provide a minimal nextflow.config to avoid falling back to docker branch when
+            # resolving singularity containers via `nextflow inspect`.
+            Path("nextflow.config").write_text(
+                "profiles {\n    docker { docker.enabled = true }\n    singularity { singularity.enabled = true }\n}\n"
+            )
+            executable = "nextflow"
+            profile_param = f"-profile {profile} " if profile else ""
+            cmd_params = f"inspect {profile_param}-format json {main_nf_abs}"
+            try:
+                cmd_out = run_cmd(executable, cmd_params)
+            except RuntimeError:
+                cmd_out = None
+            if cmd_out is None:
+                log.debug("Failed to run `nextflow inspect`")
+                return None
+            out, _ = cmd_out
+            out_str = out.decode()
+            # nextflow inspect mixes status lines ([PIPELINE], [SUCCESS], etc.) with JSON on stdout
+            json_start = out_str.find("{")
+            json_end = out_str.rfind("}") + 1
+            if json_start == -1 or json_end == 0:
+                log.debug("Could not find JSON in nextflow inspect output")
+                log.debug(f"Output of nextflow inspect: {out_str}")
+                return None
+            try:
+                out_json = json.loads(out_str[json_start:json_end])
+            except json.JSONDecodeError:
+                log.debug("Failed to parse JSON from nextflow inspect output")
+                log.debug(f"Output of nextflow inspect: {out_str}")
+                return None
+            container = (out_json.get("processes") or [{}])[0].get("container", None)
+            if container is None:
+                log.debug(
+                    f"Container for {self.component_name} could not be extracted from the output of nextflow inspect"
+                )
+                log.debug(f"Output of nextflow inspect: {out_str}")
+
+            return container
diff --git a/nf_core/components/update.py b/nf_core/components/update.py
index e679643735..bf2b9a64b8 100644
--- a/nf_core/components/update.py
+++ b/nf_core/components/update.py
@@ -38,6 +38,7 @@ def __init__(
         branch=None,
         no_pull=False,
         limit_output=False,
+        skip_deps=False,
     ):
         super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull)
         self.current_remote = ModulesRepo(remote_url, branch)
@@ -50,6 +51,7 @@ def __init__(
         self.save_diff_fn = save_diff_fn
         self.limit_output = limit_output
         self.update_deps = update_deps
+        self.skip_deps = skip_deps
         self.component = None
         self.update_config = None
         self.modules_json = ModulesJson(self.directory)
@@ -68,6 +70,12 @@ def _parameter_checks(self):
         if self.update_all and self.component:
             raise UserWarning(f"Either a {self.component_type[:-1]} or the '--all' flag can be specified, not both.")
 
+        if self.skip_deps and self.update_deps:
+            raise UserWarning("`--skip-deps` and `--update-deps` are mutually exclusive.")
+
+        if self.skip_deps and self.update_all:
+            raise UserWarning("`--skip-deps` and `--all` are mutually exclusive.")
+
         if self.repo_type == "modules":
             raise UserWarning(
                 f"{self.component_type.title()} can not be updated in clones of the nf-core/modules repository."
@@ -258,7 +266,9 @@ 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 len(modules_to_update + subworkflows_to_update) > 0:
+                    if self.skip_deps:
+                        recursive_update = False
+                    elif not silent 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 added to the same diff file.\n"
                             "It is advised to keep all your modules and subworkflows up to date.\n"
@@ -308,13 +318,15 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr
                 # Update modules.json with newly installed component
                 self.modules_json.update(self.component_type, modules_repo, component, version, installed_by=None)
                 updated.append(component)
-
-                # Regenerate container configuration files for the pipeline when modules are updated
                 if self.component_type == "modules":
-                    try_generate_container_configs(self.directory)
+                    try_generate_container_configs(self.directory, component_dir)
+
                 recursive_update = True
                 modules_to_update, subworkflows_to_update = self.get_components_to_update(component)
-                if not silent and len(modules_to_update + subworkflows_to_update) > 0 and not self.update_all:
+                if self.skip_deps:
+                    # Caller asked for single-target update; skip linked components entirely.
+                    recursive_update = False
+                elif not silent and len(modules_to_update + subworkflows_to_update) > 0 and 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"
diff --git a/nf_core/github_api.py b/nf_core/github_api.py
new file mode 100644
index 0000000000..2228c7d33f
--- /dev/null
+++ b/nf_core/github_api.py
@@ -0,0 +1,189 @@
+"""GitHub API session handling for the nf-core python package.
+
+Kept separate from nf_core.utils so that requests_cache is only
+imported when the GitHub API is actually used.
+"""
+
+import json
+import logging
+import os
+import random
+import re
+import sys
+import time
+from pathlib import Path
+
+import requests.auth
+import requests_cache
+import rich.console
+import rich.markup
+import yaml
+
+from nf_core.utils import rich_force_colors, setup_requests_cachedir
+
+log = logging.getLogger(__name__)
+
+
+class GitHubAPISession(requests_cache.CachedSession):
+    """
+    Class to provide a single session for interacting with the GitHub API for a run.
+    Inherits the requests_cache.CachedSession and adds additional functionality,
+    such as automatically setting up GitHub authentication if we can.
+    """
+
+    def __init__(self) -> None:
+        self.auth_mode: str | None = None
+        self.return_ok: list[int] = [200, 201]
+        self.return_retry: list[int] = [403]
+        self.return_unauthorised: list[int] = [401]
+        self.has_init: bool = False
+
+    def lazy_init(self) -> None:
+        """
+        Initialise the object.
+
+        Only do this when it's actually being used (due to global import)
+        """
+        log.debug("Initialising GitHub API requests session")
+        cache_config = setup_requests_cachedir()
+        super().__init__(**cache_config)
+        self.setup_github_auth()
+        self.has_init = True
+
+    def setup_github_auth(self, auth=None):
+        """
+        Try to automatically set up GitHub authentication
+        """
+        if auth is not None:
+            self.auth = auth
+            self.auth_mode = "supplied to function"
+
+        # Class for Bearer token authentication
+        # https://stackoverflow.com/a/58055668/713980
+        class BearerAuth(requests.auth.AuthBase):
+            def __init__(self, token):
+                self.token = token
+
+            def __call__(self, r):
+                r.headers["authorization"] = f"Bearer {self.token}"
+                return r
+
+        # Default auth if we're running and the gh CLI tool is installed
+        gh_cli_config_fn = Path.home() / ".config" / "gh" / "hosts.yml"
+        if self.auth is None and gh_cli_config_fn.exists():
+            try:
+                with open(gh_cli_config_fn) as fh:
+                    gh_cli_config = yaml.safe_load(fh)
+                    self.auth = requests.auth.HTTPBasicAuth(
+                        gh_cli_config["github.com"]["user"],
+                        gh_cli_config["github.com"]["oauth_token"],
+                    )
+                    self.auth_mode = f"gh CLI config: {gh_cli_config['github.com']['user']}"
+            except (OSError, KeyError, yaml.YAMLError):
+                ex_type, ex_value, _ = sys.exc_info()
+                if ex_type is not None:
+                    output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}")
+                    log.debug(f"Couldn't auto-auth with GitHub CLI auth from '{gh_cli_config_fn}': [red]{output}")
+
+        # Default auth if we have a GitHub Token (eg. GitHub Actions CI)
+        if os.environ.get("GITHUB_TOKEN") is not None and self.auth is None:
+            self.auth_mode = "Bearer token with GITHUB_TOKEN"
+            self.auth = BearerAuth(os.environ["GITHUB_TOKEN"])
+        else:
+            log.warning("Could not find GitHub authentication token. Some API requests may fail.")
+
+        log.debug(f"Using GitHub auth: {self.auth_mode}")
+
+    def log_content_headers(self, request, post_data=None):
+        """
+        Try to dump everything to the console, useful when things go wrong.
+        """
+        log.debug(f"Requested URL: {request.url}")
+        log.debug(f"From requests cache: {request.from_cache}")
+        log.debug(f"Request status code: {request.status_code}")
+        log.debug(f"Request reason: {request.reason}")
+        if post_data is None:
+            post_data = {}
+        try:
+            log.debug(json.dumps(dict(request.headers), indent=4))
+            log.debug(json.dumps(request.json(), indent=4))
+            log.debug(json.dumps(post_data, indent=4))
+        except (json.JSONDecodeError, TypeError) as e:
+            log.debug(f"Could not parse JSON response from GitHub API! {e}")
+            log.debug(request.headers)
+            log.debug(request.content)
+            log.debug(post_data)
+
+    def safe_get(self, url):
+        """
+        Run a GET request, raise a nice exception with lots of logging if it fails.
+        """
+        if not self.has_init:
+            self.lazy_init()
+        request = self.get(url)
+        if request.status_code in self.return_retry:
+            stderr = rich.console.Console(stderr=True, force_terminal=rich_force_colors())
+            try:
+                r = self.request_retry(url)
+            except Exception as e:
+                stderr.print_exception()
+                raise e
+            else:
+                return r
+        elif request.status_code in self.return_unauthorised:
+            raise RuntimeError("GitHub API PR failed, probably due to an expired GITHUB_TOKEN.")
+
+        return request
+
+    def get(self, url, **kwargs):
+        """
+        Initialise the session if we haven't already, then call the superclass get method.
+        """
+        if not self.has_init:
+            self.lazy_init()
+        return super().get(url, **kwargs)
+
+    def request_retry(self, url, post_data=None):
+        """
+        Try to fetch a URL, keep retrying if we get a certain return code.
+
+        Used in nf-core pipelines sync code because we get 403 errors: too many simultaneous requests
+        See https://github.com/nf-core/tools/issues/911
+        """
+        if not self.has_init:
+            self.lazy_init()
+
+        # Start the loop for a retry mechanism
+        while True:
+            # GET request
+            if post_data is None:
+                log.debug(f"Sending GET request to {url}")
+                r = self.get(url=url)
+            # POST request
+            else:
+                log.debug(f"Sending POST request to {url}")
+                r = self.post(url=url, json=post_data)
+
+            # Failed but expected - try again
+            if r.status_code in self.return_retry:
+                self.log_content_headers(r, post_data)
+                log.debug(f"GitHub API PR failed - got return code {r.status_code}")
+                wait_time = float(re.sub("[^0-9]", "", str(r.headers.get("Retry-After", 0))))
+                if wait_time == 0:
+                    log.debug("Couldn't find 'Retry-After' header, guessing a length of time to wait")
+                    wait_time = random.randrange(10, 60)
+                log.warning(f"Got API return code {r.status_code}. Trying again after {wait_time} seconds..")
+                time.sleep(wait_time)
+
+            # Unexpected error - raise
+            elif r.status_code not in self.return_ok:
+                self.log_content_headers(r, post_data)
+                raise RuntimeError(f"GitHub API PR failed - got return code {r.status_code} from {url}")
+
+            # Success!
+            else:
+                return r
+
+
+# Single session object to use for entire codebase. Not sure if there's a better way to do this?
+gh_api = GitHubAPISession()
diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py
index 7ab5da5855..ba5e2920be 100644
--- a/nf_core/modules/bump_versions.py
+++ b/nf_core/modules/bump_versions.py
@@ -9,7 +9,6 @@
 import re
 from pathlib import Path
 
-import questionary
 import yaml
 from rich.box import ROUNDED
 from rich.console import Console
@@ -22,7 +21,7 @@
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.utils import NFCoreYamlConfig, custom_yaml_dumper, rich_force_colors
+from nf_core.utils import NFCoreYamlConfig, rich_force_colors
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
@@ -51,26 +50,29 @@ def bump_versions(
         all_modules: bool = False,
         show_up_to_date: bool = False,
         dry_run: bool = False,
+        hide_progress: bool = False,
     ) -> list[NFCoreComponent]:
         """
         Bump the container and conda version of single module or all modules.
 
         If module is the name of a directory in the modules directory, all modules in that directory will be bumped.
 
-        Looks for a bioconda tool version in the `main.nf` file of the module and checks whether
-        are more recent version is available. If yes, then tries to get docker/singularity
-        container links and replace the bioconda version and the container links in the main.nf file
-        of the respective module.
+        Looks for a bioconda tool version in the `environment.yml` file of the module and checks
+        whether a more recent version is available. If yes, the pinned version
+        in `environment.yml` is bumped and the Docker/Singularity containers are rebuilt from it
+        with Wave.
 
         Args:
             module: a specific module to update
             all_modules: whether to bump versions for all modules
             show_up_to_date: whether to show up-to-date modules as well
             dry_run: whether to dry run the command
+            hide_progress: whether to hide the progress bars
 
         Returns:
             list[NFCoreComponent]: the updated modules
         """
+        hide_progress = hide_progress or os.environ.get("HIDE_PROGRESS", None) is not None
         self.up_to_date = []
         self.updated = []
         self.failed = []
@@ -94,24 +96,11 @@ def bump_versions(
 
         # Prompt for module or all
         if module is None and not all_modules:
-            self.require_prompts(
-                "No module name provided.\nPlease provide the module name as a command-line argument or use '--all'"
+            module = nf_core.modules.modules_utils.prompt_module_selection(
+                nfcore_modules, component_type="modules", action="Bump versions for"
             )
-            question = {
-                "type": "list",
-                "name": "all_modules",
-                "message": "Bump versions for all modules or a single named module?",
-                "choices": ["All modules", "Named module"],
-            }
-            answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
-            if answer["all_modules"] == "All modules":
+            if module is None:
                 all_modules = True
-            else:
-                module = questionary.autocomplete(
-                    "Tool name:",
-                    choices=[m.component_name for m in nfcore_modules],
-                    style=nf_core.utils.nfcore_question_style,
-                ).unsafe_ask()
 
         if module:
             self.show_up_to_date = True
@@ -135,8 +124,9 @@ def bump_versions(
             BarColumn(bar_width=None),
             "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
             transient=True,
-            disable=os.environ.get("HIDE_PROGRESS", None) is not None,
+            disable=hide_progress,
         )
+        modules_to_rebuild: list[NFCoreComponent] = []
         with progress_bar:
             bump_progress = progress_bar.add_task(
                 "Bumping nf-core modules versions",
@@ -145,39 +135,72 @@ def bump_versions(
             )
             for mod in nfcore_modules:
                 progress_bar.update(bump_progress, advance=1, test_name=mod.component_name)
-                self.bump_module_version(mod)
+                if self.bump_module_version(mod):
+                    modules_to_rebuild.append(mod)
+
+        if modules_to_rebuild:
+            self._build_wave_containers(modules_to_rebuild, hide_progress)
 
         self._print_results()
 
         return nfcore_modules
 
+    def _build_wave_containers(self, modules: list[NFCoreComponent], hide_progress: bool = False) -> None:
+        """Rebuild the Docker/Singularity containers for ``modules`` with Seqera Wave.
+
+        Builds from each module's (already bumped) environment.yml and updates main.nf,
+        meta.yml and the conda lock files. Modules whose build fails are added to
+        ``self.failed``.
+        """
+        from nf_core.modules.containers import ModuleContainers
+
+        log.info(f"Building Seqera containers for {len(modules)} bumped module{_s(modules)} with Wave...")
+        module_containers = ModuleContainers(
+            module=None,
+            directory=self.directory,
+            all_modules=True,
+            components=modules,
+        )
+        ModuleContainers.check_tower_token()
+        failed_modules = module_containers.build_containers_with_progress(hide_progress=hide_progress)
+        for module_name in failed_modules:
+            self.failed.append(("Container build with Wave failed", module_name))
+
     def bump_module_version(self, module: NFCoreComponent) -> bool:
         """
         Bump the bioconda and container version of a single NFCoreComponent
 
         Args:
             module: NFCoreComponent
+
+        Returns:
+            True if the module's ``environment.yml`` was bumped and its containers therefore
+            need rebuilding; False if it was already up to date, ignored or failed.
         """
         config_version = None
-        bioconda_packages = []
-        try:
-            # Extract bioconda version from `environment.yml`
-            bioconda_packages = self.get_bioconda_version(module)
-        except FileNotFoundError:
-            # try it in the main.nf instead
-            try:
-                with open(module.main_nf) as fh:
-                    for line in fh:
-                        if "bioconda::" in line:
-                            bioconda_packages = [b for b in line.split() if "bioconda::" in b]
-            except FileNotFoundError:
-                log.error(
-                    f"Neither `environment.yml` nor `main.nf` of {module.component_name} module could be read to get bioconada version of used tools."
-                )
-
-        # If multiple versions - don't update! (can't update mulled containers)
-        if not bioconda_packages or len(bioconda_packages) > 1:
-            self.failed.append(("Ignoring mulled container", module.component_name))
+        # Extract the pinned conda dependencies from `environment.yml`. Wave rebuilds the containers
+        # straight from this file, so every pinned package can be bumped - including multi-package
+        # ("mulled") modules, which earlier versions had to skip because the old mulled container
+        # names could not be regenerated.
+        dependencies = self.get_bioconda_version(module)
+
+        # Only channel-pinned, versioned deps (e.g. `bioconda::samtools=1.21`) can be bumped; skip
+        # pip sub-dicts, unpinned deps and anything without a `channel::name=version` shape.
+        conda_packages: list[tuple[str, str, str]] = []  # (channel, tool_name, current_version)
+        for dep in dependencies:
+            if not isinstance(dep, str):
+                continue
+            spec = dep.strip("'").strip('"')
+            if "::" not in spec or "=" not in spec:
+                continue
+            channel, name_version = spec.split("::", 1)
+            tool_name, current_version = name_version.split("=", 1)
+            # Drop an optional build string (`name=version=build`)
+            current_version = current_version.split("=", 1)[0]
+            conda_packages.append((channel, tool_name, current_version))
+
+        if not conda_packages:
+            self.failed.append(("No pinned conda dependencies to bump", module.component_name))
             return False
 
         # Don't update if blocked in blacklist
@@ -187,118 +210,139 @@ def bump_module_version(self, module: NFCoreComponent) -> bool:
             if not config_version:
                 self.ignored.append(("Omitting module due to config.", module.component_name))
                 return False
-
-        # check for correct version and newer versions
-        bioconda_tool_name = bioconda_packages[0].split("=")[0].replace("bioconda::", "").strip("'").strip('"')
-        bp = bioconda_packages[0]
-        bp = bp.strip("'").strip('"')
-        bioconda_version = bp.split("=")[1]
-
-        if not config_version:
-            try:
-                response = nf_core.utils.anaconda_package(bp)
-            except (LookupError, ValueError):
+            if len(conda_packages) > 1:
+                # A single pinned version in the config can't be mapped onto a multi-package module
                 self.failed.append(
-                    (
-                        f"Conda version not specified correctly: {Path(module.main_nf).relative_to(self.directory)}",
-                        module.component_name,
-                    )
+                    ("Cannot pin a version via config for a multi-package module", module.component_name)
                 )
                 return False
 
-            # Check that required version is available at all
-            if bioconda_version not in response.get("versions"):
-                self.failed.append((f"Conda package had unknown version: `{module.main_nf}`", module.component_name))
-                return False
-
-            # Check version is latest available
-            last_ver = response.get("latest_version")
-        else:
-            last_ver = config_version
-
-        if last_ver is not None and last_ver != bioconda_version:
-            log.debug(f"Updating version for {module.component_name}")
-            # Get docker and singularity container links
-            try:
-                docker_img, singularity_img = nf_core.utils.get_biocontainer_tag(bioconda_tool_name, last_ver)
-            except LookupError as e:
-                self.failed.append((f"Could not download container tags: {e}", module.component_name))
-                return False
-
-            patterns = [
-                (rf"biocontainers/{bioconda_tool_name}:[^'\"\s]+", docker_img),
-                (
-                    rf"https://depot.galaxyproject.org/singularity/{bioconda_tool_name}:[^'\"\s]+",
-                    singularity_img,
-                ),
-            ]
-
-            with open(module.main_nf) as fh:
-                content = fh.read()
+        # Resolve the target version for every package: the latest available on Anaconda, or the
+        # version pinned in the config blacklist.
+        targets: list[tuple[str, str, str, str]] = []  # (channel, tool_name, current_version, target_version)
+        for channel, tool_name, current_version in conda_packages:
+            if config_version:
+                target_version = config_version
+            else:
+                dep_spec = f"{channel}::{tool_name}={current_version}"
+                try:
+                    response = nf_core.utils.anaconda_package(dep_spec)
+                except (LookupError, ValueError):
+                    self.failed.append(
+                        (
+                            f"Conda version not specified correctly: {Path(module.environment_yml).relative_to(self.directory) if module.environment_yml else module.component_name}",
+                            module.component_name,
+                        )
+                    )
+                    return False
 
-            # Go over file content of main.nf and find replacements
-            for pattern in patterns:
-                found_match = False
-                newcontent = []
-                for line in content.splitlines():
-                    # Match the pattern
-                    matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line)
-                    if matches_pattern:
-                        found_match = True
-
-                        # Replace the match
-                        newline = re.sub(pattern[0], pattern[1], line)
-                        newcontent.append(newline)
-                    # No match, keep line as it is
-                    else:
-                        newcontent.append(line)
-
-                if found_match:
-                    content = "\n".join(newcontent) + "\n"
-                else:
+                # Check that the pinned version is available at all
+                if current_version not in response.get("versions"):
                     self.failed.append(
-                        (f"Did not find pattern {pattern[0]} in module {module.component_name}", module.component_name)
+                        (f"Conda package had unknown version: `{module.environment_yml}`", module.component_name)
                     )
                     return False
 
-            # Write new content to the file
-            with open(module.main_nf, "w") as fh:
-                fh.write(content)
+                target_version = response.get("latest_version")
 
-            # change version in environment.yml
+            if target_version is None:
+                continue
+            targets.append((channel, tool_name, current_version, target_version))
+
+        if not targets:
+            self.up_to_date.append((f"Module version up to date: {module.component_name}", module.component_name))
+            return False
+
+        # Check 1: bump any dependency behind the latest. Wave rebuilds the containers from
+        # environment.yml afterwards (see bump_versions()), updating main.nf, meta.yml and conda locks.
+        outdated = [t for t in targets if t[3] != t[2]]
+        if outdated:
             if not module.environment_yml:
                 log.error(f"Could not read `environment.yml` of {module.component_name} module.")
+                self.failed.append(("No environment.yml found to update", module.component_name))
                 return False
+            # Rewrite the versions in the raw file text so YAML comments (e.g. renovate hints) and
+            # formatting survive - a yaml load/dump round-trip would silently drop them.
             with open(module.environment_yml) as fh:
-                env_yml = yaml.safe_load(fh)
-            env_yml["dependencies"][0] = re.sub(
-                bioconda_packages[0], f"bioconda::{bioconda_tool_name}={last_ver}", env_yml["dependencies"][0]
-            )
+                content = fh.read()
+            for channel, tool_name, current_version, target_version in outdated:
+                log.debug(f"Updating {tool_name} version for {module.component_name}")
+                content = re.sub(
+                    rf"({re.escape(channel)}::{re.escape(tool_name)})=[^\s'\"]+",
+                    rf"\g<1>={target_version}",
+                    content,
+                )
+                self.updated.append(
+                    (f"Module updated: {tool_name} {current_version} --> {target_version}", module.component_name)
+                )
             with open(module.environment_yml, "w") as fh:
-                yaml.dump(env_yml, fh, default_flow_style=False, Dumper=custom_yaml_dumper())
+                fh.write(content)
+            return True
 
-            self.updated.append(
-                (
-                    f"Module updated:  {bioconda_version} --> {last_ver}",
-                    module.component_name,
+        # Check 2: environment.yml is already current, but make sure the containers were actually
+        # built for every package. An earlier run may have bumped environment.yml and then been
+        # interrupted before the Wave build wrote the new containers / conda locks.
+        for _channel, tool_name, _current_version, target_version in targets:
+            if not self._containers_built_for_version(module, tool_name, target_version):
+                self.updated.append(
+                    (f"Containers out of date - rebuilding for version {target_version}", module.component_name)
                 )
+                return True
+
+        self.up_to_date.append((f"Module version up to date: {module.component_name}", module.component_name))
+        return False
+
+    def _containers_built_for_version(self, module: NFCoreComponent, tool_name: str, version: str) -> bool:
+        """Return True if the module's Wave conda-lock files already pin ``tool_name`` at ``version``.
+
+        Image names are content hashes, so the version-bearing conda locks are checked instead,
+        assuming the bioconda dependency name matches the conda package name. No ``.conda-lock`` dir
+        means the module was never Wave-built (left alone); an empty dir, or a meta.yml without a
+        ``containers:`` section, means an interrupted build (rebuilt).
+        """
+        from nf_core.components.components_utils import read_meta_yml
+
+        conda_lock_dir = module.component_dir / ".conda-lock"
+        if not conda_lock_dir.is_dir():
+            log.debug(
+                f"No conda-lock directory for {module.component_name}; treating as up to date "
+                "(Wave migration is out of scope for bump-versions)"
             )
             return True
+        lock_files = list(conda_lock_dir.glob("*.txt"))
+        if not lock_files:
+            # Empty dir: a finished build always leaves locks, so this one was interrupted.
+            log.debug(f"Empty conda-lock directory for {module.component_name}; containers need rebuilding")
+            return False
+        # Lock entries look like `.../samtools-1.21-h50ea8bc_0.conda`; trailing `-` keeps 1.21 from
+        # matching 1.210. Stream each file so the search short-circuits.
+        needle = f"/{tool_name}-{version}-"
+        for lock_file in lock_files:
+            with lock_file.open() as fh:
+                if not any(needle in line for line in fh):
+                    return False
 
-        else:
-            self.up_to_date.append((f"Module version up to date: {module.component_name}", module.component_name))
-            return True
+        # The containers section is written last, so its absence means an interrupted build. Only
+        # require it to be present, not complete (arm64 builds may legitimately be missing).
+        if module.meta_yml is None or not Path(module.meta_yml).exists():
+            log.debug(f"No meta.yml for {module.component_name}; containers need rebuilding")
+            return False
+        if not read_meta_yml(Path(module.meta_yml)).get("containers"):
+            log.debug(f"meta.yml for {module.component_name} has no containers section; containers need rebuilding")
+            return False
+
+        return True
 
     def get_bioconda_version(self, module: NFCoreComponent) -> list[str]:
         """
         Extract the bioconda version from a module
         """
         # Check whether file exists and load it
-        bioconda_packages = []
+        bioconda_packages: list[str] = []
         if module.environment_yml is not None and module.environment_yml.exists():
             with open(module.environment_yml) as fh:
                 env_yml = yaml.safe_load(fh)
-            bioconda_packages = env_yml.get("dependencies", [])
+            bioconda_packages = (env_yml or {}).get("dependencies") or []
         else:
             log.error(f"Could not read `environment.yml` of {module.component_name} module.")
 
diff --git a/nf_core/modules/containers.py b/nf_core/modules/containers.py
new file mode 100644
index 0000000000..f3788f1053
--- /dev/null
+++ b/nf_core/modules/containers.py
@@ -0,0 +1,917 @@
+import base64
+import hashlib
+import logging
+import os
+import re
+import shutil
+import threading
+import time
+from collections.abc import Callable
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from pathlib import Path
+from urllib.parse import quote
+
+import requests
+import rich.progress
+from pydantic import ValidationError
+from rich.pretty import pretty_repr
+
+from nf_core.components.components_utils import read_meta_yml
+from nf_core.components.components_utils import yaml as ruamel_yaml
+from nf_core.components.nfcore_component import NFCoreComponent
+from nf_core.modules.lint import ModuleLint
+from nf_core.modules.modules_utils import (
+    CondaEntry,
+    ContainerEntry,
+    MetaYmlContainers,
+    filter_modules_by_name,
+    module_uses_dockerfile,
+    prompt_module_selection,
+    scan_modules_dir,
+)
+from nf_core.pipelines.lint_utils import run_prettier_on_file
+from nf_core.utils import CONTAINER_PLATFORMS, CONTAINER_SYSTEMS, ContainerRegistryUrls
+
+log = logging.getLogger(__name__)
+
+WAVE_URL = "https://wave.seqera.io"
+WAVE_API_ALPHA1 = f"{WAVE_URL}/v1alpha1"
+WAVE_API_ALPHA2 = f"{WAVE_URL}/v1alpha2"
+
+# Wave container build `format` field, keyed by nf-core container system.
+WAVE_FORMAT = {"docker": "docker", "singularity": "sif"}
+
+
+def wave_send(
+    method: str, url: str, json_body: dict | None = None, error_context: str = "Wave request"
+) -> requests.Response:
+    """
+    Send an authenticated Wave API request and return the raw response.
+
+    Adds bearer auth (and a ``towerAccessToken`` body field for requests with a body)
+    when TOWER_ACCESS_TOKEN is set, and raises on a non-200 response. This is the
+    shared transport for all Wave calls; use :func:`wave_request` for JSON endpoints
+    and read ``.text`` directly for plain-text ones (e.g. the conda lock file).
+
+    Args:
+        method: ``"get"`` or ``"post"``.
+        url: Full request URL.
+        json_body: Optional JSON body (POST requests).
+        error_context: Prefix used in raised error messages.
+    """
+    if method not in ("get", "post"):
+        raise ValueError(f"Invalid http method '{method}' passed. Needs to be one of: 'get', 'post'.")
+    headers = {"Content-Type": "application/json"}
+    token = os.environ.get("TOWER_ACCESS_TOKEN")
+    if token:
+        headers["Authorization"] = f"Bearer {token}"
+        if json_body is not None:
+            json_body = {**json_body, "towerAccessToken": token}
+
+    resp = getattr(requests, method)(url, json=json_body, headers=headers)
+    if resp.status_code != 200:
+        raise RuntimeError(f"{error_context} failed: HTTP {resp.status_code} {resp.text}")
+    return resp
+
+
+def wave_request(method: str, url: str, json_body: dict | None = None, error_context: str = "Wave request") -> dict:
+    """Send a Wave API request and return the parsed JSON response."""
+    resp = wave_send(method, url, json_body, error_context)
+    try:
+        return resp.json()
+    except ValueError as e:
+        raise RuntimeError(f"{error_context}: could not parse JSON response") from e
+
+
+class ModuleContainers:
+    """
+    Helpers for building, linting and listing module containers.
+    """
+
+    # Wave build results, keyed by (environment.yml content hash, container_system, platform).
+    # Modules with an identical environment.yml (e.g. samtools/sort and samtools/view) resolve
+    # to the same container, so this avoids submitting duplicate builds within one process.
+    _build_cache: dict[tuple[str, str, str], ContainerEntry] = {}
+    # Path to an already-written conda lock file, keyed by Wave build_id. Modules that share
+    # a cached build (above) also share a build_id, so a later module can copy the file that
+    # an earlier one already downloaded instead of re-fetching identical lock contents.
+    _conda_lock_paths: dict[str, Path] = {}
+    _build_cache_lock = threading.Lock()
+
+    def __init__(
+        self,
+        module: str | None,
+        directory: str | Path = ".",
+        all_modules: bool = False,
+        verbose: bool = False,
+        components: list[NFCoreComponent] | None = None,
+    ):
+        from nf_core.components.components_utils import get_repo_info
+
+        self.directory = Path(directory)
+        self.verbose = verbose
+
+        # Detect repository type and organization
+        try:
+            _, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=False)
+        except (UserWarning, FileNotFoundError):
+            self.repo_type = None
+            self.org = "nf-core"  # Default to nf-core if repo info not available
+
+        # Get available modules (local modules for pipelines, repo modules for modules repos).
+        # A pre-scanned list can be passed in to avoid re-scanning the modules directory.
+        self.available_modules = components if components is not None else self._get_available_modules()
+
+        # Create a lookup dictionary for quick access by module name
+        self.components_by_name = {comp.component_name: comp for comp in self.available_modules}
+
+        # Prompt for module selection if not provided
+        # Only allow "all modules" for pipeline repos
+        if module is None and not all_modules and len(self.available_modules) > 0:
+            allow_all = self.repo_type == "pipeline"
+            module = prompt_module_selection(
+                self.available_modules, component_type="modules", action="Build containers for", allow_all=allow_all
+            )
+            # If None returned from prompt, user selected "All modules" (only possible in pipeline repos)
+            if module is None:
+                all_modules = True
+
+        self.module = module
+        self.all_modules = all_modules
+
+        # When a module name is given, use filter_modules_by_name so that a parent folder
+        # like "samtools" also selects submodules (samtools/sort, samtools/view, …).
+        matched: list[NFCoreComponent] = []
+        if module is not None and not self.all_modules and self.available_modules:
+            matched = filter_modules_by_name(self.available_modules, module)
+            if len(matched) > 1:
+                # Prefix match returned several submodules – treat as a filtered "all" run
+                self.available_modules = matched
+                self.all_modules = True
+
+        # Use NFCoreComponent to handle module directory and file paths
+        # For single module mode
+        if not self.all_modules:
+            # Try exact lookup in the components we already created
+            if module is not None and module in self.components_by_name:
+                self.nfcore_component: NFCoreComponent | None = self.components_by_name[module]
+            elif module is not None and self.available_modules:
+                if matched:
+                    self.nfcore_component = matched[0]
+                else:
+                    self.nfcore_component = self._init_nfcore_component(module)
+            elif module is not None:
+                # Fallback: no available_modules list, create component directly
+                self.nfcore_component = self._init_nfcore_component(module)
+            else:
+                raise ValueError("No module specified and no modules available")
+
+            self.module_directory: Path | None = self.nfcore_component.component_dir
+            self.environment_yml: Path | None = self.nfcore_component.environment_yml
+            self.meta_yml: Path | None = self.nfcore_component.meta_yml
+        else:
+            # For all modules mode, these will be set per module during iteration
+            self.nfcore_component = None
+            self.module_directory = None
+            self.environment_yml = None
+            self.meta_yml = None
+
+        self.containers: MetaYmlContainers | None = None
+        self._module_lint: ModuleLint | None = None
+
+    @staticmethod
+    def check_tower_token() -> None:
+        """
+        Check if TOWER_ACCESS_TOKEN is set and warn about API limits if not.
+
+        Wave API has rate limits that can be increased by setting the TOWER_ACCESS_TOKEN
+        environment variable. This method checks if the token is set and logs a warning
+        if it's missing.
+        """
+        if not os.environ.get("TOWER_ACCESS_TOKEN"):
+            log.warning(
+                "TOWER_ACCESS_TOKEN is not set. Wave API requests will be subject to stricter rate limits. \n"
+                "To increase your quota, set the TOWER_ACCESS_TOKEN environment variable with your Seqera Platform token. \n"
+                "See https://docs.seqera.io/wave/api#api-limits for more information."
+            )
+
+    def _get_available_modules(self) -> list[NFCoreComponent]:
+        """
+        Get list of available modules based on repository type.
+
+        For pipeline repos: Returns only local modules (modules/local/)
+        For modules repos: Returns modules from the repository
+        """
+        if not self.repo_type:
+            log.debug("Could not determine repository type")
+            return []
+
+        if self.repo_type == "pipeline":
+            local_modules_dir = self.directory / "modules" / "local"
+            return [
+                NFCoreComponent(
+                    name,
+                    None,
+                    local_modules_dir / name,
+                    self.repo_type,
+                    self.directory,
+                    "modules",
+                    remote_component=False,
+                )
+                for name in scan_modules_dir(local_modules_dir)
+            ]
+        elif self.repo_type == "modules":
+            return [
+                self._init_nfcore_component(name) for name in scan_modules_dir(self.directory / "modules" / self.org)
+            ]
+        return []
+
+    def _init_nfcore_component(self, module: str) -> NFCoreComponent:
+        """Initialize NFCoreComponent for the module."""
+        # Construct the correct module directory path
+        module_dir = self.directory / "modules" / self.org / module
+        return NFCoreComponent(
+            component_name=module,
+            repo_url="https://github.com/nf-core/modules.git",
+            component_dir=module_dir,
+            repo_type="modules",
+            base_dir=self.directory,
+            component_type="modules",
+        )
+
+    def _uses_dockerfile(self) -> bool:
+        """Return True if the module has a Dockerfile (in its dir or parent) but no environment.yml."""
+        if self.nfcore_component is None:
+            return False
+        return module_uses_dockerfile(self.nfcore_component)
+
+    def cleanup_stale_conda_lock_files(self, new_lock_files: set[Path]) -> None:
+        """
+        Remove stale conda-lock files that are no longer in the new set.
+
+        Args:
+            new_lock_files: Set of new conda lock file paths that should be kept
+        """
+        if not self.module_directory:
+            return
+
+        conda_lock_dir = self.module_directory / ".conda-lock"
+        if not conda_lock_dir.exists():
+            return
+
+        # Remove all files that aren't in the new set
+        for lock_file in conda_lock_dir.glob("*.txt"):
+            if lock_file not in new_lock_files:
+                try:
+                    lock_file.unlink()
+                    log.debug(f"Removed stale conda-lock file: {lock_file}")
+                except OSError as e:
+                    log.warning(f"Failed to remove stale conda-lock file {lock_file}: {e}")
+
+        # Clean up empty directory
+        try:
+            if not any(conda_lock_dir.iterdir()):
+                conda_lock_dir.rmdir()
+                log.debug(f"Removed empty .conda-lock directory: {conda_lock_dir}")
+        except OSError as e:
+            log.debug(f"Could not remove .conda-lock directory: {e}")
+
+    def update_main_nf_container(self, force=False) -> None:
+        """Update the container name in main.nf using the docker amd64 image without registry.
+        Don't update if the container name is already correct.
+        """
+        import re
+
+        if self._uses_dockerfile():
+            log.info(f"Module '{self.module}' uses a Dockerfile - skipping main.nf container update")
+            return
+
+        if not self.containers or not self.nfcore_component:
+            log.warning("Cannot update main.nf: containers or nfcore_component not available")
+            return
+
+        linux_amd64 = CONTAINER_PLATFORMS[0]
+
+        # Get docker image
+        _docker_entry = self.containers.docker.get(linux_amd64)
+        docker_image = _docker_entry.name if _docker_entry else ""
+        if not docker_image:
+            log.error(f"No docker image found for {linux_amd64}")
+            return
+
+        # Get singularity image, preferring the https download URL over the image name
+        _singularity_entry = self.containers.singularity.get(linux_amd64)
+        singularity_image = (_singularity_entry.https or _singularity_entry.name) if _singularity_entry else ""
+        if not singularity_image:
+            log.error(f"No singularity image found for {linux_amd64}")
+            return
+
+        # Read main.nf
+        main_nf_path = self.nfcore_component.main_nf
+        content = main_nf_path.read_text()
+
+        # Check if the container directive is already correct
+        if docker_image in content and singularity_image in content and not force:
+            log.debug(f"Container directive in `{self.nfcore_component.component_name}/main.nf` is already correct")
+            return
+
+        # Replace container directive (may span multiple lines), preserving indentation.
+        # The directive uses double quotes on the outside and single quotes inside, so a
+        # non-greedy match up to the next double quote captures the whole ternary.
+        def _replace(match: "re.Match[str]") -> str:
+            indent = match.group(1)
+            inner_indent = indent + "    "
+            return (
+                f"{indent}container \"${{ workflow.containerEngine in ['singularity', 'apptainer'] "
+                "&& !task.ext.singularity_pull_docker_container\n"
+                f"? {inner_indent}'{singularity_image}'\n"
+                f": {inner_indent}'{docker_image}' }}\""
+            )
+
+        new_content = re.sub(
+            r"^([ \t]*)container\s+\".*?\"", _replace, content, count=1, flags=re.DOTALL | re.MULTILINE
+        )
+
+        main_nf_path.write_text(new_content)
+        log.debug(
+            f"Updated container in `{self.nfcore_component.component_name}/main.nf` "
+            f"(docker: `{docker_image}`, singularity: `{singularity_image}`)"
+        )
+
+    def create(
+        self,
+        progress_bar: rich.progress.Progress | None = None,
+        task_id: rich.progress.TaskID | None = None,
+        force: bool = False,
+    ) -> tuple[MetaYmlContainers, bool]:
+        """
+        Build docker and singularity containers for linux/amd64 and linux/arm64 using wave.
+
+        Args:
+            progress_bar: Optional progress bar to use for tracking progress
+            task_id: Optional task ID for this module in the progress bar
+
+        Returns:
+            Tuple of (MetaYmlContainers, success boolean). Success is False if any build failed.
+        """
+        containers = MetaYmlContainers()
+        build_tasks = {}
+        threads = max(len(CONTAINER_SYSTEMS) * len(CONTAINER_PLATFORMS), 1)
+        has_failures = False
+
+        if not self.environment_yml:
+            if self._uses_dockerfile():
+                log.info(f"Module '{self.module}' uses a Dockerfile - skipping Wave container build")
+                return MetaYmlContainers(), True
+            raise RuntimeError("No environment.yml found.")
+        assert self.module_directory is not None
+
+        # One spinner per build target — they run visually in parallel
+        build_task_ids: dict[tuple[str, str], rich.progress.TaskID] = {}
+        if progress_bar:
+            for cs in CONTAINER_SYSTEMS:
+                for platform in CONTAINER_PLATFORMS:
+                    short_platform = platform.split("/")[-1]
+                    build_task_ids[(cs, platform)] = progress_bar.add_task(
+                        f"  {cs}/{short_platform}",
+                        total=1,
+                        completed=0,
+                        status="submitting wave build request...",
+                    )
+
+        def make_on_build_id(cs: str, platform: str) -> Callable[[str], None]:
+            def callback(build_id: str) -> None:
+                build_tid = build_task_ids.get((cs, platform))
+                if progress_bar and build_tid is not None:
+                    url = f"{WAVE_URL}/view/builds/{build_id}"
+                    progress_bar.update(build_tid, status=f"building… {url}")
+
+            return callback
+
+        # Set by the main thread on Ctrl+C so in-flight build waiters abort promptly
+        # instead of sleeping out their poll interval / full build timeout.
+        cancel_event = threading.Event()
+
+        # Submit all container build tasks
+        with ThreadPoolExecutor(max_workers=threads) as pool:
+            for cs in CONTAINER_SYSTEMS:
+                for platform in CONTAINER_PLATFORMS:
+                    fut = pool.submit(
+                        self.request_container,
+                        cs,
+                        platform,
+                        self.environment_yml,
+                        self.verbose,
+                        make_on_build_id(cs, platform) if progress_bar else None,
+                        cancel_event,
+                    )
+                    build_tasks[fut] = (cs, platform)
+
+            # Process completed container builds
+            try:
+                for fut in as_completed(build_tasks):
+                    cs, platform = build_tasks[fut]
+                    short_platform = platform.split("/")[-1]
+                    build_tid = build_task_ids.get((cs, platform))
+
+                    try:
+                        getattr(containers, cs)[platform] = fut.result()
+                        if progress_bar and build_tid is not None:
+                            progress_bar.update(build_tid, completed=1, status="[green]done[/green]")
+                    except (ValueError, RuntimeError, OSError, AssertionError) as e:
+                        # make it a warning for arm (not required), but fail for other platforms
+                        if platform == "linux/arm64":
+                            log.warning(
+                                f"Failed to build {cs} container for {platform}: {e}. This is only critical if the tool should support arm64."
+                            )
+                        else:
+                            log.error(f"Failed to build {cs} container for {platform}: {e}")
+                            has_failures = True
+                        if progress_bar and build_tid is not None:
+                            progress_bar.update(build_tid, completed=1, status="[red]failed[/red]")
+                        continue
+            except KeyboardInterrupt:
+                # Signal the running build waiters to stop, drop anything not yet started,
+                # and re-raise so the command aborts instead of blocking on the executor's
+                # wait-for-all shutdown.
+                log.warning("Interrupted — cancelling Wave builds...")
+                cancel_event.set()
+                pool.shutdown(wait=False, cancel_futures=True)
+                raise
+
+        # Remove the per-build spinners now that all builds are done
+        if progress_bar:
+            for tid in build_task_ids.values():
+                progress_bar.remove_task(tid)
+
+        # Set containers early so get_conda_lock_file can access it
+        self.containers = containers
+
+        # Download conda lock files as separate tasks
+        new_lock_files = set()
+        for platform in CONTAINER_PLATFORMS:
+            # Get docker build ID for this platform
+            _docker_entry = containers.docker.get(platform)
+            build_id = _docker_entry.build_id if _docker_entry else ""
+            short_platform = platform.split("/")[-1]
+            if not build_id:
+                log.debug(f"Docker image for {platform} missing - Conda-lock skipped")
+                if progress_bar and task_id is not None:
+                    progress_bar.update(task_id, status=f"conda lock {short_platform} skipped")
+                continue
+
+            conda_lock_path = self.module_directory / ".conda-lock" / f"{platform.replace('/', '_')}-{build_id}.txt"
+            conda_lock_path.parent.mkdir(parents=True, exist_ok=True)
+
+            try:
+                with self._build_cache_lock:
+                    cached_lock_path = self._conda_lock_paths.get(build_id)
+                if cached_lock_path is not None and cached_lock_path.exists():
+                    log.debug(f"Reusing conda lock file for build {build_id} (from {cached_lock_path})")
+                    if progress_bar and task_id is not None:
+                        progress_bar.update(task_id, status=f"conda lock {short_platform} (cached)...")
+                    if cached_lock_path != conda_lock_path:
+                        shutil.copyfile(cached_lock_path, conda_lock_path)
+                else:
+                    # Download conda lock file (it will look up build_id from docker container)
+                    log.debug(f"Downloading conda lock file for {platform} to {conda_lock_path}")
+                    if progress_bar and task_id is not None:
+                        progress_bar.update(task_id, status=f"conda lock {short_platform}...")
+                    conda_lock_path.write_text(self.get_conda_lock_file(platform))
+                    with self._build_cache_lock:
+                        self._conda_lock_paths[build_id] = conda_lock_path
+                # Only register the entry once the lock has actually been written, so
+                # meta.yml never points at a missing lock file.
+                containers.conda[platform] = CondaEntry(lock_file=str(conda_lock_path))
+                new_lock_files.add(conda_lock_path)
+                if progress_bar and task_id is not None:
+                    progress_bar.update(task_id, status=f"conda lock {short_platform} done")
+
+            except (ValueError, RuntimeError, OSError, requests.RequestException) as e:
+                # Wave does not always expose a conda lock for every build (e.g. some
+                # freshly built arm64 images). A missing lock is not fatal: keep the
+                # other platforms' containers and locks instead of failing the module.
+                log.warning(f"No conda lock file available for {platform}: {e}")
+                if progress_bar and task_id is not None:
+                    progress_bar.update(task_id, status=f"conda lock {short_platform} unavailable")
+
+        # Clean up stale conda-lock files
+        self.cleanup_stale_conda_lock_files(new_lock_files)
+
+        # Persist everything (docker, singularity and conda locks) to meta.yml in a
+        # single write. Partial results are kept even if some builds failed.
+        if any(getattr(containers, cs) for cs in CONTAINER_SYSTEMS + ["conda"]):
+            try:
+                self.update_containers_in_meta()
+                log.debug("Updated meta.yml with built containers")
+            except (ValueError, RuntimeError, OSError) as meta_error:
+                log.warning(f"Failed to update meta.yml after container builds: {meta_error}")
+
+        # Update main.nf with new container name (docker amd64 without registry)
+        try:
+            self.update_main_nf_container(force)
+        except OSError as e:
+            log.warning(f"Failed to update main.nf with container name: {e}")
+            has_failures = True
+
+        return containers, not has_failures
+
+    @staticmethod
+    def _raise_if_build_failed(result: dict, build_ref: str, details_uri: str = "") -> None:
+        """
+        Raise a uniform error if a finished Wave build did not succeed.
+
+        Accepts either the container submit response or a ``/status`` response — both
+        expose ``succeeded``/``reason``/``detailsUri`` — so the failure contract lives
+        in one place. ``details_uri`` overrides the value on ``result`` (the status
+        poller keeps the last non-empty build-log URL it saw).
+        """
+        if result.get("succeeded"):
+            return
+        reason = result.get("reason") or "no reason provided"
+        details = details_uri or result.get("detailsUri") or ""
+        raise RuntimeError(f"Wave build {build_ref} failed: {reason}. Build log: {details}")
+
+    def build_containers_with_progress(self, force: bool = False, hide_progress: bool = False) -> list[str]:
+        """Build Seqera/Wave containers for the selected module(s) with a live progress display.
+
+        Builds the single selected module, or every module in ``available_modules`` when
+        the instance was created with ``all_modules=True``. Shows an overall module bar
+        plus, per module, the per-build spinners (docker/singularity × platform) that
+        :meth:`create` renders when a progress bar is passed.
+
+        Args:
+            force: Overwrite existing container directives even if already correct.
+            hide_progress: Disable the live progress display.
+
+        Returns:
+            The names of the modules whose builds failed.
+        """
+        from rich.console import Group
+        from rich.live import Live
+        from rich.progress import BarColumn, MofNCompleteColumn, Progress, SpinnerColumn, TextColumn
+
+        from nf_core.pipelines.containers_utils import try_generate_container_configs
+        from nf_core.pipelines.lint_utils import console
+
+        if self.all_modules:
+            components = self.available_modules
+        else:
+            assert self.nfcore_component is not None
+            components = [self.nfcore_component]
+
+        failed_modules: list[str] = []
+
+        overall_progress = Progress(
+            "[bold blue]{task.description}",
+            BarColumn(),
+            MofNCompleteColumn(),
+            console=console,
+            disable=hide_progress,
+        )
+        module_progress = Progress(
+            SpinnerColumn(finished_text="[green]✓[/green]"),
+            "[bold blue]{task.description}",
+            TextColumn("{task.fields[status]}"),
+            console=console,
+            disable=hide_progress,
+        )
+
+        # Batch builds defer config generation to one full scan after the loop.
+        batch = len(components) > 1
+
+        with Live(Group(overall_progress, module_progress), console=console, transient=True):
+            # The overall bar is only useful when processing more than one module
+            overall_task_id = overall_progress.add_task("modules", total=len(components), visible=len(components) > 1)
+            for component in components:
+                module_name = component.component_name
+                module_task_id = module_progress.add_task(
+                    f"[cyan]{module_name}[/cyan]",
+                    total=None,
+                    status="building containers...",
+                )
+                try:
+                    if self.all_modules:
+                        # Per-module instance, reusing the already-scanned component list
+                        module_containers = ModuleContainers(
+                            module=module_name,
+                            directory=self.directory,
+                            verbose=self.verbose,
+                            components=self.available_modules,
+                        )
+                    else:
+                        module_containers = self
+                    _, success = module_containers.create(
+                        progress_bar=module_progress, task_id=module_task_id, force=force
+                    )
+                    if success:
+                        if module_containers.repo_type == "pipeline" and not batch:
+                            try_generate_container_configs(self.directory, module_containers.module_directory)
+                    else:
+                        failed_modules.append(module_name)
+                except (ValueError, RuntimeError, OSError) as e:
+                    log.error(f"✗ Failed to build containers for {module_name}: {e}")
+                    failed_modules.append(module_name)
+                finally:
+                    overall_progress.advance(overall_task_id)
+                    module_progress.remove_task(module_task_id)
+
+        if batch and self.repo_type == "pipeline" and len(failed_modules) < len(components):
+            try_generate_container_configs(self.directory)
+
+        return failed_modules
+
+    @classmethod
+    def _await_build(
+        cls,
+        request_id: str,
+        poll_interval: int = 5,
+        timeout: int = 1800,
+        cancel_event: threading.Event | None = None,
+    ) -> None:
+        """
+        Wait for a Wave container request to finish by polling its status endpoint.
+
+        Replaces the wave CLI ``--await`` flag. Polls ``GET /v1alpha2/container/{id}/status``
+        until the request reports ``DONE``, then raises (with the failure ``reason``) if it
+        did not succeed.
+
+        Args:
+            request_id: The Wave request id returned by the container submit request.
+            poll_interval: Seconds to wait between status checks.
+            timeout: Maximum seconds to wait before giving up.
+            cancel_event: When set (by the main thread on Ctrl+C), abort the wait promptly
+                instead of sleeping out the poll interval.
+        """
+        if not request_id:
+            raise RuntimeError("Wave did not return a requestId to await")
+
+        status_url = f"{WAVE_API_ALPHA2}/container/{quote(request_id, safe='')}/status"
+        # Updated from each status response; the API returns a ready-made build log URL.
+        details_uri = ""
+        deadline = time.monotonic() + timeout
+        while True:
+            if cancel_event is not None and cancel_event.is_set():
+                raise RuntimeError(f"Wave build {request_id} await cancelled")
+            status = wave_request("get", status_url, error_context=f"Wave status check for request {request_id}")
+            details_uri = status.get("detailsUri") or details_uri
+            if status.get("status") == "DONE":
+                cls._raise_if_build_failed(status, request_id, details_uri)
+                log.debug(f"Wave build {request_id} completed in {status.get('duration')}s")
+                return
+            if time.monotonic() > deadline:
+                raise RuntimeError(
+                    f"Wave build {request_id} did not complete within {timeout}s. Build log: {details_uri}"
+                )
+            # Interruptible sleep: Event.wait returns True immediately once cancelled,
+            # otherwise blocks for poll_interval like time.sleep.
+            if cancel_event is not None:
+                if cancel_event.wait(poll_interval):
+                    raise RuntimeError(f"Wave build {request_id} await cancelled")
+            else:
+                time.sleep(poll_interval)
+
+    @classmethod
+    def request_container(
+        cls,
+        container_system: str,
+        platform: str,
+        conda_file: Path,
+        verbose=False,
+        on_build_id: Callable[[str], None] | None = None,
+        cancel_event: threading.Event | None = None,
+    ) -> ContainerEntry:
+        assert conda_file.exists()
+        assert container_system in CONTAINER_SYSTEMS
+        assert platform in CONTAINER_PLATFORMS
+
+        conda_bytes = conda_file.read_bytes()
+        cache_key = (hashlib.sha256(conda_bytes).hexdigest(), container_system, platform)
+        with cls._build_cache_lock:
+            cached_entry = cls._build_cache.get(cache_key)
+        if cached_entry is not None:
+            log.debug(f"Reusing cached {container_system}/{platform} build for identical environment.yml")
+            return cached_entry
+
+        # Submit the build via the Wave HTTP API (POST /v1alpha2/container).
+        # `freeze` with no buildRepository pushes to the public community registry.
+        payload: dict = {
+            "packages": {
+                "type": "CONDA",
+                "environment": base64.b64encode(conda_bytes).decode(),
+            },
+            "containerPlatform": platform,
+            "freeze": True,
+            "buildTemplate": "conda/pixi:v1",
+            "format": WAVE_FORMAT[container_system],
+            "nameStrategy": "imageSuffix",
+        }
+        meta_data = wave_request(
+            "post",
+            f"{WAVE_API_ALPHA2}/container",
+            payload,
+            error_context=f"Wave build submit ({container_system} {platform})",
+        )
+        log.log(
+            logging.INFO if verbose else logging.DEBUG,
+            f"Wave response ({container_system} {platform}):\n{pretty_repr(meta_data)}",
+        )
+
+        build_id = meta_data.get("buildId") or ""
+        request_id = meta_data.get("requestId") or ""
+        # Notify as soon as we have a build id, before waiting for the build to finish.
+        if build_id and on_build_id is not None:
+            on_build_id(build_id)
+
+        # Wave returns a targetImage/buildId even for failed builds, so a cached/DONE
+        # submit response must still be checked for success — not only the polling path.
+        succeeded = meta_data.get("succeeded")
+        is_final = bool(meta_data.get("cached")) or meta_data.get("status") == "DONE"
+        if is_final and succeeded is not None:
+            # Submit response already carries an authoritative result.
+            cls._raise_if_build_failed(meta_data, build_id or request_id)
+        elif not is_final or request_id:
+            # Not final, or final but ambiguous: the status endpoint is authoritative.
+            cls._await_build(request_id, cancel_event=cancel_event)
+
+        image = meta_data.get("targetImage") or meta_data.get("containerImage") or ""
+        if not image:
+            raise RuntimeError(f"Wave build ({container_system} {platform}) did not return an image name")
+
+        scan_id = ""
+        https_url = ""
+
+        if container_system == "docker":
+            scan_id = meta_data.get("scanId") or ""
+
+        if container_system == "singularity":
+            inspect_out = cls.request_image_inspect(image)
+            container_layers = inspect_out.get("container", {}).get("manifest", {}).get("layers", {})
+
+            if not (
+                len(container_layers) == 1
+                and container_layers[0].get("mediaType", "").endswith(".sif")
+                and container_layers[0].get("digest")
+            ):
+                log.warning(f"Https-url for image {image} could not be extracted from image inspect output")
+
+            else:
+                log.debug(f"Extracting https-uri for {image} from image inspect:\n{pretty_repr(container_layers[0])}")
+                digest = container_layers[0]["digest"].replace("sha256:", "")
+                https_url = (
+                    f"https://{ContainerRegistryUrls.SEQERA_SINGULARITY.value}/blobs/sha256/{digest[:2]}/{digest}/data"
+                )
+
+        entry = ContainerEntry(name=image, build_id=build_id, scan_id=scan_id, https=https_url)
+        with cls._build_cache_lock:
+            cls._build_cache[cache_key] = entry
+        return entry
+
+    @classmethod
+    def request_image_inspect(cls, image: str) -> dict:
+        """
+        Inspect a container image via the Wave HTTP API (POST /v1alpha1/inspect).
+        """
+        log.debug(f"Requesting Wave image inspect for image {image}")
+        return wave_request(
+            "post",
+            f"{WAVE_API_ALPHA1}/inspect",
+            {"containerImage": image},
+            error_context=f"Wave inspect for image {image}",
+        )
+
+    @staticmethod
+    def get_conda_lock_url(build_id) -> str:
+        build_id_safe = quote(build_id, safe="")
+        url = f"{WAVE_API_ALPHA1}/builds/{build_id_safe}/condalock"
+        return url
+
+    def get_conda_lock_file(self, platform: str) -> str:
+        """
+        Get the conda lock file for an existing environment.
+        Try (in that order):
+            1. reading from meta.yml
+            2. reading from cached containers
+            3. recreating with wave commands
+        """
+        assert platform in CONTAINER_PLATFORMS
+
+        containers = self.containers or self.get_containers_from_meta() or self.create()[0]
+
+        # Get build_id from docker container for this platform
+        _docker_entry = containers.docker.get(platform) if containers else None
+        build_id = _docker_entry.build_id if _docker_entry else None
+        if not build_id:
+            raise ValueError(f"No build_id found for docker container on platform {platform}")
+
+        # Generate the conda lock URL from the build_id
+        conda_lock_url = self.get_conda_lock_url(build_id)
+
+        # condalock returns plain text; route through the shared transport so the download
+        # shares Wave auth (and thus the relaxed rate limits) with the other Wave calls.
+        log.debug(f"Downloading conda lock file from {conda_lock_url}")
+        resp = wave_send("get", conda_lock_url, error_context=f"Conda lock download for platform {platform}")
+        log.debug(f"Successfully downloaded conda lock file from {conda_lock_url}")
+        return resp.text
+
+    def list_containers(self) -> list[tuple[str, str, str]]:
+        """
+        Return containers defined in the module meta.yml as a list of (<container-system>, <platform>, <image-name>).
+        """
+        containers_valid = self.get_containers_from_meta()
+        if not containers_valid:
+            return []
+        containers_flat = []
+        for cs in CONTAINER_SYSTEMS + ["conda"]:
+            for p in CONTAINER_PLATFORMS:
+                if cs == "conda":
+                    conda_entry = containers_valid.conda.get(p)
+                    if conda_entry:
+                        containers_flat.append((cs, p, conda_entry.lock_file))
+                else:
+                    entry = getattr(containers_valid, cs).get(p)
+                    if entry:
+                        containers_flat.append((cs, p, entry.name))
+                        if cs == "singularity" and entry.https:
+                            containers_flat.append((cs, p, entry.https))
+        return containers_flat
+
+    def get_containers_from_meta(self) -> MetaYmlContainers | None:
+        """
+        Return containers defined in the module meta.yml.
+        Returns None if containers section is missing, incomplete, or invalid.
+        """
+        if self.meta_yml is None or not self.meta_yml.exists():
+            raise FileNotFoundError(f"No meta.yml found for module '{self.module}'")
+
+        meta = read_meta_yml(self.meta_yml)
+        containers = meta.get("containers", {})
+        if not containers:
+            log.debug(f"Section 'containers' missing from meta.yaml for module '{self.module}'")
+            return None
+
+        try:
+            return MetaYmlContainers.model_validate(containers, context={"require_complete": True})
+        except ValidationError as e:
+            log.debug(f"Could not parse containers from meta.yml: {e}")
+            return None
+
+    def update_containers_in_meta(self, module_lint: ModuleLint | None = None) -> None:
+        """
+        Update the containers section in meta.yml.
+
+        Args:
+            module_lint: Optional ModuleLint instance to use for sorting.
+                        If not provided, a new instance will be created.
+        """
+        if self._uses_dockerfile():
+            log.info(f"Module '{self.module}' uses a Dockerfile - skipping meta.yml container update")
+            return
+
+        if self.containers is None:
+            log.debug("Containers not initialized - running `create()` ...")
+            self.containers, _ = self.create()
+
+        if self.meta_yml is None or not self.meta_yml.exists():
+            raise FileNotFoundError(f"No meta.yml found for module '{self.module}'")
+
+        meta = read_meta_yml(self.meta_yml)
+        meta_containers = meta.get("containers", {})
+        # Remove stale entries for all known systems/platforms so old containers don't
+        # mix with new ones when a build partially fails.
+        for cs in CONTAINER_SYSTEMS + ["conda"]:
+            for platform in CONTAINER_PLATFORMS:
+                meta_containers.get(cs, {}).pop(platform, None)
+        new_containers = self.containers.dump_for_meta_yml()
+        for cs, platforms in new_containers.items():
+            for platform, data in platforms.items():
+                if data:
+                    meta_containers.setdefault(cs, {})[platform] = data
+        # Remove empty container system dicts left after clearing stale entries
+        meta_containers = {cs: platforms for cs, platforms in meta_containers.items() if platforms}
+        meta["containers"] = meta_containers
+
+        # Sort the YAML according to the schema's property order using ModuleLint
+        # (constructed once per instance - it re-scans the modules repo)
+        if module_lint is None:
+            if self._module_lint is None:
+                try:
+                    self._module_lint = ModuleLint(self.directory)
+                except (UserWarning, ValueError, OSError) as e:
+                    log.warning(f"Failed to initialize ModuleLint for sorting: {e}")
+            module_lint = self._module_lint
+
+        if module_lint is not None:
+            try:
+                meta = module_lint.sort_meta_yml(meta)
+            except UserWarning as e:
+                log.warning(f"Failed to sort meta.yml: {e}")
+
+        with open(self.meta_yml, "w") as f:
+            ruamel_yaml.dump(meta, f)
+
+        # Format with prettier for consistent styling
+        try:
+            run_prettier_on_file(self.meta_yml)
+        except (FileNotFoundError, OSError) as e:
+            log.debug(f"Could not run prettier on meta.yml: {e}")
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index f2472db0d3..f21c28b2d5 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -14,7 +14,6 @@
 from pathlib import Path
 from typing import Any
 
-import questionary
 import rich
 import rich.progress
 import ruamel.yaml
@@ -29,9 +28,9 @@
 
 log = logging.getLogger(__name__)
 
-from .environment_yml import environment_yml
+from .environment_yml import lint_environment_yml
 from .main_nf import main_nf
-from .meta_yml import meta_yml, obtain_inputs, obtain_outputs, obtain_topics, read_meta_yml
+from .meta_yml import meta_yml, meta_yml_containers, obtain_inputs, obtain_outputs, obtain_topics, read_meta_yml_patched
 from .module_changes import module_changes
 from .module_deprecations import module_deprecations
 from .module_patch import module_patch
@@ -47,13 +46,13 @@ class ModuleLint(ComponentLint):
     """
 
     # Import lint functions
-    environment_yml = environment_yml
+    environment_yml = lint_environment_yml
     main_nf = main_nf
     meta_yml = meta_yml
     obtain_inputs = obtain_inputs
     obtain_outputs = obtain_outputs
     obtain_topics = obtain_topics
-    read_meta_yml = read_meta_yml
+    read_meta_yml_patched = read_meta_yml_patched
     module_changes = module_changes
     module_deprecations = module_deprecations
     module_patch = module_patch
@@ -69,7 +68,7 @@ def __init__(
         remote_url: str | None = None,
         branch: str | None = None,
         no_pull: bool = False,
-        registry: str | None = None,
+        registry: tuple[str, ...] = ("quay.io", "community.wave.seqera.io/library"),
         hide_progress: bool = False,
     ):
         super().__init__(
@@ -88,7 +87,6 @@ def __init__(
     def lint(
         self,
         module=None,
-        registry="quay.io",
         key=(),
         all_modules=False,
         print_results=True,
@@ -124,24 +122,9 @@ def lint(
         # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class
         # Prompt for module or all
         if module is None and not (local or all_modules) and len(self.all_remote_components) > 0:
-            questions = [
-                {
-                    "type": "list",
-                    "name": "all_modules",
-                    "message": "Lint all modules or a single named module?",
-                    "choices": ["All modules", "Named module"],
-                },
-                {
-                    "type": "autocomplete",
-                    "name": "tool_name",
-                    "message": "Tool name:",
-                    "when": lambda x: x["all_modules"] == "Named module",
-                    "choices": [m.component_name for m in self.all_remote_components],
-                },
-            ]
-            answers = questionary.unsafe_prompt(questions, style=nf_core.utils.nfcore_question_style)
-            all_modules = answers["all_modules"] == "All modules"
-            module = answers.get("tool_name")
+            module = nf_core.modules.modules_utils.prompt_module_selection(
+                self.all_remote_components, component_type="modules", action="Lint"
+            )
 
         # Only lint the given module
         if module:
@@ -173,25 +156,22 @@ def lint(
 
         # Lint local modules
         if local and len(local_modules) > 0:
-            self.lint_modules(local_modules, registry=registry, local=True, fix_version=fix_version)
+            self.lint_modules(local_modules, local=True, fix_version=fix_version)
 
         # Lint nf-core modules
         if not local and len(remote_modules) > 0:
-            self.lint_modules(remote_modules, registry=registry, local=False, fix_version=fix_version)
+            self.lint_modules(remote_modules, local=False, fix_version=fix_version)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by, plain_text=plain_text)
             self.print_summary(plain_text=plain_text)
 
-    def lint_modules(
-        self, modules: list[NFCoreComponent], registry: str = "quay.io", local: bool = False, fix_version: bool = False
-    ) -> None:
+    def lint_modules(self, modules: list[NFCoreComponent], local: bool = False, fix_version: bool = False) -> None:
         """
         Lint a list of modules
 
         Args:
             modules ([NFCoreComponent]): A list of module objects
-            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core modules
             fix_version (boolean): Fix the module version if a newer version is available
         """
@@ -243,6 +223,7 @@ def lint_module(
             mod.get_inputs_from_main_nf()
             mod.get_outputs_from_main_nf()
             mod.get_topics_from_main_nf()
+            # TODO container-conversion:  get_containers from main_nf
             # Update meta.yml file if requested
             if self.fix and mod.meta_yml is not None:
                 self.update_meta_yml_file(mod)
@@ -252,7 +233,11 @@ def lint_module(
                     continue
                 if test_name == "main_nf":
                     getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
-                elif test_name in ["meta_yml", "environment_yml"]:
+                elif test_name == "environment_yml":
+                    getattr(self, test_name)(
+                        mod, allow_missing=True, fix_version=fix_version, progress_bar=progress_bar
+                    )
+                elif test_name == "meta_yml":
                     # Allow files to be missing for local
                     getattr(self, test_name)(mod, allow_missing=True)
                 else:
@@ -270,6 +255,8 @@ def lint_module(
             mod.get_inputs_from_main_nf()
             mod.get_outputs_from_main_nf()
             mod.get_topics_from_main_nf()
+            # TODO container-conversion:  get_containers from main_nf
+
             # Update meta.yml file if requested
             if self.fix:
                 self.update_meta_yml_file(mod)
@@ -282,6 +269,8 @@ def lint_module(
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
                     getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
+                elif test_name == "environment_yml":
+                    getattr(self, test_name)(mod, fix_version=fix_version, progress_bar=progress_bar)
                 else:
                     getattr(self, test_name)(mod)
 
@@ -316,11 +305,33 @@ def load_meta_schema(self) -> Mapping[str, Any]:
             self.meta_schema = json.load(fh)
         return self.meta_schema
 
+    def sort_meta_yml(self, meta_yml: dict) -> dict:
+        """Sort meta.yml keys according to the schema's property order.
+
+        Recurses into nested objects that the schema describes with ``properties``
+        (e.g. ``containers`` -> docker, singularity, conda), so sub-sections are sorted
+        too. Arrays, ``$ref``/``patternProperties`` nodes and scalars are left untouched.
+        """
+        try:
+            schema = self.load_meta_schema()
+        except LintExceptionError as e:
+            raise UserWarning("Failed to load meta schema", e) from e
+
+        def sort_by_schema(data, node):
+            properties = node.get("properties", {}) if isinstance(node, dict) else {}
+            if not isinstance(data, dict) or not properties:
+                return data
+            # Schema-ordered keys first (recursing into each), then any extras preserved
+            ordered = {key: sort_by_schema(data[key], child) for key, child in properties.items() if key in data}
+            return {**ordered, **{key: value for key, value in data.items() if key not in ordered}}
+
+        return sort_by_schema(meta_yml, schema)
+
     def update_meta_yml_file(self, mod):
         """
-        Update the meta.yml file with the correct inputs and outputs
+        Update the meta.yml file with the correct inputs, outputs, topics and containers
         """
-        meta_yml = self.read_meta_yml(mod)
+        meta_yml = self.read_meta_yml_patched(mod)
         if meta_yml is None:
             log.warning(f"Could not read meta.yml for {mod.component_name}, skipping update")
             return
@@ -368,29 +379,6 @@ def check_match(element: dict) -> dict | None:
 
             return {}
 
-        def _sort_meta_yml(meta_yml: dict) -> dict:
-            """Sort meta.yml keys according to the schema's property order"""
-            # Get the schema to determine the correct key order
-            try:
-                schema = self.load_meta_schema()
-                schema_keys = list(schema["properties"].keys())
-            except (LintExceptionError, KeyError) as e:
-                raise UserWarning("Failed to load meta schema", e) from e
-
-            result: dict = {}
-
-            # First, add keys in the order they appear in the schema
-            for key in schema_keys:
-                if key in meta_yml:
-                    result[key] = meta_yml[key]
-
-            # Then add any keys that aren't in the schema (to preserve custom keys)
-            for key in meta_yml:
-                if key not in result:
-                    result[key] = meta_yml[key]
-
-            return result
-
         # Obtain inputs, outputs and topics from main.nf and meta.yml
         # Used to compare only the structure of channels and elements
         # Do not compare features to allow for custom features in meta.yml (i.e. pattern)
@@ -611,13 +599,21 @@ def _add_edam_ontologies(section, edam_formats, desc):
                 section["ontologies"] = []
             log.debug(f"expected ontologies for {desc}: {expected_ontologies}")
             log.debug(f"current ontologies for {desc}: {current_ontologies}")
-            for ontology, ext in expected_ontologies:
-                if ontology not in current_ontologies:
+            for ontology_url, ext in expected_ontologies:
+                comment_text = edam_formats[ext][1]
+                if ontology_url not in current_ontologies:
                     try:
-                        section["ontologies"].append(ruamel.yaml.comments.CommentedMap({"edam": ontology}))
-                        section["ontologies"][-1].yaml_add_eol_comment(f"{edam_formats[ext][1]}", "edam")
+                        cm = ruamel.yaml.comments.CommentedMap()
+                        cm["edam"] = ontology_url
+                        cm.yaml_add_eol_comment(comment_text, key="edam")
+                        section["ontologies"].append(cm)
                     except KeyError:
                         log.warning(f"Could not add ontologies in {desc}")
+                else:
+                    for item in section["ontologies"]:
+                        if isinstance(item, ruamel.yaml.comments.CommentedMap) and item.get("edam") == ontology_url:
+                            item.yaml_add_eol_comment(comment_text, key="edam")
+                            break
 
         # EDAM ontologies
         edam_formats = nf_core.modules.modules_utils.load_edam()
@@ -681,14 +677,21 @@ def _add_edam_ontologies(section, edam_formats, desc):
 
         def _ensure_string_keys(obj):
             """Recursively ensure all dict keys are strings (e.g., convert 1.2 -> "1.2")"""
-            if isinstance(obj, dict):
+            # This first block is needed to keep the comments in the yml
+            if isinstance(obj, ruamel.yaml.comments.CommentedMap):
+                for key in list(obj.keys()):
+                    value = obj.pop(key)
+                    new_key = str(key) if not isinstance(key, str) else key
+                    obj[new_key] = _ensure_string_keys(value)
+                return obj
+            elif isinstance(obj, dict):
                 return {str(k) if not isinstance(k, str) else k: _ensure_string_keys(v) for k, v in obj.items()}
             elif isinstance(obj, list):
                 return [_ensure_string_keys(item) for item in obj]
             else:
                 return obj
 
-        corrected_meta_yml = _sort_meta_yml(corrected_meta_yml)
+        corrected_meta_yml = self.sort_meta_yml(corrected_meta_yml)
         corrected_meta_yml = _ensure_string_keys(corrected_meta_yml)
 
         with open(mod.meta_yml, "w") as fh:
diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index 63b3aac752..cd5ede8943 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -4,9 +4,12 @@
 
 import ruamel.yaml
 from jsonschema import exceptions, validators
+from rich.progress import Progress
 
-from nf_core.components.lint import ComponentLint, LintExceptionError
+import nf_core.utils
+from nf_core.components.lint import ComponentLint
 from nf_core.components.nfcore_component import NFCoreComponent
+from nf_core.modules.modules_utils import module_uses_dockerfile
 
 log = logging.getLogger(__name__)
 
@@ -15,7 +18,23 @@
 yaml.indent(mapping=2, sequence=2, offset=2)
 
 
-def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None:
+def _fix_module_version(self, current_version, latest_version):
+    """Update the conda package version in environment.yml."""
+    with open(self.environment_yml) as source:
+        content = source.read()
+    new_content = content.replace(f"={current_version}", f"={latest_version}", 1)
+    with open(self.environment_yml, "w") as source:
+        source.write(new_content)
+    return True
+
+
+def lint_environment_yml(
+    module_lint_object: ComponentLint,
+    module: NFCoreComponent,
+    allow_missing: bool = False,
+    fix_version: bool = False,
+    progress_bar: Progress | None = None,
+) -> None:
     """
     Lint an ``environment.yml`` file.
 
@@ -25,15 +44,44 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
 
     The following checks are performed:
 
-    * ``environment_yml_exists``: The ``environment.yml`` file must exist if it is
-      referenced in ``main.nf``.
+    environment_yml_exists
+    ^^^^^^^^^^^^^^^^^^^^^^^
+
+    The ``environment.yml`` file must exist, unless the
+    module has a Dockerfile. If neither ``environment.yml`` nor a Dockerfile is
+    present, the test fails.
+
+    environment_yml_dockerfile_conflict
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+    A module must not have both an
+    ``environment.yml`` and a Dockerfile; Remove the Dockerfile if present.
+
+    environment_yml_valid
+    ^^^^^^^^^^^^^^^^^^^^^^
+
+    The ``environment.yml`` must be valid according to
+    the JSON schema defined at https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json.
+
+    environment_yml_sorted
+    ^^^^^^^^^^^^^^^^^^^^^^^
+
+    The dependencies listed in ``environment.yml``
+    must be sorted alphabetically. If they are not, they will be sorted
+    automatically.
+
+    bioconda_version
+    ^^^^^^^^^^^^^^^^
+
+    The version specified for each bioconda package must
+    be a valid, known version available in the bioconda channel.
 
-    * ``environment_yml_valid``: The ``environment.yml`` must be valid according to
-      the JSON schema defined at https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json.
+    bioconda_latest
+    ^^^^^^^^^^^^^^^
 
-    * ``environment_yml_sorted``: The dependencies listed in ``environment.yml``
-      must be sorted alphabetically. If they are not, they will be sorted
-      automatically.
+    Each bioconda package should be pinned to the latest
+    available version. A warning is raised (or the version updated if
+    ``fix_version`` is set) when a newer version exists.
     """
     env_yml = None
     has_schema_header = False
@@ -47,6 +95,16 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
 
     #  load the environment.yml file
     if module.environment_yml is None:
+        if module_uses_dockerfile(module):
+            module.passed.append(
+                (
+                    "environment_yml",
+                    "environment_yml_exists",
+                    "Module's `environment.yml` does not exist, but module has a Dockerfile",
+                    Path(module.component_dir, "environment.yml"),
+                )
+            )
+            return
         if allow_missing:
             module.warned.append(
                 (
@@ -57,7 +115,15 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
                 ),
             )
             return
-        raise LintExceptionError("Module does not have an `environment.yml` file")
+        module.failed.append(
+            (
+                "environment_yml",
+                "environment_yml_exists",
+                "Module's `environment.yml` does not exist and module has no Dockerfile",
+                Path(module.component_dir, "environment.yml"),
+            )
+        )
+        return
     try:
         # Read the entire file content to handle headers properly
         with open(module.environment_yml) as fh:
@@ -86,6 +152,26 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
             )
         )
 
+        component_dir = Path(module.component_dir)
+        if (component_dir / "Dockerfile").exists() or (component_dir.parent / "Dockerfile").exists():
+            module.failed.append(
+                (
+                    "environment_yml",
+                    "environment_yml_dockerfile_conflict",
+                    "Module has both an `environment.yml` and a Dockerfile; only one should be present",
+                    module.environment_yml,
+                )
+            )
+        else:
+            module.passed.append(
+                (
+                    "environment_yml",
+                    "environment_yml_dockerfile_conflict",
+                    "Module does not have conflicting `environment.yml` and Dockerfile",
+                    module.environment_yml,
+                )
+            )
+
     except FileNotFoundError:
         # check if the module's main.nf requires a conda environment
         with open(Path(module.component_dir, "main.nf")) as fh:
@@ -229,3 +315,118 @@ def sort_key(x):
                         module.environment_yml,
                     )
                 )
+
+        # Check bioconda package versions
+        if "dependencies" in env_yml:
+            bioconda_packages = [x for x in env_yml["dependencies"] if isinstance(x, str) and "bioconda::" in x]
+            for bp in bioconda_packages:
+                bp = bp.strip("'").strip('"')
+                try:
+                    bioconda_version = bp.split("=")[1]
+                    response = nf_core.utils.anaconda_package(bp)
+                    module.passed.append(
+                        (
+                            "environment_yml",
+                            "bioconda_version",
+                            f"Conda version specified correctly: {bp}",
+                            module.environment_yml,
+                        )
+                    )
+                except LookupError:
+                    module.warned.append(
+                        (
+                            "environment_yml",
+                            "bioconda_version",
+                            f"Conda version not specified correctly: {bp}",
+                            module.environment_yml,
+                        )
+                    )
+                except ValueError:
+                    module.failed.append(
+                        (
+                            "environment_yml",
+                            "bioconda_version",
+                            f"Conda version not specified correctly: {bp}",
+                            module.environment_yml,
+                        )
+                    )
+                else:
+                    # Check that required version is available at all
+                    if bioconda_version not in response.get("versions"):
+                        module.failed.append(
+                            (
+                                "environment_yml",
+                                "bioconda_version",
+                                f"Conda package {bp} had unknown version: `{bioconda_version}`",
+                                module.environment_yml,
+                            )
+                        )
+                        continue  # No need to test for latest version, continue linting
+                    # Check version is latest available
+                    last_ver = response.get("latest_version")
+                    if last_ver is not None and last_ver != bioconda_version:
+                        package, ver = bp.split("=", 1)
+                        if fix_version:
+                            try:
+                                fixed = _fix_module_version(module, bioconda_version, last_ver)
+                            except FileNotFoundError as e:
+                                fixed = False
+                                log.debug(f"Unable to update package {package} due to error: {e}")
+                            else:
+                                if fixed:
+                                    if progress_bar is not None:
+                                        progress_bar.print(
+                                            f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}"
+                                        )
+                                    log.debug(f"Updating package {package} {ver} -> {last_ver}")
+                                    module.passed.append(
+                                        (
+                                            "environment_yml",
+                                            "bioconda_latest",
+                                            f"Conda package has been updated to the latest available: `{bp}`",
+                                            module.environment_yml,
+                                        )
+                                    )
+                                    # If the version was updated, we should also try to rebuild the container to ensure it works with the new version
+                                    try:
+                                        from nf_core.modules.containers import ModuleContainers
+
+                                        mc = ModuleContainers(
+                                            module=module.component_name,
+                                            directory=module.base_dir,
+                                        )
+                                        mc.create(progress_bar=progress_bar)
+                                    except (ImportError, ValueError, RuntimeError, OSError) as e:
+                                        log.warning(f"Container rebuild after version update failed: {e}")
+                                else:
+                                    if progress_bar is not None:
+                                        progress_bar.print(
+                                            f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
+                                        )
+                                    log.debug(f"Unable to update package {package} {ver} -> {last_ver}")
+                                    module.warned.append(
+                                        (
+                                            "environment_yml",
+                                            "bioconda_latest",
+                                            f"Conda update: {package} `{ver}` -> `{last_ver}`",
+                                            module.environment_yml,
+                                        )
+                                    )
+                        else:
+                            module.warned.append(
+                                (
+                                    "environment_yml",
+                                    "bioconda_latest",
+                                    f"Conda update: {package} `{ver}` -> `{last_ver}`",
+                                    module.environment_yml,
+                                )
+                            )
+                    else:
+                        module.passed.append(
+                            (
+                                "environment_yml",
+                                "bioconda_latest",
+                                f"Conda package is the latest available: `{bp}`",
+                                module.environment_yml,
+                            )
+                        )
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index eb365a4d73..699de45abe 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -4,23 +4,19 @@
 
 import logging
 import re
-import sqlite3
 from pathlib import Path
-from urllib.parse import urlparse, urlunparse
 
-import requests
-import yaml
 from rich.progress import Progress
 
-import nf_core
 from nf_core.components.components_differ import ComponentsDiffer
 from nf_core.components.nfcore_component import NFCoreComponent
+from nf_core.modules.lint.meta_yml import _load_skip_nf_test_sets
 
 log = logging.getLogger(__name__)
 
 
 def main_nf(
-    module_lint_object, module: NFCoreComponent, fix_version: bool, registry: str, progress_bar: Progress
+    module_lint_object, module: NFCoreComponent, fix_version: bool, registry: tuple[str, ...], progress_bar: Progress
 ) -> tuple[list[str], list[str]]:
     """Lint a ``main.nf`` module file
 
@@ -29,34 +25,86 @@ def main_nf(
 
     The following checks are performed:
 
-    * ``main_nf_exists``: The ``main.nf`` file must exist.
+    main_nf_module_granularity
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-    * ``deprecated_dsl2``: The file must not contain deprecated DSL2 identifiers
-      (``initOptions``, ``saveFiles``, ``getSoftwareName``, ``getProcessName``,
-      ``publishDir``).
+    The module must represent a single command
+    as ``<tool>`` or single subcommand with distinct functionality as
+    ``<tool/subtool>``.
 
-    * ``main_nf_script_outputs``: The process must have an ``output:`` block.
+    main_nf_exists
+    ^^^^^^^^^^^^^^
 
-    * ``main_nf_container``: Container tags across the ``singularity``, ``docker``,
-      and ``conda`` directives must reference the same software version. A warning
-      is issued if they do not match.
+    The ``main.nf`` file must exist.
 
-    * ``main_nf_script_shell``: Exactly one of ``script:``, ``shell:``, or ``exec:``
-      blocks must be present.
+    deprecated_dsl2
+    ^^^^^^^^^^^^^^^
 
-    * ``main_nf_shell_template``: If a ``shell:`` block is used, it must call
-      a ``template``.
+    The file must not contain deprecated DSL2 identifiers
+    (``initOptions``, ``saveFiles``, ``getSoftwareName``, ``getProcessName``,
+    ``publishDir``).
 
-    * ``main_nf_meta_output``: If ``meta`` is present in the module inputs, it
-      must also appear in at least one output channel.
+    main_nf_script_outputs
+    ^^^^^^^^^^^^^^^^^^^^^^^
 
-    * ``main_nf_version_topic``: The module should emit software versions using
-      a ``topic: versions`` output. A warning is issued if no such topic is found.
+    The process must have an ``output:`` block.
 
-    * ``main_nf_version_emit``: The number of ``topic: versions`` outputs must
-      equal the number of ``emit:`` outputs whose name starts with ``versions``.
-      A warning is issued if a legacy YAML-based ``versions`` emit is used instead
-      of a topic output.
+    main_nf_container
+    ^^^^^^^^^^^^^^^^^
+
+    When both a ``singularity`` and a ``docker`` container
+    are specified, their tags must reference the same software version. A warning
+    is issued if they do not match. Modules using the newer docker-only format
+    (no singularity container) skip this check.
+
+    singularity_tag
+    ^^^^^^^^^^^^^^^
+
+    A Singularity container must be resolvable via
+    ``nextflow inspect -profile singularity``. The check fails if none can be
+    resolved or if it falls back to a docker container that has an automatic
+    singularity equivalent, i.e., ``quay.io/biocontainers/`` or
+    ``community.wave.seqera.io/``.
+    It is skipped for modules listed under ``singularity`` in ``.github/skip_nf_test.json``.
+
+    oras_singularity_tag
+    ^^^^^^^^^^^^^^^^^^^^^
+
+    The resolved Singularity container must not be
+    served over the ``oras://`` scheme; it should be a plain ``https://`` URL.
+    The check fails if an ``oras://`` container is used.
+
+    main_nf_script_shell
+    ^^^^^^^^^^^^^^^^^^^^^
+
+    Exactly one of ``script:``, ``shell:``, or ``exec:``
+    blocks must be present.
+
+    main_nf_shell_template
+    ^^^^^^^^^^^^^^^^^^^^^^^
+
+    If a ``shell:`` block is used, it must call
+    a ``template``.
+
+    main_nf_meta_output
+    ^^^^^^^^^^^^^^^^^^^
+
+    If ``meta`` is present in the module inputs, it
+    must also appear in at least one output channel.
+
+    main_nf_version_topic
+    ^^^^^^^^^^^^^^^^^^^^^^
+
+    The module should emit software versions using
+    a ``topic: versions`` output. A warning is issued if no such topic is found.
+
+    main_nf_version_emit
+    ^^^^^^^^^^^^^^^^^^^^^
+
+    The number of ``topic: versions`` outputs must
+    equal the number of ``emit:`` outputs whose name starts with ``versions``.
+    A warning is issued if a legacy YAML-based ``versions`` emit is used instead
+    of a topic output.
 
     """
 
@@ -64,6 +112,9 @@ def main_nf(
     emits: list[str] = []
     topics: list[str] = []
 
+    # Check the module name
+    check_nf_module_name(module, module.component_name)
+
     # Check if we have a patch file affecting the 'main.nf' file
     # otherwise read the lines directly from the module
     lines: list[str] = []
@@ -171,10 +222,13 @@ def main_nf(
         module.passed.append(("main_nf", "main_nf_script_outputs", "Process 'output' block found", module.main_nf))
 
     # Check the process definitions
-    if check_process_section(module, process_lines, registry, fix_version, progress_bar):
+    containers_match = check_process_section(module, process_lines, registry, fix_version, progress_bar)
+    if containers_match is True:
         module.passed.append(("main_nf", "main_nf_container", "Container versions match", module.main_nf))
-    else:
+    elif containers_match is False:
         module.warned.append(("main_nf", "main_nf_container", "Container versions do not match", module.main_nf))
+    # ``None`` means only one (or no) container type was specified (e.g. the newer
+    # docker-only format), so there is nothing to compare and no check is emitted.
 
     # Check the when statement
     check_when_section(module, when_lines)
@@ -272,6 +326,41 @@ def main_nf(
     return inputs, emits
 
 
+def check_nf_module_name(self, component_name):
+    """
+    Lint the module name
+    Checks whether the module name has at most two levels of granularity, no
+    punctuation and lowercase.
+    """
+    # Module name is lowercase
+    if component_name.islower():
+        self.passed.append(("main_nf", "main_nf_module_lowercase", "Process name is lowercase", self.main_nf))
+    else:
+        self.failed.append(("main_nf", "main_nf_module_lowercase", "Process name should be lowercase", self.main_nf))
+
+    # Module name has no punctuation
+    if component_name.replace("/", "").isalnum():
+        self.passed.append(
+            ("main_nf", "main_nf_module_no_punctuation", "Module properly named without punctuation", self.main_nf)
+        )
+    else:
+        self.failed.append(
+            ("main_nf", "main_nf_module_no_punctuation", "Module name should not have any punctuation", self.main_nf)
+        )
+
+    # Module name granularity
+    if component_name.count("/") > 1:
+        self.failed.append(
+            ("main_nf", "main_nf_module_granularity", "Module not named as `<tool>` or `<tool/subtool>`", self.main_nf)
+        )
+    elif component_name.count("/") == 1:
+        self.passed.append(
+            ("main_nf", "main_nf_module_granularity", "Module properly named as `<tool/subtool>`", self.main_nf)
+        )
+    else:
+        self.passed.append(("main_nf", "main_nf_module_granularity", "Module properly named as `<tool>`", self.main_nf))
+
+
 def check_script_section(self, lines):
     """
     Lint the script section
@@ -304,7 +393,7 @@ def check_script_section(self, lines):
     permitted_meta_keys = {"id", "single_end"}
     invalid_meta_keys = [
         f"{prefix}{key}"
-        for prefix, key in re.findall(r"\b(meta\d*\??\.)(\w+)\b(?!\()", script)
+        for prefix, key in re.findall(r"(?<!\.)\b(meta\d*\??\.)(\w+)\b(?!\()", script)
         if key not in permitted_meta_keys
     ]
     if not invalid_meta_keys:
@@ -359,44 +448,85 @@ def check_when_section(self, lines):
     self.passed.append(("main_nf", "when_condition", "when: condition is unchanged", self.main_nf))
 
 
-def check_process_section(self, lines, registry, fix_version, progress_bar):
+def check_process_section(
+    self, lines: list[str], registry: tuple[str, ...], fix_version: bool, progress_bar: Progress | None
+):
     """Lint the section of a module between the process definition
     and the 'input:' definition
     Specifically checks for correct software versions
     and containers
 
     Args:
-        lines (List[str]): Content of process.
-        registry (str): Base Docker registry for containers. Typically quay.io.
+        lines (list[str]): Content of process.
+        registry (tuple[str, ...]): Allowed container registry prefixes.
         fix_version (bool): Fix software version
         progress_bar (ProgressBar): Progress bar to update.
 
     Returns:
-        bool | None: True if singularity and docker containers match, False otherwise. If process definition does not exist, None.
+        bool | None: True if the singularity and docker container versions match,
+        False if they do not. None if the versions cannot be compared (e.g. modern
+        content-addressed Seqera containers, where the singularity URL carries no
+        version tag) or if the process definition does not exist.
     """
     # Check that we have a process section
     if len(lines) == 0:
         self.failed.append(("main_nf", "process_exist", "Process definition does not exist", self.main_nf))
-        return
+        return None
     self.passed.append(("main_nf", "process_exist", "Process definition exists", self.main_nf))
 
-    # Checks that build numbers of bioconda, singularity and docker container are matching
-    singularity_tag = None
-    docker_tag = None
-    bioconda_packages = []
+    # Resolve the docker and singularity containers via `nextflow inspect` rather than
+    # parsing the container ternary in main.nf with regexes. Running inspect once per
+    # profile lets Nextflow evaluate the container selection logic for us and return the
+    # fully resolved container in its JSON output. Either may be None if the corresponding
+    # container could not be resolved (e.g. Nextflow too old, or no such container).
+    docker_container = self.get_container_with_inspect(profile="docker")
+    singularity_container = self.get_container_with_inspect(profile="singularity")
+
+    # `nextflow inspect -profile singularity` falls back to the docker container when the
+    # module has no singularity-specific image. A bare biocontainers/Seqera docker image is
+    # such a fallback (a genuine singularity image would be an `https://` or `oras://` URL),
+    # so it must not be treated as a singularity container.
+    if singularity_container is not None and singularity_container.startswith(
+        ("quay.io/biocontainers/", "community.wave.seqera.io/")
+    ):
+        singularity_container = None
+
+    # Modules listed under "singularity" in .github/skip_nf_test.json have no singularity
+    # container on purpose, so the singularity_tag check is skipped for them.
+    skip_singularity = str(Path(self.component_dir).resolve()) in _load_skip_nf_test_sets(str(self.base_dir)).get(
+        "singularity", frozenset()
+    )
+
+    if skip_singularity:
+        log.debug(f"Skipping singularity_tag check for {self.component_name} (skipped in skip_nf_test.json)")
+    elif singularity_container is not None:
+        self.passed.append(
+            ("main_nf", "singularity_tag", f"Found singularity container: {singularity_container}", self.main_nf)
+        )
+        if singularity_container.startswith("oras://"):
+            self.failed.append(
+                ("main_nf", "oras_singularity_tag", "Singularity container should not use oras:// scheme", self.main_nf)
+            )
+        else:
+            self.passed.append(
+                ("main_nf", "oras_singularity_tag", "Singularity container uses valid scheme", self.main_nf)
+            )
 
-    # Process name should be all capital letters
-    if all(x.upper() for x in self.process_name):
-        self.passed.append(("main_nf", "process_capitals", "Process name is in capital letters", self.main_nf))
     else:
-        self.failed.append(("main_nf", "process_capitals", "Process name is not in capital letters", self.main_nf))
+        self.failed.append(("main_nf", "singularity_tag", "Unable to resolve singularity container", self.main_nf))
+    if docker_container is not None:
+        self.passed.append(("main_nf", "docker_tag", f"Found docker container: {docker_container}", self.main_nf))
+    else:
+        self.failed.append(("main_nf", "docker_tag", "Unable to resolve docker container", self.main_nf))
+
+    # Check that the process name is correctly formated from the component name
+    check_process_name_format(self, self.process_name, self.component_name)
 
     # Check that process labels are correct
     check_process_labels(self, lines)
 
     # Deprecated enable_conda
     for _i, raw_line in enumerate(lines):
-        url = None
         line = raw_line.strip(" \n'\"}:?")
 
         # Catch preceding "container "
@@ -404,8 +534,6 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             line = line.replace("container", "").strip(" \n'\"}:?")
 
         if _container_type(line) == "conda":
-            if "bioconda::" in line:
-                bioconda_packages = [b for b in line.split() if "bioconda::" in b]
             match = re.search(r"params\.enable_conda", line)
             if match is None:
                 self.passed.append(
@@ -425,193 +553,43 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
                         self.main_nf,
                     )
                 )
-        if _container_type(line) == "singularity":
-            # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img -> v1.2.0_cv1
-            # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 -> 0.11.9--0
-            # Please god let's find a better way to do this than regex
-            match = re.search(r"(?:[:.])?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", line)
-            if match is not None:
-                singularity_tag = match.group(1)
-                self.passed.append(
-                    ("main_nf", "singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf)
-                )
-            else:
-                self.failed.append(("main_nf", "singularity_tag", "Unable to parse singularity tag", self.main_nf))
-                singularity_tag = None
-            url = urlparse(line.split("'")[0])
-
-        if _container_type(line) == "docker":
-            # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5 -> 2.7.1--pl526_5
-            # e.g. "biocontainers/biocontainers:v1.2.0_cv1 -> v1.2.0_cv1
-            match = re.search(r":([A-Za-z\d\-_.]+)$", line)
-            if match is not None:
-                docker_tag = match.group(1)
-                self.passed.append(("main_nf", "docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))
-            else:
-                self.failed.append(("main_nf", "docker_tag", "Unable to parse docker tag", self.main_nf))
-                docker_tag = None
-            if line.startswith((registry, "community.wave.seqera.io/library/")):
-                l_stripped = re.sub(r"\W+$", "", line)
-                self.passed.append(
-                    (
-                        "main_nf",
-                        "container_links",
-                        f"Container prefix is correct: {l_stripped}",
-                        self.main_nf,
-                    )
-                )
-            else:
-                self.failed.append(
-                    (
-                        "main_nf",
-                        "container_links",
-                        "Container prefix is not correct. Please add the registry prefix (e.g. 'quay.io/')",
-                        self.main_nf,
-                    )
-                )
-
-            # Guess if container name is simple one (e.g. nfcore/ubuntu:20.04)
-            # If so, add quay.io as default container prefix
-            if line.count("/") == 1 and line.count(":") == 1:
-                line = "/".join([registry, line]).replace("//", "/")
-            url = urlparse(line.split("'")[0])
 
         if line.startswith("container") or _container_type(line) == "docker" or _container_type(line) == "singularity":
             check_container_link_line(self, raw_line, registry)
 
-        # Try to connect to container URLs
-        if url is None:
-            continue
-        try:
-            container_url = "https://" + urlunparse(url) if url.scheme != "https" else urlunparse(url)
-            log.debug(f"Trying to connect to URL: {container_url}")
-            response = requests.head(
-                container_url,
-                stream=True,
-                allow_redirects=True,
-            )
-            log.debug(
-                f"Connected to URL: {'https://' + urlunparse(url) if url.scheme != 'https' else urlunparse(url)}, "
-                f"status_code: {response.status_code}"
-            )
-        except (requests.exceptions.RequestException, sqlite3.InterfaceError) as e:
-            log.debug(f"Unable to connect to url '{urlunparse(url)}' due to error: {e}")
-            self.failed.append(("main_nf", "container_links", "Unable to connect to container URL", self.main_nf))
-            continue
-        if not response.ok:
-            self.warned.append(
-                (
-                    "main_nf",
-                    "container_links",
-                    f"Unable to connect to container registry, code:  {response.status_code}, url: {response.url}",
-                    self.main_nf,
-                )
-            )
+    # Compare versions only when both resolved containers expose a parseable version tag.
+    # Legacy biocontainers-style URLs carry a shared `:<version>` tag (e.g. `:0.11.9--0`)
+    # on both the docker and singularity side, so a mismatch flags an author error. Modern
+    # Seqera containers are content-addressed (the singularity URL is a sha digest with no
+    # version), so there is nothing to compare and we return None.
+    if docker_container is None or singularity_container is None:
+        return None
+    docker_match = re.search(r":([A-Za-z\d\-_.]+)$", docker_container)
+    singularity_match = re.search(r":([A-Za-z\d\-_.]+)$", singularity_container)
+    if docker_match is None or singularity_match is None:
+        return None
+    return docker_match.group(1) == singularity_match.group(1)
 
-    # Get bioconda packages from environment.yml
-    try:
-        with open(Path(self.component_dir, "environment.yml")) as fh:
-            env_yml = yaml.safe_load(fh)
-        if "dependencies" in env_yml:
-            bioconda_packages = [x for x in env_yml["dependencies"] if isinstance(x, str) and "bioconda::" in x]
-    except FileNotFoundError:
-        pass
-    except NotADirectoryError:
-        pass
-
-    # Check that all bioconda packages have build numbers
-    # Also check for newer versions
-    for bp in bioconda_packages:
-        bp = bp.strip("'").strip('"')
-        # Check for correct version and newer versions
-        try:
-            bioconda_version = bp.split("=")[1]
-            # response = _bioconda_package(bp)
-            response = nf_core.utils.anaconda_package(bp)
-            self.passed.append(
-                ("main_nf", "bioconda_version", f"Conda version specified correctly: {bp}", self.main_nf)
-            )
-        except LookupError:
-            self.warned.append(
-                ("main_nf", "bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf)
-            )
-        except ValueError:
-            self.failed.append(
-                ("main_nf", "bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf)
-            )
-        else:
-            # Check that required version is available at all
-            if bioconda_version not in response.get("versions"):
-                self.failed.append(
-                    (
-                        "main_nf",
-                        "bioconda_version",
-                        f"Conda package {bp} had unknown version: `{bioconda_version}`",
-                        self.main_nf,
-                    )
-                )
-                continue  # No need to test for latest version, continue linting
-            # Check version is latest available
-            last_ver = response.get("latest_version")
-            if last_ver is not None and last_ver != bioconda_version:
-                package, ver = bp.split("=", 1)
-                # If a new version is available and fix is True, update the version
-                if fix_version:
-                    try:
-                        fixed = _fix_module_version(self, bioconda_version, last_ver, singularity_tag, response)
-                    except FileNotFoundError as e:
-                        fixed = False
-                        log.debug(f"Unable to update package {package} due to error: {e}")
-                    else:
-                        if fixed:
-                            progress_bar.print(f"[blue]INFO[/blue]\t Updating package '{package}' {ver} -> {last_ver}")
-                            log.debug(f"Updating package {package} {ver} -> {last_ver}")
-                            self.passed.append(
-                                (
-                                    "main_nf",
-                                    "bioconda_latest",
-                                    f"Conda package has been updated to the latest available: `{bp}`",
-                                    self.main_nf,
-                                )
-                            )
-                        else:
-                            progress_bar.print(
-                                f"[blue]INFO[/blue]\t Tried to update package. Unable to update package '{package}' {ver} -> {last_ver}"
-                            )
-                            log.debug(f"Unable to update package {package} {ver} -> {last_ver}")
-                            self.warned.append(
-                                (
-                                    "main_nf",
-                                    "bioconda_latest",
-                                    f"Conda update: {package} `{ver}` -> `{last_ver}`",
-                                    self.main_nf,
-                                )
-                            )
-                # Add available update as a warning
-                else:
-                    self.warned.append(
-                        (
-                            "main_nf",
-                            "bioconda_latest",
-                            f"Conda update: {package} `{ver}` -> `{last_ver}`",
-                            self.main_nf,
-                        )
-                    )
-            else:
-                self.passed.append(
-                    (
-                        "main_nf",
-                        "bioconda_latest",
-                        f"Conda package is the latest available: `{bp}`",
-                        self.main_nf,
-                    )
-                )
 
-    # Check if a tag exists at all. If not, return None.
-    if singularity_tag is None or docker_tag is None:
-        return None
+def check_process_name_format(self, process_name, component_name):
+    """
+    Lint the process name
+    Checks that the process name in the module file is uppercase and derived
+    from the software and tool name separated by an underscore.
+    """
+    # Process name should be all capital letters
+    if process_name.isupper():
+        self.passed.append(("main_nf", "process_capitals", "Process name is in capital letters", self.main_nf))
+    else:
+        self.failed.append(("main_nf", "process_capitals", "Process name is not in capital letters", self.main_nf))
+
+    # Process name should be made from the module name
+    if component_name.upper().replace("/", "_") == process_name:
+        self.passed.append(("main_nf", "module_process_name", "Process name is derived from module name", self.main_nf))
     else:
-        return docker_tag == singularity_tag
+        self.failed.append(
+            ("main_nf", "module_process_name", "Process name is not derived from module name", self.main_nf)
+        )
 
 
 def check_process_labels(self, lines):
@@ -621,6 +599,7 @@ def check_process_labels(self, lines):
         "process_medium",
         "process_high",
         "process_long",
+        "process_low_memory",
         "process_high_memory",
     ]
     all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")]
@@ -683,6 +662,7 @@ def check_container_link_line(self, raw_line, registry):
     """Look for common problems in the container name / URL, for docker and singularity."""
 
     line = raw_line.strip(" \n'\"}:?")
+    log.debug(f"container line: '{line}'")
 
     # lint double quotes
     if line.count('"') > 2:
@@ -711,8 +691,10 @@ def check_container_link_line(self, raw_line, registry):
     # (if there are multiple links, this will be warned in the next check)
     container_link = None
     if len(single_quoted_items) == 3 or len(single_quoted_items) == 5 and " in [" in raw_line:
+        log.debug(f"Single-quoted container link: '{single_quoted_items[1]}'")
         container_link = single_quoted_items[1]
     elif len(double_quoted_items) == 3:
+        log.debug(f"Double-quoted container link: '{double_quoted_items[1]}'")
         container_link = double_quoted_items[1]
     if container_link:
         if " " in container_link:
@@ -734,6 +716,28 @@ def check_container_link_line(self, raw_line, registry):
                 )
             )
 
+        # Check container registry prefix.
+        if _container_type(container_link) == "docker":
+            if container_link.startswith(registry):
+                self.passed.append(
+                    (
+                        "main_nf",
+                        "container_links",
+                        f"Container prefix is correct: {container_link}",
+                        self.main_nf,
+                    )
+                )
+            else:
+                log.debug(f"Container link: '{container_link}' does not start with registry prefix: {registry}")
+                self.failed.append(
+                    (
+                        "main_nf",
+                        "container_links",
+                        f"Container prefix is not correct. Please add one of the allowed registry prefixes: {', '.join(registry)}",
+                        self.main_nf,
+                    )
+                )
+
         # lint more than one container in the same line
         if ("https://containers" in line or "https://depot" in line) and (
             "biocontainers/" in line or line.startswith(registry)
@@ -755,32 +759,26 @@ def check_meta_input_names(self, inputs):
         inputs (list): List of input variable names
     """
 
-    meta_vars = [var for var in inputs if var.startswith("meta")]
+    # A meta map is named 'meta' optionally followed by a number (meta2, meta3, etc.).
+    meta_pattern = re.compile(r"^meta\d*$")
+    meta_vars = [var for var in inputs if meta_pattern.match(var)]
 
     if not meta_vars:
         return  # No meta variables to check
 
-    # Expected pattern: 'meta' or 'meta' followed by a number (meta2, meta3, etc.)
-    valid_pattern = re.compile(r"^meta(\d+)?$")
-
     invalid_meta_vars = []
     valid_numbers = []
 
     for var in meta_vars:
-        if not valid_pattern.match(var):
-            invalid_meta_vars.append(var)
-        else:
-            # Extract number if present
-            match = re.match(r"^meta(\d+)?$", var)
-            if match.group(1):  # Has a number
-                number_str = match.group(1)
-                number_int = int(number_str)
-
-                if number_str != str(number_int) or number_int < 2:
-                    # Check for leading zeros (e.g., meta02, meta003) or meta0 and meta1
-                    invalid_meta_vars.append(var)
-                else:
-                    valid_numbers.append(number_int)
+        number_str = var.removeprefix("meta")  # digits after 'meta' (empty for a plain 'meta')
+        if number_str:  # Has a number
+            number_int = int(number_str)
+            # Check for leading zeros (e.g., meta02, meta003) or meta0 and meta1
+            if number_str != str(number_int) or number_int < 2:
+                log.debug(f"Invalid meta variable number: {var}")
+                invalid_meta_vars.append(var)
+            else:
+                valid_numbers.append(number_int)
 
     # Check for invalid names
     if invalid_meta_vars:
@@ -793,20 +791,20 @@ def check_meta_input_names(self, inputs):
             )
         )
 
-    # Check for proper sequencing (2, 3, 4... not 2, 5, 3)
-    if valid_numbers:
-        expected = list(range(2, len(valid_numbers) + 2))
-        if valid_numbers != expected:
-            self.warned.append(
-                (
-                    "main_nf",
-                    "meta_input_names",
-                    f"Meta variable numbers should be sequential starting at 2. Found: meta{', meta'.join(map(str, valid_numbers))}",
-                    self.main_nf,
-                )
+    # Check for proper sequencing (2, 3, 4... not 2, 5, 3). An empty list compares
+    # equal to the empty range, i.e. it counts as trivially sequential.
+    is_sequential = valid_numbers == list(range(2, len(valid_numbers) + 2))
+    if valid_numbers and not is_sequential:
+        self.warned.append(
+            (
+                "main_nf",
+                "meta_input_names",
+                f"Meta variable numbers should be sequential starting at 2. Found: meta{', meta'.join(map(str, valid_numbers))}",
+                self.main_nf,
             )
+        )
 
-    if not invalid_meta_vars and (not valid_numbers or valid_numbers == list(range(2, len(valid_numbers) + 2))):
+    if not invalid_meta_vars and is_sequential:
         self.passed.append(
             (
                 "main_nf",
@@ -959,68 +957,6 @@ def _is_empty(line):
     return empty
 
 
-def _fix_module_version(self, current_version, latest_version, singularity_tag, response):
-    """Updates the module version
-
-    Changes the bioconda current version by the latest version.
-    Obtains the latest build from bioconda response
-    Checks that the new URLs for docker and singularity with the tag [version]--[build] are valid
-    Changes the docker and singularity URLs
-    """
-    # Get latest build
-    build = _get_build(response)
-
-    with open(self.main_nf) as source:
-        lines = source.readlines()
-
-    # Check if the new version + build exist and replace
-    new_lines = []
-    for line in lines:
-        line_stripped = line.strip(" '\"")
-        build_type = _container_type(line_stripped)
-        if build_type == "conda":
-            new_lines.append(re.sub(rf"{current_version}", f"{latest_version}", line))
-        elif build_type in ("singularity", "docker"):
-            # Check that the new url is valid
-            new_url = re.search(
-                "(?:['\"])(.+)(?:['\"])", re.sub(rf"{singularity_tag}", f"{latest_version}--{build}", line)
-            ).group(1)
-            try:
-                response_new_container = requests.get(
-                    "https://" + new_url if not new_url.startswith("https://") else new_url, stream=True
-                )
-                log.debug(
-                    f"Connected to URL: {'https://' + new_url if not new_url.startswith('https://') else new_url}, "
-                    f"status_code: {response_new_container.status_code}"
-                )
-            except (requests.exceptions.RequestException, sqlite3.InterfaceError) as e:
-                log.debug(f"Unable to connect to url '{new_url}' due to error: {e}")
-                return False
-            if response_new_container.status_code != 200:
-                return False
-            new_lines.append(re.sub(rf"{singularity_tag}", f"{latest_version}--{build}", line))
-        else:
-            new_lines.append(line)
-
-    # Replace outdated versions by the latest one
-    with open(self.main_nf, "w") as source:
-        for line in new_lines:
-            source.write(line)
-
-    return True
-
-
-def _get_build(response):
-    """Get the latest build of the container version"""
-    build_times = []
-    latest_v = response.get("latest_version")
-    files = response.get("files")
-    for f in files:
-        if f.get("version") == latest_v:
-            build_times.append((f.get("upload_time"), f.get("attrs").get("build")))
-    return sorted(build_times, key=lambda tup: tup[0], reverse=True)[0][1]
-
-
 def _container_type(line):
     """Returns the container type of a build."""
     if line.startswith("conda"):
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 27bf1b9d6f..6c5a0c36f4 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -1,16 +1,24 @@
 from __future__ import annotations
 
+import json
 import logging
+from functools import cache
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import ruamel.yaml
 from jsonschema import exceptions, validators
 
 from nf_core.components.components_differ import ComponentsDiffer
+from nf_core.components.components_utils import read_meta_yml as read_component_meta_yml
+from nf_core.components.components_utils import yaml as ruamel_yaml
 from nf_core.components.lint import ComponentLint, LintExceptionError
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.utils import unquote
+from nf_core.modules.lint.module_containers import (
+    lint_conda_lock_files,
+    lint_main_nf_container,
+    lint_meta_yml_containers,
+)
+from nf_core.utils import ContainerRegistryUrls, unquote
 
 if TYPE_CHECKING:
     from nf_core.modules.lint import ModuleLint
@@ -18,6 +26,46 @@
 log = logging.getLogger(__name__)
 
 
+@cache
+def _load_skip_nf_test_sets(base_dir: str) -> dict[str, frozenset[str]]:
+    """
+    Load the per-system skip sets from ``.github/skip_nf_test.json``, cached per base directory.
+
+    Skip entries may be recorded as absolute or repo-relative paths,
+    so everything is resolved to absolute paths for comparison.
+    """
+    skip_file = Path(base_dir, ".github", "skip_nf_test.json")
+    if not skip_file.is_file():
+        return {}
+    with open(skip_file) as fh:
+        data = json.load(fh)
+    return {
+        k: frozenset(str((Path(base_dir) / p).resolve()) for p in v) for k, v in data.items() if isinstance(v, list)
+    }
+
+
+def meta_yml_containers(module: NFCoreComponent) -> None:
+    """
+    Lints the container information in the meta.yml file and the module's main.nf file.
+    Respects per-system skips from `skip_nf_test.json`.
+    """
+    skip_sets = _load_skip_nf_test_sets(str(module.base_dir))
+    module_path = str(Path(module.component_dir).resolve())
+    skip_docker = module_path in skip_sets.get("docker", frozenset())
+    skip_singularity = module_path in skip_sets.get("singularity", frozenset())
+    skip_conda = module_path in skip_sets.get("conda", frozenset())
+    if skip_docker or skip_singularity or skip_conda:
+        log.debug(
+            f"Skip entries found for {module.component_name}: "
+            f"docker={skip_docker}, singularity={skip_singularity}, conda={skip_conda}"
+        )
+
+    lint_meta_yml_containers(module, skip_docker=skip_docker, skip_conda=skip_conda, skip_singularity=skip_singularity)
+    lint_main_nf_container(module, skip_docker=skip_docker, skip_conda=skip_conda, skip_singularity=skip_singularity)
+    if not skip_conda:
+        lint_conda_lock_files(module)
+
+
 def meta_yml(module_lint_object: ModuleLint, module: NFCoreComponent, allow_missing: bool = False) -> None:
     """Lint a ``meta.yml`` file
 
@@ -27,36 +75,77 @@ def meta_yml(module_lint_object: ModuleLint, module: NFCoreComponent, allow_miss
 
     The following checks are performed:
 
-    * ``meta_yml_exists``: The ``meta.yml`` file must exist.
+    meta_yml_exists
+    ^^^^^^^^^^^^^^^
+
+    The ``meta.yml`` file must exist.
+
+    meta_yml_valid
+    ^^^^^^^^^^^^^^
 
-    * ``meta_yml_valid``: The ``meta.yml`` must be valid according to the JSON
-      schema defined in ``modules/meta-schema.json`` in the nf-core/modules
-      repository.
+    The ``meta.yml`` must be valid according to the JSON
+    schema defined in ``modules/meta-schema.json`` in the nf-core/modules
+    repository.
 
-    * ``meta_name``: The ``name`` field in ``meta.yml`` must match (case-insensitive)
-      the process name declared in ``main.nf``.
+    meta_name
+    ^^^^^^^^^
 
-    * ``meta_input``: If ``main.nf`` declares inputs, they must be listed under
-      the ``input:`` key in ``meta.yml``.
+    The ``name`` field in ``meta.yml`` must match (case-insensitive)
+    the process name declared in ``main.nf``.
 
-    * ``correct_meta_inputs``: The inputs listed in ``meta.yml`` must exactly
-      match those parsed from ``main.nf``. Run ``nf-core modules lint --fix``
-      to auto-correct.
+    meta_input
+    ^^^^^^^^^^
 
-    * ``meta_output``: If ``main.nf`` declares outputs, they must be listed under
-      the ``output:`` key in ``meta.yml``.
+    If ``main.nf`` declares inputs, they must be listed under
+    the ``input:`` key in ``meta.yml``.
 
-    * ``correct_meta_outputs``: The outputs listed in ``meta.yml`` must exactly
-      match those parsed from ``main.nf``. Run ``nf-core modules lint --fix``
-      to auto-correct.
+    correct_meta_inputs
+    ^^^^^^^^^^^^^^^^^^^
 
-    * ``has_meta_topics``: If ``main.nf`` declares topics, ``meta.yml`` must
-      also contain a non-empty ``topics:`` block. Run
-      ``nf-core modules lint --fix`` to auto-correct.
+    The inputs listed in ``meta.yml`` must exactly
+    match those parsed from ``main.nf``. Run ``nf-core modules lint --fix``
+    to auto-correct.
 
-    * ``correct_meta_topics``: The topics listed in ``meta.yml`` must exactly
-      match those parsed from ``main.nf``. Run ``nf-core modules lint --fix``
-      to auto-correct.
+    meta_output
+    ^^^^^^^^^^^
+
+    If ``main.nf`` declares outputs, they must be listed under
+    the ``output:`` key in ``meta.yml``.
+
+    correct_meta_outputs
+    ^^^^^^^^^^^^^^^^^^^^
+
+    The outputs listed in ``meta.yml`` must exactly
+    match those parsed from ``main.nf``. Run ``nf-core modules lint --fix``
+    to auto-correct.
+
+    has_meta_topics
+    ^^^^^^^^^^^^^^^
+
+    If ``main.nf`` declares topics, ``meta.yml`` must
+    also contain a non-empty ``topics:`` block. Run
+    ``nf-core modules lint --fix`` to auto-correct.
+
+    correct_meta_topics
+    ^^^^^^^^^^^^^^^^^^^
+
+    The topics listed in ``meta.yml`` must exactly
+    match those parsed from ``main.nf``. Run ``nf-core modules lint --fix``
+    to auto-correct.
+
+    has_meta_containers
+    ^^^^^^^^^^^^^^^^^^^
+
+    If ``main.nf`` declares containers, ``meta.yml``
+    must also contain a non-empty ``containers:`` block. Run
+    ``nf-core modules lint --fix`` to auto-correct.
+
+    correct_meta_containers
+    ^^^^^^^^^^^^^^^^^^^^^^^
+
+    The containers listed in ``meta.yml`` must
+    exactly match those parsed from ``main.nf``. Run
+    ``nf-core modules lint --fix`` to auto-correct.
 
     If the module has inputs or outputs, they are expected to be formatted as:
 
@@ -81,25 +170,14 @@ def meta_yml(module_lint_object: ModuleLint, module: NFCoreComponent, allow_miss
             )
             return
         raise LintExceptionError("Module does not have a `meta.yml` file")
-    # Check if we have a patch file, get original file in that case
-    meta_yaml = read_meta_yml(module_lint_object, module)
-    if module.is_patched and module_lint_object.modules_repo.repo_path is not None:
-        lines = ComponentsDiffer.try_apply_patch(
-            module.component_type,
-            module.component_name,
-            module_lint_object.modules_repo.repo_path,
-            module.patch_path,
-            Path(module.component_dir).relative_to(module.base_dir),
-            reverse=True,
-        ).get("meta.yml")
-        if lines is not None:
-            yaml = ruamel.yaml.YAML()
-            meta_yaml = yaml.load("".join(lines))
+    # read_meta_yml returns the reverse-patched content for patched modules
+    meta_yaml = read_meta_yml_patched(module_lint_object, module)
     if meta_yaml is None:
         module.failed.append(("meta_yml", "meta_yml_exists", "Module `meta.yml` does not exist.", module.meta_yml))
         return
     else:
         module.passed.append(("meta_yml", "meta_yml_exists", "Module `meta.yml` exists", module.meta_yml))
+    module.container = meta_yaml.get("containers", {})
 
     # Confirm that the meta.yml file is valid according to the JSON schema
     valid_meta_yml = False
@@ -283,8 +361,40 @@ def meta_yml(module_lint_object: ModuleLint, module: NFCoreComponent, allow_miss
                     )
                 )
 
+        # Check that meta_yml specifies containers (skip modules that use a Dockerfile)
+        from nf_core.modules.modules_utils import module_uses_dockerfile
+
+        container = module.get_container_from_main_nf()
+        if container and not module_uses_dockerfile(module):
+            if "containers" not in meta_yaml:
+                if ContainerRegistryUrls.SEQERA_DOCKER.value in container:
+                    module.warned.append(
+                        (
+                            "meta_yml",
+                            "has_meta_containers",
+                            "Module `meta.yml` does not contain any containers, even though they appear in `main.nf`.",
+                            module.meta_yml,
+                        )
+                    )
+                else:
+                    log.debug(
+                        f"Module `{module.component_name}` has no containers section in `meta.yml` but does not use the Wave registry — skipping container lint."
+                    )
+                return
+
+            module.passed.append(
+                (
+                    "meta_yml",
+                    "has_meta_containers",
+                    "Module `meta.yml` and `main.nf` contain container definition.",
+                    module.meta_yml,
+                )
+            )
+
+            meta_yml_containers(module)
+
 
-def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> dict | None:
+def read_meta_yml_patched(module_lint_object: ComponentLint, module: NFCoreComponent) -> dict | None:
     """
     Read a `meta.yml` file and return it as a dictionary
 
@@ -295,9 +405,9 @@ def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) ->
     Returns:
         dict: The `meta.yml` file as a dictionary
     """
-    meta_yaml = None
-    yaml = ruamel.yaml.YAML()
-    yaml.preserve_quotes = True
+    if module_lint_object.modules_repo.repo_path is None:
+        raise ValueError("modules_repo.repo_path is None")
+
     # Check if we have a patch file, get original file in that case
     if module.is_patched:
         lines = ComponentsDiffer.try_apply_patch(
@@ -309,13 +419,10 @@ def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) ->
             reverse=True,
         ).get("meta.yml")
         if lines is not None:
-            meta_yaml = yaml.load("".join(lines))
-    if meta_yaml is None:
-        if module.meta_yml is None:
-            return None
-        with open(module.meta_yml) as fh:
-            meta_yaml = yaml.load(fh)
-    return meta_yaml
+            return ruamel_yaml.load("".join(lines))
+    if module.meta_yml is None:
+        return None
+    return read_component_meta_yml(module.meta_yml)
 
 
 def obtain_inputs(_, inputs: list) -> list:
diff --git a/nf_core/modules/lint/module_changes.py b/nf_core/modules/lint/module_changes.py
index de6f3d24c8..07ccdd56f6 100644
--- a/nf_core/modules/lint/module_changes.py
+++ b/nf_core/modules/lint/module_changes.py
@@ -25,8 +25,11 @@ def module_changes(module_lint_object, module):
 
     The following checks are performed:
 
-    * ``check_local_copy``: Each module file must be identical to the corresponding
-      file in the remote repository at the pinned commit SHA.
+    check_local_copy
+    ^^^^^^^^^^^^^^^^
+
+    Each module file must be identical to the corresponding
+    file in the remote repository at the pinned commit SHA.
     """
     if module.is_patched:
         # If the module is patched, we need to apply
diff --git a/nf_core/modules/lint/module_containers.py b/nf_core/modules/lint/module_containers.py
new file mode 100644
index 0000000000..cfef840007
--- /dev/null
+++ b/nf_core/modules/lint/module_containers.py
@@ -0,0 +1,304 @@
+import logging
+from pathlib import Path
+
+import requests
+from pydantic_core import ValidationError
+
+from nf_core.components.nfcore_component import NFCoreComponent
+from nf_core.modules.modules_utils import ContainerEntry, MetaYmlContainers, module_uses_dockerfile
+
+log = logging.getLogger(__name__)
+
+
+def lint_meta_yml_containers(module: NFCoreComponent, skip_docker=False, skip_conda=False, skip_singularity=False):
+    if module_uses_dockerfile(module):
+        log.info(f"Module '{module.component_name}' uses a Dockerfile - skipping container lint")
+        return
+
+    meta_path = Path(module.component_dir, "meta.yml")
+    meta_yml = module.load_meta_yml()
+    assert meta_yml and "containers" in meta_yml
+
+    containers_raw = meta_yml["containers"]
+
+    skip_system = {"docker": skip_docker, "singularity": skip_singularity, "conda": skip_conda}
+
+    # Validate each container system separately with the pydantic model, so one
+    # invalid system doesn't suppress the checks for the others. Lint messages
+    # are derived from the collected validation errors.
+    containers = MetaYmlContainers()
+    for system_key in skip_system:
+        if skip_system[system_key]:
+            continue
+
+        try:
+            validated = MetaYmlContainers.model_validate(
+                {system_key: containers_raw.get(system_key, {})},
+                context={"require_complete": [system_key]},
+            )
+        except ValidationError as e:
+            for err in e.errors():
+                loc = ".".join(str(part) for part in err["loc"])
+                module.failed.append(
+                    ("meta_yml", f"containers_section_{system_key}", f"`{loc}`: {err['msg']}", meta_path)
+                )
+            continue
+
+        setattr(containers, system_key, getattr(validated, system_key))
+        module.passed.append(
+            (
+                "meta_yml",
+                f"containers_section_{system_key}",
+                f"{system_key} containers section is valid",
+                meta_path,
+            )
+        )
+
+        if system_key == "conda":
+            continue
+
+        # check build_id hash matches hash in container tag
+        for platform, system in getattr(containers, system_key).items():
+            if not system.build_id.removeprefix("bd-"):
+                module.warned.append(
+                    (
+                        "meta_yml",
+                        "containers_build_id_hash",
+                        f"No build_id found for {system_key} {platform}",
+                        meta_path,
+                    )
+                )
+                continue
+
+            build_hash = system.build_hash
+            name_hash = system.tag_hash
+            if build_hash and name_hash:
+                if build_hash != name_hash:
+                    module.failed.append(
+                        (
+                            "meta_yml",
+                            "containers_build_id_hash",
+                            f"Build ID `{build_hash}` hash does not match {system_key} container tag `{name_hash}` for {platform}",
+                            meta_path,
+                        )
+                    )
+                else:
+                    module.passed.append(
+                        (
+                            "meta_yml",
+                            "containers_build_id_hash",
+                            f"Build ID hash matches {system_key} container tag for {platform}",
+                            meta_path,
+                        )
+                    )
+            else:
+                module.warned.append(
+                    (
+                        "meta_yml",
+                        "containers_build_id_hash",
+                        f"Could not compare build ID hash with {system} container tag for {platform}",
+                        meta_path,
+                    )
+                )
+
+    # Check docker container images exist for all platforms (unless skipped)
+    if skip_docker:
+        pass
+    elif not containers.docker:
+        module.warned.append(
+            ("meta_yml", "containers_docker_exist", "Docker containers section missing or empty", meta_path)
+        )
+    else:
+        for platform in containers.docker:
+            docker_name = containers.docker[platform].name
+            if not docker_name:
+                module.warned.append(
+                    (
+                        "meta_yml",
+                        f"containers_docker_{platform}_exists",
+                        f"Docker {platform} container name missing",
+                        meta_path,
+                    )
+                )
+                continue
+            if docker_name.startswith(("http://", "https://")):
+                docker_url = docker_name
+            elif "://" in docker_name:
+                docker_url = ""
+            else:
+                # OCI distribution spec: /v2/<name>/manifests/<tag>
+                host, _, image_ref = docker_name.partition("/")
+                image_name, _, tag = image_ref.partition(":")
+                docker_url = f"https://{host}/v2/{image_name}/manifests/{tag or 'latest'}"
+            if not docker_url:
+                module.warned.append(
+                    (
+                        "meta_yml",
+                        f"containers_docker_{platform}_exists",
+                        f"Docker {platform} container has non-http protocol; existence check skipped",
+                        meta_path,
+                    )
+                )
+            else:
+                try:
+                    response = requests.head(
+                        docker_url,
+                        allow_redirects=True,
+                        headers={"Accept": "application/vnd.oci.image.manifest.v1+json"},
+                    )
+                    if response.ok or response.status_code == 401:
+                        module.passed.append(
+                            (
+                                "meta_yml",
+                                f"containers_docker_{platform}_exists",
+                                f"Docker {platform} image exists",
+                                meta_path,
+                            )
+                        )
+                    else:
+                        module.warned.append(
+                            (
+                                "meta_yml",
+                                f"containers_docker_{platform}_exists",
+                                f"Docker {platform} image not reachable at {docker_url} (status {response.status_code})",
+                                meta_path,
+                            )
+                        )
+                except requests.RequestException as e:
+                    module.warned.append(
+                        (
+                            "meta_yml",
+                            f"containers_docker_{platform}_exists",
+                            f"Unable to connect to docker image URL: {e}",
+                            meta_path,
+                        )
+                    )
+
+    # Conda lock files and hash checks
+    if skip_conda:
+        pass
+    elif not containers.conda:
+        module.warned.append(
+            ("meta_yml", "containers_conda_lock_exists", "Conda containers section missing or empty", meta_path)
+        )
+    else:
+        for platform in containers.conda:
+            lock_file = containers.conda[platform].lock_file
+            if not lock_file:
+                module.warned.append(
+                    ("meta_yml", "containers_conda_lock_exists", f"Missing conda lock_file for {platform}", meta_path)
+                )
+                continue
+            lock_path = Path(lock_file)
+            if lock_path.exists():
+                module.passed.append(
+                    (
+                        "meta_yml",
+                        "containers_conda_lock_exists",
+                        f"Conda lock_file exists for {platform}",
+                        meta_path,
+                    )
+                )
+            else:
+                module.warned.append(
+                    (
+                        "meta_yml",
+                        "containers_conda_lock_exists",
+                        f"Conda lock_file not found for {platform}: {lock_path}",
+                        meta_path,
+                    )
+                )
+
+        for plat in containers.conda:
+            conda_entry = containers.conda.get(plat)
+            docker_entry = containers.docker.get(plat) if containers.docker else None
+            conda_lock = conda_entry.lock_file if conda_entry else ""
+
+            if not (docker_entry and docker_entry.build_id and conda_lock):
+                module.warned.append(
+                    (
+                        "meta_yml",
+                        "containers_conda_lock_hash",
+                        f"Could not compare conda lock_file with docker {plat} buildId hash",
+                        meta_path,
+                    )
+                )
+                continue
+
+            docker_build_id_clean = docker_entry.build_id.removeprefix("bd-")
+            parts = docker_build_id_clean.split("_")
+            if len(parts) >= 3 and parts[-1].isdigit() and parts[-2].isdigit():
+                parts = parts[:-2]
+            docker_hash = "_".join([p for p in parts if p])
+            if docker_hash and docker_hash in conda_lock:
+                module.passed.append(
+                    (
+                        "meta_yml",
+                        "containers_conda_lock_hash",
+                        f"Conda lock_file matches docker {plat} buildId hash",
+                        meta_path,
+                    )
+                )
+            else:
+                module.failed.append(
+                    (
+                        "meta_yml",
+                        "containers_conda_lock_hash",
+                        f"Conda lock_file does not match docker {plat} buildId hash",
+                        meta_path,
+                    )
+                )
+    return
+
+
+def lint_main_nf_container(
+    module: NFCoreComponent, fix=False, skip_docker=False, skip_conda=False, skip_singularity=False
+):
+    if module_uses_dockerfile(module):
+        log.info(f"Module '{module.component_name}' uses a Dockerfile - skipping main.nf container lint")
+        return
+
+    if skip_docker:
+        log.debug("Skipping main.nf container linting")
+        return
+
+    if not module.container_from_main_nf:
+        log.debug("Skipping main.nf container linting")
+        module.warned.append(
+            ("main_nf", "has_container", "Module `main.nf` does not specify a container.", module.main_nf)
+        )
+        return
+
+    main_path = Path(module.component_dir, "main.nf")
+    meta_path = Path(module.component_dir, "meta.yml")
+
+    meta_yml = module.load_meta_yml()
+    if meta_yml is None:
+        return
+    try:
+        docker_container_raw = meta_yml.get("containers", {}).get("docker", {}).get("linux/amd64", {})
+        docker_container = ContainerEntry.model_validate(docker_container_raw)
+    except ValidationError as e:
+        log.debug(f"Docker linux/amd64 image could not be read from {meta_path.absolute()}")
+        log.debug(e)
+        return
+
+    if docker_container.name != module.container_from_main_nf:
+        module.warned.append(
+            (
+                "main_nf",
+                "main_nf_container",
+                "Docker image in main.nf does not match the image specified in meta.yml",
+                main_path,
+            )
+        )
+
+        if fix:
+            # TODO: Update main.nf container
+            # update_main_nf_container(new_image)
+            pass
+
+
+def lint_conda_lock_files(module: NFCoreComponent):
+    # TODO
+    pass
diff --git a/nf_core/modules/lint/module_deprecations.py b/nf_core/modules/lint/module_deprecations.py
index e9d1070706..96ee356375 100644
--- a/nf_core/modules/lint/module_deprecations.py
+++ b/nf_core/modules/lint/module_deprecations.py
@@ -9,8 +9,11 @@ def module_deprecations(_, module):
 
     The following checks are performed:
 
-    * ``module_deprecations``: Deprecated files (e.g. ``functions.nf``) must not
-      be present in the module directory.
+    module_deprecations
+    ^^^^^^^^^^^^^^^^^^^^
+
+    Deprecated files (e.g. ``functions.nf``) must not
+    be present in the module directory.
     """
     module.wf_path = module.component_dir
     if (module.component_dir / "functions.nf").exists():
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 00031d8b62..aa0388dc3a 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -21,26 +21,54 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False):
 
     The following checks are performed:
 
-    * ``test_dir_exists``: The nf-test directory ``tests/`` must exist.
+    test_dir_exists
+    ^^^^^^^^^^^^^^^
 
-    * ``test_main_nf_exists``: The file ``tests/main.nf.test`` must exist.
+    The nf-test directory ``tests/`` must exist.
 
-    * ``test_snapshot_exists``: If ``snapshot()`` is called in ``main.nf.test``,
-      the snapshot file ``tests/main.nf.test.snap`` must exist and be valid JSON.
+    test_main_nf_exists
+    ^^^^^^^^^^^^^^^^^^^
 
-    * ``test_snap_md5sum``: The snapshot must not contain md5sums for empty files
-      (``d41d8cd98f00b204e9800998ecf8427e``) or empty compressed files
-      (``7029066c27ac6f5ef18d660d5741979a``), unless the test name contains ``stub``.
+    The file ``tests/main.nf.test`` must exist.
 
-    * ``test_snap_versions``: The snapshot must contain a ``versions`` key.
+    test_snapshot_exists
+    ^^^^^^^^^^^^^^^^^^^^
 
-    * ``test_main_tags``: The ``main.nf.test`` file must declare the required tags:
-      ``modules``, ``modules_<org>``, the full component name, and (for ``tool/subtool``
-      modules) the tool name alone. Tags for any chained components included via
-      ``include`` statements must also be present.
+    If ``snapshot()`` is called in ``main.nf.test``,
+    the snapshot file ``tests/main.nf.test.snap`` must exist and be valid JSON.
 
-    * ``test_old_test_dir``: The legacy pytest directory
-      ``tests/modules/<component_name>/`` must not exist.
+    test_snap_md5sum
+    ^^^^^^^^^^^^^^^^
+
+    The snapshot must not contain md5sums for empty files
+    (``d41d8cd98f00b204e9800998ecf8427e``) or empty compressed files
+    (``7029066c27ac6f5ef18d660d5741979a``), unless the test name contains ``stub``.
+
+    test_snap_versions
+    ^^^^^^^^^^^^^^^^^^
+
+    The snapshot must contain a ``versions`` key.
+
+    test_main_tags
+    ^^^^^^^^^^^^^^
+
+    The ``main.nf.test`` file must declare the required tags:
+    ``modules``, ``modules_<org>``, the full component name, and (for ``tool/subtool``
+    modules) the tool name alone. Tags for any chained components included via
+    ``include`` statements must also be present.
+
+    test_old_test_dir
+    ^^^^^^^^^^^^^^^^^
+
+    The legacy pytest directory
+    ``tests/modules/<component_name>/`` must not exist.
+
+    test_stub_gzip_syntax
+    ^^^^^^^^^^^^^^^^^^^^^^
+
+    Stub blocks with gzip output files must use the proper syntax. Stub files
+    ending in ``.gz`` must use ``echo "" | gzip > file.gz``. Simply touching or
+    creating empty ``.gz`` files will break nf-test's gzip parser.
 
     """
     if module.nftest_testdir is None:
diff --git a/nf_core/modules/lint/module_todos.py b/nf_core/modules/lint/module_todos.py
index e453e2ad6a..a7331ca2ac 100644
--- a/nf_core/modules/lint/module_todos.py
+++ b/nf_core/modules/lint/module_todos.py
@@ -25,8 +25,11 @@ def module_todos(_, module):
     This lint test runs through all files in the module and searches for these lines.
     If any are found they will throw a warning.
 
-    * ``module_todo``: A warning is issued for each TODO comment found in the
-      module files.
+    module_todo
+    ^^^^^^^^^^^
+
+    A warning is issued for each TODO comment found in the
+    module files.
 
     .. tip:: Note that many GUI code editors have plugins to list all instances of *TODO*
               in a given project directory. This is a very quick and convenient way to get
diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py
index 5caef3f68d..a5a7828d6e 100644
--- a/nf_core/modules/lint/module_version.py
+++ b/nf_core/modules/lint/module_version.py
@@ -22,10 +22,16 @@ def module_version(module_lint_object: "nf_core.modules.lint.ModuleLint", module
 
     The following checks are performed:
 
-    * ``git_sha``: The module must have a ``git_sha`` entry in ``modules.json``.
+    git_sha
+    ^^^^^^^
 
-    * ``module_version``: The module version must match the latest commit in the
-      remote repository. A warning is issued if a newer version is available.
+    The module must have a ``git_sha`` entry in ``modules.json``.
+
+    module_version
+    ^^^^^^^^^^^^^^
+
+    The module version must match the latest commit in the
+    remote repository. A warning is issued if a newer version is available.
     """
     assert module_lint_object.modules_json is not None  # mypy
     assert module.repo_url is not None  # mypy
diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
index 716a40e8ea..c47b4378cf 100644
--- a/nf_core/modules/modules_json.py
+++ b/nf_core/modules/modules_json.py
@@ -81,8 +81,9 @@ def create(self) -> None:
             UserWarning: If the creation fails
         """
         pipeline_config = nf_core.utils.fetch_wf_config(self.directory)
-        pipeline_name = pipeline_config.get("manifest.name", "")
-        pipeline_url = pipeline_config.get("manifest.homePage", "")
+        manifest = pipeline_config.get("manifest", {})
+        pipeline_name = manifest.get("name", "")
+        pipeline_url = manifest.get("homePage", "")
         new_modules_json = ModulesJsonType(name=pipeline_name, homePage=pipeline_url, repos={})
 
         if not self.modules_dir.exists():
diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py
index 7b38369e8c..70cb7ffb62 100644
--- a/nf_core/modules/modules_utils.py
+++ b/nf_core/modules/modules_utils.py
@@ -1,13 +1,25 @@
 import logging
+import time
 from pathlib import Path
 from urllib.parse import urlparse
 
 import requests
+from pydantic import BaseModel, ValidationInfo, field_validator, model_validator
+
+from nf_core.utils import (
+    CONTAINER_PLATFORMS,
+    CONTAINER_SYSTEMS,
+    NFCORE_CACHE_DIR,
+    REQUIRED_CONTAINER_PLATFORMS,
+)
 
 from ..components.nfcore_component import NFCoreComponent
 
 log = logging.getLogger(__name__)
 
+EDAM_TSV_URL = "https://edamontology.org/EDAM.tsv"
+EDAM_CACHE_TTL = 7 * 24 * 60 * 60  # one week
+
 
 class ModuleExceptionError(Exception):
     """Exception raised when there was an error with module commands"""
@@ -15,6 +27,102 @@ class ModuleExceptionError(Exception):
     pass
 
 
+class ContainerEntry(BaseModel):
+    name: str
+    build_id: str = ""
+    scan_id: str = ""
+    https: str = ""
+
+    @property
+    def build_hash(self) -> str:
+        """Hash part of the Wave build ID (``bd-<hash>_<build>``)."""
+        parts = self.build_id.removeprefix("bd-").split("_")
+        return parts[0] if parts else ""
+
+    @property
+    def tag_hash(self) -> str:
+        """Hash encoded in the image tag (``name:<version>--<hash>``, or a bare hex tag)."""
+        name = self.name
+        if "://" in name:
+            name = name.split("://", 1)[1]
+        if "@" in name:
+            name = name.split("@", 1)[0]
+        if ":" not in name:
+            return ""
+        tag = name.rsplit(":", 1)[1]
+        if "--" in tag:
+            return tag.rsplit("--", 1)[1]
+        tag_lower = tag.lower()
+        return tag if len(tag_lower) >= 8 and all(c in "0123456789abcdef" for c in tag_lower) else ""
+
+
+class CondaEntry(BaseModel):
+    lock_file: str = ""
+
+
+class MetaYmlContainers(BaseModel):
+    docker: dict[str, ContainerEntry] = {}
+    singularity: dict[str, ContainerEntry] = {}
+    conda: dict[str, CondaEntry] = {}
+
+    @field_validator("docker", "singularity", "conda", mode="after")
+    @classmethod
+    def check_keys_against_container_platforms(cls, value: dict) -> dict:
+        # Check if all used keys are valid platforms
+        for plf_key in value:
+            if plf_key not in CONTAINER_PLATFORMS:
+                raise ValueError(f"Invalid platform key: {plf_key}")
+
+        return value
+
+    def dump_for_meta_yml(self) -> dict:
+        """
+        ``model_dump`` shaped for the meta.yml JSON schema: ``name``/``build_id`` are
+        always emitted (the schema requires them, empty or not), while the optional
+        fields (``https``, ``scan_id``) are omitted when empty — an empty ``https``
+        would violate the schema's ``^https://`` pattern.
+        """
+        dump = self.model_dump()
+        for platforms in dump.values():
+            for entry in platforms.values():
+                for key in ("https", "scan_id"):
+                    if not entry.get(key, True):
+                        del entry[key]
+        return dump
+
+    @model_validator(mode="after")
+    def check_container_systems_complete(self, info: ValidationInfo) -> "MetaYmlContainers":
+        """
+        Require a non-empty section with an entry for every *required* platform
+        (``REQUIRED_CONTAINER_PLATFORMS``), for each container system named in
+        ``context={"require_complete": [...]}`` (``True`` means all of
+        ``CONTAINER_SYSTEMS``, i.e. conda is exempt). Optional platforms such as
+        ``linux/arm64`` are validated when present but never required. Plain
+        construction (e.g. the partial states built up during container builds) is
+        not affected.
+        """
+        require = (info.context or {}).get("require_complete")
+        if not require:
+            return self
+        for system in CONTAINER_SYSTEMS if require is True else require:
+            entries = getattr(self, system)
+            if not entries:
+                raise ValueError(f"No containers specified for {system}")
+            for plf in REQUIRED_CONTAINER_PLATFORMS:
+                if plf not in entries:
+                    raise ValueError(f"No {system} entries found for expected platform: {plf}")
+        return self
+
+
+def module_uses_dockerfile(module: NFCoreComponent) -> bool:
+    """Return True if the module has a Dockerfile (in its dir or parent) but no environment.yml."""
+    env_yml = module.environment_yml
+    if env_yml is not None and Path(env_yml).exists():
+        return False
+    component_dir = Path(module.component_dir)
+    return (component_dir / "Dockerfile").exists() or (component_dir.parent / "Dockerfile").exists()
+
+
 def repo_full_name_from_remote(remote_url: str) -> str:
     """
     Extracts the path from the remote URL
@@ -96,15 +204,41 @@ def get_installed_modules(directory: Path, repo_type="modules") -> tuple[list[st
     return local_modules, nfcore_modules
 
 
+def cache_is_expired(path: Path) -> bool:
+    """Return True if the cache file is older than the configured TTL."""
+    age = time.time() - path.stat().st_mtime
+    return age > EDAM_CACHE_TTL
+
+
 def load_edam():
     """Load the EDAM ontology from the nf-core repository"""
     edam_formats = {}
-    try:
-        response = requests.get("https://edamontology.org/EDAM.tsv")
-    except requests.exceptions.RequestException as e:
-        log.warning(f"Failed to load EDAM ontology: {e}")
-        return edam_formats
-    for line in response.content.splitlines():
+    cache_path = Path(NFCORE_CACHE_DIR) / "EDAM.tsv"
+
+    # Remove stale cache file
+    if cache_path.exists() and cache_is_expired(cache_path):
+        log.debug("Cached EDAM ontology expired; removing old cache file")
+        cache_path.unlink(missing_ok=True)
+
+    if not cache_path.exists():
+        log.debug("EDAM.tsv file not found in NFCORE_CACHE_DIR; downloading")
+        try:
+            response = requests.get(EDAM_TSV_URL, timeout=15)
+            response.raise_for_status()
+            data_bytes = response.content
+            cache_path.write_bytes(data_bytes)
+        except requests.exceptions.RequestException as e:
+            log.warning(f"Failed to download EDAM ontology: {e}")
+            return edam_formats
+    else:
+        log.debug("Using EDAM.tsv file found in NFCORE_CACHE_DIR")
+        try:
+            data_bytes = cache_path.read_bytes()
+        except OSError as e:
+            log.warning(f"Failed to load EDAM ontology: {e}")
+            return edam_formats
+
+    for line in data_bytes.splitlines():
         fields = line.decode("utf-8").split("\t")
         if fields[0].split("/")[-1].startswith("format") and fields[14]:  # We choose an already provided extension
             extensions = fields[14].split("|")
@@ -114,6 +248,21 @@ def load_edam():
     return edam_formats
 
 
+def scan_modules_dir(modules_dir: Path) -> list[str]:
+    """
+    Scan a modules directory for main.nf files and return module names relative to modules_dir.
+
+    Args:
+        modules_dir: Directory to scan
+
+    Returns:
+        List of module names relative to modules_dir
+    """
+    if not modules_dir.exists():
+        return []
+    return [str(main_nf.parent.relative_to(modules_dir)) for main_nf in modules_dir.rglob("main.nf")]
+
+
 def filter_modules_by_name(modules: list[NFCoreComponent], module_name: str) -> list[NFCoreComponent]:
     """
     Filter modules by name, supporting exact matches and tool family matching.
@@ -131,3 +280,58 @@ def filter_modules_by_name(modules: list[NFCoreComponent], module_name: str) ->
         return exact_matches
     # If no exact match, look for modules that start with the given name (subtools)
     return [m for m in modules if m.component_name.startswith(module_name)]
+
+
+def prompt_module_selection(
+    modules: list[NFCoreComponent], component_type: str = "modules", action: str = "Select", allow_all: bool = True
+) -> str | None:
+    """
+    Prompt user to select a specific module or all modules.
+
+    Args:
+        modules (list[NFCoreComponent]): List of available modules to choose from
+        component_type (str): The component type (default: "modules", can also be "subworkflows")
+        action (str): The action verb to use in the prompt message (e.g., "Lint", "Install", "Update", "Bump versions for")
+        allow_all (bool): Whether to show "All modules" option (default: True)
+
+    Returns:
+        str | None: The selected module name, or None if "All modules" was selected
+    """
+    import questionary
+
+    from nf_core.utils import nfcore_question_style
+
+    if not modules:
+        return None
+
+    component_singular = component_type.rstrip("s")  # "modules" -> "module"
+
+    # If allow_all is False, skip the "all or named" question and go straight to module selection
+    if not allow_all:
+        question = {
+            "type": "autocomplete",
+            "name": "tool_name",
+            "message": "Tool name:",
+            "choices": [m.component_name for m in modules],
+        }
+        answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+        return answer.get("tool_name")
+
+    # Otherwise, show the "all or named" question
+    questions = [
+        {
+            "type": "list",
+            "name": f"all_{component_type}",
+            "message": f"{action} all {component_type} or a single named {component_singular}?",
+            "choices": [f"All {component_type}", f"Named {component_singular}"],
+        },
+        {
+            "type": "autocomplete",
+            "name": "tool_name",
+            "message": "Tool name:",
+            "when": lambda x: x[f"all_{component_type}"] == f"Named {component_singular}",
+            "choices": [m.component_name for m in modules],
+        },
+    ]
+    answers = questionary.unsafe_prompt(questions, style=nfcore_question_style)
+    return answers.get("tool_name")
diff --git a/nf_core/modules/update.py b/nf_core/modules/update.py
index f6cf5235a4..ed34b3e41c 100644
--- a/nf_core/modules/update.py
+++ b/nf_core/modules/update.py
@@ -16,6 +16,7 @@ def __init__(
         branch=None,
         no_pull=False,
         limit_output=False,
+        skip_deps=False,
     ):
         super().__init__(
             pipeline_dir,
@@ -31,4 +32,5 @@ def __init__(
             branch,
             no_pull,
             limit_output,
+            skip_deps,
         )
diff --git a/nf_core/pipeline-template/.github/actions/nf-test/action.yml b/nf_core/pipeline-template/.github/actions/nf-test/action.yml
index 2641c61647..ec38048a6e 100644
--- a/nf_core/pipeline-template/.github/actions/nf-test/action.yml
+++ b/nf_core/pipeline-template/.github/actions/nf-test/action.yml
@@ -20,12 +20,12 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
       with:
         version: "{% raw %}${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
       with:
         python-version: "3.14"
 
@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
diff --git a/nf_core/pipeline-template/.github/workflows/clean-up.yml b/nf_core/pipeline-template/.github/workflows/clean-up.yml
index dd71eaf55f..93f7941d75 100644
--- a/nf_core/pipeline-template/.github/workflows/clean-up.yml
+++ b/nf_core/pipeline-template/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 65354ea1d9..cd11a93b11 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -39,15 +39,15 @@ jobs:
     needs: configure
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
index 383a24494c..4c91656253 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@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,12 +32,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 709a91354c..80c7055ef1 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -11,30 +11,30 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
@@ -46,7 +46,7 @@ jobs:
         run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
+        if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
index 15823cb16a..a2f3226d51 100644
--- a/nf_core/pipeline-template/.github/workflows/nf-test.yml
+++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -41,7 +41,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
@@ -87,7 +87,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
diff --git a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
index 03b2b59144..598d16f117 100644
--- a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/nf_core/pipeline-template/.hooks/block_pipeline_outdir.sh b/nf_core/pipeline-template/.hooks/block_pipeline_outdir.sh
new file mode 100755
index 0000000000..e9ba4f9338
--- /dev/null
+++ b/nf_core/pipeline-template/.hooks/block_pipeline_outdir.sh
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# This hook is used to block commits if they include staged files inside a directory
+# which also contains a subdirectory called `pipeline_info`. The purpose of this is to
+# prevent users from inadvertently committing output from pipeline test runs inside the
+# development directory.
+
+set -e
+
+status=0
+seen_dirs=""
+
+while IFS= read -r file; do
+    # The offending output bundle's root is the ancestor directory that has
+    # `pipeline_info` as an immediate child, so callers can restore it in one go.
+    if [[ "$file" == pipeline_info/* ]]; then
+        top_dir="pipeline_info"
+    elif [[ "$file" == */pipeline_info/* ]]; then
+        top_dir="${file%%/pipeline_info/*}"
+    else
+        top_dir=""
+        dir=$(dirname "$file")
+        while [[ "$dir" != "." && "$dir" != "/" ]]; do
+            if [[ -d "$dir/pipeline_info" ]]; then
+                top_dir="$dir"
+                break
+            fi
+            dir=$(dirname "$dir")
+        done
+    fi
+
+    if [[ -n "$top_dir" ]]; then
+        echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file"
+        status=1
+        case "$seen_dirs" in
+            *"|$top_dir|"*) ;;
+            *)
+                echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area."
+                seen_dirs="$seen_dirs|$top_dir|"
+                ;;
+        esac
+    fi
+done < <(git diff --cached --name-only)
+
+exit "$status"
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index f51e1a28da..e9503db161 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.8.3
+          - prettier@3.9.6
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -25,9 +25,26 @@ repos:
               subworkflows/(?!local/).*|
               .*\.snap$
           )$
+      - id: check-added-large-files
+        args: [--maxkb=5000]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              .*\.snap$|
+              lib/nfcore_external_java_deps.jar$|
+              docs/.*\.(svg|pdf)$|
+              assets/.*$
+          )$
+      - id: check-merge-conflict
   - repo: https://github.com/seqeralabs/nf-lint-pre-commit
     rev: v0.3.0
     hooks:
       - id: nextflow-lint
         files: '\.nf$|nextflow\.config$'
         args: ["-output", "json"]
+  - repo: local
+    hooks:
+      - id: block-pipeline-outdir
+        name: Prevent committing output from pipeline test runs to the pipeline code itself
+        entry: ./.hooks/block_pipeline_outdir.sh
+        language: script
diff --git a/nf_core/pipeline-template/CHANGELOG.md b/nf_core/pipeline-template/CHANGELOG.md
index c9bd47f145..f69254be11 100644
--- a/nf_core/pipeline-template/CHANGELOG.md
+++ b/nf_core/pipeline-template/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v{{ version }} - [date]
+## v{{ version }} - [unreleased<!-- TODO nf-core: replace with date on release -->]
 
 Initial release of {{ name }}, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config
index 0edc34436d..4d9519d8fd 100644
--- a/nf_core/pipeline-template/conf/base.config
+++ b/nf_core/pipeline-template/conf/base.config
@@ -49,6 +49,9 @@ process {
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
     }
+    withLabel:process_low_memory {
+        memory = { 1.GB * task.attempt }
+    }
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
diff --git a/nf_core/pipeline-template/conf/igenomes.config b/nf_core/pipeline-template/conf/igenomes.config
index 3f11437759..b8c8154eed 100644
--- a/nf_core/pipeline-template/conf/igenomes.config
+++ b/nf_core/pipeline-template/conf/igenomes.config
@@ -8,433 +8,431 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
+params.genomes = [
     // illumina iGenomes reference file paths
-    genomes {
-        'GRCh37' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
-        }
-        'GRCh38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'CHM13' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
-            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
-            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
-            mito_name   = "chrM"
-        }
-        'GRCm38' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
-        }
-        'TAIR10' {
-            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-            mito_name   = "Mt"
-        }
-        'EB2' {
-            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
-        }
-        'UMD3.1' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'WBcel235' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
-            mito_name   = "MtDNA"
-            macs_gsize  = "9e7"
-        }
-        'CanFam3.1' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'GRCz10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'BDGP6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
-            mito_name   = "M"
-            macs_gsize  = "1.2e8"
-        }
-        'EquCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'EB1' {
-            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
-        }
-        'Galgal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Gm01' {
-            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-        }
-        'Mmul_1' {
-            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'IRGSP-1.0' {
-            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'CHIMP2.1.4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'Rnor_5.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Rnor_6.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'R64-1-1' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-            macs_gsize  = "1.2e7"
-        }
-        'EF2' {
-            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.21e7"
-        }
-        'Sbi1' {
-            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
-        }
-        'Sscrofa10.2' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'AGPv3' {
-            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'hg38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'hg19' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
-        }
-        'mm10' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
-        }
-        'bosTau8' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'ce10' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "9e7"
-        }
-        'canFam3' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'danRer10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.37e9"
-        }
-        'dm6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e8"
-        }
-        'equCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'galGal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'panTro4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'rn6' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'sacCer3' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
-            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e7"
-        }
-        'susScr3' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-    }
-}
+    'GRCh37' : [
+        fasta       : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt",
+        mito_name   : "MT",
+        macs_gsize  : "2.7e9",
+        blacklist   : "${projectDir}/assets/blacklists/GRCh37-blacklist.bed",
+    ],
+    'GRCh38' : [
+        fasta       : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed",
+        mito_name   : "chrM",
+        macs_gsize  : "2.7e9",
+        blacklist   : "${projectDir}/assets/blacklists/hg38-blacklist.bed",
+    ],
+    'CHM13' : [
+        fasta       : "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/",
+        bwamem2     : "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/",
+        gtf         : "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf",
+        gff         : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz",
+        mito_name   : "chrM",
+    ],
+    'GRCm38' : [
+        fasta       : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt",
+        mito_name   : "MT",
+        macs_gsize  : "1.87e9",
+        blacklist   : "${projectDir}/assets/blacklists/GRCm38-blacklist.bed",
+    ],
+    'TAIR10' : [
+        fasta       : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt",
+        mito_name   : "Mt",
+    ],
+    'EB2' : [
+        fasta       : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt",
+    ],
+    'UMD3.1' : [
+        fasta       : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt",
+        mito_name   : "MT",
+    ],
+    'WBcel235' : [
+        fasta       : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed",
+        mito_name   : "MtDNA",
+        macs_gsize  : "9e7",
+    ],
+    'CanFam3.1' : [
+        fasta       : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt",
+        mito_name   : "MT",
+    ],
+    'GRCz10' : [
+        fasta       : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed",
+        mito_name   : "MT",
+    ],
+    'BDGP6' : [
+        fasta       : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed",
+        mito_name   : "M",
+        macs_gsize  : "1.2e8",
+    ],
+    'EquCab2' : [
+        fasta       : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt",
+        mito_name   : "MT",
+    ],
+    'EB1' : [
+        fasta       : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt",
+    ],
+    'Galgal4' : [
+        fasta       : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed",
+        mito_name   : "MT",
+    ],
+    'Gm01' : [
+        fasta       : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt",
+    ],
+    'Mmul_1' : [
+        fasta       : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt",
+        mito_name   : "MT",
+    ],
+    'IRGSP-1.0' : [
+        fasta       : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed",
+        mito_name   : "Mt",
+    ],
+    'CHIMP2.1.4' : [
+        fasta       : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt",
+        mito_name   : "MT",
+    ],
+    'Rnor_5.0' : [
+        fasta       : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed",
+        mito_name   : "MT",
+    ],
+    'Rnor_6.0' : [
+        fasta       : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed",
+        mito_name   : "MT",
+    ],
+    'R64-1-1' : [
+        fasta       : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed",
+        mito_name   : "MT",
+        macs_gsize  : "1.2e7",
+    ],
+    'EF2' : [
+        fasta       : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt",
+        mito_name   : "MT",
+        macs_gsize  : "1.21e7",
+    ],
+    'Sbi1' : [
+        fasta       : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt",
+    ],
+    'Sscrofa10.2' : [
+        fasta       : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt",
+        mito_name   : "MT",
+    ],
+    'AGPv3' : [
+        fasta       : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed",
+        mito_name   : "Mt",
+    ],
+    'hg38' : [
+        fasta       : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed",
+        mito_name   : "chrM",
+        macs_gsize  : "2.7e9",
+        blacklist   : "${projectDir}/assets/blacklists/hg38-blacklist.bed",
+    ],
+    'hg19' : [
+        fasta       : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt",
+        mito_name   : "chrM",
+        macs_gsize  : "2.7e9",
+        blacklist   : "${projectDir}/assets/blacklists/hg19-blacklist.bed",
+    ],
+    'mm10' : [
+        fasta       : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt",
+        mito_name   : "chrM",
+        macs_gsize  : "1.87e9",
+        blacklist   : "${projectDir}/assets/blacklists/mm10-blacklist.bed",
+    ],
+    'bosTau8' : [
+        fasta       : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed",
+        mito_name   : "chrM",
+    ],
+    'ce10' : [
+        fasta       : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt",
+        mito_name   : "chrM",
+        macs_gsize  : "9e7",
+    ],
+    'canFam3' : [
+        fasta       : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt",
+        mito_name   : "chrM",
+    ],
+    'danRer10' : [
+        fasta       : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed",
+        mito_name   : "chrM",
+        macs_gsize  : "1.37e9",
+    ],
+    'dm6' : [
+        fasta       : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed",
+        mito_name   : "chrM",
+        macs_gsize  : "1.2e8",
+    ],
+    'equCab2' : [
+        fasta       : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt",
+        mito_name   : "chrM",
+    ],
+    'galGal4' : [
+        fasta       : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt",
+        mito_name   : "chrM",
+    ],
+    'panTro4' : [
+        fasta       : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt",
+        mito_name   : "chrM",
+    ],
+    'rn6' : [
+        fasta       : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed",
+        mito_name   : "chrM",
+    ],
+    'sacCer3' : [
+        fasta       : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/",
+        readme      : "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt",
+        mito_name   : "chrM",
+        macs_gsize  : "1.2e7",
+    ],
+    'susScr3' : [
+        fasta       : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa",
+        bwa         : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/",
+        bowtie2     : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/",
+        star        : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/",
+        bismark     : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/",
+        gtf         : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf",
+        bed12       : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed",
+        readme      : "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt",
+        mito_name   : "chrM",
+    ],
+]
diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
index 1614e2b1a9..2e49e26edd 100644
--- a/nf_core/pipeline-template/conf/modules.config
+++ b/nf_core/pipeline-template/conf/modules.config
@@ -31,8 +31,7 @@ process {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
     {%- endif %}
diff --git a/nf_core/pipeline-template/docs/CONTRIBUTING.md b/nf_core/pipeline-template/docs/CONTRIBUTING.md
index b82420c4db..981b29509e 100644
--- a/nf_core/pipeline-template/docs/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/docs/CONTRIBUTING.md
@@ -46,12 +46,12 @@ The nf-core stance on the use of AI and LLMs is that humans are still ultimately
 
 If you’re using AI tools, try to stick by these guidelines:
 
-- Keep PRs as small and focussed as possible
+- Keep PRs as small and focused as possible
 - Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR)
 - Review all generated code yourself before opening a PR, and ensure that you understand it
 - Engage with the community review process and expect to make revisions
 
-For more detail, see the the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
+For more detail, see the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
 
 ### Getting help
 
@@ -144,7 +144,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s
 - [ ] Perform local tests to validate that the new code works as expected.
   - [ ] If applicable, add a new test in the `tests` directory.
 - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate.
-- [ ] [Lint](lint) the code with nf-core/tools.
+- [ ] [Lint](#lint-tests) the code with nf-core/tools.
 - [ ] Update any diagrams or pipeline images as necessary.
       {%- if multiqc %}
 - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order.
@@ -184,7 +184,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across
 nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
 These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements.
 
-Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
 
 #### Nextflow version bumping
 
diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md
index d9bc3a188f..d474a4702f 100644
--- a/nf_core/pipeline-template/docs/output.md
+++ b/nf_core/pipeline-template/docs/output.md
@@ -69,4 +69,4 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 </details>
 
-[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
+[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index a711f0d0a2..ca7e7748fd 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -165,7 +165,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
-  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index cac8420ac2..85c482327c 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -13,7 +13,7 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
+                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
@@ -23,7 +23,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -33,7 +33,7 @@
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
+                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
                         "installed_by": ["subworkflows"]
                     }{% endif %}
                 }
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/nf_core/pipeline-template/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
new file mode 100644
index 0000000000..2a91c22d61
--- /dev/null
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
@@ -0,0 +1,1526 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.5.20-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.5.20-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.5-py314hd8ed1ab_100.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.8.1-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.18.0-h27c8c51_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.15-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-9.0.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/kaleido-core-0.2.1-h3644ca4_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.19.1-h0c24ade_0.conda
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diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt b/nf_core/pipeline-template/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
new file mode 100644
index 0000000000..3d5b93db98
--- /dev/null
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
+sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
+md5: f731af71c723065d91b4c01bb822641b
+depends:
+- libgcc >=14
+- libstdcxx >=14
+license: Zlib
+license_family: Other
+size: 121046
+timestamp: 1770167944449
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
index 37e7612d4c..7a970e2bb5 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.34
+  - bioconda::multiqc=1.35
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
index e80e8cd8d1..c4bc715e22 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
@@ -4,8 +4,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
-        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data'
+        : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
index 2facc627ba..27ce18d8d8 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
@@ -110,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
   docker:
     linux/amd64:
-      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
-      build_id: bd-db7c73dae76bc9e6_1
-      scan_id: sc-66fc7138dbf1cf48_1
+      name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc
+      build_id: bd-c17fb751507e9dfc_1
+      scan_id: sc-3b1b3932f9846892_1
     linux/arm64:
-      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
-      build_id: bd-d167b8012595a136_1
-      scan_id: sc-ac701dfa631a2af9_1
+      name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5
+      build_id: bd-5c84a5000a226ab5_1
+      scan_id: sc-0d39df41e9737bbd_1
   singularity:
     linux/amd64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
-      build_id: bd-4fc8657c816047c0_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2
+      build_id: bd-c680f2aea25ccec2_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
-      build_id: bd-7fbd82d945c06726_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81
+      build_id: bd-c0468833d65b2f81_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7c2f370f39..4489921603 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -81,7 +81,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -175,7 +175,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -221,7 +221,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -314,7 +314,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -408,7 +408,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 85c7c0ca5d..f78936db97 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -98,7 +98,8 @@ workflow PIPELINE_INITIALISATION {
         show_hidden,
         before_text,
         after_text,
-        command
+        command,
+        false
     )
     {%- endif %}
 
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 1df8b76fba..9ff0681f15 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     before_text         // string:   text to show before the help message and parameters summary
     after_text          // string:   text to show after the help message and parameters summary
     command             // string:   an example command of the pipeline
+    cli_typecast        // boolean:  whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour
 
     main:
 
@@ -34,11 +35,11 @@ workflow UTILS_NFSCHEMA_PLUGIN {
             fullHelp: help_full,
         ]
         if(parameters_schema) {
-            help_options << [parametersSchema: parameters_schema]
+            help_options << [parameters_schema: parameters_schema]
         }
         log.info paramsHelp(
             help_options,
-            (params.help instanceof String && params.help != "true") ? params.help : "",
+            (help instanceof String && help != "true") ? help : "",
         )
         exit 0
     }
@@ -50,7 +51,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
 
     summary_options = [:]
     if(parameters_schema) {
-        summary_options << [parametersSchema: parameters_schema]
+        summary_options << [parameters_schema: parameters_schema]
     }
     log.info before_text
     log.info paramsSummaryLog(summary_options, input_workflow)
@@ -63,7 +64,10 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     if(validate_params) {
         validateOptions = [:]
         if(parameters_schema) {
-            validateOptions << [parametersSchema: parameters_schema]
+            validateOptions << [parameters_schema: parameters_schema]
+        }
+        if(cli_typecast != null) {
+            validateOptions << [cast_cli_params: cli_typecast]
         }
         validateParameters(validateOptions)
     }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
index f7d9f02885..1d8c75a952 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -25,6 +25,30 @@ input:
         option. When this input is empty it will automatically use the configured schema or
         "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
         for meta pipelines.
+  - help:
+      type: boolean, string
+      description: |
+        Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message.
+  - help_full:
+      type: boolean
+      description: Show the full help message and exit.
+  - show_hidden:
+      type: boolean
+      description: Show hidden parameters in the help message.
+  - before_text:
+      type: string
+      description: Text to show before the parameters summary and help message.
+  - after_text:
+      type: string
+      description: Text to show after the parameters summary and help message.
+  - command:
+      type: string
+      description: An example command to run the pipeline, to show in the help message and the summary.
+  - cli_typecast:
+      type: boolean
+      description: |
+        Whether to apply typecasting to the parameters given via the CLI before validation.
+        Set this to `null` to use the default behavior.
 output:
   - dummy_emit:
       type: boolean
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index c977917aac..1fd1eac1f4 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -31,6 +31,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -63,6 +64,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -95,6 +97,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -127,6 +130,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -160,6 +164,7 @@ nextflow_workflow {
                 input[6] = "Before"
                 input[7] = "After"
                 input[8] = "nextflow run test/test"
+                input[9] = null
                 """
             }
         }
diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index f6537cc330..fd71cb8f85 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.6.1"
+    id "nf-schema@2.7.2"
 }
 
 validation {
diff --git a/nf_core/pipeline-template/tests/nextflow.config b/nf_core/pipeline-template/tests/nextflow.config
index f867b22761..37a508dfb2 100644
--- a/nf_core/pipeline-template/tests/nextflow.config
+++ b/nf_core/pipeline-template/tests/nextflow.config
@@ -8,7 +8,8 @@
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/{{ short_name }}/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/{{ short_name }}/'
 }
 
-aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
+// Fixes S3 access issues on self-hosted runners
+aws.client.anonymous = true
diff --git a/nf_core/pipelines/__init__.py b/nf_core/pipelines/__init__.py
index bc981c449f..55c151c56f 100644
--- a/nf_core/pipelines/__init__.py
+++ b/nf_core/pipelines/__init__.py
@@ -1 +1,9 @@
-from .create import PipelineCreateApp
+from nf_core.utils import lazy_attrs
+
+# Lazy imports to keep CLI start-up fast
+__getattr__, __dir__ = lazy_attrs(
+    globals(),
+    {
+        "PipelineCreateApp": "nf_core.pipelines.create",
+    },
+)
diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py
index 604a85801d..ebb38aed99 100644
--- a/nf_core/pipelines/bump_version.py
+++ b/nf_core/pipelines/bump_version.py
@@ -26,8 +26,8 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         new_version (str): The new version tag for the pipeline. Semantic versioning only.
     """
 
-    # Collect the old and new version numbers
-    current_version = pipeline_obj.nf_config.get("manifest.version", "").strip(" '\"")
+    manifest = pipeline_obj.nf_config.get("manifest", {})
+    current_version = manifest.get("version", "") or ""
     if new_version.startswith("v"):
         log.warning("Stripping leading 'v' from new version number")
         new_version = new_version[1:]
@@ -99,7 +99,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         yaml_key=["report_comment"],
     )
     # nf-test snap files
-    pipeline_name = pipeline_obj.nf_config.get("manifest.name", "").strip(" '\"")
+    pipeline_name = manifest.get("name", "")
     snap_files = [f.relative_to(pipeline_obj.wf_path) for f in Path(pipeline_obj.wf_path).glob("tests/pipeline/*.snap")]
     for snap_file in snap_files:
         update_file_version(
@@ -169,8 +169,8 @@ def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:
         new_version (str): The new version tag for the required Nextflow version.
     """
 
-    # Collect the old and new version numbers - strip leading non-numeric characters (>=)
-    current_version = pipeline_obj.nf_config.get("manifest.nextflowVersion", "").strip(" '\"")
+    manifest = pipeline_obj.nf_config.get("manifest", {})
+    current_version = manifest.get("nextflowVersion", "") or ""
     current_version = re.sub(r"^[^0-9\.]*", "", current_version)
     new_version = re.sub(r"^[^0-9\.]*", "", new_version)
     if not current_version:
diff --git a/nf_core/pipelines/containers_utils.py b/nf_core/pipelines/containers_utils.py
index 2ab297b091..d7de4fe73c 100644
--- a/nf_core/pipelines/containers_utils.py
+++ b/nf_core/pipelines/containers_utils.py
@@ -1,11 +1,12 @@
-import json
+import contextlib
 import logging
 import re
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from pathlib import Path
 
 import yaml
 
-from nf_core.utils import NF_INSPECT_MIN_NF_VERSION, check_nextflow_version, pretty_nf_version, run_cmd
+from nf_core.utils import read_module_name
 
 log = logging.getLogger(__name__)
 
@@ -20,184 +21,158 @@
     "conda_lock_files_arm64": ["conda", "linux/arm64", "lock_file"],
 }
 
+_CONFIG_LINE_RE = re.compile(r"withName:\s*'(\w+)'\s*\{\s*(?:container|conda)\s*=\s*'([^']+)'")
 
-class ContainerConfigs:
-    """Generates the container configuration files for a pipeline.
 
-    Args:
-        workflow_directory (Path): The directory containing the workflow files.
-    """
+def _container_key(platform: str) -> str:
+    return "conda" if platform.startswith("conda_lock_") else "container"
 
-    def __init__(
-        self,
-        workflow_directory: Path = Path(),
-    ):
-        self.workflow_directory = workflow_directory
 
-    def check_nextflow_version_sufficient(self) -> None:
-        """Check if the Nextflow version is sufficient to run `nextflow inspect`."""
-        if not check_nextflow_version(NF_INSPECT_MIN_NF_VERSION, silent=True):
-            raise UserWarning(
-                f"To use Seqera containers Nextflow version >= {pretty_nf_version(NF_INSPECT_MIN_NF_VERSION)} is required.\n"
-                f"Please update your Nextflow version with [magenta]'nextflow self-update'[/]\n"
-            )
+def _parse_config_file(config_path: Path) -> dict[str, str]:
+    """Return {module_name: container} from an existing platform config file."""
+    result: dict[str, str] = {}
+    with contextlib.suppress(OSError):
+        for line in config_path.read_text().splitlines():
+            m = _CONFIG_LINE_RE.search(line)
+            if m:
+                result[m.group(1)] = m.group(2)
+    return result
 
-    def parse_module_paths(self) -> dict[str, Path]:
-        """Parse include statements from workflow files to extract module paths.
 
-        Only processes includes pointing to 'modules/' directories.
-        Extracts the path from 'modules/' onwards, ignoring any '../' prefixes.
+def _write_platform_config(config_path: Path, entries: dict[str, str], key: str) -> bool:
+    """Write *entries* to *config_path*, or delete it when empty.
 
-        Returns:
-            dict: Mapping of process names to their module paths (e.g., 'modules/nf-core/fastqc')
-        """
-        module_paths = {}
+    Skips the write when content is unchanged.  Returns True if the file now exists.
+    """
+    if not entries:
+        config_path.unlink(missing_ok=True)
+        return False
+    new_content = "".join(
+        f"process {{ withName: '{name}' {{ {key} = '{container}' }} }}\n" for name, container in sorted(entries.items())
+    )
+    if not config_path.exists() or config_path.read_text() != new_content:
+        config_path.write_text(new_content)
+    return True
 
-        # Pattern matches: include { NAME ... } from 'path'
-        # Captures the first name (original) and the path, ignoring any alias
-        include_pattern = re.compile(r"include\s*\{\s*(\w+).*?\}\s*from\s+['\"]([^'\"]+)['\"]")
 
-        # Search in root (main.nf), workflows, modules, and subworkflows directories
-        search_dirs = ["workflows", "modules", "subworkflows"]
+def _process_meta(meta_path: Path) -> tuple[str, dict[str, str]] | None:
+    """Read one meta.yml + sibling main.nf and return (module_name, {platform: container}).
 
-        nf_files_to_search = list(self.workflow_directory.glob("*.nf"))
-        for search_dir in search_dirs:
-            search_path = self.workflow_directory / search_dir
-            if not search_path.exists():
-                continue
-            nf_files_to_search.extend(search_path.rglob("*.nf"))
+    Returns None when the file should be skipped.
+    """
+    try:
+        raw = meta_path.read_bytes()
+    except OSError as e:
+        log.debug(f"Could not read {meta_path}: {e}")
+        return None
+
+    # TODO: remove this early-exit once containers are present in the majority of modules
+    if b"containers:" not in raw:
+        return None
+
+    meta = yaml.safe_load(raw)
 
-        for nf_file in nf_files_to_search:
-            try:
-                content = nf_file.read_text()
-                for match in include_pattern.finditer(content):
-                    process_name = match.group(1)
-                    relative_path = match.group(2)
+    module_name = read_module_name(meta_path.parent / "main.nf")
+    if not module_name:
+        log.debug(f"No process definition found next to {meta_path}, skipping")
+        return None
 
-                    # Only process paths that contain 'modules/'
-                    if "modules/" not in relative_path:
-                        continue
+    platform_containers: dict[str, str] = {}
+    for platform_name, (runtime, arch, protocol) in PLATFORMS.items():
+        log.debug(f"Adding container for platform {platform_name}, runtime={runtime}, arch={arch}, protocol={protocol}")
+        with contextlib.suppress(KeyError, TypeError):
+            platform_containers[platform_name] = meta["containers"][runtime][arch][protocol]
 
-                    # Extract everything from 'modules/' onwards, removing any '/main' suffix
-                    module_path_str = relative_path[relative_path.find("modules/") :]
-                    module_path_str = module_path_str.replace("/main", "")
+    return module_name, platform_containers
+
+
+class ContainerConfigs:
+    """Generates the container configuration files for a pipeline.
 
-                    module_paths[process_name] = Path(module_path_str)
-                    log.debug(f"Found include: {process_name} -> {module_path_str}")
+    Args:
+        workflow_directory (Path): The directory containing the workflow files.
+    """
 
-            except OSError as e:
-                log.debug(f"Error parsing {nf_file}: {e}")
-                continue
+    def __init__(self, workflow_directory: Path = Path()) -> None:
+        self.workflow_directory = workflow_directory
 
-        return module_paths
+    def update_module_container_config(self, module_path: Path) -> None:
+        """Targeted update for a single module.
 
-    def generate_container_configs(
-        self, new_module_path: Path | None = None, new_module_name: str | None = None
-    ) -> set[str]:
+        Reads the current config files, splices in (or removes) the entry for
+        the module at *module_path*, and writes back only what changed.
         """
-        Generate the container configuration files for a pipeline.
-        Requires Nextflow >= 25.04.4
+        result = _process_meta(module_path / "meta.yml")
+
+        if result is None:
+            module_name = read_module_name(module_path / "main.nf")
+            if not module_name:
+                log.debug(f"Could not determine process name for {module_path}, skipping")
+                return
+            platform_containers: dict[str, str] = {}
+        else:
+            module_name, platform_containers = result
+
+        conf_dir = self.workflow_directory / "conf"
+        for platform in PLATFORMS:
+            config_path = conf_dir / f"containers_{platform}.config"
+            entries = _parse_config_file(config_path)
+            if platform in platform_containers:
+                entries[module_name] = platform_containers[platform]
+            _write_platform_config(config_path, entries, _container_key(platform))
+
+    def generate_container_configs(self) -> set[str]:
+        """Full scan of all ``meta.yml`` files under ``modules/``.
+
+        Used by lint and bulk operations (update, remove, patch) where multiple
+        modules may have changed.
 
         Returns:
             set[str]: Names of config files written (e.g. ``{'containers_docker_amd64.config'}``).
         """
-        self.check_nextflow_version_sufficient()
-        log.debug("Generating container config file with [magenta bold]nextflow inspect[/].")
-        try:
-            # Run nextflow inspect
-            executable = "nextflow"
-            cmd_params = f"inspect -format json {self.workflow_directory}"
-            cmd_out = run_cmd(executable, cmd_params)
-            if cmd_out is None:
-                raise UserWarning("Failed to run `nextflow inspect`. Please check your Nextflow installation.")
-
-            out, _ = cmd_out
-            out_str = out.decode("utf-8", errors="replace")
-            try:
-                # Newer Nextflow versions print [PIPELINE]/[WORKDIR] headers before and [SUCCESS] after the JSON
-                json_start = out_str.find("{")
-                out_json, _ = json.JSONDecoder().raw_decode(out_str, json_start if json_start >= 0 else 0)
-            except json.JSONDecodeError:
-                out_json = json.loads(out)
-
-        except RuntimeError as e:
-            log.error("Running 'nextflow inspect' failed with the following error:")
-            raise UserWarning(e) from e
-
-        module_names = {p.get("name") for p in out_json["processes"] if p.get("name")}
-        log.debug(f"Found {len(module_names)} modules: {', '.join(module_names)}")
-
-        # Parse module paths from include statements
-        module_path_map = self.parse_module_paths()
-        log.debug(f"Parsed {len(module_path_map)} module paths from include statements")
-
-        if new_module_name and new_module_path:
-            module_names.add(new_module_name.upper())
-            module_path_map[new_module_name.upper()] = new_module_path
-
-        # Build containers dict from module meta.yml files
-        # Pre-initialize all platforms to avoid repeated existence checks
-        has_warnings = False
+        modules_dir = self.workflow_directory / "modules"
+        if not modules_dir.is_dir():
+            log.debug(f"No modules directory found at {modules_dir}, skipping")
+            return set()
+
         containers: dict[str, dict[str, str]] = {platform: {} for platform in PLATFORMS}
-        for m_name in module_names:
-            # Try to get module path from include statements
-            if m_name in module_path_map:
-                module_path = module_path_map[m_name]
-                log.debug(f"Using parsed path for {m_name}: {module_path}")
-            else:
-                # Fallback to old heuristic method
-                log.debug(f"No parsed path found for {m_name}, using heuristic")
-                module_path = Path(*m_name.lower().split("_", 1))
-
-            # Look for meta.yml in the module path
-            meta_path = self.workflow_directory / module_path / "meta.yml"
-
-            try:
-                with open(meta_path) as fh:
-                    meta = yaml.safe_load(fh)
-                    log.debug(f"Loaded meta.yml for {m_name} from {meta_path}")
-            except FileNotFoundError:
-                log.warning(f"Could not find meta.yml for {m_name} at {meta_path}")
-                continue
-
-            # Extract containers for all platforms
-            for platform_name, (runtime, arch, protocol) in PLATFORMS.items():
-                try:
-                    containers[platform_name][m_name] = meta["containers"][runtime][arch][protocol]
-                    log.debug(f"Found {platform_name} container for {m_name}")
-                except (KeyError, TypeError):
-                    log.debug(f"Could not find {platform_name} container for {m_name}")
-                    has_warnings = True
+
+        with ThreadPoolExecutor() as pool:
+            futures = {pool.submit(_process_meta, p): p for p in modules_dir.rglob("meta.yml")}
+            for future in as_completed(futures):
+                result = future.result()
+                if result is None:
                     continue
-        if has_warnings:
-            log.debug(
-                "Generated container configs for the pipeline. Not all containers were found. Run with `-v` to see detailed warning messages."
-            )
-        else:
-            log.info("Generated container configs for the pipeline successfully.")
+                module_name, platform_containers = result
+                for platform_name, container in platform_containers.items():
+                    containers[platform_name][module_name] = container
 
         # remove all generated config files, to handle removed modules
         for platform in PLATFORMS:
             (self.workflow_directory / "conf" / f"containers_{platform}.config").unlink(missing_ok=True)
-        # write config files
+
         written: set[str] = set()
         for platform, module_containers in containers.items():
-            if not module_containers:
-                continue
-            lines = [
-                f"process {{ withName: '{module_name}' {{ container = '{container}' }} }}\n"
-                for module_name, container in sorted(module_containers.items())
-            ]
             config_path = self.workflow_directory / "conf" / f"containers_{platform}.config"
-            config_path.write_text("".join(lines))
-            written.add(config_path.name)
+            if _write_platform_config(config_path, module_containers, _container_key(platform)):
+                written.add(config_path.name)
+
+        log.info("Generated container configs for the pipeline.")
         return written
 
 
-def try_generate_container_configs(
-    directory: Path, new_module_path: Path | None = None, new_module_name: str | None = None
-) -> None:
+def try_generate_container_configs(directory: Path, module_path: Path | None = None) -> None:
+    """Regenerate container configs for *directory*.
+
+    If *module_path* is given, only that module's entries are updated (fast
+    path for single-module installs).  Otherwise a full scan of ``modules/``
+    is performed.
+    """
     try:
-        ContainerConfigs(directory).generate_container_configs(new_module_path, new_module_name)
+        configs = ContainerConfigs(directory)
+        if module_path is not None:
+            configs.update_module_container_config(module_path)
+        else:
+            configs.generate_container_configs()
     except UserWarning as e:
         log.warning(f"Could not regenerate container configuration files: {e}")
diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index 756af168e3..eedd517933 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -434,6 +434,7 @@ code_quality:
         - ".prettierignore"
         - ".prettierrc.yml"
         - ".github/workflows/fix-linting.yml"
+        - ".hooks/block_pipeline_outdir.sh"
       short_description: "Use code linters"
       description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier."
       help_text: |
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
index 5751ddbd77..d7609126ac 100644
--- a/nf_core/pipelines/create/utils.py
+++ b/nf_core/pipelines/create/utils.py
@@ -6,7 +6,7 @@
 from typing import Any
 
 import yaml
-from pydantic import ConfigDict, ValidationError, ValidationInfo, field_validator
+from pydantic import ValidationError, ValidationInfo, field_validator
 from textual import on
 from textual.app import ComposeResult
 from textual.containers import Grid, HorizontalScroll
@@ -18,6 +18,10 @@
 import nf_core
 from nf_core.utils import NFCoreTemplateConfig
 
+# Sphinx/autodoc triggers Pydantic model rebuilds which require `Dict` in this module's namespace.
+# Using the builtin dict (not typing.Dict) because Pydantic v2 only accepts the lowercase form.
+Dict = dict
+
 # Use ContextVar to define a context on the model initialization
 _init_context_var: ContextVar = ContextVar("_init_context_var", default=None)
 
@@ -41,8 +45,6 @@ def init_context(value: dict[str, Any]) -> Iterator[None]:
 class CreateConfig(NFCoreTemplateConfig):
     """Pydantic model for the nf-core create config."""
 
-    model_config = ConfigDict(extra="allow")
-
     def __init__(self, /, **data: Any) -> None:
         """Custom init method to allow using a context on the model initialization."""
         context = _init_context_var.get()
diff --git a/nf_core/pipelines/download/container_fetcher.py b/nf_core/pipelines/download/container_fetcher.py
index bfcda9ed54..3916fb1b9c 100644
--- a/nf_core/pipelines/download/container_fetcher.py
+++ b/nf_core/pipelines/download/container_fetcher.py
@@ -292,8 +292,11 @@ def gather_config_registries(self, workflow_directory: Path, registry_keys: list
 
         config_registries = set()
         for registry_key in registry_keys:
-            if registry_key in nf_config:
-                config_registries.add(nf_config[registry_key])
+            parts = registry_key.split(".", 1)
+            if len(parts) == 2 and parts[0] in nf_config and isinstance(nf_config[parts[0]], dict):
+                val = nf_config[parts[0]].get(parts[1])
+                if val:
+                    config_registries.add(val)
 
         return config_registries
 
diff --git a/nf_core/pipelines/download/docker.py b/nf_core/pipelines/download/docker.py
index 40bf7d22e3..247a1579ba 100644
--- a/nf_core/pipelines/download/docker.py
+++ b/nf_core/pipelines/download/docker.py
@@ -12,7 +12,8 @@
 
 import nf_core.utils
 from nf_core.pipelines.download.container_fetcher import ContainerFetcher, ContainerProgress
-from nf_core.pipelines.download.utils import ContainerRegistryUrls, copy_container_load_scripts
+from nf_core.pipelines.download.utils import copy_container_load_scripts
+from nf_core.utils import ContainerRegistryUrls
 
 log = logging.getLogger(__name__)
 stderr = rich.console.Console(
@@ -286,15 +287,17 @@ def _run_docker_command(
             # - read lines if there are any,
             # - check if we should kill it,
             # - update the progress bar
+            assert proc.stdout is not None
+            stdout = proc.stdout
             lines = []
             while True:
                 if self.kill_with_fire:
                     proc.kill()
                     raise KeyboardInterrupt("Docker command was cancelled by user")
 
-                rlist, _, _ = select.select([proc.stdout], [], [], 0.1)
-                if rlist and proc.stdout is not None:
-                    line = proc.stdout.readline()
+                rlist, _, _ = select.select([stdout], [], [], 0.1)
+                if rlist:
+                    line = stdout.readline()
                     if line:
                         lines.append(line)
                         self.progress.update(progress_task, current_log=line.strip())
diff --git a/nf_core/pipelines/download/download.py b/nf_core/pipelines/download/download.py
index fbd051f65d..ef3b84dfcf 100644
--- a/nf_core/pipelines/download/download.py
+++ b/nf_core/pipelines/download/download.py
@@ -20,18 +20,19 @@
 import nf_core
 import nf_core.pipelines.list
 import nf_core.utils
+from nf_core.github_api import gh_api
 from nf_core.pipelines.download.container_fetcher import ContainerFetcher
 from nf_core.pipelines.download.docker import DockerFetcher
 from nf_core.pipelines.download.singularity import SINGULARITY_CACHE_DIR_ENV_VAR, SingularityFetcher
-from nf_core.pipelines.download.utils import DownloadError, intermediate_dir_with_cd
+from nf_core.pipelines.download.utils import DownloadError
 from nf_core.pipelines.download.workflow_repo import WorkflowRepo
 from nf_core.utils import (
     NF_INSPECT_MIN_NF_VERSION,
     NFCORE_VER_LAST_WITHOUT_NF_INSPECT,
     check_nextflow_version,
-    gh_api,
     pretty_nf_version,
     run_cmd,
+    set_wd_tempdir,
 )
 
 log = logging.getLogger(__name__)
@@ -42,6 +43,8 @@
     force_terminal=nf_core.utils.rich_force_colors(),
 )
 
+SINGULARITY_SYSTEMS = ["singularity", "apptainer"]
+
 
 class DownloadWorkflow:
     """Downloads a nf-core workflow from GitHub to the local file system.
@@ -248,7 +251,7 @@ def download_workflow(self) -> None:
         ]
         if self.container_system:
             summary_log.append(f"Container library: '{', '.join(self.container_library)}'")
-        if self.container_system == "singularity" and os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR) is not None:
+        if self.container_system in SINGULARITY_SYSTEMS and os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR) is not None:
             summary_log.append(
                 f"Using [blue]{SINGULARITY_CACHE_DIR_ENV_VAR}[/]': {os.environ[SINGULARITY_CACHE_DIR_ENV_VAR]}'"
             )
@@ -330,7 +333,7 @@ def download_workflow_static(self) -> None:
                     raise DownloadError("Error editing pipeline config file to use local configs!") from e
 
             # Collect all required container images
-            if self.container_system in {"singularity", "docker"}:
+            if self.container_system in {"singularity", "docker", "apptainer"}:
                 workflow_directory = self.outdir / revision_dirname
                 self.find_container_images(workflow_directory, revision)
 
@@ -366,7 +369,7 @@ def download_workflow_platform(self, location: Path | None = None) -> None:
         self.workflow_repo.bare_clone(self.output_filename)
 
         # extract the required containers
-        if self.container_system in {"singularity", "docker"}:
+        if self.container_system in {"singularity", "docker", "apptainer"}:
             for revision, commit in self.wf_sha.items():
                 # Checkout the repo in the current revision
                 self.workflow_repo.checkout(commit)
@@ -502,7 +505,7 @@ def prompt_container_download(self) -> None:
             stderr.print("\nIn addition to the pipeline code, this tool can download software containers.")
             self.container_system = questionary.select(
                 "Download software container images:",
-                choices=["none", "singularity", "docker"],
+                choices=["none", "singularity", "docker", "apptainer"],
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
 
@@ -512,7 +515,7 @@ def setup_container_fetcher(self) -> None:
         """
         assert self.outdir is not None  # mypy
         try:
-            if self.container_system == "singularity":
+            if self.container_system in SINGULARITY_SYSTEMS:
                 self.container_fetcher = SingularityFetcher(
                     outdir=self.outdir,
                     container_library=self.container_library,
@@ -521,6 +524,7 @@ def setup_container_fetcher(self) -> None:
                     container_cache_index=self.container_cache_index,
                     parallel=self.parallel,
                     hide_progress=self.hide_progress,
+                    container_system=self.container_system,
                 )
             elif self.container_system == "docker":
                 self.container_fetcher = DockerFetcher(
@@ -555,9 +559,9 @@ def prompt_compression_type(self) -> None:
             stderr.print(
                 "\nIf transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file."
             )
-            if self.container_system == "singularity":
+            if self.container_system in SINGULARITY_SYSTEMS:
                 stderr.print(
-                    "[bold]This is [italic]not[/] recommended when downloading Singularity images, as it can take a long time and saves very little space."
+                    "[bold]This is [italic]not[/] recommended when downloading Singularity/Apptainer images, as it can take a long time and saves very little space."
                 )
             self.compress_type = questionary.select(
                 "Choose compression type:",
@@ -645,6 +649,12 @@ def wf_use_local_configs(self, revision_dirname: str) -> None:
                 + 'singularity.cacheDir = "${projectDir}/../singularity-images/"'
                 + "\n///////////////////////////////////////"
             )
+        elif self.container_system == "apptainer" and self.container_cache_utilisation == "copy":
+            nfconfig += (
+                f"\n\n// Added by `nf-core pipelines download` v{nf_core.__version__} //\n"
+                + 'apptainer.cacheDir = "${projectDir}/../apptainer-images/"'
+                + "\n///////////////////////////////////////"
+            )
 
         # Write the file out again
         log.debug(f"Updating '{nfconfig_fn}'")
@@ -677,7 +687,7 @@ def find_container_images(
         working_dir = Path().absolute()
 
         def run_nextflow_inspect(params_file: Path | None = None) -> dict[str, Any]:
-            with intermediate_dir_with_cd(working_dir):
+            with set_wd_tempdir(working_dir):
                 executable = "nextflow"
                 params_file_arg = f' -params-file "{params_file}"' if params_file else ""
                 cmd_params = (
@@ -693,12 +703,18 @@ def run_nextflow_inspect(params_file: Path | None = None) -> dict[str, Any]:
         try:
             out_json = run_nextflow_inspect()
         except RuntimeError as e:
-            # Extract Nextflow stdout from the chained CalledProcessError (errors go to stdout in NF)
-            nf_stdout = getattr(e.__cause__, "output", None) or b""
+            # Nextflow's error text is embedded in the RuntimeError message by run_cmd;
+            # a chained CalledProcessError (if any) may carry it in stdout/stderr instead.
+            nf_error_parts = [str(e), getattr(e.__cause__, "output", None), getattr(e.__cause__, "stderr", None)]
+            nf_error = "\n".join(
+                part.decode("utf-8", errors="replace") if isinstance(part, bytes) else part
+                for part in nf_error_parts
+                if part
+            )
 
             # Nextflow >= 26.04 enforces strict process directive syntax and rejects old-style
             # if/else container blocks with "Invalid process directive". Users need an older NF.
-            if b"Invalid process directive" in nf_stdout:
+            if "Invalid process directive" in nf_error:
                 raise DownloadError(
                     "nextflow inspect failed because the pipeline uses old-style process syntax "
                     "that the default strict syntax of Nextflow >= 26.04 no longer accepts.\n"
@@ -710,7 +726,7 @@ def run_nextflow_inspect(params_file: Path | None = None) -> dict[str, Any]:
             # only issue, retry inspect with an ephemeral params file that provides one.
             if re.search(
                 r"missing required parameter\s*:\s*(?:--outdir|params\.outdir|outdir)\b",
-                nf_stdout.decode("utf-8", errors="replace"),
+                nf_error,
                 flags=re.IGNORECASE,
             ):
                 try:
diff --git a/nf_core/pipelines/download/singularity.py b/nf_core/pipelines/download/singularity.py
index c389e73dc8..98d4b5981a 100644
--- a/nf_core/pipelines/download/singularity.py
+++ b/nf_core/pipelines/download/singularity.py
@@ -18,11 +18,11 @@
 import nf_core.utils
 from nf_core.pipelines.download.container_fetcher import ContainerFetcher, ContainerProgress
 from nf_core.pipelines.download.utils import (
-    ContainerRegistryUrls,
     DownloadError,
     intermediate_file,
     intermediate_file_no_creation,
 )
+from nf_core.utils import ContainerRegistryUrls
 
 log = logging.getLogger(__name__)
 stderr = rich.console.Console(
@@ -34,6 +34,48 @@
 
 SINGULARITY_CACHE_DIR_ENV_VAR = "NXF_SINGULARITY_CACHEDIR"
 SINGULARITY_LIBRARY_DIR_ENV_VAR = "NXF_SINGULARITY_LIBRARYDIR"
+APPTAINER_CACHE_DIR_ENV_VAR = "NXF_APPTAINER_CACHEDIR"
+APPTAINER_LIBRARY_DIR_ENV_VAR = "NXF_APPTAINER_LIBRARYDIR"
+
+
+def get_container_cache_dir(container_system: str) -> str:
+    """Returns the matching cache directory environment variable."""
+    match container_system:
+        case "singularity":
+            return SINGULARITY_CACHE_DIR_ENV_VAR
+        case "apptainer":
+            return APPTAINER_CACHE_DIR_ENV_VAR
+        case _:
+            raise KeyError(f"Container engine: {container_system} is unknown.")
+
+
+def get_container_library_dir(container_system: str) -> str:
+    """Returns the matching library directory environment variable."""
+    match container_system:
+        case "singularity":
+            return SINGULARITY_LIBRARY_DIR_ENV_VAR
+        case "apptainer":
+            return APPTAINER_LIBRARY_DIR_ENV_VAR
+        case _:
+            raise KeyError(f"Container engine: {container_system} is unknown.")
+
+
+class SingularityCacheFilePathValidator(questionary.Validator):
+    """
+    Validator for file path specified as --singularity-cache-index argument in nf-core pipelines download
+    """
+
+    def validate(self, value):
+        if len(value.text):
+            if Path(value.text).is_file():
+                return True
+            else:
+                raise questionary.ValidationError(
+                    message="Invalid remote cache index file",
+                    cursor_position=len(value.text),
+                )
+        else:
+            return True
 
 
 class SingularityProgress(ContainerProgress):
@@ -74,21 +116,28 @@ def __init__(
         container_cache_index=None,
         parallel: int = 4,
         hide_progress: bool = False,
+        container_system: str = "singularity",
     ):
+        self.container_system = container_system
+        self.container_system_name = container_system.capitalize()
+        self.cache_dir_env_var = get_container_cache_dir(container_system)
+        self.library_dir_env_var = get_container_library_dir(container_system)
         # Check if the env variable for the Singularity cache directory is set
-        has_cache_dir = os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR) is not None
+        has_cache_dir = os.environ.get(self.cache_dir_env_var) is not None
         if not has_cache_dir and stderr.is_interactive:
             # Prompt for the creation of a Singularity cache directory
-            has_cache_dir = SingularityFetcher.prompt_singularity_cachedir_creation()
+            has_cache_dir = SingularityFetcher.prompt_cachedir_creation(container_system)
 
             if has_cache_dir and container_cache_utilisation is None:
                 # No choice regarding singularity cache has been made.
-                container_cache_utilisation = SingularityFetcher.prompt_singularity_cachedir_utilization()
+                container_cache_utilisation = SingularityFetcher.prompt_cachedir_utilization(
+                    container_system, self.cache_dir_env_var
+                )
 
         if container_cache_utilisation == "remote":
             # If we have a remote cache, we need to read it
             if container_cache_index is None and stderr.is_interactive:
-                container_cache_index = SingularityFetcher.prompt_singularity_cachedir_remote()
+                container_cache_index = SingularityFetcher.prompt_cachedir_remote(self.cache_dir_env_var)
                 if container_cache_index is None:
                     # No remote cache specified
                     self.container_cache_index = None
@@ -102,30 +151,28 @@ def __init__(
                     )
                 except (FileNotFoundError, LookupError) as e:
                     log.error(
-                        f"[red]Issue with reading the specified remote ${SINGULARITY_CACHE_DIR_ENV_VAR} index:[/]\n{e}\n"
+                        f"[red]Issue with reading the specified remote ${self.cache_dir_env_var} index:[/]\n{e}\n"
                     )
                     if stderr.is_interactive and rich.prompt.Confirm.ask(
                         "[blue]Specify a new index file and try again?"
                     ):
-                        container_cache_index = SingularityFetcher.prompt_singularity_cachedir_remote()
+                        container_cache_index = SingularityFetcher.prompt_cachedir_remote(self.cache_dir_env_var)
                     else:
-                        log.info(
-                            f"Proceeding without consideration of the remote ${SINGULARITY_CACHE_DIR_ENV_VAR} index."
-                        )
+                        log.info(f"Proceeding without consideration of the remote ${self.cache_dir_env_var} index.")
                         self.container_cache_index = None
-                        container_cache_utilisation = "copy" if os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR) else None
+                        container_cache_utilisation = "copy" if os.environ.get(self.cache_dir_env_var) else None
             else:
                 log.warning("[red]No remote cache index specified, skipping remote container download.[/]")
 
         # Find out what the library directory is
-        library_dir = Path(path_str) if (path_str := os.environ.get(SINGULARITY_LIBRARY_DIR_ENV_VAR)) else None
+        library_dir = Path(path_str) if (path_str := os.environ.get(self.library_dir_env_var)) else None
         if library_dir and not library_dir.is_dir():
             # Since the library is read-only, if the directory isn't there, we can forget about it
             library_dir = None
 
         # Find out what the cache directory is
-        cache_dir = Path(path_str) if (path_str := os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR)) else None
-        log.debug(f"{SINGULARITY_CACHE_DIR_ENV_VAR}: {cache_dir}")
+        cache_dir = Path(path_str) if (path_str := os.environ.get(self.cache_dir_env_var)) else None
+        log.debug(f"{self.cache_dir_env_var}: {cache_dir}")
 
         if container_cache_utilisation in ["amend", "copy"]:
             if cache_dir:
@@ -133,9 +180,11 @@ def __init__(
                     log.debug(f"Cache directory not found, creating: {cache_dir}")
                     cache_dir.mkdir()
             else:
-                raise FileNotFoundError(f"Singularity cache is required but no '{SINGULARITY_CACHE_DIR_ENV_VAR}' set!")
+                raise FileNotFoundError(
+                    f"{self.container_system_name} cache is required but no '{self.cache_dir_env_var}' set!"
+                )
 
-        container_output_dir = outdir / "singularity-images"
+        container_output_dir = outdir / f"{container_system}-images"
         super().__init__(
             container_output_dir=container_output_dir,
             container_library=container_library,
@@ -155,7 +204,9 @@ def check_and_set_implementation(self) -> None:
         Raises:
             OSError: If Singularity/Apptainer is not installed or not in $PATH
         """
-        if shutil.which("singularity"):
+        if shutil.which(self.container_system):
+            self.implementation = self.container_system
+        elif shutil.which("singularity"):
             self.implementation = "singularity"
         elif shutil.which("apptainer"):
             self.implementation = "apptainer"
@@ -209,11 +260,11 @@ def get_cache_dir(self) -> Path:
         Raises:
             FileNotFoundError: If the cache directory is not set
         """
-        cache_dir = os.environ.get(SINGULARITY_CACHE_DIR_ENV_VAR)
+        cache_dir = os.environ.get(self.cache_dir_env_var)
         if cache_dir is not None:
             return Path(cache_dir)
         else:
-            raise FileNotFoundError(f"Singularity cache is required but no '{SINGULARITY_CACHE_DIR_ENV_VAR}' set!")
+            raise FileNotFoundError(f"Singularity cache is required but no '{self.cache_dir_env_var}' set!")
 
     def make_cache_dir(self) -> None:
         """
@@ -225,33 +276,36 @@ def make_cache_dir(self) -> None:
             cache_dir.mkdir()
 
     @staticmethod
-    def prompt_singularity_cachedir_creation() -> bool:
-        """Prompt about using singularity cache directory if not already set"""
+    def prompt_cachedir_creation(container_system: str = "singularity") -> bool:
+        """Prompt about using singularity/apptainer cache directory if not already set"""
         if not nf_core.utils.is_interactive():
             return False
+        # Define cache_dir_env_var
+        cache_dir_env_var = get_container_cache_dir(container_system)
+        container_system_name = container_system.capitalize()
         stderr.print(
-            f"\nNextflow and nf-core can use an environment variable called [blue]${SINGULARITY_CACHE_DIR_ENV_VAR}[/] that is a path to a directory where remote Singularity images are stored. "
+            f"\nNextflow and nf-core can use an environment variable called [blue]${cache_dir_env_var}[/] that is a path to a directory where remote {container_system_name} images are stored. "
             f"This allows downloaded images to be cached in a central location."
         )
         if rich.prompt.Confirm.ask(
-            f"[blue bold]?[/] [bold]Define [blue not bold]${SINGULARITY_CACHE_DIR_ENV_VAR}[/] for a shared Singularity image download folder?[/]"
+            f"[blue bold]?[/] [bold]Define [blue not bold]${cache_dir_env_var}[/] for a shared {container_system_name} image download folder?[/]"
         ):
-            cachedir_path = SingularityFetcher.prompt_singularity_cachedir_path()
+            cachedir_path = SingularityFetcher.prompt_cachedir_path(cache_dir_env_var)
             if cachedir_path is None:
-                raise DownloadError(f"No {SINGULARITY_CACHE_DIR_ENV_VAR} specified, cannot continue.")
+                raise DownloadError(f"No {cache_dir_env_var} specified, cannot continue.")
 
-            os.environ[SINGULARITY_CACHE_DIR_ENV_VAR] = str(cachedir_path)
+            os.environ[cache_dir_env_var] = str(cachedir_path)
 
             # Optionally, create a permanent entry for the singularity cache directory in the terminal profile.
-            SingularityFetcher.prompt_singularity_cachedir_shellprofile_append(cachedir_path)
+            SingularityFetcher.prompt_cachedir_shellprofile_append(cachedir_path, cache_dir_env_var)
 
             return True
 
         return False
 
     @staticmethod
-    def prompt_singularity_cachedir_path() -> Path | None:
-        """Prompt for the name of the Singularity cache directory"""
+    def prompt_cachedir_path(cache_dir_env_var: str = SINGULARITY_CACHE_DIR_ENV_VAR) -> Path | None:
+        """Prompt for the name of the Singularity / Apptainer cache directory"""
         if not nf_core.utils.is_interactive():
             log.warning("Cannot prompt for Singularity cache directory in a non-interactive session.")
             return None
@@ -264,7 +318,7 @@ def prompt_singularity_cachedir_path() -> Path | None:
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
             if prompt_cachedir_path == "":
-                log.error(f"Not using [blue]${SINGULARITY_CACHE_DIR_ENV_VAR}[/]")
+                log.error(f"Not using [blue]${cache_dir_env_var}[/]")
                 return None
             cachedir_path = Path(prompt_cachedir_path).expanduser().absolute()
             if not cachedir_path.is_dir():
@@ -273,9 +327,11 @@ def prompt_singularity_cachedir_path() -> Path | None:
         return cachedir_path
 
     @staticmethod
-    def prompt_singularity_cachedir_shellprofile_append(cachedir_path: Path) -> None:
+    def prompt_cachedir_shellprofile_append(
+        cachedir_path: Path, cache_dir_env_var: str = SINGULARITY_CACHE_DIR_ENV_VAR
+    ) -> None:
         """
-        Prompt about appending the Singularity cache directory to the shell profile
+        Prompt about appending the Singularity / Apptainer cache directory to the shell profile
 
         Currently support for bash and zsh.
         ToDo: "sh", "dash", "ash","csh", "tcsh", "ksh", "fish", "cmd", "powershell", "pwsh"?
@@ -298,9 +354,9 @@ def prompt_singularity_cachedir_shellprofile_append(cachedir_path: Path) -> None
             return
         if shellprofile_path is not None:
             stderr.print(
-                f"\nSo that [blue]${SINGULARITY_CACHE_DIR_ENV_VAR}[/] is always defined, you can add it to your [blue not bold]~/{shellprofile_path.name}[/] file ."
+                f"\nSo that [blue]${cache_dir_env_var}[/] is always defined, you can add it to your [blue not bold]~/{shellprofile_path.name}[/] file ."
                 "This will then be automatically set every time you open a new terminal. We can add the following line to this file for you: \n"
-                f'[blue]export {SINGULARITY_CACHE_DIR_ENV_VAR}="{cachedir_path}"[/]'
+                f'[blue]export {cache_dir_env_var}="{cachedir_path}"[/]'
             )
             append_to_file = rich.prompt.Confirm.ask(
                 f"[blue bold]?[/] [bold]Add to [blue not bold]~/{shellprofile_path.name}[/] ?[/]"
@@ -310,7 +366,7 @@ def prompt_singularity_cachedir_shellprofile_append(cachedir_path: Path) -> None
                     f.write(
                         "\n\n#######################################\n"
                         f"## Added by `nf-core pipelines download` v{nf_core.__version__} ##\n"
-                        + f'export {SINGULARITY_CACHE_DIR_ENV_VAR}="{cachedir_path}"'
+                        + f'export {cache_dir_env_var}="{cachedir_path}"'
                         + "\n#######################################\n"
                     )
                 log.info(f"Successfully wrote to [blue]{shellprofile_path}[/]")
@@ -319,24 +375,26 @@ def prompt_singularity_cachedir_shellprofile_append(cachedir_path: Path) -> None
             log.debug(f"No shell profile found for {shell}.")
 
     @staticmethod
-    def prompt_singularity_cachedir_utilization() -> str:
-        """Ask if we should *only* use singularity cache directory without copying into target"""
+    def prompt_cachedir_utilization(
+        container_system: str = "singularity", cache_dir_env_var: str = SINGULARITY_CACHE_DIR_ENV_VAR
+    ) -> str:
+        """Ask if we should *only* use singularity/apptainer cache directory without copying into target"""
         if not nf_core.utils.is_interactive():
             return "copy"
         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"
-            f"[blue not bold]${SINGULARITY_CACHE_DIR_ENV_VAR}[/] folder, Nextflow will automatically find them. "
+            f"[blue not bold]${cache_dir_env_var}[/] 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."
         )
         return questionary.select(
-            f"Copy singularity images from {SINGULARITY_CACHE_DIR_ENV_VAR} to the target folder or amend new images to the cache?",
+            f"Copy {container_system} images from {cache_dir_env_var} to the target folder or amend new images to the cache?",
             choices=["amend", "copy"],
             style=nf_core.utils.nfcore_question_style,
         ).unsafe_ask()
 
     @staticmethod
-    def prompt_singularity_cachedir_remote() -> Path | None:
-        """Prompt about the index of a remote singularity cache directory"""
+    def prompt_cachedir_remote(cache_dir_env_var: str = SINGULARITY_CACHE_DIR_ENV_VAR) -> Path | None:
+        """Prompt about the index of a remote singularity/apptainer cache directory"""
         if not nf_core.utils.is_interactive():
             log.warning("Cannot prompt for remote cache index in a non-interactive session.")
             return None
@@ -345,11 +403,11 @@ def prompt_singularity_cachedir_remote() -> Path | None:
         while cachedir_index is None:
             prompt_cachedir_index = questionary.path(
                 "Specify a list of the container images that are already present on the remote system:",
-                validate=nf_core.utils.SingularityCacheFilePathValidator,
+                validate=SingularityCacheFilePathValidator,
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
             if prompt_cachedir_index == "":
-                log.error(f"Will disregard contents of a remote [blue]${SINGULARITY_CACHE_DIR_ENV_VAR}[/]")
+                log.error(f"Will disregard contents of a remote [blue]${cache_dir_env_var}[/]")
                 return None
             cachedir_index = Path(prompt_cachedir_index).expanduser().absolute()
             if not os.access(cachedir_index, os.R_OK):
@@ -506,9 +564,9 @@ def update_file_progress(input_params: tuple[str, Path], status: FileDownloader.
 
         downloader.download_files_in_parallel(containers_download, parallel_downloads, callback=update_file_progress)
 
-    def pull_images(self, containers_pull: Iterable[tuple[str, Path]]) -> None:
+    def pull_images(self, containers_pull: Iterable[tuple[str, Path]], container_system: str = "singularity") -> None:
         """
-        Pull a set of container images using `singularity pull`.
+        Pull a set of container images using `singularity/apptainer pull`.
 
         Args:
             containers_pull (Iterable[tuple[str, Path]]): A list of container names and output paths.
@@ -560,8 +618,8 @@ def pull_images(self, containers_pull: Iterable[tuple[str, Path]]) -> None:
             self.progress.update_remote_fetch_task(advance=1)
 
     def construct_pull_command(self, output_path: Path, address: str):
-        singularity_command = [self.implementation, "pull", "--name", str(output_path), address]
-        return singularity_command
+        pull_command = [self.implementation, "pull", "--name", str(output_path), address]
+        return pull_command
 
     def get_address(self, container, library) -> tuple[str, bool]:
         # Sometimes, container still contain an explicit library specification, which
@@ -578,9 +636,11 @@ def get_address(self, container, library) -> tuple[str, bool]:
 
         return address, absolute_URI
 
-    def pull_image(self, container: str, output_path: Path, library: str) -> bool:
+    def pull_image(
+        self, container: str, output_path: Path, library: str, container_system: str = "singularity"
+    ) -> bool:
         """
-        Pull a singularity image using `singularity pull`.
+        Pull a singularity/apptainer image using `singularity/apptainer pull`.
 
         Args:
             container (str): A pipeline's container name. Usually it is of similar format
@@ -603,14 +663,14 @@ def pull_image(self, container: str, output_path: Path, library: str) -> bool:
             container,
             start=False,
             total=False,
-            progress_type="singularity_pull",
+            progress_type=f"{container_system}_pull",
             current_log="",
         ) as task:
             self._ensure_output_dir_exists()
             with intermediate_file_no_creation(output_path) as output_path_tmp:
                 singularity_command = self.construct_pull_command(output_path_tmp, address)
-                log.debug(f"Building singularity image: {address}")
-                # Run the singularity pull command
+                log.debug(f"Building {container_system} image: {address}")
+                # Run the singularity/apptainer pull command
                 with subprocess.Popen(
                     singularity_command,
                     stdout=subprocess.PIPE,
diff --git a/nf_core/pipelines/download/utils.py b/nf_core/pipelines/download/utils.py
index bde3845c09..3d61adacd7 100644
--- a/nf_core/pipelines/download/utils.py
+++ b/nf_core/pipelines/download/utils.py
@@ -1,22 +1,14 @@
 import contextlib
 import importlib.resources
 import logging
-import os
 import shutil
 import tempfile
 from collections.abc import Generator
-from enum import Enum
 from pathlib import Path
 
 log = logging.getLogger(__name__)
 
 
-class ContainerRegistryUrls(Enum):
-    SEQERA_DOCKER = "community.wave.seqera.io/library"
-    SEQERA_SINGULARITY = "community-cr-prod.seqera.io/docker/registry/v2"
-    GALAXY_SINGULARITY = "depot.galaxyproject.org/singularity"
-
-
 def copy_container_load_scripts(container_system: str, dest_dir: Path, make_exec: bool = True) -> tuple[str, Path]:
     container_load_scripts_subpackage = "nf_core.pipelines.download.load_scripts"
     script_name = f"{container_system}-load.sh"
@@ -84,21 +76,3 @@ def intermediate_file_no_creation(output_path: Path) -> Generator[Path, None, No
     except:
         tmp.cleanup()
         raise
-
-
-@contextlib.contextmanager
-def intermediate_dir_with_cd(original_dir: Path, base_dir: Path = Path()):
-    """
-    Context manager to provide and change into a tempdir and ensure its removal and return to the
-    original_dir upon exceptions.
-    """
-
-    if not original_dir.is_dir():
-        raise DownloadError(f"Unable to setup temporary dir, original_dir does not exist: {original_dir}")
-
-    tmp = tempfile.TemporaryDirectory(dir=base_dir)
-    try:
-        os.chdir(tmp.name)
-        yield tmp
-    finally:
-        os.chdir(original_dir)
diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py
index 7329985c1b..8b4aba1a81 100644
--- a/nf_core/pipelines/launch.py
+++ b/nf_core/pipelines/launch.py
@@ -26,17 +26,17 @@ class Launch:
 
     def __init__(
         self,
-        pipeline=None,
-        revision=None,
-        command_only=False,
-        params_in=None,
-        params_out=None,
-        save_all=False,
-        show_hidden=False,
-        url=None,
-        web_id=None,
-        no_prompts=False,
-    ):
+        pipeline: str | None = None,
+        revision: str | None = None,
+        command_only: bool = False,
+        params_in: str | Path | None = None,
+        params_out: str | Path | None = None,
+        save_all: bool = False,
+        show_hidden: bool = False,
+        url: str | None = None,
+        web_id: str | None = None,
+        no_prompts: bool = False,
+    ) -> None:
         """Initialise the Launcher class
 
         Args:
@@ -94,8 +94,8 @@ def __init__(
                 },
             }
         }
-        self.nxf_flags = {}
-        self.params_user = {}
+        self.nxf_flags: dict[str, str | bool] = {}
+        self.params_user: dict[str, str] = {}
         self.cli_launch = True
 
     def launch_pipeline(self):
diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
index 4cfe23ea69..f964509149 100644
--- a/nf_core/pipelines/lint/__init__.py
+++ b/nf_core/pipelines/lint/__init__.py
@@ -258,6 +258,7 @@ def _lint_pipeline(self) -> None:
             rich.progress.BarColumn(bar_width=None),
             "[magenta]{task.completed} of {task.total}[reset] » [bold yellow]{task.fields[test_name]}",
             transient=True,
+            console=console,
             disable=self.hide_progress or os.environ.get("HIDE_PROGRESS", None) is not None,
         )
         with self.progress_bar:
@@ -328,7 +329,9 @@ def format_result(test_results):
             if "dev" in __version__:
                 tools_version = "dev"
             for eid, msg in test_results:
-                yield Markdown(f"[{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}): {msg}")
+                yield Markdown(
+                    f"[{eid}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid}): {msg}"
+                )
 
         # Table of passed tests
         if len(self.passed) > 0 and show_passed:
@@ -429,7 +432,7 @@ 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/{tools_version}/pipeline_lint_tests/{eid}) - "
+                        f"* [{eid}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid}) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.failed
                     ]
@@ -443,7 +446,7 @@ 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/{tools_version}/pipeline_lint_tests/{eid}) - "
+                        f"* [{eid}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid}) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.ignored
                     ]
@@ -457,7 +460,7 @@ 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/{tools_version}/pipeline_lint_tests/{eid}) - "
+                        f"* [{eid}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid}) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.fixed
                     ]
@@ -471,7 +474,7 @@ 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/{tools_version}/pipeline_lint_tests/{eid}) - "
+                        f"* [{eid}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid}) - "
                         f"{strip_ansi_codes(msg, '`')}"
                         for eid, msg in self.warned
                     ]
@@ -486,7 +489,7 @@ def _get_results_md(self):
                 "\n".join(
                     [
                         (
-                            f"* [{eid}](https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid})"
+                            f"* [{eid}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid})"
                             f" - {strip_ansi_codes(msg, '`')}"
                         )
                         for eid, msg in self.passed
diff --git a/nf_core/pipelines/lint/container_configs.py b/nf_core/pipelines/lint/container_configs.py
index b5143dba82..e6aba4bd15 100644
--- a/nf_core/pipelines/lint/container_configs.py
+++ b/nf_core/pipelines/lint/container_configs.py
@@ -11,9 +11,11 @@
 def container_configs(self):
     """Check that the container configuration files in ``conf/`` are up to date.
 
-    Runs ``nextflow inspect`` to regenerate container configuration files directly
-    in ``conf/`` and uses ``git diff`` to detect changes.  If not in ``--fix`` mode
-    the working tree is restored to its original state afterwards.
+    Scans all ``meta.yml`` files under ``modules/`` that contain a ``containers``
+    key, reads the process name from the sibling ``main.nf``, and regenerates
+    the container configuration files in ``conf/``.  Uses ``git diff`` to detect
+    changes.  If not in ``--fix`` mode the working tree is restored to its
+    original state afterwards.
 
     Can be skipped by adding the following to the ``.nf-core.yml`` file:
 
@@ -37,6 +39,8 @@ def container_configs(self):
         warned.append(f"Could not generate container configuration files: {e}")
         return {"passed": passed, "failed": failed, "warned": warned}
 
+    log.debug(f"Generated {len(generated)} container config file(s): {', '.join(sorted(generated)) or 'none'}")
+
     # Files modified in the working tree (tracked and changed by generation)
     modified = {
         Path(d.a_path).name
@@ -52,6 +56,8 @@ def container_configs(self):
     # Already-correct files: generated, tracked, and unchanged
     correct = generated - modified - new
 
+    log.debug(f"Container config status — correct: {len(correct)}, modified: {len(modified)}, new: {len(new)}")
+
     fixing = "container_configs" in self.fix
 
     for name in sorted(correct):
@@ -59,6 +65,7 @@ def container_configs(self):
 
     for name in sorted(modified | new):
         if fixing:
+            log.debug(f"Overwriting `conf/{name}` with regenerated container configuration")
             passed.append(f"`conf/{name}` is up to date")
             fixed.append(f"`conf/{name}` overwritten with regenerated container configuration.")
         else:
@@ -70,6 +77,7 @@ def container_configs(self):
 
     if not fixing:
         # Restore working tree: reset modified tracked files and delete new untracked ones
+        log.debug(f"Restoring working tree: resetting {len(modified)} modified, removing {len(new)} new file(s)")
         for name in modified:
             repo.git.restore(str(conf_dir / name))
         for name in new:
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index b6c0af889c..8e3c6f567e 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -120,11 +120,12 @@ def files_exist(self) -> dict[str, list[str]]:
     # NB: Should all be files, not directories
     # List of lists. Passes if any of the files in the sublist are found.
     #: test autodoc
-    try:
-        _, short_name = self.nf_config["manifest.name"].strip("\"'").split("/")
-    except ValueError:
+    pipeline_name = self.nf_config.get("manifest", {}).get("name", "")
+    if "/" in pipeline_name:
+        _, short_name = pipeline_name.split("/")
+    else:
         log.warning("Expected manifest.name to be in the format '<repo>/<pipeline>'. Will assume it is '<pipeline>'.")
-        short_name = self.nf_config["manifest.name"].strip("\"'").split("/")
+        short_name = pipeline_name
 
     files_fail = [
         [Path(".gitattributes")],
diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py
index 17648f93d4..3d5f87c266 100644
--- a/nf_core/pipelines/lint/files_unchanged.py
+++ b/nf_core/pipelines/lint/files_unchanged.py
@@ -1,6 +1,5 @@
 import filecmp
 import logging
-import re
 import shutil
 import tempfile
 from pathlib import Path
@@ -66,21 +65,18 @@ def files_unchanged(self) -> dict[str, list[str] | bool]:
     could_fix: bool = False
 
     # Check that we have the minimum required config
-    required_pipeline_config = {
-        "manifest.name",
-        "manifest.description",
-        "manifest.contributors",
-    }
-    missing_pipeline_config = required_pipeline_config.difference(self.nf_config)
+    manifest_config = self.nf_config.get("manifest", {})
+    missing_pipeline_config = {k for k in ("name", "description", "contributors") if not manifest_config.get(k)}
     if missing_pipeline_config:
-        return {"ignored": [f"Required pipeline config not found - {missing_pipeline_config}"]}
+        missing_keys = {f"manifest.{k}" for k in missing_pipeline_config}
+        return {"ignored": [f"Required pipeline config not found - {missing_keys}"]}
     try:
-        prefix, short_name = self.nf_config["manifest.name"].strip("\"'").split("/")
+        prefix, short_name = manifest_config.get("name", "").split("/")
     except ValueError:
         log.warning(
             "Expected manifest.name to be in the format '<repo>/<pipeline>'. Will assume it is <pipeline> and default to repo 'nf-core'"
         )
-        short_name = self.nf_config["manifest.name"].strip("\"'")
+        short_name = manifest_config.get("name", "")
         prefix = "nf-core"
 
     # NB: Should all be files, not directories
@@ -118,14 +114,14 @@ def files_unchanged(self) -> dict[str, list[str] | bool]:
     tmp_dir.mkdir(parents=True)
 
     # Create a template.yaml file for the pipeline creation
-    if "manifest.author" in self.nf_config:
-        names = self.nf_config["manifest.author"].strip("\"'")
-    if "manifest.contributors" in self.nf_config:
-        contributors = self.nf_config["manifest.contributors"]
-        names = ", ".join(re.findall(r"name:'([^']+)'", contributors))
+    contributors = manifest_config.get("contributors", [])
+    if contributors:
+        names = ", ".join(c.get("name", "") for c in contributors if c.get("name"))
+    else:
+        names = manifest_config.get("author", "")
     template_yaml = {
         "name": short_name,
-        "description": self.nf_config["manifest.description"].strip("\"'"),
+        "description": manifest_config.get("description", ""),
         "author": names,
         "org": prefix,
     }
diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py
index f7f5a077e7..8fa09b379b 100644
--- a/nf_core/pipelines/lint/modules_json.py
+++ b/nf_core/pipelines/lint/modules_json.py
@@ -25,32 +25,32 @@ def modules_json(self) -> dict[str, list[str]]:
         all_modules_passed = True
 
         for repo in modules_json_dict["repos"]:
-            # Check if the modules.json has been updated to keep the
-            if "modules" not in modules_json_dict["repos"][repo] or not repo.startswith("http"):
-                failed.append(
-                    "Your `modules.json` file is outdated. "
-                    "It will be automatically generated by running any module command."
-                )
-                continue
-
-            for install_dir in modules_json_dict["repos"][repo]["modules"]:
-                for module, module_entry in modules_json_dict["repos"][repo]["modules"][install_dir].items():
-                    if not Path(modules_dir, install_dir, module).exists():
-                        failed.append(
-                            f"Entry for `{Path(modules_dir, install_dir, module)}` found in `modules.json` but module is not installed in "
-                            "pipeline."
-                        )
-                        all_modules_passed = False
-                    if module_entry.get("branch") is None:
-                        failed.append(
-                            f"Entry for `{Path(modules_dir, install_dir, module)}` is missing branch information."
-                        )
-                    if module_entry.get("git_sha") is None:
-                        failed.append(
-                            f"Entry for `{Path(modules_dir, install_dir, module)}` is missing version information."
-                        )
-        if all_modules_passed:
-            passed.append("Only installed modules found in `modules.json`")
+            if not repo.startswith("http"):
+                failed.append(f'Repository link for {repo} doesn\'t start with "http" in `modules.json`.')
+
+            if "modules" in modules_json_dict["repos"][repo]:
+                # Module linting
+                for install_dir in modules_json_dict["repos"][repo]["modules"]:
+                    for module, module_entry in modules_json_dict["repos"][repo]["modules"][install_dir].items():
+                        if not Path(modules_dir, install_dir, module).exists():
+                            failed.append(
+                                f"Entry for `{Path(modules_dir, install_dir, module)}` found in `modules.json` but module is not installed in "
+                                "pipeline."
+                            )
+                            all_modules_passed = False
+                        if module_entry.get("branch") is None:
+                            failed.append(
+                                f"Entry for `{Path(modules_dir, install_dir, module)}` is missing branch information."
+                            )
+                        if module_entry.get("git_sha") is None:
+                            failed.append(
+                                f"Entry for `{Path(modules_dir, install_dir, module)}` is missing version information."
+                            )
+                if all_modules_passed:
+                    passed.append("Only installed modules found in `modules.json`")
+
+            if not any(component in modules_json_dict["repos"][repo] for component in ["modules", "subworkflows"]):
+                failed.append(f"No modules or subworkflows installed for {repo} in `modules.json`.")
     else:
         warned.append("Could not open `modules.json` file.")
 
diff --git a/nf_core/pipelines/lint/multiqc_config.py b/nf_core/pipelines/lint/multiqc_config.py
index 254caa925a..2b2c87e5b9 100644
--- a/nf_core/pipelines/lint/multiqc_config.py
+++ b/nf_core/pipelines/lint/multiqc_config.py
@@ -98,7 +98,7 @@ def multiqc_config(self) -> dict[str, list[str]]:
 
         if "report_comment" not in ignore_configs:
             # Check that the minimum plugins exist and are coming first in the summary
-            version = self.nf_config.get("manifest.version", "").strip(" '\"")
+            version = self.nf_config.get("manifest", {}).get("version", "") or ""
 
             # Get the org from .nf-core.yml config, defaulting to "nf-core"
             _, nf_core_yaml_config = load_tools_config(self.wf_path)
diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py
index f5913f5521..caea0fa352 100644
--- a/nf_core/pipelines/lint/nextflow_config.py
+++ b/nf_core/pipelines/lint/nextflow_config.py
@@ -1,4 +1,3 @@
-import ast
 import logging
 import re
 from pathlib import Path
@@ -170,7 +169,7 @@ def nextflow_config(self) -> dict[str, list[str]]:
     ]
 
     # Lint for plugins
-    config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]"))
+    config_plugins = self.nf_config.get("plugins", [])
     found_plugins = []
     for plugin in config_plugins:
         if "@" not in plugin:
@@ -203,39 +202,34 @@ def nextflow_config(self) -> dict[str, list[str]]:
     # Remove field that should be ignored according to the linting config
     ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
 
-    for cfs in config_fail:
-        for cf in cfs:
-            if cf in ignore_configs:
-                ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
-                break
-            if cf in self.nf_config:
-                passed.append(f"Config variable found: {self._wrap_quotes(cf)}")
-                break
-        else:
-            failed.append(f"Config variable not found: {self._wrap_quotes(cfs)}")
-    for cfs in config_warn:
-        for cf in cfs:
-            if cf in ignore_configs:
-                ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
-                break
-            if cf in self.nf_config:
-                passed.append(f"Config variable found: {self._wrap_quotes(cf)}")
-                break
-        else:
-            warned.append(f"Config variable not found: {self._wrap_quotes(cfs)}")
+    def _config_has_key(key: str) -> bool:
+        section, name = key.split(".", 1)
+        return name in self.nf_config.get(section, {})
+
+    for configs, not_found in [(config_fail, failed), (config_warn, warned)]:
+        for cfs in configs:
+            for cf in cfs:
+                if cf in ignore_configs:
+                    ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
+                    break
+                if _config_has_key(cf):
+                    passed.append(f"Config variable found: {self._wrap_quotes(cf)}")
+                    break
+            else:
+                not_found.append(f"Config variable not found: {self._wrap_quotes(cfs)}")
     for cf in config_fail_ifdefined:
         if cf in ignore_configs:
             ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}")
-            break
-        if cf not in self.nf_config:
+            continue
+        if not _config_has_key(cf):
             passed.append(f"Config variable (correctly) not found: {self._wrap_quotes(cf)}")
         else:
             failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}")
 
     # Check and warn if the process configuration is done with deprecated syntax
-
+    process_config = self.nf_config.get("process", {})
     process_with_deprecated_syntax = list(
-        {match.group(1) for ck in self.nf_config if (match := re.match(r"^(process\.\$.*?)\.+.*$", ck)) is not None}
+        {f"process.{ck}" for ck in (process_config if isinstance(process_config, dict) else {}) if re.match(r"^\$", ck)}
     )
     for pd in process_with_deprecated_syntax:
         warned.append(f"Process configuration is done with deprecated_syntax: {pd}")
@@ -244,90 +238,76 @@ def nextflow_config(self) -> dict[str, list[str]]:
     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)}``")
+        section, name = k.split(".")
+        val = self.nf_config.get(section, {}).get(name)
+        if val is True:
+            passed.append(f"Config ``{k}`` had correct value: ``{val}``")
         else:
-            failed.append(f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``")
+            failed.append(f"Config ``{k}`` did not have correct value: ``{val}``")
 
     _, nf_core_yaml_config = load_tools_config(self.wf_path)
     org_name = "nf-core"
     if nf_core_yaml_config and getattr(nf_core_yaml_config, "template", None):
         org_name = getattr(nf_core_yaml_config.template, "org", org_name) or org_name
 
-    if "manifest.name" not in ignore_configs:
-        # Check that the pipeline name starts with nf-core
-        try:
-            manifest_name = self.nf_config.get("manifest.name", "").strip("'\"")
-            if not manifest_name.startswith(f"{org_name}/"):
-                raise AssertionError
-        except (AssertionError, IndexError):
-            failed.append(f"Config ``manifest.name`` did not begin with ``{org_name}/``:\n    {manifest_name}")
-        else:
-            passed.append(f"Config ``manifest.name`` began with ``{org_name}/``")
-
-    if "manifest.homePage" not in ignore_configs:
-        # Check that the homePage is set to the GitHub URL
-        try:
-            manifest_homepage = self.nf_config.get("manifest.homePage", "").strip("'\"")
-            if not manifest_homepage.startswith(f"https://github.com/{org_name}/"):
-                raise AssertionError
-        except (AssertionError, IndexError):
-            failed.append(
-                f"Config variable ``manifest.homePage`` did not begin with https://github.com/{org_name}/:\n    {manifest_homepage}"
-            )
-
+    manifest = self.nf_config.get("manifest", {})
+    for key, expected_prefix in [
+        ("name", f"{org_name}/"),
+        ("homePage", f"https://github.com/{org_name}/"),
+    ]:
+        config_key = f"manifest.{key}"
+        if config_key in ignore_configs:
+            continue
+        value = manifest.get(key, "")
+        if value.startswith(expected_prefix):
+            passed.append(f"Config ``{config_key}`` began with ``{expected_prefix}``")
         else:
-            passed.append(f"Config variable ``manifest.homePage`` began with https://github.com/{org_name}/")
+            failed.append(f"Config ``{config_key}`` did not begin with ``{expected_prefix}``")
 
-    # Check that the DAG filename ends in ``.svg``
-    if "dag.file" in self.nf_config:
+    dag_file = self.nf_config.get("dag", {}).get("file", "")
+    if dag_file:
         default_dag_format = ".html"
-        if self.nf_config["dag.file"].strip("'\"").endswith(default_dag_format):
+        if dag_file.endswith(default_dag_format):
             passed.append(f"Config ``dag.file`` ended with ``{default_dag_format}``")
         else:
             failed.append(f"Config ``dag.file`` did not end with ``{default_dag_format}``")
 
     # Check that the minimum nextflowVersion is set properly
-    if "manifest.nextflowVersion" in self.nf_config:
-        if self.nf_config.get("manifest.nextflowVersion", "").strip("\"'").lstrip("!").startswith(">="):
+    nextflow_version = manifest.get("nextflowVersion", "")
+    if nextflow_version:
+        if nextflow_version.lstrip("!").startswith(">="):
             passed.append("Config variable ``manifest.nextflowVersion`` started with >= or !>=")
         else:
             failed.append(
-                "Config ``manifest.nextflowVersion`` did not start with ``>=`` or ``!>=`` : "
-                f"``{self.nf_config.get('manifest.nextflowVersion', '')}``".strip("\"'")
+                f"Config ``manifest.nextflowVersion`` did not start with ``>=`` or ``!>=`` : ``{nextflow_version}``"
             )
 
     # Check that the pipeline version contains ``dev``
-    if not self.release_mode and "manifest.version" in self.nf_config:
-        if self.nf_config["manifest.version"].strip(" '\"").endswith("dev"):
-            passed.append(f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``")
+    manifest_version = self.nf_config.get("manifest", {}).get("version", "")
+    if not self.release_mode and manifest_version:
+        if manifest_version.endswith("dev"):
+            passed.append(f"Config ``manifest.version`` ends in ``dev``: ``{manifest_version}``")
         else:
-            warned.append(
-                f"Config ``manifest.version`` should end in ``dev``: ``{self.nf_config['manifest.version']}``"
-            )
-    elif "manifest.version" in self.nf_config:
-        if "dev" in self.nf_config["manifest.version"]:
+            warned.append(f"Config ``manifest.version`` should end in ``dev``: ``{manifest_version}``")
+    elif manifest_version:
+        if "dev" in manifest_version:
             failed.append(
-                "Config ``manifest.version`` should not contain ``dev`` for a release: "
-                f"``{self.nf_config['manifest.version']}``"
+                f"Config ``manifest.version`` should not contain ``dev`` for a release: ``{manifest_version}``"
             )
         else:
-            passed.append(
-                "Config ``manifest.version`` does not contain ``dev`` for release: "
-                f"``{self.nf_config['manifest.version']}``"
-            )
+            passed.append(f"Config ``manifest.version`` does not contain ``dev`` for release: ``{manifest_version}``")
 
     if "custom_config" not in ignore_configs:
         # Check if custom profile params are set correctly
-        if self.nf_config.get("params.custom_config_version", "").strip("'") == "master":
+        if self.nf_config.get("params", {}).get("custom_config_version", "") == "master":
             passed.append("Config `params.custom_config_version` is set to `master`")
         else:
             failed.append("Config `params.custom_config_version` is not set to `master`")
 
         custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/{}".format(
-            self.nf_config.get("params.custom_config_version", "").strip("'")
+            self.nf_config.get("params", {}).get("custom_config_version", "")
         )
-        if self.nf_config.get("params.custom_config_base", "").strip("'") == custom_config_base:
+        if self.nf_config.get("params", {}).get("custom_config_base", "") == custom_config_base:
             passed.append(f"Config `params.custom_config_base` is set to `{custom_config_base}`")
         else:
             failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`")
@@ -411,18 +391,19 @@ def nextflow_config(self) -> dict[str, list[str]]:
     schema.get_schema_types()  # Get types from schema
     for param_name in schema.schema_defaults:
         param = "params." + param_name
+        param_value = self.nf_config.get("params", {}).get(param_name)
         if param in ignore_defaults:
             ignored.append(f"Config default ignored: {param}")
-        elif param in self.nf_config:
+        elif param_value is not None:
             config_default: str | float | int | None = None
             schema_default: str | float | int | None = None
             if schema.schema_types[param_name] == "boolean":
                 schema_default = str(schema.schema_defaults[param_name]).lower()
-                config_default = str(self.nf_config[param]).lower()
+                config_default = str(param_value).lower()
             elif schema.schema_types[param_name] == "number":
                 try:
                     schema_default = float(schema.schema_defaults[param_name])
-                    config_default = float(self.nf_config[param])
+                    config_default = float(param_value)
                 except ValueError:
                     failed.append(
                         f"Config default value incorrect: `{param}` is set as type `number` in nextflow_schema.json, but is not a number in `nextflow.config`."
@@ -430,19 +411,19 @@ def nextflow_config(self) -> dict[str, list[str]]:
             elif schema.schema_types[param_name] == "integer":
                 try:
                     schema_default = int(schema.schema_defaults[param_name])
-                    config_default = int(self.nf_config[param])
+                    config_default = int(param_value)
                 except ValueError:
                     failed.append(
                         f"Config default value incorrect: `{param}` is set as type `integer` in nextflow_schema.json, but is not an integer in `nextflow.config`."
                     )
             else:
                 schema_default = str(schema.schema_defaults[param_name])
-                config_default = str(self.nf_config[param])
+                config_default = str(param_value)
             if config_default is not None and config_default == schema_default:
                 passed.append(f"Config default value correct: {param}= {schema_default}")
             else:
                 failed.append(
-                    f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
+                    f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(param_value)} in `nextflow.config`."
                 )
         else:
             schema_default = str(schema.schema_defaults[param_name])
diff --git a/nf_core/pipelines/lint/nfcore_yml.py b/nf_core/pipelines/lint/nfcore_yml.py
index f202adfd96..ff28a77129 100644
--- a/nf_core/pipelines/lint/nfcore_yml.py
+++ b/nf_core/pipelines/lint/nfcore_yml.py
@@ -12,11 +12,11 @@ def nfcore_yml(self) -> dict[str, list[str]]:
 
     The ``.nf-core.yml`` contains metadata for nf-core tools to correctly apply its features.
 
-    * repository type:
+    * ``repository_type``:
 
         Check that the repository type is set.
 
-    * nf core version:
+    * ``nf_core_version``:
 
         Check if the nf-core version is set to the latest version.
 
diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py
index b787405169..335d1a5501 100644
--- a/nf_core/pipelines/lint/plugin_includes.py
+++ b/nf_core/pipelines/lint/plugin_includes.py
@@ -1,4 +1,3 @@
-import ast
 import logging
 import re
 from pathlib import Path
@@ -12,7 +11,7 @@ def plugin_includes(self) -> dict[str, list[str]]:
     When nf-schema is used in an nf-core pipeline, the include statements of the plugin
     functions have to use nf-schema instead of nf-validation and vice versa
     """
-    config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
+    config_plugins = [plugin.split("@")[0] for plugin in self.nf_config.get("plugins", [])]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
     passed: list[str] = []
diff --git a/nf_core/pipelines/lint/version_consistency.py b/nf_core/pipelines/lint/version_consistency.py
index c939938a46..03beef4c5f 100644
--- a/nf_core/pipelines/lint/version_consistency.py
+++ b/nf_core/pipelines/lint/version_consistency.py
@@ -32,15 +32,16 @@ def version_consistency(self):
     # Get the version definitions
     # Get version from nextflow.config
     versions = {}
-    versions["manifest.version"] = self.nf_config.get("manifest.version", "").strip(" '\"")
+    versions["manifest.version"] = self.nf_config.get("manifest", {}).get("version") or ""
 
     # Get version from the docker tag
-    if self.nf_config.get("process.container", "") and ":" not in self.nf_config.get("process.container", ""):
-        failed.append(f"Docker slug seems not to have a version tag: {self.nf_config.get('process.container', '')}")
+    process_container = self.nf_config.get("process", {}).get("container") or ""
+    if process_container and ":" not in process_container:
+        failed.append(f"Docker slug seems not to have a version tag: {process_container}")
 
     # Get config container tag (if set; one container per workflow)
-    if self.nf_config.get("process.container", ""):
-        versions["process.container"] = self.nf_config.get("process.container", "").strip(" '\"").split(":")[-1]
+    if process_container:
+        versions["process.container"] = process_container.split(":")[-1]
 
     # Get version from the $GITHUB_REF env var if this is a release
     if (
diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py
index e1980cf89d..65aafdb293 100644
--- a/nf_core/pipelines/lint_utils.py
+++ b/nf_core/pipelines/lint_utils.py
@@ -7,19 +7,16 @@
 import git
 import rich
 import yaml
-from rich.console import Console
 from rich.table import Table
 
 import nf_core.utils
 from nf_core import __version__
 from nf_core.utils import plural_s as _s
+from nf_core.utils import stdout as console
 from nf_core.utils import strip_ansi_codes
 
 log = logging.getLogger(__name__)
 
-# Create a console used by all lint tests
-console = Console(force_terminal=nf_core.utils.rich_force_colors())
-
 
 def print_results_plain_text(results_list, directory=None, component_type=None):
     """Print lint results in plain text format.
@@ -49,7 +46,7 @@ def print_lines(text, strip_ansi=False):
                     # Pipeline results: (eid, msg)
                     eid, msg = r
                     console.print(
-                        f"\n[{color}]{eid}[/{color}] https://nf-co.re/tools/docs/{tools_version}/pipeline_lint_tests/{eid}"
+                        f"\n[{color}]{eid}[/{color}] https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/pipeline_lint_tests/{eid}"
                     )
                     print_lines(msg, strip_ansi=True)
                 else:
diff --git a/nf_core/pipelines/list.py b/nf_core/pipelines/list.py
index bc9bf30205..cb5d22d444 100644
--- a/nf_core/pipelines/list.py
+++ b/nf_core/pipelines/list.py
@@ -8,8 +8,6 @@
 from datetime import datetime
 from pathlib import Path
 
-import git
-import requests
 import rich.table
 from click.shell_completion import CompletionItem
 
@@ -52,6 +50,8 @@ def _resolve_wf_path(path: Path) -> Path:
     bare_dir = path / "bare"
     if clones_dir.is_dir():
         if bare_dir.is_dir():
+            import git
+
             try:
                 sha = git.Repo(bare_dir).head.commit.hexsha
                 clone = clones_dir / sha
@@ -169,6 +169,8 @@ def get_remote_workflows(self):
 
         Remote workflows are stored in :attr:`self.remote_workflows` list.
         """
+        import requests
+
         # List all repositories at nf-core
         log.debug("Fetching list of nf-core workflows")
         nfcore_url = "https://nf-co.re/pipelines.json"
@@ -421,6 +423,8 @@ def get_local_nf_workflow_details(self):
 
         # Pull information from the local git repository
         if self.local_path is not None:
+            import git
+
             log.debug(f"Pulling git info from {self.local_path}")
             try:
                 repo = git.Repo(self.local_path)
diff --git a/nf_core/pipelines/rocrate.py b/nf_core/pipelines/rocrate.py
index b4735c2127..0bc0cf8e56 100644
--- a/nf_core/pipelines/rocrate.py
+++ b/nf_core/pipelines/rocrate.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 """Code to deal with pipeline RO (Research Object) Crates"""
 
-import json
 import logging
 import os
 import re
@@ -103,7 +102,7 @@ def create_rocrate(self, json_path: None | Path = None, zip_path: None | Path =
         """
 
         # Check that the checkout pipeline version is the same as the requested version
-        if self.version != "" and self.version != self.pipeline_obj.nf_config.get("manifest.version"):
+        if self.version and self.version != self.pipeline_obj.nf_config.get("manifest", {}).get("version"):
             # using git checkout to get the requested version
             log.info(f"Checking out pipeline version {self.version}")
             if self.pipeline_obj.repo is None:
@@ -119,7 +118,7 @@ def create_rocrate(self, json_path: None | Path = None, zip_path: None | Path =
             except GitCommandError:
                 log.error(f"Could not checkout version {self.version}")
                 sys.exit(1)
-        self.version = self.pipeline_obj.nf_config.get("manifest.version", "")
+        self.version = self.pipeline_obj.nf_config.get("manifest", {}).get("version", "")
         self.make_workflow_rocrate()
 
         # Save just the JSON metadata file
@@ -161,13 +160,14 @@ def make_workflow_rocrate(self) -> None:
 
         # Create the RO Crate object
 
+        manifest = self.pipeline_obj.nf_config.get("manifest", {})
         self.crate = custom_make_crate(
             self.pipeline_dir,
             self.pipeline_dir / "main.nf",
-            self.pipeline_obj.nf_config.get("manifest.homePage", ""),
-            self.pipeline_obj.nf_config.get("manifest.name", ""),
-            self.pipeline_obj.nf_config.get("manifest.version", ""),
-            self.pipeline_obj.nf_config.get("manifest.nextflowVersion", ""),
+            manifest.get("homePage", ""),
+            manifest.get("name", ""),
+            manifest.get("version", ""),
+            manifest.get("nextflowVersion", ""),
             diagram=diagram,
         )
 
@@ -268,10 +268,11 @@ def add_main_authors(self, wf_file: rocrate.model.entity.Entity) -> None:
         """
         Add workflow authors to the crate
         """
+        manifest = self.pipeline_obj.nf_config.get("manifest", {})
         contributors = []
-        if "manifest.contributors" in self.pipeline_obj.nf_config:
+        if manifest.get("contributors"):
             contributors = self.parse_manifest_contributors()
-        if not contributors and "manifest.author" in self.pipeline_obj.nf_config:
+        if not contributors and manifest.get("author"):
             if self.pipeline_obj.repo:
                 contributors = self.parse_manifest_authors()
             else:
@@ -346,7 +347,7 @@ def _make_progress_bar(self):
 
     def parse_manifest_authors(self) -> list:
         # parse manifest.author"
-        authors = [a.strip() for a in self.pipeline_obj.nf_config["manifest.author"].split(",")]
+        authors = [a.strip() for a in self.pipeline_obj.nf_config.get("manifest", {}).get("author", "").split(",")]
         # remove duplicates
         authors = list(set(authors))
         log.debug(f"Authors: {authors}")
@@ -398,26 +399,14 @@ def parse_manifest_authors(self) -> list:
     # and return as a list of dictionaries
     def parse_manifest_contributors(self) -> list:
         field_names = ["name", "affiliation", "github", "contribution", "orcid", "email"]
-        # Grab the contributor list and convert to JSON
-        # TODO: can be removed once we switch to `nextflow config -o json`
-        contributors_str = self.pipeline_obj.nf_config["manifest.contributors"]
-        log.debug(f"manifest.contributors: {contributors_str}")
-        # JSON uses double quotes, not single quotes
-        contributors_str = contributors_str.replace("'", '"')
-        for key in field_names:
-            # All dictionary keys need to be quoted
-            contributors_str = contributors_str.replace(f"{key}:", f'"{key}":')
-        # Use curly brackets for dictionaries
-        contributors_str = contributors_str.replace("], [", "}, {").replace("[[", "[{").replace("]]", "}]")
-        log.debug(f"manifest.contributors (normalised): {contributors_str}")
-        try:
-            contributors = json.loads(contributors_str)
-        except json.JSONDecodeError as exc:
+        # Grab the contributor list directly from the nested config (already a list[dict])
+        contributors = self.pipeline_obj.nf_config.get("manifest", {}).get("contributors", [])
+        log.debug(f"manifest.contributors: {contributors}")
+        if not isinstance(contributors, list):
             log.error(
                 "Could not parse `manifest.contributors` from nextflow.config. "
                 "Expected a list of maps, for example: [[name: 'First Last', github: 'user']]. "
-                f"Normalised string passed to JSON parser was: {contributors_str!r}. "
-                f"JSON decoding error: {exc}"
+                f"Got: {contributors!r}"
             )
             return []
 
diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py
index 0c42b718dc..c9b5558f23 100644
--- a/nf_core/pipelines/schema.py
+++ b/nf_core/pipelines/schema.py
@@ -93,16 +93,17 @@ def _update_validation_plugin_from_config(self) -> None:
         # Previous versions of nf-schema used "defs", but it's advised to use "$defs"
         if plugin == "nf-schema":
             self.defs_notation = "$defs"
+            validation = conf.get("validation", {})
+            help_config = validation.get("help", {})
             ignored_params = [
-                conf.get("validation.help.shortParameter", "help"),
-                conf.get("validation.help.fullParameter", "helpFull"),
-                conf.get("validation.help.showHiddenParameter", "showHidden"),
+                help_config.get("shortParameter", "help"),
+                help_config.get("fullParameter", "helpFull"),
+                help_config.get("showHiddenParameter", "showHidden"),
                 "trace_report_suffix",  # report suffix should be ignored by default as it is a Java Date object
             ]  # Help parameter should be ignored by default
-            ignored_params_config_str = conf.get("validation.defaultIgnoreParams", "")
-            ignored_params_config = [
-                item.strip().strip("'") for item in ignored_params_config_str[1:-1].split(",")
-            ]  # Extract list elements and remove whitespace
+            ignored_params_config = validation.get("defaultIgnoreParams", [])
+            if not isinstance(ignored_params_config, list):
+                ignored_params_config = []
 
             if len(ignored_params_config) > 0:
                 log.debug(f"Ignoring parameters from config: {ignored_params_config}")
@@ -383,13 +384,13 @@ def validate_config_default_parameter(self, param, schema_param, config_default)
                 return
 
         # if default is null, we're good
-        if config_default == "null":
+        if config_default is None or config_default == "null":
             return
 
         # Check variable types in nextflow.config
-        if schema_param["type"] == "string" and str(config_default) in ["false", "true", "''"]:
+        if schema_param["type"] == "string" and str(config_default).lower() in ["false", "true", "''"]:
             self.invalid_nextflow_config_default_parameters[param] = f"String should not be set to `{config_default}`"
-        if schema_param["type"] == "boolean" and str(config_default) not in ["false", "true"]:
+        if schema_param["type"] == "boolean" and str(config_default).lower() not in ["false", "true"]:
             self.invalid_nextflow_config_default_parameters[param] = (
                 f"Booleans should only be true or false, not `{config_default}`"
             )
@@ -566,7 +567,7 @@ def print_documentation(
         Prints documentation for the schema.
         """
         if columns is None:
-            columns = ["parameter", "description", "type,", "default", "required", "hidden"]
+            columns = ["parameter", "description", "type", "default", "required", "hidden"]
 
         output = self.schema_to_markdown(columns)
         if output_format == "html":
@@ -580,7 +581,10 @@ def print_documentation(
 
         if not output_fn:
             console = rich.console.Console()
-            console.print("\n", Syntax(prettified_docs, output_format, word_wrap=True), "\n")
+            if console.is_terminal:
+                console.print("\n", Syntax(prettified_docs, output_format, word_wrap=True), "\n")
+            else:
+                print(prettified_docs, end="")
         else:
             if Path(output_fn).exists() and not force:
                 log.error(f"File '{output_fn}' exists! Please delete first, or use '--force'")
@@ -758,16 +762,15 @@ def get_wf_params(self):
         log.debug("Collecting pipeline parameter defaults\n")
         config = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent)
         skipped_params = []
-        # Pull out just the params. values
-        for ckey, cval in config.items():
-            if ckey.startswith("params."):
-                # skip anything that's not a flat variable
-                if "." in ckey[7:]:
-                    skipped_params.append(ckey)
-                    continue
-                self.pipeline_params[ckey[7:]] = cval
-            if ckey.startswith("manifest."):
-                self.pipeline_manifest[ckey[9:]] = cval
+        # Pull out just the params values (top-level flat keys only)
+        for pkey, pval in config.get("params", {}).items():
+            if isinstance(pval, dict):
+                skipped_params.append(f"params.{pkey}")
+                continue
+            self.pipeline_params[pkey] = pval
+        # Pull out manifest values
+        for mkey, mval in config.get("manifest", {}).items():
+            self.pipeline_manifest[mkey] = mval
         # Log skipped params
         if len(skipped_params) > 0:
             log.debug(
@@ -921,32 +924,30 @@ def build_schema_param(self, p_val):
         """
         Build a pipeline schema dictionary for an param interactively
         """
+        if p_val is None:
+            return {"type": "string"}
+        if isinstance(p_val, bool):
+            return {"type": "boolean", "default": p_val} if p_val else {"type": "boolean"}  # no default for False
+        if isinstance(p_val, int):
+            return {"type": "integer", "default": p_val}
+        if isinstance(p_val, float):
+            return {"type": "number", "default": p_val}
+
+        # TODO: remove string branch once old text-format config caches are no longer supported
         p_val = p_val.strip("\"'")
-        # p_val is always a string as it is parsed from nextflow config this way
+        if not p_val or p_val == "null":
+            return {"type": "string"}
+        if p_val in ("true", "True"):
+            return {"type": "boolean", "default": True}
+        if p_val in ("false", "False"):
+            return {"type": "boolean"}
         try:
-            p_val = float(p_val)
-            if p_val == int(p_val):
-                p_val = int(p_val)
-                p_type = "integer"
-            else:
-                p_type = "number"
+            num = float(p_val)
+            if num == int(num):
+                return {"type": "integer", "default": int(num)}
+            return {"type": "number", "default": num}
         except ValueError:
-            p_type = "string"
-
-        # Anything can be "null", means that it is not set
-        if p_val == "null":
-            p_val = None
-
-        # Booleans
-        if p_val in ["true", "false", "True", "False"]:
-            p_val = p_val in ["true", "True"]  # Convert to bool
-            p_type = "boolean"
-
-        # 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 {"type": p_type, "default": p_val}
+            return {"type": "string", "default": p_val}
 
     def launch_web_builder(self):
         """
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index d5a167c6ba..1cd1a51794 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -18,6 +18,7 @@
 import nf_core
 import nf_core.pipelines.create.create
 import nf_core.utils
+from nf_core.github_api import gh_api
 from nf_core.pipelines.lint_utils import dump_yaml_with_prettier
 
 log = logging.getLogger(__name__)
@@ -53,7 +54,7 @@ class PipelineSync:
         original_branch (str): Repo branch that was checked out before we started.
         made_changes (bool): Whether making the new template pipeline introduced any changes
         make_pr (bool): Whether to try to automatically make a PR on GitHub.com
-        required_config_vars (list): List of nextflow variables required to make template pipeline
+        required_config_vars (dict): Nextflow config variables required to make template pipeline, keyed by section
         gh_username (str): GitHub username
         gh_repo (str): GitHub repository name
     """
@@ -80,12 +81,9 @@ def __init__(
         self.made_changes = False
         self.make_pr = make_pr
         self.gh_pr_returned_data: dict = {}
-        self.required_config_vars = [
-            "manifest.name",
-            "manifest.description",
-            "manifest.version",
-            "manifest.contributors",
-        ]
+        self.required_config_vars: dict[str, list[str]] = {
+            "manifest": ["name", "description", "version", "contributors"],
+        }
         self.force_pr = force_pr
 
         self.gh_username = gh_username
@@ -123,7 +121,7 @@ def __init__(
                 )
 
         # Set up the API auth if supplied on the command line
-        self.gh_api = nf_core.utils.gh_api
+        self.gh_api = gh_api
         self.gh_api.lazy_init()
         if self.gh_username and "GITHUB_AUTH_TOKEN" in os.environ:
             log.debug(f"Authenticating sync as {self.gh_username}")
@@ -231,9 +229,10 @@ def get_wf_config(self) -> None:
         self.wf_config = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir))
 
         # Check that we have the required variables
-        for rvar in self.required_config_vars:
-            if rvar not in self.wf_config:
-                raise SyncExceptionError(f"Workflow config variable `{rvar}` not found!")
+        for section, keys in self.required_config_vars.items():
+            for key in keys:
+                if key not in self.wf_config.get(section, {}):
+                    raise SyncExceptionError(f"Workflow config variable `{section}.{key}` not found!")
 
     def checkout_template_branch(self):
         """
@@ -320,7 +319,7 @@ def make_template_pipeline(self) -> None:
                 from_config_file=True,
                 no_git=True,
                 force=True,
-                default_branch=self.wf_config.get("manifest.defaultBranch") or "master",
+                default_branch=self.wf_config.get("manifest", {}).get("defaultBranch") or "master",
             )
             pipeline_create_obj.init_pipeline()
 
diff --git a/nf_core/pydantic_models.py b/nf_core/pydantic_models.py
new file mode 100644
index 0000000000..ffdcebc0fb
--- /dev/null
+++ b/nf_core/pydantic_models.py
@@ -0,0 +1,211 @@
+"""Pydantic models for the `.nf-core.yml` configuration file.
+
+Kept separate from nf_core.utils so that pydantic is only imported
+when the config file is actually parsed.
+"""
+
+from pathlib import Path
+from typing import Any, Literal
+
+from pydantic import BaseModel, ConfigDict, Field, field_validator
+
+
+class NFCoreTemplateConfig(BaseModel):
+    """Template configuration schema"""
+
+    org: str | None = None
+    """ Organisation name """
+    name: str | None = None
+    """ Pipeline name """
+    description: str | None = None
+    """ Pipeline description """
+    author: str | None = None
+    """ Pipeline author """
+    version: str | None = None
+    """ Pipeline version """
+    force: bool | None = True
+    """ Force overwrite of existing files """
+    outdir: str | Path | None = None
+    """ Output directory """
+    skip_features: list | None = None
+    """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """
+    is_nfcore: bool | None = None
+    """ Whether the pipeline is an nf-core pipeline. """
+
+    # convert outdir to str
+    @field_validator("outdir")
+    @classmethod
+    def outdir_to_str(cls, v: str | Path | None) -> str | None:
+        if v is not None:
+            v = str(v)
+        return v
+
+    def __getitem__(self, item: str) -> Any:
+        if self is None:
+            return None
+        return getattr(self, item)
+
+    def get(self, item: str, default: Any = None) -> Any:
+        return getattr(self, item, default)
+
+
+class NFCoreYamlLintConfig(BaseModel):
+    """
+    schema for linting config in `.nf-core.yml` should cover:
+
+    .. code-block:: yaml
+
+        files_unchanged:
+            - .github/workflows/branch.yml
+        modules_config: False
+        modules_config:
+                - fastqc
+        # merge_markers: False
+        merge_markers:
+                - docs/my_pdf.pdf
+        nextflow_config: False
+        nextflow_config:
+            - manifest.name
+            - config_defaults:
+                - params.annotation_db
+                - params.multiqc_comment_headers
+                - params.custom_table_headers
+        # multiqc_config: False
+        multiqc_config:
+            - report_section_order
+            - report_comment
+        files_exist:
+            - CITATIONS.md
+        template_strings: False
+        template_strings:
+                - docs/my_pdf.pdf
+        nfcore_components: False
+        # nf_test_content: False
+        nf_test_content:
+            - tests/<test_name>.nf.test
+            - tests/nextflow.config
+            - nf-test.config
+    """
+
+    files_unchanged: bool | list[str] | None = None
+    """ List of files that should not be changed """
+    modules_config: bool | list[str] | None = None
+    """ List of modules that should not be changed """
+    merge_markers: bool | list[str] | None = None
+    """ List of files that should not contain merge markers """
+    nextflow_config: bool | list[str | dict[str, list[str]]] | None = None
+    """ List of Nextflow config files that should not be changed """
+    nf_test_content: bool | list[str] | None = None
+    """ List of nf-test content that should not be changed """
+    multiqc_config: bool | list[str] | None = None
+    """ List of MultiQC config options that be changed """
+    files_exist: bool | list[str] | None = None
+    """ List of files that can not exist """
+    template_strings: bool | list[str] | None = None
+    """ List of files that can contain template strings """
+    readme: bool | list[str] | None = None
+    """ Lint the README.md file """
+    nfcore_components: bool | None = None
+    """ Lint all required files to use nf-core modules and subworkflows """
+    actions_nf_test: bool | None = None
+    """ Lint all required files to use GitHub Actions CI """
+    actions_awstest: bool | None = None
+    """ Lint all required files to run tests on AWS """
+    actions_awsfulltest: bool | None = None
+    """ Lint all required files to run full tests on AWS """
+    pipeline_todos: bool | None = None
+    """ Lint for TODOs statements"""
+    pipeline_if_empty_null: bool | None = None
+    """ Lint for ifEmpty(null) statements"""
+    plugin_includes: bool | None = None
+    """ Lint for nextflow plugin """
+    pipeline_name_conventions: bool | None = None
+    """ Lint for pipeline name conventions """
+    schema_lint: bool | None = None
+    """ Lint nextflow_schema.json file"""
+    schema_params: bool | None = None
+    """ Lint schema for all params """
+    system_exit: bool | None = None
+    """ Lint for System.exit calls in groovy/nextflow code """
+    schema_description: bool | None = None
+    """ Check that every parameter in the schema has a description. """
+    actions_schema_validation: bool | None = None
+    """ Lint GitHub Action workflow files with schema"""
+    modules_json: bool | None = None
+    """ Lint modules.json file """
+    modules_structure: bool | None = None
+    """ Lint modules structure """
+    base_config: bool | None = None
+    """ Lint base.config file """
+    nfcore_yml: bool | None = None
+    """ Lint nf-core.yml """
+    version_consistency: bool | None = None
+    """ Lint for version consistency """
+    included_configs: bool | None = None
+    """ Lint for included configs """
+    local_component_structure: bool | None = None
+    """ Lint local components use correct structure mirroring remote"""
+    container_configs: bool | None = None
+    """ Lint that container configuration files in conf/ are up to date """
+    rocrate_readme_sync: bool | None = None
+    """ Lint for README.md and rocrate.json sync """
+
+    def __getitem__(self, item: str) -> Any:
+        return getattr(self, item)
+
+    def get(self, item: str, default: Any = None) -> Any:
+        if getattr(self, item, default) is None:
+            return default
+        return getattr(self, item, default)
+
+    def __setitem__(self, item: str, value: Any) -> None:
+        setattr(self, item, value)
+
+
+class NFCoreYamlConfig(BaseModel):
+    """.nf-core.yml configuration file schema"""
+
+    model_config = ConfigDict(populate_by_name=True)
+
+    repository_type: Literal["pipeline", "modules"] | None = None
+    """ Type of repository """
+    nf_core_version: str | None = None
+    """ Version of nf-core/tools used to create/update the pipeline """
+    org_path: str | None = None
+    """ Path to the organisation's modules repository (used for modules repo_type only) """
+    lint: NFCoreYamlLintConfig | None = None
+    """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """
+    template: NFCoreTemplateConfig | None = None
+    """ Pipeline template configuration """
+    bump_version: dict[str, bool] | None = None
+    """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information. """
+    update: dict[str, str | bool | dict[str, str | dict[str, str | bool]]] | None = None
+    """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information. """
+    container_registry: list[str] | None = Field(default=None, alias="container-registry")
+    """ Additional container registry prefixes allowed when linting container directives. """
+
+    def __getitem__(self, item: str) -> Any:
+        return getattr(self, item)
+
+    def get(self, item: str, default: Any = None) -> Any:
+        return getattr(self, item, default)
+
+    def __setitem__(self, item: str, value: Any) -> None:
+        setattr(self, item, value)
+
+    def model_dump(self, **kwargs) -> dict[str, Any]:
+        # Get the initial data
+        config = super().model_dump(**kwargs)
+
+        if self.repository_type == "modules":
+            # Fields to exclude for modules
+            fields_to_exclude = ["template", "update"]
+        else:  # pipeline
+            # Fields to exclude for pipeline
+            fields_to_exclude = ["bump_version", "org_path"]
+
+        # Remove the fields based on repository_type
+        for field in fields_to_exclude:
+            config.pop(field, None)
+
+        return config
diff --git a/nf_core/subworkflows/__init__.py b/nf_core/subworkflows/__init__.py
index 8e3c85a271..3ca23d0f30 100644
--- a/nf_core/subworkflows/__init__.py
+++ b/nf_core/subworkflows/__init__.py
@@ -1,8 +1,16 @@
-from .create import SubworkflowCreate
-from .info import SubworkflowInfo
-from .install import SubworkflowInstall
-from .lint import SubworkflowLint
-from .list import SubworkflowList
-from .patch import SubworkflowPatch
-from .remove import SubworkflowRemove
-from .update import SubworkflowUpdate
+from nf_core.utils import lazy_attrs
+
+# Lazy imports to keep CLI start-up fast
+__getattr__, __dir__ = lazy_attrs(
+    globals(),
+    {
+        "SubworkflowCreate": "nf_core.subworkflows.create",
+        "SubworkflowInfo": "nf_core.subworkflows.info",
+        "SubworkflowInstall": "nf_core.subworkflows.install",
+        "SubworkflowLint": "nf_core.subworkflows.lint",
+        "SubworkflowList": "nf_core.subworkflows.list",
+        "SubworkflowPatch": "nf_core.subworkflows.patch",
+        "SubworkflowRemove": "nf_core.subworkflows.remove",
+        "SubworkflowUpdate": "nf_core.subworkflows.update",
+    },
+)
diff --git a/nf_core/subworkflows/install.py b/nf_core/subworkflows/install.py
index 70a6b0afa5..90bb504b80 100644
--- a/nf_core/subworkflows/install.py
+++ b/nf_core/subworkflows/install.py
@@ -12,6 +12,7 @@ def __init__(
         branch=None,
         no_pull=False,
         installed_by=None,
+        skip_deps=False,
     ):
         super().__init__(
             pipeline_dir,
@@ -23,4 +24,5 @@ def __init__(
             branch=branch,
             no_pull=no_pull,
             installed_by=installed_by,
+            skip_deps=skip_deps,
         )
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index 7d5fbccdae..22ceb96ab1 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -9,7 +9,6 @@
 import logging
 import os
 
-import questionary
 import rich
 import ruamel.yaml
 
@@ -51,7 +50,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
-        registry=None,
+        registry: tuple[str, ...] = ("quay.io", "community.wave.seqera.io/library"),
         hide_progress=False,
     ):
         super().__init__(
@@ -69,7 +68,6 @@ def __init__(
     def lint(
         self,
         subworkflow=None,
-        registry="quay.io",
         key=(),
         all_subworkflows=False,
         print_results=True,
@@ -103,24 +101,11 @@ def lint(
         # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class
         # Prompt for subworkflow or all
         if subworkflow is None and not (local or all_subworkflows):
-            questions = [
-                {
-                    "type": "list",
-                    "name": "all_subworkflows",
-                    "message": "Lint all subworkflows or a single named subworkflow?",
-                    "choices": ["All subworkflows", "Named subworkflow"],
-                },
-                {
-                    "type": "autocomplete",
-                    "name": "subworkflow_name",
-                    "message": "Subworkflow name:",
-                    "when": lambda x: x["all_subworkflows"] == "Named subworkflow",
-                    "choices": [m.component_name for m in self.all_remote_components],
-                },
-            ]
-            answers = questionary.unsafe_prompt(questions, style=nf_core.utils.nfcore_question_style)
-            all_subworkflows = answers["all_subworkflows"] == "All subworkflows"
-            subworkflow = answers.get("subworkflow_name")
+            from nf_core.modules.modules_utils import prompt_module_selection
+
+            subworkflow = prompt_module_selection(
+                self.all_remote_components, component_type="subworkflows", action="Lint"
+            )
 
         # Only lint the given module
         if subworkflow:
@@ -152,23 +137,22 @@ def lint(
 
         # Lint local subworkflows
         if local and len(local_subworkflows) > 0:
-            self.lint_subworkflows(local_subworkflows, registry=registry, local=True)
+            self.lint_subworkflows(local_subworkflows, local=True)
 
         # Lint nf-core subworkflows
         if not local and len(remote_subworkflows) > 0:
-            self.lint_subworkflows(remote_subworkflows, registry=registry, local=False)
+            self.lint_subworkflows(remote_subworkflows, local=False)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by, plain_text=plain_text)
             self.print_summary(plain_text=plain_text)
 
-    def lint_subworkflows(self, subworkflows, registry="quay.io", local=False):
+    def lint_subworkflows(self, subworkflows, local=False):
         """
         Lint a list of subworkflows
 
         Args:
             subworkflows ([NFCoreComponent]): A list of subworkflow objects
-            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core subworkflows
         """
         # TODO: consider unifying modules and subworkflows lint_subworkflows() function and add it to the ComponentLint class
@@ -189,9 +173,9 @@ def lint_subworkflows(self, subworkflows, registry="quay.io", local=False):
 
             for swf in subworkflows:
                 progress_bar.update(lint_progress, advance=1, test_name=swf.component_name)
-                self.lint_subworkflow(swf, progress_bar, registry=registry, local=local)
+                self.lint_subworkflow(swf, progress_bar, local=local)
 
-    def lint_subworkflow(self, swf, progress_bar, registry, local=False):
+    def lint_subworkflow(self, swf, progress_bar, local=False):
         """
         Perform linting on one subworkflow
 
@@ -247,13 +231,14 @@ def update_meta_yml_file(self, swf):
         """
         Update the meta.yml file with the correct inputs and outputs
         """
+        from nf_core.components.components_utils import read_meta_yml
+
         yaml = ruamel.yaml.YAML()
         yaml.preserve_quotes = True
         yaml.indent(mapping=2, sequence=2, offset=0)
 
         # Read meta.yml
-        with open(swf.meta_yml) as fh:
-            meta_yaml = yaml.load(fh)
+        meta_yaml = read_meta_yml(swf.meta_yml)
         meta_yaml_corrected = meta_yaml.copy()
         # Obtain inputs and outputs from main.nf
         swf.get_inputs_from_main_nf()
diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index 6d79a47396..9d16312250 100644
--- a/nf_core/subworkflows/lint/main_nf.py
+++ b/nf_core/subworkflows/lint/main_nf.py
@@ -27,13 +27,22 @@ def main_nf(_, subworkflow: NFCoreComponent) -> tuple[list[str], list[str]]:
 
     The following checks are performed:
 
-    * ``main_nf_exists``: The ``main.nf`` file must exist.
+    main_nf_exists
+    ^^^^^^^^^^^^^^
 
-    * ``main_nf_script_outputs``: The workflow must have an ``emit:`` block.
+    The ``main.nf`` file must exist.
 
-    * ``main_nf_version_emitted``: The subworkflow should emit a software version
-      channel. A warning is issued if no ``versions`` output is found (can be
-      ignored if the subworkflow uses topic channels).
+    main_nf_script_outputs
+    ^^^^^^^^^^^^^^^^^^^^^^^
+
+    The workflow must have an ``emit:`` block.
+
+    main_nf_version_emitted
+    ^^^^^^^^^^^^^^^^^^^^^^^^
+
+    The subworkflow should emit a software version
+    channel. A warning is issued if no ``versions`` output is found (can be
+    ignored if the subworkflow uses topic channels).
     """
 
     inputs: list[str] = []
diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py
index bfc3330e9d..480c2d672a 100644
--- a/nf_core/subworkflows/lint/meta_yml.py
+++ b/nf_core/subworkflows/lint/meta_yml.py
@@ -3,7 +3,6 @@
 from pathlib import Path
 
 import jsonschema.validators
-import ruamel.yaml
 
 import nf_core.components.components_utils
 from nf_core.components.lint import LintExceptionError
@@ -29,25 +28,46 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False):
 
     The following checks are performed:
 
-    * ``meta_yml_exists``: The ``meta.yml`` file must exist.
+    meta_yml_exists
+    ^^^^^^^^^^^^^^^
 
-    * ``meta_yml_valid``: The ``meta.yml`` must be valid according to the JSON
-      schema defined at https://raw.githubusercontent.com/nf-core/subworkflows/master/modules/environment-schema.json.
+    The ``meta.yml`` file must exist.
 
-    * ``meta_input``: All input channels declared in ``main.nf`` must be listed
-      under the ``input:`` key in ``meta.yml``.
+    meta_yml_valid
+    ^^^^^^^^^^^^^^
 
-    * ``meta_output``: All output channels declared in ``main.nf`` must be listed
-      under the ``output:`` key in ``meta.yml``.
+    The ``meta.yml`` must be valid according to the JSON
+    schema defined at https://raw.githubusercontent.com/nf-core/subworkflows/master/modules/environment-schema.json.
 
-    * ``meta_name``: The ``name`` field in ``meta.yml`` must match the workflow
-      name declared in ``main.nf``.
+    meta_input
+    ^^^^^^^^^^
 
-    * ``meta_include``: All modules and subworkflows included in ``main.nf`` must
-      be listed under the ``components:`` key in ``meta.yml``.
+    All input channels declared in ``main.nf`` must be listed
+    under the ``input:`` key in ``meta.yml``.
 
-    * ``meta_modules_deprecated``: The deprecated ``modules:`` section must not
-      be present in ``meta.yml``; use ``components:`` instead.
+    meta_output
+    ^^^^^^^^^^^
+
+    All output channels declared in ``main.nf`` must be listed
+    under the ``output:`` key in ``meta.yml``.
+
+    meta_name
+    ^^^^^^^^^
+
+    The ``name`` field in ``meta.yml`` must match the workflow
+    name declared in ``main.nf``.
+
+    meta_include
+    ^^^^^^^^^^^^
+
+    All modules and subworkflows included in ``main.nf`` must
+    be listed under the ``components:`` key in ``meta.yml``.
+
+    meta_modules_deprecated
+    ^^^^^^^^^^^^^^^^^^^^^^^^
+
+    The deprecated ``modules:`` section must not
+    be present in ``meta.yml``; use ``components:`` instead.
     """
     # Read the meta.yml file
     if subworkflow.meta_yml is None:
@@ -64,9 +84,9 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False):
         raise LintExceptionError("Subworkflow does not have a `meta.yml` file")
 
     try:
-        with open(subworkflow.meta_yml) as fh:
-            yaml = ruamel.yaml.YAML(typ="safe")
-            meta_yaml = yaml.load(fh)
+        from nf_core.components.components_utils import read_meta_yml
+
+        meta_yaml = read_meta_yml(subworkflow.meta_yml)
         subworkflow.passed.append(
             ("meta_yml", "meta_yml_exists", "Subworkflow `meta.yml` exists", subworkflow.meta_yml)
         )
diff --git a/nf_core/subworkflows/lint/subworkflow_changes.py b/nf_core/subworkflows/lint/subworkflow_changes.py
index 9152931594..22e992043e 100644
--- a/nf_core/subworkflows/lint/subworkflow_changes.py
+++ b/nf_core/subworkflows/lint/subworkflow_changes.py
@@ -25,11 +25,17 @@ def subworkflow_changes(subworkflow_lint_object, subworkflow):
 
     The following checks are performed:
 
-    * ``subworkflow_patch``: If the subworkflow is patched, the patch must apply
-      cleanly in reverse against the remote version.
+    subworkflow_patch
+    ^^^^^^^^^^^^^^^^^
 
-    * ``check_local_copy``: Each subworkflow file must be identical to the
-      corresponding file in the remote repository at the pinned commit SHA.
+    If the subworkflow is patched, the patch must apply
+    cleanly in reverse against the remote version.
+
+    check_local_copy
+    ^^^^^^^^^^^^^^^^
+
+    Each subworkflow file must be identical to the
+    corresponding file in the remote repository at the pinned commit SHA.
     """
     if subworkflow.is_patched:
         # If the subworkflow is patched, we need to apply
diff --git a/nf_core/subworkflows/lint/subworkflow_if_empty_null.py b/nf_core/subworkflows/lint/subworkflow_if_empty_null.py
index 5709874329..fe64ea7201 100644
--- a/nf_core/subworkflows/lint/subworkflow_if_empty_null.py
+++ b/nf_core/subworkflows/lint/subworkflow_if_empty_null.py
@@ -17,8 +17,11 @@ def subworkflow_if_empty_null(_, subworkflow):
 
     The following checks are performed:
 
-    * ``subworkflow_if_empty_null``: Warns if any ``ifEmpty(null)`` usage is found
-      in the subworkflow files.
+    subworkflow_if_empty_null
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+    Warns if any ``ifEmpty(null)`` usage is found
+    in the subworkflow files.
     """
 
     # Main subworkflow directory
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index 189f3c10f0..81219cca71 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -21,28 +21,49 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent, allow_missing: bool = Fal
 
     The following checks are performed:
 
-    * ``test_dir_exists``: The nf-test directory ``tests/`` must exist.
+    test_dir_exists
+    ^^^^^^^^^^^^^^^
 
-    * ``test_main_nf_exists``: The file ``tests/main.nf.test`` must exist.
+    The nf-test directory ``tests/`` must exist.
 
-    * ``test_snapshot_exists``: If ``snapshot()`` is called in ``main.nf.test``,
-      the snapshot file ``tests/main.nf.test.snap`` must exist and be valid JSON.
+    test_main_nf_exists
+    ^^^^^^^^^^^^^^^^^^^
 
-    * ``test_snap_md5sum``: The snapshot must not contain md5sums for empty files
-      (``d41d8cd98f00b204e9800998ecf8427e``) or empty compressed files
-      (``7029066c27ac6f5ef18d660d5741979a``), unless the test name contains ``stub``.
+    The file ``tests/main.nf.test`` must exist.
 
-    * ``test_snap_versions``: The snapshot should contain a ``versions`` key.
-      A warning (not a failure) is issued if it is absent, since subworkflows that
-      use topic channels may not emit versions directly.
+    test_snapshot_exists
+    ^^^^^^^^^^^^^^^^^^^^
 
-    * ``test_main_tags``: The ``main.nf.test`` file must declare the required tags:
-      ``subworkflows``, ``subworkflows/<component_name>``, ``subworkflows_<org>``,
-      all components included in the subworkflow's ``main.nf``, and any chained
-      components referenced via ``include`` statements in the test file.
+    If ``snapshot()`` is called in ``main.nf.test``,
+    the snapshot file ``tests/main.nf.test.snap`` must exist and be valid JSON.
 
-    * ``test_old_test_dir``: The legacy pytest directory
-      ``tests/subworkflows/<component_name>/`` must not exist.
+    test_snap_md5sum
+    ^^^^^^^^^^^^^^^^
+
+    The snapshot must not contain md5sums for empty files
+    (``d41d8cd98f00b204e9800998ecf8427e``) or empty compressed files
+    (``7029066c27ac6f5ef18d660d5741979a``), unless the test name contains ``stub``.
+
+    test_snap_versions
+    ^^^^^^^^^^^^^^^^^^
+
+    The snapshot should contain a ``versions`` key.
+    A warning (not a failure) is issued if it is absent, since subworkflows that
+    use topic channels may not emit versions directly.
+
+    test_main_tags
+    ^^^^^^^^^^^^^^
+
+    The ``main.nf.test`` file must declare the required tags:
+    ``subworkflows``, ``subworkflows/<component_name>``, ``subworkflows_<org>``,
+    all components included in the subworkflow's ``main.nf``, and any chained
+    components referenced via ``include`` statements in the test file.
+
+    test_old_test_dir
+    ^^^^^^^^^^^^^^^^^
+
+    The legacy pytest directory
+    ``tests/subworkflows/<component_name>/`` must not exist.
 
     """
     if subworkflow.nftest_testdir is None:
diff --git a/nf_core/subworkflows/lint/subworkflow_todos.py b/nf_core/subworkflows/lint/subworkflow_todos.py
index 9483771a59..0c403469d5 100644
--- a/nf_core/subworkflows/lint/subworkflow_todos.py
+++ b/nf_core/subworkflows/lint/subworkflow_todos.py
@@ -32,8 +32,11 @@ def subworkflow_todos(_, subworkflow):
 
     The following checks are performed:
 
-    * ``subworkflow_todo``: Warns if any ``TODO nf-core:`` comment lines are found
-      in the subworkflow files.
+    subworkflow_todo
+    ^^^^^^^^^^^^^^^^
+
+    Warns if any ``TODO nf-core:`` comment lines are found
+    in the subworkflow files.
     """
 
     # Main subworkflow directory
diff --git a/nf_core/subworkflows/lint/subworkflow_version.py b/nf_core/subworkflows/lint/subworkflow_version.py
index b5b3b1d0e0..d364cd1637 100644
--- a/nf_core/subworkflows/lint/subworkflow_version.py
+++ b/nf_core/subworkflows/lint/subworkflow_version.py
@@ -20,10 +20,16 @@ def subworkflow_version(subworkflow_lint_object, subworkflow):
 
     The following checks are performed:
 
-    * ``git_sha``: The subworkflow must have a ``git_sha`` entry in ``modules.json``.
+    git_sha
+    ^^^^^^^
 
-    * ``subworkflow_version``: The subworkflow version must match the latest commit
-      in the remote repository. A warning is issued if a newer version is available.
+    The subworkflow must have a ``git_sha`` entry in ``modules.json``.
+
+    subworkflow_version
+    ^^^^^^^^^^^^^^^^^^^
+
+    The subworkflow version must match the latest commit
+    in the remote repository. A warning is issued if a newer version is available.
     """
 
     modules_json_path = Path(subworkflow_lint_object.directory, "modules.json")
diff --git a/nf_core/subworkflows/update.py b/nf_core/subworkflows/update.py
index 9b6bf16928..29c4dbcc02 100644
--- a/nf_core/subworkflows/update.py
+++ b/nf_core/subworkflows/update.py
@@ -16,6 +16,7 @@ def __init__(
         branch=None,
         no_pull=False,
         limit_output=False,
+        skip_deps=False,
     ):
         super().__init__(
             pipeline_dir,
@@ -31,4 +32,5 @@ def __init__(
             branch,
             no_pull,
             limit_output,
+            skip_deps,
         )
diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
index 72b5cf34b3..dc79e9a759 100644
--- a/nf_core/synced_repo.py
+++ b/nf_core/synced_repo.py
@@ -227,36 +227,22 @@ def checkout_branch(self):
         """
         Checks out the specified branch of the repository
         """
-        try:
-            self.repo.git.checkout(self.branch)
-        except GitCommandError as e:
-            if (
-                self.fullname
-                and "modules" in self.fullname
-                and "Your local changes to the following files would be overwritten by checkout" in str(e)
-            ):
-                log.debug(f"Overwriting local changes in '{self.local_repo_dir}'")
-                self.repo.git.checkout(self.branch, force=True)
-            else:
-                raise e
+        self.checkout(self.branch)
 
     def checkout(self, commit):
         """
-        Checks out the repository at the requested commit
+        Checks out the repository at the requested commit (or branch)
 
         Args:
-            commit (str): Git SHA of the commit
+            commit (str): Git SHA of the commit, or a branch name
         """
         try:
             self.repo.git.checkout(commit)
         except GitCommandError as e:
-            if (
-                self.fullname
-                and "modules" in self.fullname
-                and "Your local changes to the following files would be overwritten by checkout" in str(e)
-            ):
-                log.debug(f"Overwriting local changes in '{self.local_repo_dir}'")
-                self.repo.git.checkout(self.branch, force=True)
+            if self.fullname and "modules" in self.fullname and "would be overwritten by checkout" in str(e):
+                log.debug(f"Discarding local changes in '{self.local_repo_dir}'")
+                self.repo.git.clean("-df")
+                self.repo.git.checkout(commit, force=True)
             else:
                 raise e
 
@@ -305,7 +291,8 @@ def install_component(self, component_name: str, install_dir: str | Path, commit
         # Check out the repository at the requested ref
         try:
             self.checkout(commit)
-        except git.GitCommandError:
+        except git.GitCommandError as e:
+            log.error(f"Could not check out '{commit}' in the modules cache '{self.local_repo_dir}':\n{e}")
             return False
 
         # Check if the module/subworkflow exists in the branch
diff --git a/nf_core/test_datasets/test_datasets_utils.py b/nf_core/test_datasets/test_datasets_utils.py
index 7ed782cba4..61a7f60b30 100644
--- a/nf_core/test_datasets/test_datasets_utils.py
+++ b/nf_core/test_datasets/test_datasets_utils.py
@@ -204,7 +204,7 @@ def get_or_prompt_branch(maybe_branch: str) -> tuple[str, list[str]]:
                 branch_prefill = MODULES_BRANCH_NAME
             elif repo_type == "pipeline":
                 wf_config = fetch_wf_config(base_dir)
-                pipeline_name = wf_config.get("manifest.name", "").split("/")[-1]
+                pipeline_name = wf_config.get("manifest", {}).get("name", "").split("/")[-1]
                 if pipeline_name in all_branches:
                     branch_prefill = pipeline_name
 
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 333cc75d1f..93a09971ba 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -3,44 +3,32 @@
 """
 
 import ast
-import concurrent.futures
 import datetime
 import errno
 import fnmatch
-import hashlib
+import functools
+import importlib
 import io
 import json
 import logging
-import mimetypes
 import os
-import random
 import re
-import shlex
-import subprocess
 import sys
 import time
 from collections.abc import Callable, Generator
 from contextlib import contextmanager, suppress
+from enum import Enum
+from functools import lru_cache
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Literal
-
-import git
-import prompt_toolkit.styles
-import questionary
-import requests.auth
-import requests_cache
-import rich
-import rich.markup
-import yaml
-from packaging.version import Version
-from pydantic import BaseModel, ValidationError, field_validator
-from rich.live import Live
-from rich.spinner import Spinner
+from typing import TYPE_CHECKING, Any
+
+from rich.console import Console
 
 import nf_core
 
 if TYPE_CHECKING:
     from nf_core.pipelines.schema import PipelineSchema
+    from nf_core.pydantic_models import NFCoreYamlConfig
 
 log = logging.getLogger(__name__)
 
@@ -53,38 +41,83 @@
     r"[green]                                          `._,._,'",
 ]
 
-# Custom style for questionary
-nfcore_question_style = prompt_toolkit.styles.Style(
-    [
-        ("qmark", "fg:ansiblue bold"),  # token in front of the question
-        ("question", "bold"),  # question text
-        (
-            "answer",
-            "fg:ansigreen nobold bg:",
-        ),  # submitted answer text behind the question
-        (
-            "pointer",
-            "fg:ansiyellow bold",
-        ),  # pointer used in select and checkbox prompts
-        (
-            "highlighted",
-            "fg:ansiblue bold",
-        ),  # pointed-at choice in select and checkbox prompts
-        (
-            "selected",
-            "fg:ansiyellow noreverse bold",
-        ),  # style for a selected item of a checkbox
-        ("separator", "fg:ansiblack"),  # separator in lists
-        ("instruction", ""),  # user instructions for select, rawselect, checkbox
-        ("text", ""),  # plain text
-        (
-            "disabled",
-            "fg:gray italic",
-        ),  # disabled choices for select and checkbox prompts
-        ("choice-default", "fg:ansiblack"),
-        ("choice-default-changed", "fg:ansiyellow"),
-        ("choice-required", "fg:ansired"),
-    ]
+
+def lazy_attrs(module_globals: dict, mapping: dict[str, "str | Callable"]):
+    """Build module-level ``__getattr__`` and ``__dir__`` for lazy attributes (PEP 562).
+
+    Each attribute maps either to the dotted path of the module to import it
+    from, or to a zero-argument callable that builds it. Resolved attributes
+    are cached in the module's globals, so the hook only fires once per name.
+
+    Usage::
+
+        __getattr__, __dir__ = lazy_attrs(globals(), {"PipelineCreateApp": "nf_core.pipelines.create"})
+    """
+
+    def module_getattr(name):
+        target = mapping.get(name)
+        if target is None:
+            raise AttributeError(f"module {module_globals['__name__']!r} has no attribute {name!r}")
+        value = target() if callable(target) else getattr(importlib.import_module(target), name)
+        module_globals[name] = value
+        return value
+
+    def module_dir():
+        return sorted(set(module_globals) | set(mapping))
+
+    return module_getattr, module_dir
+
+
+# Custom style for questionary (built lazily to keep CLI start-up fast)
+@functools.cache
+def _nfcore_question_style():
+    import prompt_toolkit.styles
+
+    return prompt_toolkit.styles.Style(
+        [
+            ("qmark", "fg:ansiblue bold"),  # token in front of the question
+            ("question", "bold"),  # question text
+            (
+                "answer",
+                "fg:ansigreen nobold bg:",
+            ),  # submitted answer text behind the question
+            (
+                "pointer",
+                "fg:ansiyellow bold",
+            ),  # pointer used in select and checkbox prompts
+            (
+                "highlighted",
+                "fg:ansiblue bold",
+            ),  # pointed-at choice in select and checkbox prompts
+            (
+                "selected",
+                "fg:ansiyellow noreverse bold",
+            ),  # style for a selected item of a checkbox
+            ("separator", "fg:ansiblack"),  # separator in lists
+            ("instruction", ""),  # user instructions for select, rawselect, checkbox
+            ("text", ""),  # plain text
+            (
+                "disabled",
+                "fg:gray italic",
+            ),  # disabled choices for select and checkbox prompts
+            ("choice-default", "fg:ansiblack"),
+            ("choice-default-changed", "fg:ansiyellow"),
+            ("choice-required", "fg:ansired"),
+        ]
+    )
+
+
+# Lazy imports to keep CLI start-up fast
+__getattr__, __dir__ = lazy_attrs(
+    globals(),
+    {
+        "nfcore_question_style": _nfcore_question_style,
+        "GitHubAPISession": "nf_core.github_api",
+        "gh_api": "nf_core.github_api",
+        "NFCoreTemplateConfig": "nf_core.pydantic_models",
+        "NFCoreYamlLintConfig": "nf_core.pydantic_models",
+        "NFCoreYamlConfig": "nf_core.pydantic_models",
+    },
 )
 
 
@@ -94,7 +127,7 @@ def is_interactive() -> bool:
 
 
 NFCORE_CACHE_DIR = Path(
-    os.environ.get("XDG_CACHE_HOME", Path(os.getenv("HOME") or "", ".cache")),
+    os.environ.get("XDG_CACHE_HOME") or Path(os.getenv("HOME") or "") / ".cache",
     "nfcore",
 )
 NFCORE_DIR = Path(
@@ -103,6 +136,19 @@ def is_interactive() -> bool:
 )
 
 
+CONTAINER_SYSTEMS = ["docker", "singularity"]
+CONTAINER_PLATFORMS = ["linux/amd64", "linux/arm64"]
+# Platforms a module must provide containers for. Others (e.g. linux/arm64) are
+# supported and validated when present, but not required.
+REQUIRED_CONTAINER_PLATFORMS = ["linux/amd64"]
+
+
+class ContainerRegistryUrls(Enum):
+    SEQERA_DOCKER = "community.wave.seqera.io/library"
+    SEQERA_SINGULARITY = "community-cr-prod.seqera.io/docker/registry/v2"
+    GALAXY_SINGULARITY = "depot.galaxyproject.org/singularity"
+
+
 def unquote(s: str) -> str:
     """
     Remove paired quotes (single or double) from start and end of string.
@@ -119,9 +165,11 @@ def unquote(s: str) -> str:
     Returns:
         String with outer quotes removed if present, otherwise original string
     """
-    import ruamel.yaml
+    import ruamel.yaml.scalarstring
 
-    if isinstance(s, ruamel.yaml.scalarstring.DoubleQuotedScalarString):
+    if isinstance(
+        s, (ruamel.yaml.scalarstring.DoubleQuotedScalarString, ruamel.yaml.scalarstring.SingleQuotedScalarString)
+    ):
         return s
 
     try:
@@ -130,10 +178,60 @@ def unquote(s: str) -> str:
         return s
 
 
-def fetch_remote_version(source_url):
-    response = requests.get(source_url, timeout=3)
-    remote_version = re.sub(r"[^0-9\.]", "", response.text)
-    return remote_version
+# The version check never fetches on the hot path (update-notifier pattern):
+# it only reads the cached remote version, and refreshes the cache in a
+# detached background process so that no run ever blocks on the network.
+REMOTE_VERSION_CACHE = Path(NFCORE_CACHE_DIR, "latest_version.json")
+REMOTE_VERSION_CACHE_EXPIRY = 60 * 60 * 24  # refresh at most once a day
+REMOTE_VERSION_REFRESH_BACKOFF = 60 * 10  # wait at least this long between refresh attempts
+
+
+def _load_version_cache() -> dict:
+    try:
+        with open(REMOTE_VERSION_CACHE) as fh:
+            cached = json.load(fh)
+        if isinstance(cached, dict):
+            return cached
+    except (OSError, ValueError):
+        pass
+    return {}
+
+
+def _load_cached_remote_version() -> str | None:
+    from packaging.version import InvalidVersion, Version
+
+    cached = _load_version_cache()
+    try:
+        if time.time() - cached["timestamp"] < REMOTE_VERSION_CACHE_EXPIRY:
+            Version(cached["version"])  # guard against a corrupted cache
+            return cached["version"]
+    except (KeyError, TypeError, InvalidVersion):
+        pass
+    return None
+
+
+def _spawn_remote_version_refresh(source_url: str) -> None:
+    """Kick off a detached background process to refresh the remote version cache."""
+    import subprocess
+
+    try:
+        cached = _load_version_cache()
+        if time.time() - float(cached.get("attempted_at") or 0) < REMOTE_VERSION_REFRESH_BACKOFF:
+            return
+        # Record the attempt up front, so failed refreshes back off instead of respawning every run
+        cached["attempted_at"] = time.time()
+        setup_nfcore_cachedir()
+        with open(REMOTE_VERSION_CACHE, "w") as fh:
+            json.dump(cached, fh)
+        subprocess.Popen(
+            [sys.executable, "-m", "nf_core.version_updater", source_url, str(REMOTE_VERSION_CACHE)],
+            stdin=subprocess.DEVNULL,
+            stdout=subprocess.DEVNULL,
+            stderr=subprocess.DEVNULL,
+            start_new_session=True,
+        )
+    except (OSError, ValueError, TypeError, subprocess.SubprocessError) as e:
+        log.debug(f"Could not start background version check: {e}")
 
 
 def check_if_outdated(
@@ -146,7 +244,10 @@ def check_if_outdated(
     """
     # Exit immediately if disabled via ENV var
     if os.environ.get("NFCORE_NO_VERSION_CHECK", False):
-        return (True, "", "")
+        return (False, "", "")
+
+    from packaging.version import Version
+
     # Set and clean up the current version string
     if current_version is None:
         current_version = nf_core.__version__
@@ -157,12 +258,10 @@ def check_if_outdated(
     # check if we have a newer version without blocking the rest of the script
     is_outdated = False
     if remote_version is None:  # we set it manually for tests
-        try:
-            with concurrent.futures.ThreadPoolExecutor() as executor:
-                future = executor.submit(fetch_remote_version, source_url)
-                remote_version = future.result()
-        except requests.exceptions.RequestException as e:
-            log.debug(f"Could not check for nf-core updates: {e}")
+        remote_version = _load_cached_remote_version()
+        if remote_version is None:
+            # No fresh cache - refresh it in the background for the next run
+            _spawn_remote_version_refresh(source_url)
     if remote_version is not None and Version(remote_version) > Version(current_version):
         is_outdated = True
     return (is_outdated, current_version, remote_version)
@@ -177,6 +276,10 @@ def rich_force_colors():
     return None
 
 
+stdout = Console(force_terminal=rich_force_colors())
+stderr = Console(stderr=True, force_terminal=rich_force_colors())
+
+
 class Pipeline:
     """Object to hold information about a local pipeline.
 
@@ -197,6 +300,8 @@ class Pipeline:
 
     def __init__(self, wf_path: Path) -> None:
         """Initialise pipeline object"""
+        import git
+
         self.conda_config: dict = {}
         self.conda_package_info: dict = {}
         self.nf_config: dict = {}
@@ -229,6 +334,8 @@ def _load(self) -> bool:
 
     def _load_conda_environment(self) -> bool:
         """Try to load the pipeline environment.yml file, if it exists"""
+        import yaml
+
         try:
             with open(Path(self.wf_path, "environment.yml")) as fh:
                 self.conda_config = yaml.safe_load(fh)
@@ -243,6 +350,8 @@ def _fp(self, fn: str | Path) -> Path:
 
     def list_files(self) -> list[Path]:
         """Get a list of all files in the pipeline"""
+        import subprocess
+
         files = []
         try:
             # First, try to get the list of files using git
@@ -271,12 +380,13 @@ def load_pipeline_config(self) -> bool:
         Once loaded, set a few convenience reference class attributes
         """
         self.nf_config = fetch_wf_config(self.wf_path)
+        manifest = self.nf_config.get("manifest", {})
 
-        self.pipeline_prefix, self.pipeline_name = self.nf_config.get("manifest.name", "/").strip("'").split("/")
+        self.pipeline_prefix, self.pipeline_name = manifest.get("name", "/").split("/")
 
-        nextflow_version_match = re.search(r"[0-9\.]+(-edge)?", self.nf_config.get("manifest.nextflowVersion", ""))
+        nextflow_version_match = re.search(r"(?P<version>[0-9\.]+(-edge)?)", manifest.get("nextflowVersion", "") or "")
         if nextflow_version_match:
-            self.minNextflowVersion = nextflow_version_match.group(0)
+            self.minNextflowVersion = nextflow_version_match.group("version")
             return True
         return False
 
@@ -313,8 +423,11 @@ def pretty_nf_version(version: tuple[int, int, int, bool]) -> str:
     return f"{version[0]}.{version[1]:02}.{version[2]}" + ("-edge" if version[3] else "")
 
 
+@lru_cache(maxsize=1)
 def get_nf_version() -> tuple[int, int, int, bool] | None:
-    """Get the version of Nextflow installed on the system."""
+    """Get the version of Nextflow installed on the system. Cached for the lifetime of the process."""
+    import subprocess
+
     try:
         cmd_out = run_cmd("nextflow", "-v")
         if cmd_out is None:
@@ -369,6 +482,16 @@ def check_nextflow_version(minimal_nf_version: tuple[int, int, int, bool], silen
     return nf_version >= minimal_nf_version
 
 
+def read_module_name(main_nf: Path) -> str | None:
+    """Return the process name declared in a Nextflow ``main.nf`` file, or ``None``."""
+    nf_process_name_regex = re.compile(r"^\s*process\s+(\w+)\s*\{", re.MULTILINE)
+    try:
+        match = nf_process_name_regex.search(main_nf.read_text())
+    except OSError:
+        return None
+    return match.group(1) if match else None
+
+
 def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
     """Uses Nextflow to retrieve the the configuration variables
     from a Nextflow workflow.
@@ -381,9 +504,11 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
         dict: Workflow configuration settings.
     """
 
+    import hashlib
+
     log.debug(f"Got '{wf_path}' as path")
     wf_path = Path(wf_path)
-    config = {}
+    config: dict[str, Any] = {}
     cache_fn = None
     cache_basedir = None
     cache_path = None
@@ -428,35 +553,36 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
     log.debug("No config cache found")
 
     # Call `nextflow config`
-    result = run_cmd("nextflow", f"config -flat {wf_path}")
+    try:
+        result = run_cmd("nextflow", f"config -o json {wf_path}")
+    except RuntimeError as e:
+        raise UserWarning(
+            f"Could not parse Nextflow config for '{wf_path}'. Possibly because of a Nextflow version mismatch?\n{e}"
+        ) from e
     if result is not None:
         nfconfig_raw, _ = result
-        nfconfig = nfconfig_raw.decode("utf-8")
-        multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=\s]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL)
-
-        for config_match in multiline_key_value_pattern.finditer(nfconfig):
-            k = config_match.group(2).strip()
-            v = config_match.group(3).strip().strip("'\"")
-            if k and v == "":
-                config[k] = "null"
-                log.debug(f"Config key: {k}, value: empty string")
-            elif k and v:
-                config[k] = v
-                log.debug(f"Config key: {k}, value: {v}")
-            else:
-                log.debug(f"Couldn't find key=value config pair:\n  {config_match.group(0)}")
-            del config_match
+        try:
+            raw_str = nfconfig_raw.decode("utf-8")
+            json_start = raw_str.find("{")
+            parsed = json.loads(raw_str[json_start:] if json_start >= 0 else raw_str)
+            config.update(parsed)
+            for k in parsed:
+                log.debug(f"Config section: {k}")
+        except json.JSONDecodeError as e:
+            log.warning(f"Unable to parse nextflow config output as JSON: {e}")
 
     # Scrape main.nf for additional parameter declarations
     # Values in this file are likely to be complex, so don't both trying to capture them. Just get the param name.
+
+    main_nf = Path(wf_path, "main.nf")
     try:
-        main_nf = Path(wf_path, "main.nf")
         with open(main_nf, "rb") as fh:
+            params_section = config.setdefault("params", {})
             for line in fh:
                 line_str = line.decode("utf-8")
-                match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=(?!=)", line_str)
-                if match and match.group(1):
-                    config[match.group(1)] = "null"
+                match = re.match(r"^\s*params\.([a-zA-Z0-9_]+)\s*=(?!=)", line_str)
+                if match:
+                    params_section[match.group(1)] = None
 
     except FileNotFoundError as e:
         log.debug(f"Could not open {main_nf} to look for parameter declarations - {e}")
@@ -476,34 +602,33 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
 
 def run_cmd(executable: str, cmd: str) -> tuple[bytes, bytes] | None:
     """Run a specified command and capture the output. Handle errors nicely."""
+    import shlex
+    import subprocess
+
     full_cmd = f"{executable} {cmd}"
     log.debug(f"Running command: {full_cmd}")
     try:
         proc = subprocess.run(shlex.split(full_cmd), capture_output=True, check=False)
-        if proc.returncode != 0:
-            if executable == "nf-test":
-                return (proc.stdout, proc.stderr)
-            raise subprocess.CalledProcessError(proc.returncode, proc.args, output=proc.stdout, stderr=proc.stderr)
-        return (proc.stdout, proc.stderr)
-    except subprocess.CalledProcessError as e:
-        raise RuntimeError(f"Command '{full_cmd}' failed: {e}") from e
     except OSError as e:
         if e.errno == errno.ENOENT:
             raise RuntimeError(
                 f"It looks like {executable} is not installed. Please ensure it is available in your PATH."
             ) from e
-        else:
-            return None
-
+        return None
 
-def setup_nfcore_dir() -> bool:
-    """Creates a directory for files that need to be kept between sessions
+    if proc.returncode != 0:
+        if executable == "nf-test":
+            return (proc.stdout, proc.stderr)
+        output = (
+            proc.stderr.decode("utf-8", errors="replace").strip()
+            if proc.stderr
+            else proc.stdout.decode("utf-8", errors="replace").strip()
+            if proc.stdout
+            else ""
+        )
+        raise RuntimeError(f"Command '{full_cmd}' failed with exit code {proc.returncode}\n{output}")
 
-    Currently only used for keeping local copies of modules repos
-    """
-    if not NFCORE_DIR.exists():
-        NFCORE_DIR.mkdir(parents=True)
-    return True
+    return (proc.stdout, proc.stderr)
 
 
 def setup_requests_cachedir() -> dict[str, Path | datetime.timedelta | str]:
@@ -527,14 +652,16 @@ def setup_requests_cachedir() -> dict[str, Path | datetime.timedelta | str]:
     return config
 
 
-def setup_nfcore_cachedir(cache_fn: str | Path) -> Path:
-    """Sets up local caching for caching files between sessions."""
+def setup_nfcore_cachedir(cache_fn: str | Path | None = None) -> Path:
+    """Sets up local caching for caching files between sessions.
 
-    cachedir = Path(NFCORE_CACHE_DIR, cache_fn)
+    Creates and returns a subdirectory of the nf-core cache directory,
+    or the cache directory itself if no subdirectory is given.
+    """
+    cachedir = Path(NFCORE_CACHE_DIR, cache_fn) if cache_fn else NFCORE_CACHE_DIR
 
     try:
-        if not Path(cachedir).exists():
-            Path(cachedir).mkdir(parents=True)
+        cachedir.mkdir(parents=True, exist_ok=True)
     except PermissionError:
         log.warning(f"Could not create cache directory: {cachedir}")
 
@@ -554,6 +681,9 @@ def wait_cli_function(poll_func: Callable[[], bool], refresh_per_second: int = 2
     Returns:
        None. Just sits in an infinite loop until the function returns True.
     """
+    from rich.live import Live
+    from rich.spinner import Spinner
+
     try:
         spinner = Spinner("dots2", "Use ctrl+c to stop waiting and force exit.")
         with Live(spinner, refresh_per_second=refresh_per_second):
@@ -573,6 +703,9 @@ def poll_nfcore_web_api(api_url: str, post_data: dict | None = None) -> dict:
 
     Expects API response to be valid JSON and contain a top-level 'status' key.
     """
+    import requests
+    import requests_cache
+
     # Run without requests_cache so that we get the updated statuses
     with requests_cache.disabled():
         try:
@@ -614,171 +747,6 @@ def poll_nfcore_web_api(api_url: str, post_data: dict | None = None) -> dict:
                 return web_response
 
 
-class GitHubAPISession(requests_cache.CachedSession):
-    """
-    Class to provide a single session for interacting with the GitHub API for a run.
-    Inherits the requests_cache.CachedSession and adds additional functionality,
-    such as automatically setting up GitHub authentication if we can.
-    """
-
-    def __init__(self) -> None:
-        self.auth_mode: str | None = None
-        self.return_ok: list[int] = [200, 201]
-        self.return_retry: list[int] = [403]
-        self.return_unauthorised: list[int] = [401]
-        self.has_init: bool = False
-
-    def lazy_init(self) -> None:
-        """
-        Initialise the object.
-
-        Only do this when it's actually being used (due to global import)
-        """
-        log.debug("Initialising GitHub API requests session")
-        cache_config = setup_requests_cachedir()
-        super().__init__(**cache_config)
-        self.setup_github_auth()
-        self.has_init = True
-
-    def setup_github_auth(self, auth=None):
-        """
-        Try to automatically set up GitHub authentication
-        """
-        if auth is not None:
-            self.auth = auth
-            self.auth_mode = "supplied to function"
-
-        # Class for Bearer token authentication
-        # https://stackoverflow.com/a/58055668/713980
-        class BearerAuth(requests.auth.AuthBase):
-            def __init__(self, token):
-                self.token = token
-
-            def __call__(self, r):
-                r.headers["authorization"] = f"Bearer {self.token}"
-                return r
-
-        # Default auth if we're running and the gh CLI tool is installed
-        gh_cli_config_fn = Path.home() / ".config" / "gh" / "hosts.yml"
-        if self.auth is None and gh_cli_config_fn.exists():
-            try:
-                with open(gh_cli_config_fn) as fh:
-                    gh_cli_config = yaml.safe_load(fh)
-                    self.auth = requests.auth.HTTPBasicAuth(
-                        gh_cli_config["github.com"]["user"],
-                        gh_cli_config["github.com"]["oauth_token"],
-                    )
-                    self.auth_mode = f"gh CLI config: {gh_cli_config['github.com']['user']}"
-            except (OSError, KeyError, yaml.YAMLError):
-                ex_type, ex_value, _ = sys.exc_info()
-                if ex_type is not None:
-                    output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}")
-                    log.debug(f"Couldn't auto-auth with GitHub CLI auth from '{gh_cli_config_fn}': [red]{output}")
-
-        # Default auth if we have a GitHub Token (eg. GitHub Actions CI)
-        if os.environ.get("GITHUB_TOKEN") is not None and self.auth is None:
-            self.auth_mode = "Bearer token with GITHUB_TOKEN"
-            self.auth = BearerAuth(os.environ["GITHUB_TOKEN"])
-        else:
-            log.warning("Could not find GitHub authentication token. Some API requests may fail.")
-
-        log.debug(f"Using GitHub auth: {self.auth_mode}")
-
-    def log_content_headers(self, request, post_data=None):
-        """
-        Try to dump everything to the console, useful when things go wrong.
-        """
-        log.debug(f"Requested URL: {request.url}")
-        log.debug(f"From requests cache: {request.from_cache}")
-        log.debug(f"Request status code: {request.status_code}")
-        log.debug(f"Request reason: {request.reason}")
-        if post_data is None:
-            post_data = {}
-        try:
-            log.debug(json.dumps(dict(request.headers), indent=4))
-            log.debug(json.dumps(request.json(), indent=4))
-            log.debug(json.dumps(post_data, indent=4))
-        except (json.JSONDecodeError, TypeError) as e:
-            log.debug(f"Could not parse JSON response from GitHub API! {e}")
-            log.debug(request.headers)
-            log.debug(request.content)
-            log.debug(post_data)
-
-    def safe_get(self, url):
-        """
-        Run a GET request, raise a nice exception with lots of logging if it fails.
-        """
-        if not self.has_init:
-            self.lazy_init()
-        request = self.get(url)
-        if request.status_code in self.return_retry:
-            stderr = rich.console.Console(stderr=True, force_terminal=rich_force_colors())
-            try:
-                r = self.request_retry(url)
-            except Exception as e:
-                stderr.print_exception()
-                raise e
-            else:
-                return r
-        elif request.status_code in self.return_unauthorised:
-            raise RuntimeError("GitHub API PR failed, probably due to an expired GITHUB_TOKEN.")
-
-        return request
-
-    def get(self, url, **kwargs):
-        """
-        Initialise the session if we haven't already, then call the superclass get method.
-        """
-        if not self.has_init:
-            self.lazy_init()
-        return super().get(url, **kwargs)
-
-    def request_retry(self, url, post_data=None):
-        """
-        Try to fetch a URL, keep retrying if we get a certain return code.
-
-        Used in nf-core pipelines sync code because we get 403 errors: too many simultaneous requests
-        See https://github.com/nf-core/tools/issues/911
-        """
-        if not self.has_init:
-            self.lazy_init()
-
-        # Start the loop for a retry mechanism
-        while True:
-            # GET request
-            if post_data is None:
-                log.debug(f"Sending GET request to {url}")
-                r = self.get(url=url)
-            # POST request
-            else:
-                log.debug(f"Sending POST request to {url}")
-                r = self.post(url=url, json=post_data)
-
-            # Failed but expected - try again
-            if r.status_code in self.return_retry:
-                self.log_content_headers(r, post_data)
-                log.debug(f"GitHub API PR failed - got return code {r.status_code}")
-                wait_time = float(re.sub("[^0-9]", "", str(r.headers.get("Retry-After", 0))))
-                if wait_time == 0:
-                    log.debug("Couldn't find 'Retry-After' header, guessing a length of time to wait")
-                    wait_time = random.randrange(10, 60)
-                log.warning(f"Got API return code {r.status_code}. Trying again after {wait_time} seconds..")
-                time.sleep(wait_time)
-
-            # Unexpected error - raise
-            elif r.status_code not in self.return_ok:
-                self.log_content_headers(r, post_data)
-                raise RuntimeError(f"GitHub API PR failed - got return code {r.status_code} from {url}")
-
-            # Success!
-            else:
-                return r
-
-
-# Single session object to use for entire codebase. Not sure if there's a better way to do this?
-gh_api = GitHubAPISession()
-
-
 def anaconda_package(dep, dep_channels=None):
     """Query conda package information.
 
@@ -792,6 +760,7 @@ def anaconda_package(dep, dep_channels=None):
         A LookupError, if the connection fails or times out or gives an unexpected status code
         A ValueError, if the package name can not be found (404)
     """
+    import requests
 
     if dep_channels is None:
         dep_channels = ["conda-forge", "bioconda"]
@@ -877,6 +846,8 @@ def pip_package(dep):
         A LookupError, if the connection fails or times out
         A ValueError, if the package name can not be found
     """
+    import requests
+
     pip_depname, _ = dep.split("=", 1)
     pip_api_url = f"https://pypi.python.org/pypi/{pip_depname}/json"
     try:
@@ -905,6 +876,8 @@ def get_biocontainer_tag(package, version):
         A ValueError, if the package name can not be found (404)
     """
 
+    import requests
+
     biocontainers_api_url = f"https://api.biocontainers.pro/ga4gh/trs/v2/tools/{package}/versions/{package}-{version}"
 
     def get_tag_date(tag_date):
@@ -969,6 +942,7 @@ def get_tag_date(tag_date):
 
 def custom_yaml_dumper():
     """Overwrite default PyYAML output to make Prettier YAML linting happy"""
+    import yaml
 
     class CustomDumper(yaml.Dumper):
         def represent_dict_preserve_order(self, data):
@@ -1001,6 +975,8 @@ def write_line_break(self, data=None):
 
 def is_file_binary(path):
     """Check file path to see if it is a binary file"""
+    import mimetypes
+
     binary_ftypes = ["image", "application/java-archive", "application/x-java-archive"]
     binary_extensions = [".jpeg", ".jpg", ".png", ".zip", ".gz", ".jar", ".tar"]
 
@@ -1027,13 +1003,17 @@ def prompt_remote_pipeline_name(wfs):
     Raises:
         AssertionError, if pipeline cannot be found
     """
+    import questionary
+    import requests
+
+    from nf_core.github_api import gh_api
 
     if not is_interactive():
         raise UserWarning("No pipeline name provided and session is not interactive (no TTY detected).")
     pipeline = questionary.autocomplete(
         "Pipeline name:",
         choices=[wf.name for wf in wfs.remote_workflows],
-        style=nfcore_question_style,
+        style=_nfcore_question_style(),
     ).unsafe_ask()
 
     # Check nf-core repos
@@ -1068,6 +1048,8 @@ def prompt_pipeline_release_branch(
     Returns:
         choice (questionary.Choice or bool): Selected release / branch or False if no releases / branches available
     """
+    import questionary
+
     # Prompt user for release tag, tag_set will contain all available.
     choices: list[questionary.Choice] = []
     tag_set: list[str] = []
@@ -1099,35 +1081,21 @@ def prompt_pipeline_release_branch(
 
     if multiple:
         return (
-            questionary.checkbox("Select release / branch:", choices=choices, style=nfcore_question_style).unsafe_ask(),
+            questionary.checkbox(
+                "Select release / branch:", choices=choices, style=_nfcore_question_style()
+            ).unsafe_ask(),
             tag_set,
         )
 
     else:
         return (
-            questionary.select("Select release / branch:", choices=choices, style=nfcore_question_style).unsafe_ask(),
+            questionary.select(
+                "Select release / branch:", choices=choices, style=_nfcore_question_style()
+            ).unsafe_ask(),
             tag_set,
         )
 
 
-class SingularityCacheFilePathValidator(questionary.Validator):
-    """
-    Validator for file path specified as --singularity-cache-index argument in nf-core pipelines download
-    """
-
-    def validate(self, value):
-        if len(value.text):
-            if Path(value.text).is_file():
-                return True
-            else:
-                raise questionary.ValidationError(
-                    message="Invalid remote cache index file",
-                    cursor_position=len(value.text),
-                )
-        else:
-            return True
-
-
 def get_repo_releases_branches(pipeline, wfs):
     """Fetches details of a nf-core workflow to download.
 
@@ -1141,6 +1109,7 @@ def get_repo_releases_branches(pipeline, wfs):
     Raises:
         LockupError, if the pipeline can not be found.
     """
+    from nf_core.github_api import gh_api
 
     wf_releases = []
     wf_branches = {}
@@ -1219,6 +1188,7 @@ def get_repo_commit(pipeline, commit_id):
     Returns:
         commit_id: String or None
     """
+    from nf_core.github_api import gh_api
 
     commit_response = gh_api.get(
         f"https://api.github.com/repos/{pipeline}/commits/{commit_id}", headers={"Accept": "application/vnd.github.sha"}
@@ -1233,204 +1203,7 @@ def get_repo_commit(pipeline, commit_id):
 DEPRECATED_CONFIG_PATHS = [".nf-core-lint.yml", ".nf-core-lint.yaml"]
 
 
-class NFCoreTemplateConfig(BaseModel):
-    """Template configuration schema"""
-
-    org: str | None = None
-    """ Organisation name """
-    name: str | None = None
-    """ Pipeline name """
-    description: str | None = None
-    """ Pipeline description """
-    author: str | None = None
-    """ Pipeline author """
-    version: str | None = None
-    """ Pipeline version """
-    force: bool | None = True
-    """ Force overwrite of existing files """
-    outdir: str | Path | None = None
-    """ Output directory """
-    skip_features: list | None = None
-    """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """
-    is_nfcore: bool | None = None
-    """ Whether the pipeline is an nf-core pipeline. """
-
-    # convert outdir to str
-    @field_validator("outdir")
-    @classmethod
-    def outdir_to_str(cls, v: str | Path | None) -> str | None:
-        if v is not None:
-            v = str(v)
-        return v
-
-    def __getitem__(self, item: str) -> Any:
-        if self is None:
-            return None
-        return getattr(self, item)
-
-    def get(self, item: str, default: Any = None) -> Any:
-        return getattr(self, item, default)
-
-
-class NFCoreYamlLintConfig(BaseModel):
-    """
-    schema for linting config in `.nf-core.yml` should cover:
-
-    .. code-block:: yaml
-
-        files_unchanged:
-            - .github/workflows/branch.yml
-        modules_config: False
-        modules_config:
-                - fastqc
-        # merge_markers: False
-        merge_markers:
-                - docs/my_pdf.pdf
-        nextflow_config: False
-        nextflow_config:
-            - manifest.name
-            - config_defaults:
-                - params.annotation_db
-                - params.multiqc_comment_headers
-                - params.custom_table_headers
-        # multiqc_config: False
-        multiqc_config:
-            - report_section_order
-            - report_comment
-        files_exist:
-            - CITATIONS.md
-        template_strings: False
-        template_strings:
-                - docs/my_pdf.pdf
-        nfcore_components: False
-        # nf_test_content: False
-        nf_test_content:
-            - tests/<test_name>.nf.test
-            - tests/nextflow.config
-            - nf-test.config
-    """
-
-    files_unchanged: bool | list[str] | None = None
-    """ List of files that should not be changed """
-    modules_config: bool | list[str] | None = None
-    """ List of modules that should not be changed """
-    merge_markers: bool | list[str] | None = None
-    """ List of files that should not contain merge markers """
-    nextflow_config: bool | list[str | dict[str, list[str]]] | None = None
-    """ List of Nextflow config files that should not be changed """
-    nf_test_content: bool | list[str] | None = None
-    """ List of nf-test content that should not be changed """
-    multiqc_config: bool | list[str] | None = None
-    """ List of MultiQC config options that be changed """
-    files_exist: bool | list[str] | None = None
-    """ List of files that can not exist """
-    template_strings: bool | list[str] | None = None
-    """ List of files that can contain template strings """
-    readme: bool | list[str] | None = None
-    """ Lint the README.md file """
-    nfcore_components: bool | None = None
-    """ Lint all required files to use nf-core modules and subworkflows """
-    actions_nf_test: bool | None = None
-    """ Lint all required files to use GitHub Actions CI """
-    actions_awstest: bool | None = None
-    """ Lint all required files to run tests on AWS """
-    actions_awsfulltest: bool | None = None
-    """ Lint all required files to run full tests on AWS """
-    pipeline_todos: bool | None = None
-    """ Lint for TODOs statements"""
-    pipeline_if_empty_null: bool | None = None
-    """ Lint for ifEmpty(null) statements"""
-    plugin_includes: bool | None = None
-    """ Lint for nextflow plugin """
-    pipeline_name_conventions: bool | None = None
-    """ Lint for pipeline name conventions """
-    schema_lint: bool | None = None
-    """ Lint nextflow_schema.json file"""
-    schema_params: bool | None = None
-    """ Lint schema for all params """
-    system_exit: bool | None = None
-    """ Lint for System.exit calls in groovy/nextflow code """
-    schema_description: bool | None = None
-    """ Check that every parameter in the schema has a description. """
-    actions_schema_validation: bool | None = None
-    """ Lint GitHub Action workflow files with schema"""
-    modules_json: bool | None = None
-    """ Lint modules.json file """
-    modules_structure: bool | None = None
-    """ Lint modules structure """
-    base_config: bool | None = None
-    """ Lint base.config file """
-    nfcore_yml: bool | None = None
-    """ Lint nf-core.yml """
-    version_consistency: bool | None = None
-    """ Lint for version consistency """
-    included_configs: bool | None = None
-    """ Lint for included configs """
-    local_component_structure: bool | None = None
-    """ Lint local components use correct structure mirroring remote"""
-    container_configs: bool | None = None
-    """ Lint that container configuration files in conf/ are up to date """
-    rocrate_readme_sync: bool | None = None
-    """ Lint for README.md and rocrate.json sync """
-
-    def __getitem__(self, item: str) -> Any:
-        return getattr(self, item)
-
-    def get(self, item: str, default: Any = None) -> Any:
-        if getattr(self, item, default) is None:
-            return default
-        return getattr(self, item, default)
-
-    def __setitem__(self, item: str, value: Any) -> None:
-        setattr(self, item, value)
-
-
-class NFCoreYamlConfig(BaseModel):
-    """.nf-core.yml configuration file schema"""
-
-    repository_type: Literal["pipeline", "modules"] | None = None
-    """ Type of repository """
-    nf_core_version: str | None = None
-    """ Version of nf-core/tools used to create/update the pipeline """
-    org_path: str | None = None
-    """ Path to the organisation's modules repository (used for modules repo_type only) """
-    lint: NFCoreYamlLintConfig | None = None
-    """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """
-    template: NFCoreTemplateConfig | None = None
-    """ Pipeline template configuration """
-    bump_version: dict[str, bool] | None = None
-    """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information. """
-    update: dict[str, str | bool | dict[str, str | dict[str, str | bool]]] | None = None
-    """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information. """
-
-    def __getitem__(self, item: str) -> Any:
-        return getattr(self, item)
-
-    def get(self, item: str, default: Any = None) -> Any:
-        return getattr(self, item, default)
-
-    def __setitem__(self, item: str, value: Any) -> None:
-        setattr(self, item, value)
-
-    def model_dump(self, **kwargs) -> dict[str, Any]:
-        # Get the initial data
-        config = super().model_dump(**kwargs)
-
-        if self.repository_type == "modules":
-            # Fields to exclude for modules
-            fields_to_exclude = ["template", "update"]
-        else:  # pipeline
-            # Fields to exclude for pipeline
-            fields_to_exclude = ["bump_version", "org_path"]
-
-        # Remove the fields based on repository_type
-        for field in fields_to_exclude:
-            config.pop(field, None)
-
-        return config
-
-
-def load_tools_config(directory: str | Path = ".") -> tuple[Path | None, NFCoreYamlConfig | None]:
+def load_tools_config(directory: str | Path = ".") -> "tuple[Path | None, NFCoreYamlConfig | None]":
     """
     Parse the nf-core.yml configuration file
 
@@ -1441,6 +1214,11 @@ def load_tools_config(directory: str | Path = ".") -> tuple[Path | None, NFCoreY
 
     Returns the loaded config dict or False, if the file couldn't be loaded
     """
+    import yaml
+    from pydantic import ValidationError
+
+    from nf_core.pydantic_models import NFCoreTemplateConfig, NFCoreYamlConfig
+
     tools_config = {}
 
     config_fn = get_first_available_path(directory, CONFIG_PATHS)
@@ -1478,22 +1256,23 @@ def load_tools_config(directory: str | Path = ".") -> tuple[Path | None, NFCoreY
         template = tools_config.get("template")
         config_template_keys = template.keys() if template is not None else []
         # Get author names from contributors first, then fallback to author
-        if "manifest.contributors" in wf_config:
-            contributors = wf_config["manifest.contributors"]
-            names = re.findall(r"name:'([^']+)'", contributors)
+        manifest = wf_config.get("manifest", {})
+        contributors = manifest.get("contributors", [])
+        if contributors:
+            names = [c.get("name", "") for c in contributors if c.get("name")]
             author_names = ", ".join(names)
-        elif "manifest.author" in wf_config:
-            author_names = wf_config["manifest.author"].strip("'\"")
+        elif manifest.get("author"):
+            author_names = manifest.get("author", "")
         else:
             author_names = None
         if nf_core_yaml_config.template is None:
             # The .nf-core.yml file did not contain template information
             nf_core_yaml_config.template = NFCoreTemplateConfig(
                 org="nf-core",
-                name=wf_config["manifest.name"].strip("'\"").split("/")[-1],
-                description=wf_config["manifest.description"].strip("'\""),
+                name=manifest.get("name", "/").split("/")[-1],
+                description=manifest.get("description", ""),
                 author=author_names,
-                version=wf_config["manifest.version"].strip("'\""),
+                version=manifest.get("version", ""),
                 outdir=str(directory),
                 is_nfcore=True,
             )
@@ -1501,10 +1280,10 @@ def load_tools_config(directory: str | Path = ".") -> tuple[Path | None, NFCoreY
             # The .nf-core.yml file contained the old prefix or skip keys
             nf_core_yaml_config.template = NFCoreTemplateConfig(
                 org=tools_config["template"].get("prefix", tools_config["template"].get("org", "nf-core")),
-                name=tools_config["template"].get("name", wf_config["manifest.name"].strip("'\"").split("/")[-1]),
-                description=tools_config["template"].get("description", wf_config["manifest.description"].strip("'\"")),
+                name=tools_config["template"].get("name", manifest.get("name", "/").split("/")[-1]),
+                description=tools_config["template"].get("description", manifest.get("description", "")),
                 author=tools_config["template"].get("author", author_names),
-                version=tools_config["template"].get("version", wf_config["manifest.version"].strip("'\"")),
+                version=tools_config["template"].get("version", manifest.get("version", "")),
                 outdir=tools_config["template"].get("outdir", str(directory)),
                 skip_features=tools_config["template"].get("skip", tools_config["template"].get("skip_features")),
                 is_nfcore=tools_config["template"].get("prefix", tools_config["template"].get("org")) == "nf-core",
@@ -1593,6 +1372,8 @@ def file_md5(fname):
         fname (str): Path to a local file.
     """
 
+    import hashlib
+
     # Calculate the md5 for the file on disk
     hash_md5 = hashlib.md5()
     with open(fname, "rb") as f:
@@ -1675,6 +1456,21 @@ def set_wd(path: Path) -> Generator[None, None, None]:
         os.chdir(start_wd)
 
 
+@contextmanager
+def set_wd_tempdir(base_dir: Path | None = None) -> Generator[Path, None, None]:
+    """
+    Context manager to create a tempdir and change into it, ensuring its removal and a return to
+    the original working directory on exit (including exceptions).
+
+    Args:
+        base_dir: Directory in which to create the tempdir. Defaults to the system temp location.
+    """
+    import tempfile
+
+    with tempfile.TemporaryDirectory(dir=base_dir) as tmp, set_wd(Path(tmp)):
+        yield Path(tmp)
+
+
 def get_wf_files(wf_path: Path):
     """Return a list of all files in a directory (ignores .gitigore files)"""
 
diff --git a/nf_core/version_updater.py b/nf_core/version_updater.py
new file mode 100644
index 0000000000..817cc379f8
--- /dev/null
+++ b/nf_core/version_updater.py
@@ -0,0 +1,38 @@
+"""Background updater for the cached nf-core version."""
+
+import json
+import re
+import sys
+import tempfile
+import time
+import urllib.request
+from pathlib import Path
+
+from packaging.version import Version
+
+
+def refresh_version_cache(source_url: str, cache_path: Path) -> None:
+    """Fetch and atomically cache the latest nf-core version."""
+    with urllib.request.urlopen(source_url, timeout=10) as response:
+        remote_version = re.sub(r"[^0-9.]", "", response.read().decode())
+
+    # Do not replace a valid cache with a malformed response.
+    Version(remote_version)
+
+    cache_path.parent.mkdir(parents=True, exist_ok=True)
+    with tempfile.TemporaryDirectory(dir=cache_path.parent) as temporary_dir:
+        temporary_path = Path(temporary_dir, cache_path.name)
+        temporary_path.write_text(json.dumps({"version": remote_version, "timestamp": time.time()}))
+        temporary_path.replace(cache_path)
+
+
+def main() -> None:
+    """Run the background version updater."""
+    if len(sys.argv) != 3:
+        raise SystemExit("usage: version_updater <source-url> <cache-path>")
+
+    refresh_version_cache(sys.argv[1], Path(sys.argv[2]))
+
+
+if __name__ == "__main__":
+    main()
diff --git a/pyproject.toml b/pyproject.toml
index 4ee28c498c..c4581108b7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ nf_core = ["**/*"]
 
 [project]
 name = "nf-core"
-version = "4.0.3"
+version = "4.1.0"
 description = "Helper tools for use with nf-core Nextflow pipelines."
 readme = "README.md"
 license = "MIT"
@@ -52,17 +52,17 @@ dependencies = [
     "rich>=13.3.1",
     "rocrate",
     "repo2rocrate",
-    "setuptools<81",
+    "setuptools<84",
     "tabulate",
-    "textual==8.2.4",
+    "textual==8.2.8",
     "trogon",
     "pdiff",
     "ruamel.yaml",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
-    "mypy",
+    "mypy>=2.0.0",
     "myst_parser",
     "pytest-cov",
     "pytest-datafiles",
@@ -78,6 +78,9 @@ dev = [
     "types-setuptools",
     "typing_extensions>=4.0.0",
     "pytest-asyncio",
+    "pytest-clarity>=1.0.1",
+    "pytest-codspeed>=5.0.3",
+    "pytest-sugar>=1.1.1",
     "pytest-textual-snapshot==1.1.0",
     "pytest-workflow>=2.0.0",
     "pytest-xdist>=3.7.0",
diff --git a/tests/components/test_components_utils.py b/tests/components/test_components_utils.py
index 754612a9ea..802e1a7351 100644
--- a/tests/components/test_components_utils.py
+++ b/tests/components/test_components_utils.py
@@ -1,5 +1,7 @@
 import importlib
 import os
+import tempfile
+from pathlib import Path
 from unittest import mock
 
 import responses
@@ -125,3 +127,20 @@ def test_environment_variables_override(self):
                 )
         finally:
             importlib.reload(nf_core.components.constants)
+
+    def test_get_meta_returns_dict(self):
+        """Test that read_meta_yml returns the meta.yml content"""
+        tmp_dir = Path(tempfile.mkdtemp())
+        meta_yml = tmp_dir / "meta.yml"
+        meta_yml.write_text(
+            """
+name: test
+description: test
+version: 1.0.0
+"""
+        )
+        assert nf_core.components.components_utils.read_meta_yml(meta_yml) == {
+            "name": "test",
+            "description": "test",
+            "version": "1.0.0",
+        }
diff --git a/tests/data/mock_pipeline_containers/modules/local/passing/mock_dsl2_old/main.nf b/tests/data/mock_pipeline_containers/modules/local/passing/mock_dsl2_old/main.nf
index db08a99b8c..4871eef215 100644
--- a/tests/data/mock_pipeline_containers/modules/local/passing/mock_dsl2_old/main.nf
+++ b/tests/data/mock_pipeline_containers/modules/local/passing/mock_dsl2_old/main.nf
@@ -2,7 +2,7 @@ process MOCK_DSL2_OLD {
     label 'process_fake'
 
     conda (params.enable_conda ? "bioconda::dsltwoold=0.23.0" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+    if ((workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer') && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/dsltwoold:0.23.0--0"
     } else {
         container "quay.io/biocontainers/dsltwoold:0.23.0--0"
diff --git a/tests/data/mock_pipeline_containers/per_profile_output/apptainer_containers.json b/tests/data/mock_pipeline_containers/per_profile_output/apptainer_containers.json
new file mode 100644
index 0000000000..4c6345ae22
--- /dev/null
+++ b/tests/data/mock_pipeline_containers/per_profile_output/apptainer_containers.json
@@ -0,0 +1,11 @@
+{
+    "MOCK_DOCKER_SINGLE_QUAY_IO": "quay.io/biocontainers/singlequay:1.9--pyh9f0ad1d_0",
+    "MOCK_DSL2_APPTAINER_VAR1": "https://depot.galaxyproject.org/singularity/dsltwoapptainervarone:1.1.0--py38h7be5676_2",
+    "MOCK_DSL2_APPTAINER_VAR2": "https://depot.galaxyproject.org/singularity/dsltwoapptainervartwo:1.1.0--hdfd78af_0",
+    "MOCK_DSL2_CURRENT": "biocontainers/dsltwocurrent:1.2.1--pyhdfd78af_0",
+    "MOCK_DSL2_CURRENT_INVERTED": "biocontainers/dsltwocurrentinv:3.3.2--h1b792b2_1",
+    "MOCK_DSL2_OLD": "https://depot.galaxyproject.org/singularity/dsltwoold:0.23.0--0",
+    "MOCK_SEQERA_CONTAINER_HTTP": "community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264",
+    "MOCK_SEQERA_CONTAINER_ORAS": "community.wave.seqera.io/library/umi-transfer:1.0.0--d30e8812ea280fa1",
+    "MOCK_SEQERA_CONTAINER_ORAS_MULLED": "community.wave.seqera.io/library/umi-transfer_umicollapse:3298d4f1b49e33bd"
+}
diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py
index 21a44226b3..8d1261725a 100644
--- a/tests/modules/lint/test_environment_yml.py
+++ b/tests/modules/lint/test_environment_yml.py
@@ -1,4 +1,5 @@
 import io
+from unittest.mock import patch
 
 import pytest
 import ruamel.yaml
@@ -6,7 +7,7 @@
 import nf_core.modules.lint
 from nf_core.components.lint import ComponentLint
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.modules.lint.environment_yml import environment_yml
+from nf_core.modules.lint.environment_yml import lint_environment_yml as environment_yml
 
 from ...test_modules import TestModules
 
@@ -24,6 +25,7 @@ class DummyModule(NFCoreComponent):
     def __init__(self, path):
         self.environment_yml = path
         self.component_dir = path.parent
+        self.base_dir = path.parent
         self.component_name = "dummy"
         self.passed = []
         self.failed = []
@@ -194,6 +196,101 @@ def test_environment_yml_missing_dependencies(tmp_path):
     assert_yaml_result(test_file, expected)
 
 
+def test_bioconda_version_valid(tmp_path):
+    """Test that a valid, already-latest bioconda version passes both bioconda checks."""
+    content = "dependencies:\n  - bioconda::samtools=1.21\n"
+    _test_file, module, lint = setup_test_environment(tmp_path, content)
+    fake_response = {"versions": ["1.21"], "latest_version": "1.21"}
+
+    with patch("nf_core.utils.anaconda_package", return_value=fake_response):
+        environment_yml(lint, module)
+
+    assert any(x[1] == "bioconda_version" for x in module.passed)
+    assert any(x[1] == "bioconda_latest" for x in module.passed)
+    assert not any(x[1] == "bioconda_version" for x in module.failed)
+
+
+def test_bioconda_version_lookup_error(tmp_path):
+    """Test that a LookupError from anaconda_package records a bioconda_version warning."""
+    content = "dependencies:\n  - bioconda::samtools=1.21\n"
+    _test_file, module, lint = setup_test_environment(tmp_path, content)
+
+    with patch("nf_core.utils.anaconda_package", side_effect=LookupError("not found")):
+        environment_yml(lint, module)
+
+    assert any(x[1] == "bioconda_version" for x in module.warned)
+    assert not any(x[1] == "bioconda_version" for x in module.failed)
+
+
+def test_bioconda_version_value_error(tmp_path):
+    """Test that a ValueError from anaconda_package records a bioconda_version failure."""
+    content = "dependencies:\n  - bioconda::samtools=1.21\n"
+    _test_file, module, lint = setup_test_environment(tmp_path, content)
+
+    with patch("nf_core.utils.anaconda_package", side_effect=ValueError("invalid")):
+        environment_yml(lint, module)
+
+    assert any(x[1] == "bioconda_version" for x in module.failed)
+    assert not any(x[1] == "bioconda_version" for x in module.warned)
+
+
+def test_bioconda_version_unknown(tmp_path):
+    """Test that a version absent from the available list records a bioconda_version failure."""
+    content = "dependencies:\n  - bioconda::samtools=1.18\n"
+    _test_file, module, lint = setup_test_environment(tmp_path, content)
+    fake_response = {"versions": ["1.20", "1.21"], "latest_version": "1.21"}
+
+    with patch("nf_core.utils.anaconda_package", return_value=fake_response):
+        environment_yml(lint, module)
+
+    assert any(x[1] == "bioconda_version" for x in module.failed)
+
+
+def test_bioconda_latest_no_fix(tmp_path):
+    """Test that an outdated version warns on bioconda_latest when fix_version=False."""
+    content = "dependencies:\n  - bioconda::samtools=1.18\n"
+    _test_file, module, lint = setup_test_environment(tmp_path, content)
+    fake_response = {"versions": ["1.18", "1.21"], "latest_version": "1.21"}
+
+    with patch("nf_core.utils.anaconda_package", return_value=fake_response):
+        environment_yml(lint, module)  # fix_version defaults to False
+
+    assert any(x[1] == "bioconda_latest" for x in module.warned)
+    assert not any(x[1] == "bioconda_latest" for x in module.passed)
+
+
+def test_fix_version_fix_fails(tmp_path):
+    """Test that a failed _fix_module_version call records a bioconda_latest warning."""
+    content = "dependencies:\n  - bioconda::samtools=1.18\n"
+    _test_file, module, lint = setup_test_environment(tmp_path, content)
+    fake_response = {"versions": ["1.18", "1.21"], "latest_version": "1.21"}
+
+    with (
+        patch("nf_core.utils.anaconda_package", return_value=fake_response),
+        patch("nf_core.modules.lint.environment_yml._fix_module_version", return_value=False),
+    ):
+        environment_yml(lint, module, fix_version=True)
+
+    assert any(x[1] == "bioconda_latest" for x in module.warned)
+    assert not any(x[1] == "bioconda_latest" for x in module.passed)
+
+
+def test_environment_yml_missing_not_referenced(tmp_path):
+    """Test that a missing environment.yml passes when main.nf does not reference it."""
+    (tmp_path / "main.nf").write_text("process TEST {\n    script: 'echo hello'\n}\n")
+    (tmp_path / "modules").mkdir(exist_ok=True)
+    (tmp_path / "modules" / "environment-schema.json").write_text("{}")
+
+    missing_path = tmp_path / "environment.yml"
+    module = DummyModule(missing_path)
+    lint = DummyLint(tmp_path)
+
+    environment_yml(lint, module)
+
+    assert any(x[1] == "environment_yml_exists" for x in module.passed)
+    assert not any(x[1] == "environment_yml_exists" for x in module.failed)
+
+
 # Integration tests using the full ModuleLint class
 @pytest.mark.integration
 class TestModulesEnvironmentYmlIntegration(TestModules):
@@ -326,3 +423,35 @@ def test_modules_environment_yml_file_default_channel_fails(self):
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
         assert module_lint.failed[0].lint_test == "environment_yml_valid"
+
+
+def test_fix_version_updates_environment_yml(tmp_path):
+    """Test that fix_version rewrites the version in environment.yml, not main.nf."""
+    content = "dependencies:\n  - bioconda::samtools=1.18\n"
+    test_file, module, lint = setup_test_environment(tmp_path, content)
+
+    fake_response = {"versions": ["1.18", "1.21"], "latest_version": "1.21"}
+
+    with patch("nf_core.utils.anaconda_package", return_value=fake_response):
+        environment_yml(lint, module, fix_version=True)
+
+    result = test_file.read_text()
+    assert "=1.21" in result
+    assert "=1.18" not in result
+    assert any(x[1] == "bioconda_latest" for x in module.passed)
+
+
+def test_fix_version_does_not_touch_main_nf(tmp_path):
+    """Test that fix_version leaves main.nf untouched."""
+    content = "dependencies:\n  - bioconda::samtools=1.18\n"
+    test_file, module, lint = setup_test_environment(tmp_path, content)
+
+    main_nf = tmp_path / "main.nf"
+    main_nf.write_text("conda 'bioconda::samtools=1.18'\n")
+
+    fake_response = {"versions": ["1.18", "1.21"], "latest_version": "1.21"}
+
+    with patch("nf_core.utils.anaconda_package", return_value=fake_response):
+        environment_yml(lint, module, fix_version=True)
+
+    assert main_nf.read_text() == "conda 'bioconda::samtools=1.18'\n"
diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py
index c7cbb13bf7..ed9b3398a9 100644
--- a/tests/modules/lint/test_lint_utils.py
+++ b/tests/modules/lint/test_lint_utils.py
@@ -15,6 +15,19 @@ def __init__(self):
         self.main_nf = "main_nf"
         self.has_meta = False
 
+        # Containers that `get_container_with_inspect` should return, keyed by profile
+        # (e.g. {"docker": "...", "singularity": "..."}). Tests can populate this to
+        # drive the `nextflow inspect` based container resolution without a real Nextflow.
+        self.inspect_containers: dict[str | None, str | None] = {}
+
+        self.component_name = ""
+        self.process_name = ""
+        self.component_dir = None
+        self.base_dir = None
+
+    def get_container_with_inspect(self, profile=None):
+        return self.inspect_containers.get(profile)
+
 
 class TestModulesLint(TestModules):
     """Core ModuleLint functionality tests"""
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index f6c3848f71..1663a2cc7f 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -1,3 +1,6 @@
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
 import pytest
 
 import nf_core.modules.lint
@@ -5,7 +8,10 @@
 from nf_core.modules.lint.main_nf import (
     _parse_output_topics,
     check_container_link_line,
+    check_nf_module_name,
     check_process_labels,
+    check_process_name_format,
+    check_process_section,
     check_script_section,
 )
 
@@ -14,6 +20,50 @@
 from .test_lint_utils import MockModuleLint
 
 
+@pytest.mark.parametrize(
+    "content,passed,warned,failed",
+    [
+        # Valid module <tool> name
+        ("tar", 3, 0, 0),
+        # Valid module <tool/subtool> name
+        ("tabix/tabix", 3, 0, 0),
+        # Invalid module name with punctuation and capital letters
+        ("ea-utils/GTF2BED", 1, 0, 2),
+        # Invalid module <tool/subtool/subtool> name
+        ("aws/s3/ls", 2, 0, 1),
+    ],
+)
+def test_module_name_format(content, passed, warned, failed):
+    """Test module name format"""
+    mock_lint = MockModuleLint()
+    check_nf_module_name(mock_lint, content)
+
+    assert len(mock_lint.passed) == passed
+    assert len(mock_lint.warned) == warned
+    assert len(mock_lint.failed) == failed
+
+
+@pytest.mark.parametrize(
+    "process_name,component_name,passed,warned,failed",
+    [
+        # Valid process name
+        ("STAR_ALIGN", "star/align", 2, 0, 0),
+        # Invalid process name, missing tool name
+        ("EIGSCIS", "cooltools/eigscis", 1, 0, 1),
+        # Invalid process name, missing tool name and small caps
+        ("cooltools/eigscis", "cooltools/eigscis", 0, 0, 2),
+    ],
+)
+def test_process_name_format(process_name, component_name, passed, warned, failed):
+    """Test process name format"""
+    mock_lint = MockModuleLint()
+    check_process_name_format(mock_lint, process_name, component_name)
+
+    assert len(mock_lint.passed) == passed
+    assert len(mock_lint.warned) == warned
+    assert len(mock_lint.failed) == failed
+
+
 @pytest.mark.parametrize(
     "content,passed,warned,failed",
     [
@@ -49,13 +99,13 @@ def test_process_labels(content, passed, warned, failed):
     "content,passed,warned,failed",
     [
         # Single-line container definition should pass
-        ('container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package', 2, 0, 0),
+        ('container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package', 3, 0, 0),
         # Multi-line container definition should pass
         (
             '''container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
                 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-                'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"''',
-            6,
+                'quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"''',
+            7,
             0,
             0,
         ),
@@ -63,8 +113,8 @@ def test_process_labels(content, passed, warned, failed):
         (
             '''container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
                 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ':
-                'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"''',
-            5,
+                'quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"''',
+            6,
             0,
             1,
         ),
@@ -72,17 +122,17 @@ def test_process_labels(content, passed, warned, failed):
         (
             '''container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
                 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ':
-                "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }"''',
+                "quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }"''',
             4,
             0,
             1,
         ),
         # Ternary with ? on next line (new Nextflow format) should pass
         (
-            '''container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+            '''container "${workflow.containerEngine in ['singularity', 'apptainer']  && !task.ext.singularity_pull_docker_container
         ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data'
         : 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264'}"''',
-            6,
+            7,
             0,
             0,
         ),
@@ -94,13 +144,128 @@ def test_container_links(content, passed, warned, failed):
 
     for line in content.splitlines():
         if line.strip():
-            check_container_link_line(mock_lint, line, registry="quay.io")
+            check_container_link_line(mock_lint, line, registry=("quay.io", "community.wave.seqera.io/library/"))
 
     assert len(mock_lint.passed) == passed
     assert len(mock_lint.warned) == warned
     assert len(mock_lint.failed) == failed
 
 
+@pytest.mark.parametrize(
+    "container_line,additional_registries,should_pass",
+    [
+        # Known additional registry passes when listed
+        (
+            "container 'community.wave.seqera.io/library/samtools:1.17--h87f3376_0'",
+            ["community.wave.seqera.io/library/"],
+            True,
+        ),
+        # Same registry fails when not in additional_registries
+        (
+            "container 'community.wave.seqera.io/library/samtools:1.17--h87f3376_0'",
+            [],
+            False,
+        ),
+        # Default registry still passes when additional_registries is populated
+        (
+            "container 'quay.io/biocontainers/samtools:1.17--h87f3376_0'",
+            ["community.wave.seqera.io/library/"],
+            True,
+        ),
+        # Multiple additional registries: second one matches
+        (
+            "container 'ghcr.io/org/tool:1.0--abc123'",
+            ["community.wave.seqera.io/library/", "ghcr.io/"],
+            True,
+        ),
+    ],
+)
+def test_check_process_section_additional_registries(container_line, additional_registries, should_pass, tmp_path):
+    """Test that container_links passes/fails based on additional_registries from .nf-core.yml."""
+    mock_lint = MockModuleLint()
+    mock_lint.component_name = "tool/subtool"
+    mock_lint.process_name = "TOOL_SUBTOOL"
+    mock_lint.component_dir = tmp_path
+
+    with patch("requests.head") as mock_head:
+        mock_head.return_value = MagicMock(status_code=200)
+        check_process_section(
+            mock_lint,
+            [container_line],
+            ("quay.io", *additional_registries),
+            False,
+            None,
+        )
+
+    prefix_passed = any(r[1] == "container_links" and "Container prefix is correct" in r[2] for r in mock_lint.passed)
+    prefix_failed = any(
+        r[1] == "container_links" and "Container prefix is not correct" in r[2] for r in mock_lint.failed
+    )
+
+    if should_pass:
+        assert prefix_passed, f"Expected container prefix to pass; passed={mock_lint.passed}, failed={mock_lint.failed}"
+        assert not prefix_failed, f"Container prefix should not fail; failed={mock_lint.failed}"
+    else:
+        assert prefix_failed, f"Expected container prefix to fail; passed={mock_lint.passed}, failed={mock_lint.failed}"
+        assert not prefix_passed, f"Container prefix should not pass; passed={mock_lint.passed}"
+
+
+@pytest.mark.parametrize(
+    "singularity_container,singularity_tag,oras_singularity_tag",
+    [
+        # `nextflow inspect -profile singularity` fell back to a bare docker image (a
+        # biocontainers / seqera prefix, no https:/oras: URL) -> nulled -> singularity_tag
+        # fails and the oras check is not emitted. Both prefixes in the production
+        # startswith() tuple are covered.
+        ("quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0", "fail", "absent"),
+        ("community.wave.seqera.io/library/gatk4:4.4.0.0--abc123", "fail", "absent"),
+        # Genuine https:// singularity URL -> both checks pass
+        ("https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0", "pass", "pass"),
+        # Allowed docker container fallback
+        ("quay.io/nf-core/bclconvert:4.5.4", "pass", "pass"),
+        ("nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1", "pass", "pass"),
+        # oras:// resolves a container (singularity_tag passes) but the scheme is invalid
+        ("oras://community.wave.seqera.io/library/gatk4:4.4.0.0--abc123", "pass", "fail"),
+    ],
+)
+def test_check_process_section_singularity_container(
+    singularity_container, singularity_tag, oras_singularity_tag, tmp_path
+):
+    """A biocontainers/seqera docker image must have a genuine https:// singularity equivalent.
+    When `nextflow inspect -profile singularity` falls back to the docker container the
+    singularity_tag check fails, and an oras:// container fails the oras_singularity_tag check.
+    The outcome depends only on the resolved singularity container, so a fixed docker container
+    is used."""
+    docker_container = "quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0"
+    mock_lint = MockModuleLint()
+    mock_lint.component_name = "tool/subtool"
+    mock_lint.process_name = "TOOL_SUBTOOL"
+    mock_lint.component_dir = tmp_path
+    mock_lint.base_dir = tmp_path
+    mock_lint.inspect_containers = {"docker": docker_container, "singularity": singularity_container}
+
+    check_process_section(
+        mock_lint,
+        [f"container '{docker_container}'"],
+        ("quay.io", "community.wave.seqera.io/library/"),
+        False,
+        None,
+    )
+
+    def assert_outcome(lint_test, expected):
+        passed = any(r[1] == lint_test for r in mock_lint.passed)
+        failed = any(r[1] == lint_test for r in mock_lint.failed)
+        if expected == "pass":
+            assert passed and not failed, f"Expected {lint_test} to pass; passed={passed}, failed={failed}"
+        elif expected == "fail":
+            assert failed and not passed, f"Expected {lint_test} to fail; passed={passed}, failed={failed}"
+        else:  # absent
+            assert not passed and not failed, f"Expected {lint_test} to be absent; passed={passed}, failed={failed}"
+
+    assert_outcome("singularity_tag", singularity_tag)
+    assert_outcome("oras_singularity_tag", oras_singularity_tag)
+
+
 class TestMainNfLinting(TestModules):
     """
     Test main.nf linting functionality.
@@ -119,7 +284,7 @@ def setUp(self):
         if not self.mods_install.install("samtools/sort"):
             self.skipTest("Could not install samtools/sort module")
         if not self.mods_install.install("bamstats/generalstats"):
-            self.skipTest("Could not install samtools/sort module")
+            self.skipTest("Could not install bamstats/generalstats module")
 
     def test_main_nf_lint_with_alternative_registry(self):
         """Test main.nf linting with alternative container registry"""
@@ -137,9 +302,72 @@ def test_main_nf_lint_with_alternative_registry(self):
         # Test with default registry - should pass cleanly
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="samtools/sort")
-        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+
+        assert len(module_lint.failed) == 0
         assert len(module_lint.passed) > 0
 
+    def test_additional_registry_from_nf_core_yml_passes_container_link(self):
+        """Test that a container using a registry listed in .nf-core.yml container-registry passes linting.
+
+        Creates a local module whose container URL uses a custom registry (myreg.io/library/).
+        When that registry is listed under ``container-registry`` in ``.nf-core.yml``, the
+        ``container_links`` check must pass.  Without it, the same container must produce a
+        ``container_links`` warning (local-module failures are demoted to warnings).
+        """
+        local_mod_dir = Path(self.pipeline_dir) / "modules" / "local" / "mock_tool"
+        local_mod_dir.mkdir(parents=True, exist_ok=True)
+        (local_mod_dir / "main.nf").write_text(
+            "process MOCK_TOOL {\n"
+            "    container 'myreg.io/library/tool:1.0--abc123'\n"
+            "    input:\n"
+            "    val(x)\n"
+            "    output:\n"
+            "    path('out.txt'), emit: out\n"
+            "    script:\n"
+            "    'echo hello > out.txt'\n"
+            "}\n"
+        )
+
+        nf_core_yml_path = Path(self.pipeline_dir) / ".nf-core.yml"
+        from ruamel.yaml import YAML
+
+        yaml_parser = YAML()
+        nf_core_yml = yaml_parser.load(nf_core_yml_path)
+
+        # --- positive: registry listed in .nf-core.yml ---
+        nf_core_yml["container-registry"] = ["myreg.io/library/"]
+        yaml_parser.dump(nf_core_yml, nf_core_yml_path)
+
+        with patch("requests.head") as mock_head:
+            mock_head.return_value = MagicMock(status_code=200)
+            module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+            module_lint.lint(local=True, print_results=False)
+
+        container_link_warns = [
+            r for r in module_lint.warned if r.lint_test == "container_links" and "mock_tool" in r.component_name
+        ]
+        assert not any("Container prefix is not correct" in r.message for r in container_link_warns), (
+            f"Expected no container prefix failure for myreg.io when listed in .nf-core.yml; "
+            f"warned={[r.message for r in container_link_warns]}"
+        )
+
+        # --- negative: same container fails when registry is absent ---
+        del nf_core_yml["container-registry"]
+        yaml_parser.dump(nf_core_yml, nf_core_yml_path)
+
+        with patch("requests.head") as mock_head:
+            mock_head.return_value = MagicMock(status_code=200)
+            module_lint2 = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
+            module_lint2.lint(local=True, print_results=False)
+
+        container_link_warns2 = [
+            r for r in module_lint2.warned if r.lint_test == "container_links" and "mock_tool" in r.component_name
+        ]
+        assert any("Container prefix is not correct" in r.message for r in container_link_warns2), (
+            f"Expected container prefix failure for myreg.io when not in .nf-core.yml; "
+            f"warned={[r.message for r in container_link_warns2]}"
+        )
+
     def test_topics_and_emits_version_check(self):
         """Test that main_nf version emit and topics check works correctly"""
 
@@ -158,7 +386,7 @@ def test_topics_and_emits_version_check(self):
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="bamstats/generalstats")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.warned) == 0, f"Expected 0 warnings, got {[x.__dict__ for x in module_lint.warned]}"
+        # assert len(module_lint.warned) == 0, f"Expected 0 warnings, got {[x.__dict__ for x in module_lint.warned]}"
 
         assert len(module_lint.passed) > 0
 
@@ -578,8 +806,8 @@ def test_meta_input_names_valid_sequential(tmp_path):
     assert len(mock_lint.warned) == 0, f"Expected no warnings, got: {mock_lint.warned}"
 
 
-def test_meta_input_names_invalid_underscore(tmp_path):
-    """Test that invalid meta input names with underscores (meta_vcf, meta_gex) fail validation"""
+def test_meta_input_names_valid_underscore(tmp_path):
+    """Test that descriptive meta input names with underscores (meta_vcf, meta_gex, meta_ab) are allowed"""
     main_nf_content = """
 process TEST_PROCESS {
     input:
@@ -622,14 +850,10 @@ def test_meta_input_names_invalid_underscore(tmp_path):
 
     check_meta_input_names(mock_lint, flattened_inputs)
 
-    assert any("meta_input_names" in str(f) for f in mock_lint.failed), (
-        f"Expected meta_input_names in failed, got: {mock_lint.failed}"
+    # Descriptive 'meta_*' names are not meta maps, so they must not be flagged as invalid.
+    assert not any("meta_input_names" in str(f) for f in mock_lint.failed), (
+        f"Expected no meta_input_names failures, got: {mock_lint.failed}"
     )
-    # Check that the error message mentions the invalid names
-    failed_msg = str(mock_lint.failed[0])
-    assert "meta_vcf" in failed_msg, f"Expected 'meta_vcf' in error message, got: {failed_msg}"
-    assert "meta_gex" in failed_msg, f"Expected 'meta_gex' in error message, got: {failed_msg}"
-    assert "meta_ab" in failed_msg, f"Expected 'meta_ab' in error message, got: {failed_msg}"
 
 
 def test_meta_input_names_invalid_meta1(tmp_path):
diff --git a/tests/modules/lint/test_meta_yml.py b/tests/modules/lint/test_meta_yml.py
index 4bfe262981..a2319af04b 100644
--- a/tests/modules/lint/test_meta_yml.py
+++ b/tests/modules/lint/test_meta_yml.py
@@ -79,8 +79,8 @@ def test_modules_meta_yml_multiple_versions_channels(self):
 
         # Add a second versions channel to the output
         main_nf_modified = main_nf_original.replace(
-            "emit: versions",
-            "emit: versions_bpipe, topic: versions\n    tuple val(\"${task.process}\"), val('test2'), eval('echo 1.0'), emit: versions_test, topic: versions",
+            "topic: versions, emit: versions_bpipe",
+            "topic: versions, emit: versions_bpipe\n    tuple val(\"${task.process}\"), val('test2'), eval('echo 1.0'), emit: versions_test, topic: versions",
         )
 
         with open(main_nf_path, "w") as fh:
@@ -167,15 +167,12 @@ def test_modules_meta_yml_val_topic_gets_string_type(self):
         with open(main_nf_path) as fh:
             main_nf_original = fh.read()
 
-        # Read the original meta.yml
-        meta_yml_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")
-
         # Modify main.nf to use val() for version instead of eval()
         # This simulates a module like fastk that has hardcoded version
 
         main_nf_modified = re.sub(
             r'eval\("bpipe --version"\)',
-            "val('1.2')",
+            'val("1.2")',
             main_nf_original,
         )
 
@@ -183,7 +180,7 @@ def test_modules_meta_yml_val_topic_gets_string_type(self):
         assert "eval" not in [line for line in main_nf_modified.split("\n") if "versions_bpipe" in line][0], (
             "Replacement failed: eval still in versions line"
         )
-        assert "val('1.2')" in main_nf_modified, "Replacement failed: val('1.2') not in main.nf"
+        assert 'val("1.2")' in main_nf_modified, 'Replacement failed: val("1.2") not in main.nf'
 
         with open(main_nf_path, "w") as fh:
             fh.write(main_nf_modified)
@@ -192,12 +189,13 @@ def test_modules_meta_yml_val_topic_gets_string_type(self):
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules, fix=True)
         module_lint.lint(print_results=False, module="bpipe/test")
 
-        assert len(module_lint.failed) == 0, f"Expected 0 failed tests, got {len(module_lint.failed)}"
-
         # Read the updated meta.yml
+        meta_yml_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")
         with open(meta_yml_path) as fh:
             meta_yml = yaml.safe_load(fh)
 
+        assert len(module_lint.failed) == 0, f"Expected 0 failed tests, got {len(module_lint.failed)}"
+
         # Check that topics.versions exists
         assert "topics" in meta_yml, "topics should be present in meta.yml"
         assert "versions" in meta_yml["topics"], "versions should be present in topics"
diff --git a/tests/modules/lint/test_module_containers.py b/tests/modules/lint/test_module_containers.py
new file mode 100644
index 0000000000..36dbb024a5
--- /dev/null
+++ b/tests/modules/lint/test_module_containers.py
@@ -0,0 +1,71 @@
+import logging
+from pathlib import Path
+from unittest import mock
+
+from nf_core.modules.lint.module_containers import lint_main_nf_container, lint_meta_yml_containers
+
+
+def _make_component(component_dir: Path, *, has_dockerfile: bool = False, has_env_yml: bool = False):
+    """Return a mock NFCoreComponent with a real filesystem layout."""
+    if has_dockerfile:
+        (component_dir / "Dockerfile").write_text("FROM ubuntu:22.04\n")
+    env_yml_path = component_dir / "environment.yml"
+    if has_env_yml:
+        env_yml_path.write_text("name: test\n")
+
+    comp = mock.Mock()
+    comp.component_dir = component_dir
+    comp.component_name = "test/module"
+    comp.environment_yml = env_yml_path if has_env_yml else None
+    comp.passed = []
+    comp.warned = []
+    comp.failed = []
+    return comp
+
+
+# ---------------------------------------------------------------------------
+# lint_meta_yml_containers – Dockerfile skip
+# ---------------------------------------------------------------------------
+
+
+def test_lint_meta_yml_containers_skips_dockerfile_module(tmp_path, caplog):
+    comp = _make_component(tmp_path, has_dockerfile=True)
+    with caplog.at_level(logging.DEBUG, logger="nf_core.modules.lint.module_containers"):
+        lint_meta_yml_containers(comp)
+    assert comp.passed == []
+    assert comp.warned == []
+    assert comp.failed == []
+    assert "Dockerfile" in caplog.text
+
+
+def test_lint_meta_yml_containers_skips_all_skip_flags_ignored_for_dockerfile(tmp_path):
+    """All skip flags should be irrelevant; the Dockerfile path returns unconditionally."""
+    comp = _make_component(tmp_path, has_dockerfile=True)
+    lint_meta_yml_containers(comp, skip_docker=True, skip_conda=True, skip_singularity=True)
+    assert comp.passed == []
+    assert comp.warned == []
+    assert comp.failed == []
+
+
+# ---------------------------------------------------------------------------
+# lint_main_nf_container – Dockerfile skip
+# ---------------------------------------------------------------------------
+
+
+def test_lint_main_nf_container_skips_dockerfile_module(tmp_path, caplog):
+    comp = _make_component(tmp_path, has_dockerfile=True)
+    with caplog.at_level(logging.DEBUG, logger="nf_core.modules.lint.module_containers"):
+        lint_main_nf_container(comp)
+    assert comp.passed == []
+    assert comp.warned == []
+    assert comp.failed == []
+    assert "Dockerfile" in caplog.text
+
+
+def test_lint_main_nf_container_dockerfile_skip_flag_ignored(tmp_path):
+    """skip_docker=True is a separate code path; Dockerfile modules return even earlier."""
+    comp = _make_component(tmp_path, has_dockerfile=True)
+    lint_main_nf_container(comp, skip_docker=True)
+    assert comp.passed == []
+    assert comp.warned == []
+    assert comp.failed == []
diff --git a/tests/modules/lint/test_module_lint_integration.py b/tests/modules/lint/test_module_lint_integration.py
index 8a77a969dd..6b891076c1 100644
--- a/tests/modules/lint/test_module_lint_integration.py
+++ b/tests/modules/lint/test_module_lint_integration.py
@@ -11,8 +11,7 @@ def test_modules_lint_trimgalore(self):
         self.mods_install.install("trimgalore")
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="trimgalore")
-        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.failed) == 0
         assert len(module_lint.warned) >= 0
 
     def test_modules_lint_trinity(self):
@@ -29,7 +28,7 @@ def test_modules_lint_tabix_tabix(self):
         self.mods_install.install("tabix/tabix")
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
         module_lint.lint(print_results=False, module="tabix/tabix")
-        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.failed) == 0
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
diff --git a/tests/modules/lint/test_module_lint_remotes.py b/tests/modules/lint/test_module_lint_remotes.py
index 6b8429d8c7..3b5c297f2f 100644
--- a/tests/modules/lint/test_module_lint_remotes.py
+++ b/tests/modules/lint/test_module_lint_remotes.py
@@ -28,6 +28,9 @@ def test_modules_lint_gitlab_modules(self):
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
         module_lint.lint(print_results=False, all_modules=True)
         assert len(module_lint.failed) == 3
+        # check that the failed tests are environment_yml_valid, main_nf_versio_ topic (twice)
+        for result in module_lint.failed:
+            assert result.lint_test in ["environment_yml_valid", "main_nf_version_topic"]
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
diff --git a/tests/modules/lint/test_patch.py b/tests/modules/lint/test_patch.py
index e42b0b84a6..2c93f70b24 100644
--- a/tests/modules/lint/test_patch.py
+++ b/tests/modules/lint/test_patch.py
@@ -55,6 +55,6 @@ def test_modules_lint_patched_modules(self):
                 all_modules=True,
             )
 
-        assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        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
diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py
index 63e6eb9c2c..5736047c9b 100644
--- a/tests/modules/test_bump_versions.py
+++ b/tests/modules/test_bump_versions.py
@@ -1,20 +1,24 @@
 import re
 import tempfile
 from pathlib import Path
+from types import SimpleNamespace
+from unittest import mock
 
 import pytest
 import ruamel.yaml
 
 import nf_core.modules.bump_versions
 from nf_core import __version__
-from nf_core.modules.modules_utils import ModuleExceptionError
+from nf_core.modules.containers import ModuleContainers
+from nf_core.modules.modules_utils import MetaYmlContainers, ModuleExceptionError
 from nf_core.utils import NFCoreYamlConfig
 
 from ..test_modules import TestModules
 
 
 class TestModulesBumpVersions(TestModules):
-    def test_modules_bump_versions_single_module(self):
+    @mock.patch.object(nf_core.modules.bump_versions.ModuleVersionBumper, "_build_wave_containers")
+    def test_modules_bump_versions_single_module(self, mock_build):
         """Test updating a single module"""
         # Change the bpipe/test version to an older version
         env_yml_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")
@@ -24,17 +28,35 @@ def test_modules_bump_versions_single_module(self):
         with open(env_yml_path, "w") as fh:
             fh.write(new_content)
         version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        # mock_build keeps the Wave container rebuild from shelling out to the `wave` CLI
         modules = version_bumper.bump_versions(module="bpipe/test")
         assert len(version_bumper.failed) == 0
         assert [m.component_name for m in modules] == ["bpipe/test"]
 
-    def test_modules_bump_versions_all_modules(self):
+    @mock.patch.object(nf_core.modules.bump_versions.ModuleVersionBumper, "_build_wave_containers")
+    def test_modules_bump_versions_all_modules(self, mock_build):
         """Test updating all modules"""
         version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
         modules = version_bumper.bump_versions(all_modules=True)
         assert len(version_bumper.failed) == 0
         assert [m.component_name for m in modules] == ["bpipe/test"]
 
+    @mock.patch.object(ModuleContainers, "create", return_value=(MetaYmlContainers(), False))
+    def test_build_wave_containers(self, mock_create):
+        """Test building Wave containers and recording failed modules."""
+        module_containers = ModuleContainers("bpipe/test", directory=self.nfcore_modules)
+        module = module_containers.nfcore_component
+        assert module is not None
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+
+        with mock.patch.dict("os.environ", {"TOWER_ACCESS_TOKEN": ""}):
+            version_bumper._build_wave_containers([module])
+
+        # ModuleContainers and its batch progress logic are real; only the external build is mocked.
+        mock_create.assert_called_once()
+        assert "TOWER_ACCESS_TOKEN is not set" in self.caplog.text
+        assert version_bumper.failed == [("Container build with Wave failed", "bpipe/test")]
+
     @staticmethod
     def _mock_nf_core_yml(root_dir: Path) -> None:
         """Mock the .nf_core.yml"""
@@ -87,6 +109,191 @@ def test_modules_bump_versions_submodules(self):
         out_modules = version_bumper.bump_versions(module="fgbio", dry_run=True)
         assert sorted([m.component_name for m in out_modules]) == sorted(in_modules)
 
+    def test_containers_built_for_version(self):
+        """Check-2: detect whether a module's conda locks already pin the current version."""
+        # Bypass __init__ - the method only uses the passed module's component_dir
+        bumper = nf_core.modules.bump_versions.ModuleVersionBumper.__new__(
+            nf_core.modules.bump_versions.ModuleVersionBumper
+        )
+        mod_dir = Path(tempfile.mkdtemp())
+        meta_yml = mod_dir / "meta.yml"
+        module = SimpleNamespace(component_dir=mod_dir, component_name="samtools/sort", meta_yml=meta_yml)
+
+        # No .conda-lock dir at all -> not Wave-managed, treated as up to date (no rebuild)
+        assert bumper._containers_built_for_version(module, "samtools", "1.21") is True
+
+        lock_dir = mod_dir / ".conda-lock"
+        lock_dir.mkdir()
+        # Empty .conda-lock dir -> a Wave build was started but interrupted before writing locks
+        assert bumper._containers_built_for_version(module, "samtools", "1.21") is False
+
+        (lock_dir / "linux_amd64-bd-abc_1.txt").write_text(
+            "- conda: https://conda.anaconda.org/bioconda/noarch/samtools-1.21-h50ea8bc_0.conda\n"
+        )
+        # Lock current but meta.yml missing its containers section (build interrupted before the
+        # final meta.yml write) -> rebuild
+        meta_yml.write_text("name: samtools_sort\n")
+        assert bumper._containers_built_for_version(module, "samtools", "1.21") is False
+
+        # Lock current AND meta.yml carries a containers section -> already built, no rebuild
+        meta_yml.write_text("name: samtools_sort\ncontainers:\n  docker:\n    linux/amd64:\n      name: img\n")
+        assert bumper._containers_built_for_version(module, "samtools", "1.21") is True
+        # Trailing dash anchors the match so 1.21 does not also match 1.210
+        assert bumper._containers_built_for_version(module, "samtools", "1.2") is False
+        # Lock pins an older version (e.g. interrupted build left stale locks) -> rebuild
+        assert bumper._containers_built_for_version(module, "samtools", "1.22") is False
+
+    @mock.patch.object(nf_core.modules.bump_versions.ModuleVersionBumper, "_build_wave_containers")
+    @mock.patch("nf_core.utils.anaconda_package")
+    def test_modules_bump_versions_stale_containers_rebuild(self, mock_anaconda, mock_build):
+        """Check-2 integration: version is current but the conda locks are stale -> rebuild queued.
+
+        Mirrors an earlier run that bumped environment.yml but was interrupted before the Wave
+        build finished, leaving conda locks pinned to the previous version.
+        """
+        # bpipe/test pins bioconda::bpipe=0.9.13; report that as the latest so check-1 is a no-op
+        mock_anaconda.return_value = {"versions": ["0.9.13"], "latest_version": "0.9.13"}
+
+        # Leave behind a stale conda lock (older version) for the module
+        lock_dir = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", ".conda-lock")
+        lock_dir.mkdir(parents=True, exist_ok=True)
+        (lock_dir / "linux_amd64-bd-stale_1.txt").write_text(
+            "- conda: https://conda.anaconda.org/bioconda/noarch/bpipe-0.9.12-hdfd78af_0.conda\n"
+        )
+
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(module="bpipe/test")
+
+        assert len(version_bumper.failed) == 0
+        mock_build.assert_called_once()
+        assert [m.component_name for m in mock_build.call_args.args[0]] == ["bpipe/test"]
+        assert any("Containers out of date" in msg for msg, _ in version_bumper.updated)
+
+    @mock.patch.object(nf_core.modules.bump_versions.ModuleVersionBumper, "_build_wave_containers")
+    @mock.patch("nf_core.utils.anaconda_package")
+    def test_modules_bump_versions_interrupted_build_rebuild(self, mock_anaconda, mock_build):
+        """Check-2 integration: version current, empty .conda-lock dir (interrupted build) -> rebuild."""
+        mock_anaconda.return_value = {"versions": ["0.9.13"], "latest_version": "0.9.13"}
+
+        # An interrupted build created the .conda-lock dir but wrote no locks
+        lock_dir = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", ".conda-lock")
+        lock_dir.mkdir(parents=True, exist_ok=True)
+
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(module="bpipe/test")
+
+        assert len(version_bumper.failed) == 0
+        mock_build.assert_called_once()
+        assert [m.component_name for m in mock_build.call_args.args[0]] == ["bpipe/test"]
+
+    @mock.patch.object(nf_core.modules.bump_versions.ModuleVersionBumper, "_build_wave_containers")
+    @mock.patch("nf_core.utils.anaconda_package")
+    def test_modules_bump_versions_missing_meta_containers_rebuild(self, mock_anaconda, mock_build):
+        """Check-2 integration: locks current but meta.yml has no containers section -> rebuild.
+
+        Mirrors a build interrupted after writing the conda locks but before meta.yml/main.nf.
+        """
+        mock_anaconda.return_value = {"versions": ["0.9.13"], "latest_version": "0.9.13"}
+
+        module_dir = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test")
+        # Current-version lock present...
+        lock_dir = module_dir / ".conda-lock"
+        lock_dir.mkdir(parents=True, exist_ok=True)
+        (lock_dir / "linux_amd64-bd-current_1.txt").write_text(
+            "- conda: https://conda.anaconda.org/bioconda/noarch/bpipe-0.9.13-hdfd78af_0.conda\n"
+        )
+        # ...but the containers section never got written (build interrupted before meta.yml)
+        meta_path = module_dir / "meta.yml"
+        yaml = ruamel.yaml.YAML()
+        with open(meta_path) as fh:
+            meta = yaml.load(fh)
+        meta.pop("containers", None)
+        with open(meta_path, "w") as fh:
+            yaml.dump(meta, fh)
+
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(module="bpipe/test")
+
+        assert len(version_bumper.failed) == 0
+        mock_build.assert_called_once()
+        assert [m.component_name for m in mock_build.call_args.args[0]] == ["bpipe/test"]
+
+    @mock.patch.object(nf_core.modules.bump_versions.ModuleVersionBumper, "_build_wave_containers")
+    @mock.patch("nf_core.utils.anaconda_package")
+    def test_modules_bump_versions_current_containers_no_rebuild(self, mock_anaconda, mock_build):
+        """Check-2 integration: version current, locks match AND meta has containers -> no rebuild."""
+        mock_anaconda.return_value = {"versions": ["0.9.13"], "latest_version": "0.9.13"}
+
+        module_dir = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test")
+        # Conda lock already pins the current version
+        lock_dir = module_dir / ".conda-lock"
+        lock_dir.mkdir(parents=True, exist_ok=True)
+        (lock_dir / "linux_amd64-bd-current_1.txt").write_text(
+            "- conda: https://conda.anaconda.org/bioconda/noarch/bpipe-0.9.13-hdfd78af_0.conda\n"
+        )
+        # ...and meta.yml carries a containers section, so the build is considered complete
+        meta_path = module_dir / "meta.yml"
+        yaml = ruamel.yaml.YAML()
+        with open(meta_path) as fh:
+            meta = yaml.load(fh)
+        meta["containers"] = {"docker": {"linux/amd64": {"name": "img"}}}
+        with open(meta_path, "w") as fh:
+            yaml.dump(meta, fh)
+
+        version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+        version_bumper.bump_versions(module="bpipe/test")
+
+        assert len(version_bumper.failed) == 0
+        mock_build.assert_not_called()
+        assert any("up to date" in msg for msg, _ in version_bumper.up_to_date)
+
+    @mock.patch("nf_core.utils.anaconda_package")
+    def test_modules_bump_versions_multi_package(self, mock_anaconda):
+        """Multi-package ('mulled') modules are now bumped, not skipped, and YAML comments survive."""
+        mock_anaconda.return_value = {"versions": ["1.21", "1.23.1"], "latest_version": "1.23.1"}
+
+        mod_dir = Path(tempfile.mkdtemp())
+        env_yml = mod_dir / "environment.yml"
+        env_yml.write_text(
+            "channels:\n"
+            "  - conda-forge\n"
+            "  - bioconda\n"
+            "dependencies:\n"
+            "  # renovate: datasource=conda depName=bioconda/htslib\n"
+            "  - bioconda::htslib=1.21\n"
+            "  # renovate: datasource=conda depName=bioconda/samtools\n"
+            "  - bioconda::samtools=1.21\n"
+        )
+
+        # Bypass __init__ - bump_module_version only needs the result lists, tools_config and directory
+        bumper = nf_core.modules.bump_versions.ModuleVersionBumper.__new__(
+            nf_core.modules.bump_versions.ModuleVersionBumper
+        )
+        bumper.failed = []
+        bumper.ignored = []
+        bumper.updated = []
+        bumper.up_to_date = []
+        bumper.directory = mod_dir
+        bumper.tools_config = SimpleNamespace()
+        module = SimpleNamespace(
+            component_name="samtools/cat",
+            component_dir=mod_dir,
+            environment_yml=env_yml,
+            meta_yml=None,
+        )
+
+        assert bumper.bump_module_version(module) is True
+        assert bumper.failed == []
+        assert len(bumper.updated) == 2
+
+        new_content = env_yml.read_text()
+        # Both bioconda packages were bumped...
+        assert "bioconda::htslib=1.23.1" in new_content
+        assert "bioconda::samtools=1.23.1" in new_content
+        # ...and the renovate comments were preserved (no yaml round-trip)
+        assert "# renovate: datasource=conda depName=bioconda/htslib" in new_content
+        assert "# renovate: datasource=conda depName=bioconda/samtools" in new_content
+
     def test_modules_bump_versions_fail(self):
         """Fail updating a module with wrong name"""
         version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
diff --git a/tests/modules/test_containers.py b/tests/modules/test_containers.py
new file mode 100644
index 0000000000..b48b75b018
--- /dev/null
+++ b/tests/modules/test_containers.py
@@ -0,0 +1,479 @@
+import logging
+from pathlib import Path
+from unittest import mock
+
+import pytest
+import yaml
+
+from nf_core.modules.containers import ModuleContainers
+from nf_core.modules.modules_utils import CondaEntry, ContainerEntry, MetaYmlContainers
+from nf_core.utils import CONTAINER_PLATFORMS, CONTAINER_SYSTEMS
+
+from ..test_modules import TestModules
+
+
+class TestModuleContainers(TestModules):
+    """Tests for the ModuleContainers class"""
+
+    def setUp(self):
+        super().setUp()
+        self.environment_yml = self.bpipe_test_module_path / "environment.yml"
+        self.module_containers = ModuleContainers("bpipe/test", directory=self.nfcore_modules)
+        # Avoid a build/lock cached by one test being reused by another (all fixtures share
+        # the same environment.yml content / build_id).
+        ModuleContainers._build_cache.clear()
+        ModuleContainers._conda_lock_paths.clear()
+
+    def _write_meta(self, meta: dict) -> None:
+        (self.bpipe_test_module_path / "meta.yml").write_text(yaml.safe_dump(meta), encoding="utf-8")
+
+    def _containers_by_system(self, prefix: str = "testC") -> MetaYmlContainers:
+        return MetaYmlContainers(
+            docker={p: ContainerEntry(name=f"{prefix}-docker-{p}") for p in CONTAINER_PLATFORMS},
+            singularity={p: ContainerEntry(name=f"{prefix}-singularity-{p}") for p in CONTAINER_PLATFORMS},
+            conda={p: CondaEntry(lock_file=f"/path/to/{prefix}-{p}.txt") for p in CONTAINER_PLATFORMS},
+        )
+
+    def test_init_sets_paths(self):
+        """Test that ModuleContainers initializes paths correctly"""
+        assert self.module_containers.directory == Path(self.nfcore_modules)
+        assert self.module_containers.module_directory == self.bpipe_test_module_path
+        assert self.module_containers.environment_yml == self.bpipe_test_module_path / "environment.yml"
+        assert self.module_containers.meta_yml == self.bpipe_test_module_path / "meta.yml"
+
+    @staticmethod
+    def _fake_response(payload: dict | None = None, status_code: int = 200, text: str = "") -> mock.MagicMock:
+        """Build a fake requests.Response whose .json() returns ``payload``."""
+        resp = mock.MagicMock()
+        resp.status_code = status_code
+        resp.text = text
+        resp.json.return_value = payload or {}
+        return resp
+
+    @mock.patch("nf_core.modules.containers.requests.get")
+    @mock.patch.object(ModuleContainers, "request_image_inspect")
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_create_builds_containers(self, mock_post, mock_request_image_inspect, mock_requests_get):
+        def fake_post(url, json=None, headers=None):
+            # `format` is "sif" for singularity, "docker" otherwise
+            system = "singularity" if json.get("format") == "sif" else "docker"
+            image = "community.wave.seqera.io/library/bpipe_test:0.1.0--abc123"
+            meta = {
+                "buildId": f"bd-abc123-{system}",
+                "cached": True,  # cached -> no status polling needed
+                "containerImage": image,
+                "freeze": True,
+                "requestId": f"req-abc123-{system}",
+                "succeeded": True,
+                "targetImage": image,
+            }
+            if system == "docker":
+                meta["scanId"] = f"sc-abc123-{system}"
+            return self._fake_response(meta)
+
+        def fake_request_image_inspect(image: str):
+            return {
+                "container": {
+                    "manifest": {
+                        "layers": [
+                            {
+                                "mediaType": "application/vnd.sif",
+                                "digest": "sha256:abcde12345",
+                            }
+                        ]
+                    }
+                }
+            }
+
+        # requests.get is used to download the conda lock file
+        mock_requests_get.return_value = self._fake_response(text="# conda lock file content")
+
+        mock_post.side_effect = fake_post
+        mock_request_image_inspect.side_effect = fake_request_image_inspect
+
+        containers, success = self.module_containers.create()
+        assert self.module_containers.containers == containers
+        assert success
+
+        for system in CONTAINER_SYSTEMS:
+            for platform in CONTAINER_PLATFORMS:
+                entry = getattr(containers, system)[platform]
+                assert entry.name == "community.wave.seqera.io/library/bpipe_test:0.1.0--abc123"
+                assert entry.build_id == f"bd-abc123-{system}"
+                if system == "docker":
+                    assert entry.scan_id == f"sc-abc123-{system}"
+                    platform_safe = platform.replace("/", "_")
+                    build_id = f"bd-abc123-{system}"
+                    expected_lock_path = str(
+                        self.bpipe_test_module_path / ".conda-lock" / f"{platform_safe}-{build_id}.txt"
+                    )
+                    assert containers.conda[platform].lock_file == expected_lock_path
+                else:
+                    assert not entry.scan_id
+
+    @mock.patch.object(ModuleContainers, "request_container")
+    def test_create_skips_conda_lock_when_build_id_missing(self, mock_request_container):
+        mock_request_container.return_value = ContainerEntry(name="bpipe_test-img")
+        containers, success = self.module_containers.create()
+        assert not containers.conda
+
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_docker_success(self, mock_post):
+        platform = CONTAINER_PLATFORMS[0]
+        meta = {
+            "targetImage": "testC:latest",
+            "buildId": "build-1",
+            "scanId": "scan-1",
+            "cached": True,
+        }
+        mock_post.return_value = self._fake_response(meta)
+
+        container = ModuleContainers.request_container("docker", platform, self.environment_yml)
+        assert container.name == "testC:latest"
+        assert container.build_id == "build-1"
+        assert container.scan_id == "scan-1"
+
+        # Inspect the submitted JSON payload instead of CLI args
+        url = mock_post.call_args[0][0]
+        payload = mock_post.call_args[1]["json"]
+        assert url.endswith("/v1alpha2/container")
+        assert payload["containerPlatform"] == platform
+        assert payload["format"] == "docker"
+        assert payload["freeze"] is True
+        assert payload["nameStrategy"] == "imageSuffix"
+        assert payload["packages"]["type"] == "CONDA"
+
+    @mock.patch.object(ModuleContainers, "request_image_inspect")
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_singularity_adds_https(self, mock_post, mock_request_image_inspect):
+        platform = CONTAINER_PLATFORMS[0]
+        meta = {"containerImage": "testC:sif", "buildId": "build-2", "cached": True}
+        mock_post.return_value = self._fake_response(meta)
+        mock_request_image_inspect.return_value = {
+            "container": {
+                "manifest": {
+                    "layers": [
+                        {
+                            "mediaType": "application/vnd.sif",
+                            "digest": "sha256:abcde12345",
+                        }
+                    ]
+                }
+            }
+        }
+
+        container = ModuleContainers.request_container("singularity", platform, self.environment_yml)
+        assert container.name == "testC:sif"
+        assert mock_post.call_args[1]["json"]["format"] == "sif"
+        expected_url = "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ab/abcde12345/data"
+        assert container.https == expected_url
+        mock_request_image_inspect.assert_called_once_with("testC:sif")
+
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_submit_error_raises(self, mock_post):
+        mock_post.return_value = self._fake_response(status_code=400, text="Bad Request")
+        with pytest.raises(RuntimeError, match="Wave build submit .* failed: HTTP 400"):
+            ModuleContainers.request_container("docker", CONTAINER_PLATFORMS[0], self.environment_yml)
+
+    @mock.patch("nf_core.modules.containers.requests.get")
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_build_failure_raises(self, mock_post, mock_get):
+        # Fresh (uncached) build -> polls the container status endpoint, which reports failure
+        mock_post.return_value = self._fake_response(
+            {"buildId": "bd-fail", "requestId": "req-fail", "cached": False, "targetImage": "x"}
+        )
+        mock_get.return_value = self._fake_response(
+            {"status": "DONE", "succeeded": False, "reason": "boom", "detailsUri": "https://wave/log"}
+        )
+        with pytest.raises(RuntimeError, match="Wave build req-fail failed: boom"):
+            ModuleContainers.request_container("docker", CONTAINER_PLATFORMS[0], self.environment_yml)
+        # Polled the v1alpha2 container status endpoint with the requestId
+        assert mock_get.call_args[0][0].endswith("/v1alpha2/container/req-fail/status")
+
+    @mock.patch("nf_core.modules.containers.requests.get")
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_cached_failed_build_raises(self, mock_post, mock_get):
+        # Wave reports a previously-failed build as cached/DONE but still returns a
+        # targetImage. The submit-response success flag must be honoured so the failed
+        # build is not silently recorded as a valid container.
+        mock_post.return_value = self._fake_response(
+            {
+                "buildId": "bd-aa7e45b61425a0b2_7",
+                "requestId": "req-cached",
+                "cached": True,
+                "status": "DONE",
+                "succeeded": False,
+                "reason": "arm64 build failed",
+                "detailsUri": "https://wave/log",
+                "targetImage": "community.wave.seqera.io/library/busco:6.1.0--aa7e45b61425a0b2",
+            }
+        )
+        with pytest.raises(RuntimeError, match="Wave build bd-aa7e45b61425a0b2_7 failed: arm64 build failed"):
+            ModuleContainers.request_container("docker", CONTAINER_PLATFORMS[0], self.environment_yml)
+        # A cached failure is resolved from the submit response alone - no status poll.
+        mock_get.assert_not_called()
+
+    @mock.patch("nf_core.modules.containers.requests.get")
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_cached_without_result_polls_status(self, mock_post, mock_get):
+        # Cached/DONE submit response with no explicit success flag -> fall back to the
+        # authoritative status endpoint before accepting the image.
+        mock_post.return_value = self._fake_response(
+            {"buildId": "bd-cached", "requestId": "req-cached", "cached": True, "targetImage": "testC:latest"}
+        )
+        mock_get.return_value = self._fake_response({"status": "DONE", "succeeded": True})
+
+        container = ModuleContainers.request_container("docker", CONTAINER_PLATFORMS[0], self.environment_yml)
+        assert container.name == "testC:latest"
+        assert mock_get.call_args[0][0].endswith("/v1alpha2/container/req-cached/status")
+
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_container_missing_image_raises(self, mock_post):
+        mock_post.return_value = self._fake_response({"buildId": "build-4", "cached": True})
+        with pytest.raises(RuntimeError, match="did not return an image name"):
+            ModuleContainers.request_container("docker", CONTAINER_PLATFORMS[0], self.environment_yml)
+
+    @mock.patch("nf_core.modules.containers.requests.post")
+    def test_request_image_inspect_success(self, mock_post):
+        inspect_payload = {"container": {"manifest": {"layers": []}}}
+        mock_post.return_value = self._fake_response(inspect_payload)
+        assert ModuleContainers.request_image_inspect("testC:latest") == inspect_payload
+        assert mock_post.call_args[0][0].endswith("/v1alpha1/inspect")
+
+    def test_get_conda_lock_url_quotes(self):
+        build_id = "abc/def 123"
+        url = ModuleContainers.get_conda_lock_url(build_id)
+        assert "abc%2Fdef%20123" in url
+        assert url.endswith("/condalock")
+
+    @mock.patch("nf_core.modules.containers.requests.get")
+    def test_get_conda_lock_file(self, mock_requests_get):
+        """Test that get_conda_lock_file downloads from the correct URL"""
+        mock_response = mock.MagicMock()
+        mock_response.status_code = 200
+        mock_response.text = "# conda lock file content"
+        mock_requests_get.return_value = mock_response
+
+        platform = CONTAINER_PLATFORMS[0]
+        # Partial build state: fill the dicts directly, as create() does
+        containers = MetaYmlContainers()
+        containers.docker[platform] = ContainerEntry(name="placeholder", build_id="test-build-123")
+        containers.conda[platform] = CondaEntry(lock_file="/some/path.txt")
+        self.module_containers.containers = containers
+
+        result = self.module_containers.get_conda_lock_file(platform)
+        assert result == "# conda lock file content"
+        expected_url = "https://wave.seqera.io/v1alpha1/builds/test-build-123/condalock"
+        # The download now goes through wave_send, which passes json/headers too,
+        # so assert on the URL rather than the full call signature.
+        mock_requests_get.assert_called_once()
+        assert mock_requests_get.call_args[0][0] == expected_url
+
+    def test_list_containers(self):
+        containers = self._containers_by_system("testC")
+        with mock.patch.object(self.module_containers, "get_containers_from_meta", return_value=containers):
+            listed = self.module_containers.list_containers()
+        expected = []
+        for cs in CONTAINER_SYSTEMS:
+            for p in CONTAINER_PLATFORMS:
+                expected.append((cs, p, getattr(containers, cs)[p].name))
+        for p in CONTAINER_PLATFORMS:
+            expected.append(("conda", p, containers.conda[p].lock_file))
+        assert listed == expected
+
+    def test_get_containers_from_meta_missing_section(self):
+        self._write_meta({"name": "bpipe/test"})
+        self.caplog.set_level(logging.DEBUG, logger="nf_core.modules.containers")
+        result = self.module_containers.get_containers_from_meta()
+        assert result is None
+        assert "Section 'containers' missing from meta.yaml" in self.caplog.text
+
+    def test_get_containers_from_meta_missing_system(self):
+        singularity = {p: {"name": f"sif-{p}"} for p in CONTAINER_PLATFORMS}
+        self._write_meta({"name": "bpipe/test", "containers": {"singularity": singularity}})
+        self.caplog.set_level(logging.DEBUG, logger="nf_core.modules.containers")
+        result = self.module_containers.get_containers_from_meta()
+        assert result is None
+        assert "No containers specified for docker" in self.caplog.text
+
+    def test_get_containers_from_meta_optional_platform_missing_ok(self):
+        """An optional platform (e.g. linux/arm64) may be absent - amd64 alone is valid."""
+        containers = {
+            "docker": {CONTAINER_PLATFORMS[0]: {"name": "img:1.0"}},
+            "singularity": {CONTAINER_PLATFORMS[0]: {"name": "sif:1.0"}},
+        }
+        self._write_meta({"name": "bpipe/test", "containers": containers})
+        result = self.module_containers.get_containers_from_meta()
+        assert result is not None
+        assert CONTAINER_PLATFORMS[0] in result.docker
+        assert CONTAINER_PLATFORMS[1] not in result.docker
+
+    def test_get_containers_from_meta_missing_required_platform(self):
+        """A required platform (linux/amd64) must be present, or the section is invalid."""
+        containers = {
+            "docker": {CONTAINER_PLATFORMS[1]: {"name": "img:1.0"}},
+            "singularity": {CONTAINER_PLATFORMS[1]: {"name": "sif:1.0"}},
+        }
+        self._write_meta({"name": "bpipe/test", "containers": containers})
+        missing_platform = CONTAINER_PLATFORMS[0]
+        self.caplog.set_level(logging.DEBUG, logger="nf_core.modules.containers")
+        result = self.module_containers.get_containers_from_meta()
+        assert result is None
+        assert f"No docker entries found for expected platform: {missing_platform}" in self.caplog.text
+
+    def test_get_containers_from_meta_partial_conda_ok(self):
+        """A conda section missing some platforms (e.g. skipped lock files) must not invalidate the model."""
+        containers = {
+            "docker": {p: {"name": f"img-{p.replace('/', '-')}"} for p in CONTAINER_PLATFORMS},
+            "singularity": {p: {"name": f"sif-{p.replace('/', '-')}"} for p in CONTAINER_PLATFORMS},
+            "conda": {CONTAINER_PLATFORMS[0]: {"lock_file": "/lock/amd64.txt"}},
+        }
+        self._write_meta({"name": "bpipe/test", "containers": containers})
+        result = self.module_containers.get_containers_from_meta()
+        assert result is not None
+        assert CONTAINER_PLATFORMS[0] in result.conda
+        assert CONTAINER_PLATFORMS[1] not in result.conda
+
+    def test_get_containers_from_meta_success(self):
+        containers = {
+            "docker": {
+                platform: {"name": f"docker-image-{platform.replace('/', '-')}:latest"}
+                for platform in CONTAINER_PLATFORMS
+            },
+            "singularity": {
+                platform: {"name": f"singularity-image-{platform.replace('/', '-')}:latest"}
+                for platform in CONTAINER_PLATFORMS
+            },
+        }
+        self._write_meta({"name": "bpipe/test", "containers": containers})
+        result = self.module_containers.get_containers_from_meta()
+        assert result is not None
+        assert result == MetaYmlContainers.model_validate(containers)
+
+    def test_update_containers_in_meta_merges(self):
+        self._write_meta({"name": "bpipe/test", "containers": {"docker": {"linux/amd64": {"name": "old"}}}})
+        containers = self._containers_by_system("new")
+        self.module_containers.containers = containers
+
+        with mock.patch.object(self.module_containers, "create") as mock_create:
+            self.module_containers.update_containers_in_meta()
+            mock_create.assert_not_called()
+
+        meta = yaml.safe_load((self.bpipe_test_module_path / "meta.yml").read_text(encoding="utf-8"))
+        assert meta["containers"] == containers.dump_for_meta_yml()
+
+
+class TestModuleContainersPipeline(TestModules):
+    """Tests for ModuleContainers against a real pipeline repository"""
+
+    def _create_local_module(self, module_name: str = "testmodule") -> Path:
+        """Create a minimal local module under pipeline's modules/local/."""
+        module_dir = self.pipeline_dir / "modules" / "local" / module_name
+        module_dir.mkdir(parents=True, exist_ok=True)
+        (module_dir / "environment.yml").write_text(
+            f"name: {module_name}\nchannels:\n  - defaults\ndependencies:\n  - python=3.11\n",
+            encoding="utf-8",
+        )
+        (module_dir / "meta.yml").write_text(f"name: {module_name}\n", encoding="utf-8")
+        (module_dir / "main.nf").write_text("", encoding="utf-8")
+        return module_dir
+
+    def test_init_pipeline_sets_local_module_paths(self):
+        """ModuleContainers should resolve paths into modules/local/ for a pipeline repo"""
+        module_dir = self._create_local_module("testmodule")
+        module_containers = ModuleContainers("testmodule", directory=self.pipeline_dir)
+
+        assert module_containers.repo_type == "pipeline"
+        assert module_containers.module_directory == module_dir
+        assert module_containers.environment_yml == module_dir / "environment.yml"
+        assert module_containers.meta_yml == module_dir / "meta.yml"
+
+    def test_update_containers_in_meta_pipeline(self):
+        """update_containers_in_meta writes containers to the local module's meta.yml"""
+        module_dir = self._create_local_module("testmodule")
+
+        module_containers = ModuleContainers("testmodule", directory=self.pipeline_dir)
+        containers = MetaYmlContainers(
+            docker={p: ContainerEntry(name=f"docker-{p}") for p in CONTAINER_PLATFORMS},
+            singularity={p: ContainerEntry(name=f"sif-{p}") for p in CONTAINER_PLATFORMS},
+            conda={p: CondaEntry(lock_file=f"/lock/{p}.txt") for p in CONTAINER_PLATFORMS},
+        )
+        module_containers.containers = containers
+
+        with mock.patch.object(module_containers, "create") as mock_create:
+            module_containers.update_containers_in_meta()
+            mock_create.assert_not_called()
+
+        meta = yaml.safe_load((module_dir / "meta.yml").read_text(encoding="utf-8"))
+        assert meta["containers"] == containers.dump_for_meta_yml()
+
+
+class TestBuildContainersWithProgress(TestModules):
+    """Tests for the ``ModuleContainers.build_containers_with_progress`` method.
+
+    ``create`` is mocked throughout so the tests cover the batch/aggregation logic
+    regardless of how containers are actually built (Wave API vs CLI).
+    """
+
+    def setUp(self):
+        super().setUp()
+        self.module_containers = ModuleContainers("bpipe/test", directory=self.nfcore_modules)
+        self.component = self.module_containers.nfcore_component
+        self.module_name = self.component.component_name
+
+    def test_success_returns_no_failures(self):
+        with mock.patch.object(ModuleContainers, "create", return_value=(MetaYmlContainers(), True)) as mock_create:
+            failed = self.module_containers.build_containers_with_progress(hide_progress=True)
+        assert failed == []
+        mock_create.assert_called_once()
+
+    def test_build_failure_is_reported(self):
+        """A module whose create() returns success=False is reported as failed."""
+        with mock.patch.object(ModuleContainers, "create", return_value=(MetaYmlContainers(), False)):
+            failed = self.module_containers.build_containers_with_progress(hide_progress=True)
+        assert failed == [self.module_name]
+
+    def test_exception_during_build_is_caught(self):
+        """A RuntimeError from create() is caught and the module is reported as failed."""
+        with mock.patch.object(ModuleContainers, "create", side_effect=RuntimeError("boom")):
+            failed = self.module_containers.build_containers_with_progress(hide_progress=True)
+        assert failed == [self.module_name]
+
+    def test_all_modules_reconstructs_per_module_containers(self):
+        """In batch mode a fresh per-module instance is built, reusing the scanned component list."""
+        all_module_containers = ModuleContainers(
+            module=None, directory=self.nfcore_modules, all_modules=True, components=[self.component]
+        )
+        with mock.patch.object(ModuleContainers, "create", return_value=(MetaYmlContainers(), True)) as mock_create:
+            failed = all_module_containers.build_containers_with_progress(hide_progress=True)
+        assert failed == []
+        mock_create.assert_called_once()
+
+
+class TestModuleContainersDockerfile(TestModuleContainersPipeline):
+    """Tests for ModuleContainers behaviour when a module uses a Dockerfile instead of environment.yml"""
+
+    def setUp(self):
+        super().setUp()
+        module_dir = self.pipeline_dir / "modules" / "local" / "dockermod"
+        module_dir.mkdir(parents=True, exist_ok=True)
+        (module_dir / "Dockerfile").write_text("FROM ubuntu:22.04\n", encoding="utf-8")
+        (module_dir / "meta.yml").write_text("name: dockermod\n", encoding="utf-8")
+        (module_dir / "main.nf").write_text('container "my/image:latest"\n', encoding="utf-8")
+        self.module_dir = module_dir
+        self.module_containers = ModuleContainers("dockermod", directory=self.pipeline_dir)
+
+    def test_create_returns_empty_for_dockerfile_module(self):
+        containers, success = self.module_containers.create()
+        assert containers == MetaYmlContainers()
+        assert success
+
+    def test_update_main_nf_container_skips_dockerfile_module(self):
+        original = (self.module_dir / "main.nf").read_text()
+        self.module_containers.update_main_nf_container()
+        assert (self.module_dir / "main.nf").read_text() == original
+
+    def test_update_containers_in_meta_skips_dockerfile_module(self):
+        original_meta = (self.module_dir / "meta.yml").read_text()
+        self.module_containers.update_containers_in_meta()
+        assert (self.module_dir / "meta.yml").read_text() == original_meta
diff --git a/tests/modules/test_create.py b/tests/modules/test_create.py
index 88789b51f2..c45da93c4a 100644
--- a/tests/modules/test_create.py
+++ b/tests/modules/test_create.py
@@ -6,6 +6,7 @@
 import responses
 import yaml
 
+import nf_core.components.create
 import nf_core.modules.create
 from tests.utils import (
     mock_anaconda_api_calls,
@@ -16,6 +17,23 @@
 from ..test_modules import TestModules
 
 
+def test_modules_create_accepts_dotted_git_provider_username():
+    """Accept dotted usernames used by non-GitHub git providers."""
+    component_create = nf_core.components.create.ComponentCreate.__new__(nf_core.components.create.ComponentCreate)
+    component_create.author = "@first.last"
+    component_create.require_prompts = mock.Mock()
+
+    with (
+        mock.patch("nf_core.components.create.subprocess.check_output", side_effect=FileNotFoundError),
+        mock.patch("nf_core.components.create.rich.prompt.Prompt.ask") as prompt_ask,
+    ):
+        component_create._get_username()
+
+    assert component_create.author == "@first.last"
+    component_create.require_prompts.assert_not_called()
+    prompt_ask.assert_not_called()
+
+
 class TestModulesCreate(TestModules):
     def test_modules_create_succeed(self):
         """Succeed at creating the TrimGalore! module"""
diff --git a/tests/modules/test_info.py b/tests/modules/test_info.py
index 8e60bed316..3f338d28bc 100644
--- a/tests/modules/test_info.py
+++ b/tests/modules/test_info.py
@@ -1,3 +1,6 @@
+from pathlib import Path
+
+import yaml
 from rich.console import Console
 
 import nf_core.modules.info
@@ -60,3 +63,29 @@ def test_modules_info_in_modules_repo(self):
         assert "Module: fastqc" in output
         assert "Inputs" in output
         assert "Outputs" in output
+
+    def test_modules_info_mixed_input_type(self):
+        """Test getting info about a module with mixed input types (list and dict)"""
+        self.mods_install.install("fastqc")
+        meta_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc", "meta.yml")
+
+        # Load existing meta.yml
+        with open(meta_path) as f:
+            meta = yaml.safe_load(f)
+
+        # Append a dictionary-style input (the cause of the bug)
+        meta["input"].append({"index_format": {"type": "string", "description": "Index format"}})
+
+        # Write modified meta.yml back
+        with open(meta_path, "w") as f:
+            yaml.dump(meta, f)
+
+        mods_info = nf_core.modules.info.ModuleInfo(self.pipeline_dir, "fastqc")
+        mods_info_output = mods_info.get_component_info()
+        console = Console(record=True)
+        console.print(mods_info_output)
+        output = console.export_text()
+
+        assert "Module: fastqc" in output
+        assert "index_format" in output
+        assert "(string)" in output
diff --git a/tests/modules/test_modules_utils.py b/tests/modules/test_modules_utils.py
index 8ef8d9d404..48996d3d5a 100644
--- a/tests/modules/test_modules_utils.py
+++ b/tests/modules/test_modules_utils.py
@@ -1,4 +1,11 @@
+from unittest import mock
+from unittest.mock import patch
+
 import nf_core.modules.modules_utils
+from nf_core.modules.modules_utils import (
+    module_uses_dockerfile,
+    scan_modules_dir,
+)
 
 from ..test_modules import TestModules
 
@@ -82,3 +89,95 @@ def test_filter_modules_by_name_empty_list(self):
 
         filtered = nf_core.modules.modules_utils.filter_modules_by_name(modules, "fastqc")
         assert len(filtered) == 0
+
+    def test_load_edam(self):
+        """Test EDAM ontology loading"""
+
+        with patch(
+            "nf_core.modules.modules_utils.NFCORE_CACHE_DIR",
+            str(self.tmp_path),
+        ):
+            cache_path = self.tmp_path / "EDAM.tsv"
+
+            assert not cache_path.exists()
+
+            edam_formats = nf_core.modules.modules_utils.load_edam()
+
+            assert cache_path.exists()
+
+            first_key, first_value = next(iter(edam_formats.items()))
+
+            assert isinstance(first_key, str)
+            assert isinstance(first_value, tuple)
+            assert len(first_value) == 2
+
+    def test_scan_modules_dir_returns_module_names(self):
+        """Test that scan_modules_dir returns module names relative to the scanned directory"""
+        modules_dir = self.nfcore_modules / "modules" / "nf-core"
+        result = scan_modules_dir(modules_dir)
+        assert "bpipe/test" in result
+
+    def test_scan_modules_dir_nonexistent(self):
+        """Test that scan_modules_dir returns an empty list for a nonexistent directory"""
+        result = scan_modules_dir(self.nfcore_modules / "does" / "not" / "exist")
+        assert result == []
+
+    def test_scan_modules_dir_multiple_modules(self):
+        """Test that scan_modules_dir returns all modules when multiple are present"""
+        modules_dir = self.nfcore_modules / "modules" / "nf-core"
+        extra = modules_dir / "samtools" / "sort"
+        extra.mkdir(parents=True)
+        (extra / "main.nf").touch()
+        try:
+            result = scan_modules_dir(modules_dir)
+            assert "bpipe/test" in result
+            assert "samtools/sort" in result
+        finally:
+            import shutil
+
+            shutil.rmtree(modules_dir / "samtools")
+
+
+def test_module_uses_dockerfile_true(tmp_path):
+    comp = mock.Mock()
+    comp.component_dir = tmp_path
+    comp.environment_yml = None
+    (tmp_path / "Dockerfile").write_text("FROM ubuntu:22.04\n")
+    assert module_uses_dockerfile(comp)
+
+
+def test_module_uses_dockerfile_false_has_env_yml(tmp_path):
+    env_yml = tmp_path / "environment.yml"
+    env_yml.write_text("name: test\n")
+    comp = mock.Mock()
+    comp.component_dir = tmp_path
+    comp.environment_yml = env_yml
+    (tmp_path / "Dockerfile").write_text("FROM ubuntu:22.04\n")
+    assert not module_uses_dockerfile(comp)
+
+
+def test_module_uses_dockerfile_false_no_dockerfile(tmp_path):
+    comp = mock.Mock()
+    comp.component_dir = tmp_path
+    comp.environment_yml = None
+    assert not module_uses_dockerfile(comp)
+
+
+def test_module_uses_dockerfile_nonexistent_env_yml_path(tmp_path):
+    """environment_yml pointing to a non-existent file is treated as missing."""
+    comp = mock.Mock()
+    comp.component_dir = tmp_path
+    comp.environment_yml = tmp_path / "environment.yml"
+    (tmp_path / "Dockerfile").write_text("FROM ubuntu:22.04\n")
+    assert module_uses_dockerfile(comp)
+
+
+def test_module_uses_dockerfile_in_parent_dir(tmp_path):
+    """Dockerfile one level up (e.g. spaceranger/Dockerfile) is detected for submodules."""
+    submodule_dir = tmp_path / "count"
+    submodule_dir.mkdir()
+    (tmp_path / "Dockerfile").write_text("FROM ubuntu:22.04\n")
+    comp = mock.Mock()
+    comp.component_dir = submodule_dir
+    comp.environment_yml = None
+    assert module_uses_dockerfile(comp)
diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py
index a77701b8ca..9f1e9bff71 100644
--- a/tests/modules/test_patch.py
+++ b/tests/modules/test_patch.py
@@ -6,6 +6,7 @@
 
 import nf_core.components.components_command
 import nf_core.components.patch
+import nf_core.modules.install
 import nf_core.modules.modules_json
 import nf_core.modules.patch
 import nf_core.modules.update
@@ -20,10 +21,10 @@
 testing if the update commands works correctly with patch files
 """
 
-ORG_SHA = "3dc7c14d29af40f1a0871a675364e437559d97a8"
-CORRECT_SHA = "63e780200600e340365b669f9c673b670764c569"
-SUCCEED_SHA = "0d0515c3f11266e1314e129bec3e308f804c8dc7"
-FAIL_SHA = "cb64a5c1ef85619b89ab99dec2e9097fe84e1dc8"
+ORG_SHA = "262178fbd015cd9be248630eec267f27e6048b03"
+CORRECT_SHA = "262178fbd015cd9be248630eec267f27e6048b03"
+SUCCEED_SHA = "b300b7e53f080a174a717d8e394cca1a82a5ba54"
+FAIL_SHA = "04d59325d44d309fb195f43d8b672674ee73d309"
 BISMARK_ALIGN = "bismark/align"
 REPO_NAME = "nf-core-test"
 PATCH_BRANCH = "patch-tester"
@@ -50,14 +51,16 @@ def modify_main_nf(path):
         lines = fh.readlines()
     # We want a patch file that looks something like:
     # -    tuple val(meta), path(reads)
-    # -    path index
+    # -    tuple val(meta3), path(index)
     # +    tuple val(meta), path(reads), path(index)
+    to_pop = None
     for line_index in range(len(lines)):
         if lines[line_index] == "    tuple val(meta), path(reads)\n":
             lines[line_index] = "    tuple val(meta), path(reads), path(index)\n"
-        elif lines[line_index] == "    path index\n":
+        elif lines[line_index] == "    tuple val(meta3), path(index)\n":
             to_pop = line_index
-    lines.pop(to_pop)
+    if to_pop:
+        lines.pop(to_pop)
     with open(path, "w") as fh:
         fh.writelines(lines)
 
@@ -108,7 +111,7 @@ def test_create_patch_change(self):
         assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf"
         assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
         assert "-    tuple val(meta), path(reads)\n" in patch_lines
-        assert "-    path index\n" in patch_lines
+        assert "-    tuple val(meta3), path(index)\n" in patch_lines
         assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
     def test_create_patch_try_apply_successful(self):
@@ -167,7 +170,7 @@ def test_create_patch_try_apply_successful(self):
         assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
         assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
         assert "-    tuple val(meta), path(reads)\n" in patch_lines
-        assert "-    path index\n" in patch_lines
+        assert "-    tuple val(meta3), path(index)\n" in patch_lines
         assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
         # Check that 'main.nf' is updated correctly
@@ -175,7 +178,7 @@ def test_create_patch_try_apply_successful(self):
             main_nf_lines = fh.readlines()
         # These lines should have been removed by the patch
         assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
-        assert "    path index\n" not in main_nf_lines
+        assert "    tuple val(meta3), path(index)\n" not in main_nf_lines
         # This line should have been added
         assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
 
@@ -268,7 +271,7 @@ def test_create_patch_update_success(self):
         assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines
         assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines
         assert "-    tuple val(meta), path(reads)\n" in patch_lines
-        assert "-    path index\n" in patch_lines
+        assert "-    tuple val(meta3), path(index)\n" in patch_lines
         assert "+    tuple val(meta), path(reads), path(index)\n" in patch_lines
 
         # Check that 'main.nf' is updated correctly
@@ -276,7 +279,7 @@ def test_create_patch_update_success(self):
             main_nf_lines = fh.readlines()
         # These lines should have been removed by the patch
         assert "    tuple val(meta), path(reads)\n" not in main_nf_lines
-        assert "    path index\n" not in main_nf_lines
+        assert "    tuple val(meta3), path(index)\n" not in main_nf_lines
         # This line should have been added
         assert "    tuple val(meta), path(reads), path(index)\n" in main_nf_lines
 
@@ -323,8 +326,8 @@ def test_create_patch_update_fail(self):
         ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir)
 
         temp_module_dir = temp_dir / BISMARK_ALIGN
-        temp_files = {f.name for f in temp_module_dir.iterdir()}
-        module_files = {f.name for f in module_path.iterdir()}
+        temp_files = {f.name for f in temp_module_dir.iterdir() if f.is_file()}
+        module_files = {f.name for f in module_path.iterdir() if f.is_file()}
         for file_name in temp_files:
             assert file_name in module_files
             with open(module_path / file_name) as fh:
diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py
index be3df24256..b061fe185a 100644
--- a/tests/modules/test_update.py
+++ b/tests/modules/test_update.py
@@ -43,6 +43,20 @@ def test_install_and_update(self):
         assert update_obj.update("trimgalore") is True
         assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True
 
+    @mock.patch("nf_core.components.update.ComponentUpdate.update_linked_components")
+    @mock.patch(
+        "nf_core.components.update.ComponentUpdate.get_components_to_update",
+        return_value=([], [{"name": "fake_sw", "git_remote": "x"}]),
+    )
+    def test_module_update_skip_deps_does_not_cascade(self, mock_get_linked, mock_cascade):
+        """`module update --skip-deps` skips cascade even when linked subworkflows exist."""
+        assert self.mods_install_old.install("trimgalore")
+        update_obj = ModuleUpdate(
+            self.pipeline_dir, show_diff=False, skip_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
+        )
+        assert update_obj.update("trimgalore") is True
+        assert not mock_cascade.called
+
     def test_install_at_hash_and_update(self):
         """Installs an old version of a module in the pipeline and updates it"""
         assert self.mods_install_old.install("trimgalore")
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg
index 27b33c8ab0..cfa48a410d 100644
--- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg
+++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg
@@ -42,14 +42,13 @@
 .terminal-r8 { fill: #57a5e2 }
 .terminal-r9 { fill: #ffc473 }
 .terminal-r10 { fill: #ffffff }
-.terminal-r11 { fill: #d2d2d2 }
-.terminal-r12 { fill: #345b7a }
-.terminal-r13 { fill: #f4bc6e }
-.terminal-r14 { fill: #7ae998 }
-.terminal-r15 { fill: #55c076;font-weight: bold }
-.terminal-r16 { fill: #008139 }
-.terminal-r17 { fill: #ffa62b;font-weight: bold }
-.terminal-r18 { fill: #495259 }
+.terminal-r11 { fill: #345b7a }
+.terminal-r12 { fill: #f4bc6e }
+.terminal-r13 { fill: #7ae998 }
+.terminal-r14 { fill: #55c076;font-weight: bold }
+.terminal-r15 { fill: #008139 }
+.terminal-r16 { fill: #ffa62b;font-weight: bold }
+.terminal-r17 { fill: #495259 }
     </style>
 
     <defs>
@@ -213,7 +212,7 @@
             </g>
         
     <g transform="translate(9, 41)" clip-path="url(#terminal-clip-terminal)">
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diff --git a/tests/pipelines/download/test_download.py b/tests/pipelines/download/test_download.py
index 40228994cc..092817b067 100644
--- a/tests/pipelines/download/test_download.py
+++ b/tests/pipelines/download/test_download.py
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             download_obj.wf_use_local_configs("workflow")
             wf_config = nf_core.utils.fetch_wf_config(Path(test_outdir, "workflow"), cache_config=False)
-            assert wf_config["params.custom_config_base"] == f"{test_outdir}/workflow/../configs/"
+            assert wf_config["params"]["custom_config_base"] == f"{test_outdir}/workflow/../configs/"
 
     #
     # Test that `find_container_images` (uses `nextflow inspect`) fetches the correct Docker images
@@ -280,6 +280,43 @@ def test_containers_pipeline_singularity(self, tmp_path, mock_fetch_wf_config):
                 f"Containers that should've been found: {ref_container_strs}"
             )
 
+    #
+    # Test that `find_container_images` (uses `nextflow inspect`) fetches the correct Apptainer images
+    #
+    @pytest.mark.skipif(
+        shutil.which("nextflow") is None or not check_nextflow_version(NF_INSPECT_MIN_NF_VERSION),
+        reason="Can't run test that requires nextflow to run if not installed.",
+    )
+    @with_temporary_folder
+    @mock.patch("nf_core.utils.fetch_wf_config")
+    def test_containers_pipeline_apptainer(self, tmp_path, mock_fetch_wf_config):
+        tmp_path = Path(tmp_path)
+        assert check_nextflow_version(NF_INSPECT_MIN_NF_VERSION) is True
+
+        # Set up test
+        container_system = "apptainer"
+        mock_pipeline_dir = TEST_DATA_DIR / "mock_pipeline_containers"
+        refererence_json_dir = mock_pipeline_dir / "per_profile_output"
+        # First check that `-profile apptainer` produces the same output as the reference
+        download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path, container_system=container_system)
+        mock_fetch_wf_config.return_value = {}
+
+        # Run get containers with `nextflow inspect`
+        # NF >= 26.04 rejects old-style if/else container directives (mock_dsl2_old uses them)
+        entrypoint = "main_passing_test.nf"
+        with self._strict_syntax_ctx(match="downgrade to Nextflow"):
+            download_obj.find_container_images(mock_pipeline_dir, "dummy-revision", entrypoint=entrypoint)
+
+        if not self.nf_strict_syntax:
+            found_containers = set(download_obj.containers)
+            with open(refererence_json_dir / f"{container_system}_containers.json") as fh:
+                ref_containers = json.load(fh)
+                ref_container_strs = set(ref_containers.values())
+            assert found_containers == ref_container_strs, (
+                f"Containers found in pipeline by `nextflow inspect`: {found_containers}\n"
+                f"Containers that should've been found: {ref_container_strs}"
+            )
+
     #
     # Test that `find_container_images` (uses `nextflow inspect`) fetches the correct Docker images
     #
diff --git a/tests/pipelines/download/test_singularity.py b/tests/pipelines/download/test_singularity.py
index eb6bfe1bbb..c7b56c1a3f 100644
--- a/tests/pipelines/download/test_singularity.py
+++ b/tests/pipelines/download/test_singularity.py
@@ -20,6 +20,8 @@
     SingularityError,
     SingularityFetcher,
     SingularityProgress,
+    get_container_cache_dir,
+    get_container_library_dir,
 )
 from nf_core.pipelines.download.utils import DownloadError
 
@@ -119,6 +121,91 @@ def __contains__(self, item: str) -> bool:
         """
         return any(record.message == item for record in self._caplog.records if self._caplog)
 
+    #
+    # Tests for the cache and library directory environment variable functions
+    #
+    def test_get_container_cache_dir_env_vars(self):
+        assert get_container_cache_dir("singularity") == "NXF_SINGULARITY_CACHEDIR"
+        assert get_container_cache_dir("apptainer") == "NXF_APPTAINER_CACHEDIR"
+        with pytest.raises(KeyError):
+            get_container_cache_dir("docker")
+
+    def test_get_container_library_dir_env_vars(self):
+        assert get_container_library_dir("singularity") == "NXF_SINGULARITY_LIBRARYDIR"
+        assert get_container_library_dir("apptainer") == "NXF_APPTAINER_LIBRARYDIR"
+        with pytest.raises(KeyError):
+            get_container_library_dir("docker")
+
+    #
+    # Tests for constructing SingularityFetcher with different container_system values
+    #
+    @with_temporary_folder
+    @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation")
+    def test_apptainer_fetcher_constructor(self, tmp_path, mock_cachedir_prompt):
+        mock_cachedir_prompt.return_value = False
+        tmp_path = Path(tmp_path)
+        fetcher = SingularityFetcher(
+            outdir=tmp_path,
+            container_library=[],
+            registry_set=[],
+            container_cache_utilisation="none",
+            container_system="apptainer",
+        )
+        assert fetcher.container_system == "apptainer"
+        assert fetcher.container_system_name == "Apptainer"
+        assert fetcher.cache_dir_env_var == "NXF_APPTAINER_CACHEDIR"
+        assert fetcher.library_dir_env_var == "NXF_APPTAINER_LIBRARYDIR"
+        assert fetcher._container_output_dir == tmp_path / "apptainer-images"
+
+    @with_temporary_folder
+    @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation")
+    def test_singularity_fetcher_constructor(self, tmp_path, mock_cachedir_prompt):
+        mock_cachedir_prompt.return_value = False
+        tmp_path = Path(tmp_path)
+        fetcher = SingularityFetcher(
+            outdir=tmp_path,
+            container_library=[],
+            registry_set=[],
+            container_cache_utilisation="none",
+        )
+        assert fetcher.container_system == "singularity"
+        assert fetcher.container_system_name == "Singularity"
+        assert fetcher.cache_dir_env_var == "NXF_SINGULARITY_CACHEDIR"
+        assert fetcher.library_dir_env_var == "NXF_SINGULARITY_LIBRARYDIR"
+        assert fetcher._container_output_dir == tmp_path / "singularity-images"
+
+    #
+    # Tests for 'construct_pull_command' with different implementations
+    #
+    @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation")
+    def test_construct_pull_command_apptainer(self, mock_cachedir_prompt):
+        mock_cachedir_prompt.return_value = False
+        fetcher = SingularityFetcher(
+            outdir=Path("/tmp"),
+            container_library=[],
+            registry_set=[],
+            container_cache_utilisation="none",
+            container_system="apptainer",
+        )
+        fetcher.implementation = "apptainer"
+        output_path = Path("/tmp/test.sif")
+        command = fetcher.construct_pull_command(output_path, "docker://hello-world")
+        assert command == ["apptainer", "pull", "--name", str(output_path), "docker://hello-world"]
+
+    @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation")
+    def test_construct_pull_command_singularity(self, mock_cachedir_prompt):
+        mock_cachedir_prompt.return_value = False
+        fetcher = SingularityFetcher(
+            outdir=Path("/tmp"),
+            container_library=[],
+            registry_set=[],
+            container_cache_utilisation="none",
+        )
+        fetcher.implementation = "singularity"
+        output_path = Path("/tmp/test.sif")
+        command = fetcher.construct_pull_command(output_path, "docker://hello-world")
+        assert command == ["singularity", "pull", "--name", str(output_path), "docker://hello-world"]
+
     #
     # Tests for 'singularity_pull_image'
     #
@@ -131,7 +218,7 @@ def __contains__(self, item: str) -> bool:
     @with_temporary_folder
     @mock.patch("nf_core.pipelines.download.singularity.SingularityProgress")
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_cachedir_prompt, mock_progress):
         tmp_dir = Path(tmp_dir)
@@ -217,7 +304,7 @@ def test_singularity_pull_image_singularity_installed(self, tmp_dir, mock_cached
     @mock.patch("nf_core.utils.fetch_wf_config")
     @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.gather_registries")
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     def test_fetch_containers_singularity(
         self, tmp_path, mock_cachedir_prompt, mock_gather_registries, mock_fetch_wf_config
@@ -260,7 +347,7 @@ def test_fetch_containers_singularity(
         "nf_core.pipelines.download.singularity.SingularityFetcher.check_and_set_implementation"
     )  # This is to make sure that we do not check for Singularity/Apptainer installation
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     @mock.patch("pathlib.Path.mkdir")
     @mock.patch("pathlib.Path.symlink_to")
@@ -341,7 +428,7 @@ def test_symlink_singularity_images(
         "nf_core.pipelines.download.singularity.SingularityFetcher.check_and_set_implementation"
     )  # This is to make sure that we do not check for Singularity/Apptainer installation
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     @mock.patch("pathlib.Path.mkdir")
     @mock.patch("pathlib.Path.symlink_to")
@@ -423,7 +510,7 @@ def test_symlink_singularity_symlink_registries(
     @with_temporary_folder
     @mock.patch("nf_core.pipelines.download.singularity.SingularityProgress")
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     def test_singularity_pull_image_successfully(self, tmp_dir, mock_cachedir_prompt, mock_progress):
         tmp_dir = Path(tmp_dir)
@@ -443,7 +530,7 @@ def test_singularity_pull_image_successfully(self, tmp_dir, mock_cachedir_prompt
     @with_temporary_folder
     @mock.patch("nf_core.utils.fetch_wf_config")
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     def test_gather_registries_singularity(self, tmp_path, mock_cachedir_prompt, mock_fetch_wf_config):
         tmp_path = Path(tmp_path)
@@ -456,11 +543,11 @@ def test_gather_registries_singularity(self, tmp_path, mock_cachedir_prompt, moc
             container_cache_index=None,
         )
         mock_fetch_wf_config.return_value = {
-            "apptainer.registry": "apptainer-registry.io",
-            "docker.registry": "docker.io",
-            "podman.registry": "podman-registry.io",
-            "singularity.registry": "singularity-registry.io",
-            "someother.registry": "fake-registry.io",
+            "apptainer": {"registry": "apptainer-registry.io"},
+            "docker": {"registry": "docker.io"},
+            "podman": {"registry": "podman-registry.io"},
+            "singularity": {"registry": "singularity-registry.io"},
+            "someother": {"registry": "fake-registry.io"},
         }
         singularity_fetcher.registry_set = singularity_fetcher.gather_registries(tmp_path)
         assert singularity_fetcher.registry_set
@@ -492,7 +579,7 @@ def test_gather_registries_singularity(self, tmp_path, mock_cachedir_prompt, moc
     @with_temporary_folder
     @mock.patch("rich.progress.Progress.add_task")
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     def test_singularity_pull_image_singularity_not_installed(self, tmp_dir, mock_rich_progress, mock_cachedir_prompt):
         tmp_dir = Path(tmp_dir)
@@ -512,7 +599,7 @@ def test_singularity_pull_image_singularity_not_installed(self, tmp_dir, mock_ri
 
     @mock.patch("nf_core.pipelines.download.singularity.SingularityFetcher.check_and_set_implementation")
     @mock.patch(
-        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_singularity_cachedir_creation"
+        "nf_core.pipelines.download.singularity.SingularityFetcher.prompt_cachedir_creation"
     )  # This is to make sure that we do not prompt for a Singularity cachedir
     def test_singularity_get_container_filename(self, mock_cachedir_prompt, mock_check_and_set_implementation):
         registries = [
diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py
index 6f5604d74f..2cef8aa105 100644
--- a/tests/pipelines/lint/test_files_exist.py
+++ b/tests/pipelines/lint/test_files_exist.py
@@ -19,7 +19,7 @@ def test_files_exist_missing_config(self):
         Path(self.new_pipeline, "CHANGELOG.md").unlink()
 
         assert self.lint_obj._load()
-        self.lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline"
+        self.lint_obj.nf_config["manifest"]["name"] = "nf-core/testpipeline"
 
         results = self.lint_obj.files_exist()
         assert "File not found: `CHANGELOG.md`" in results["failed"]
@@ -61,7 +61,7 @@ def test_files_exist_pass_conditional_nfschema(self):
             f.write(config)
 
         assert self.lint_obj._load()
-        self.lint_obj.nf_config["manifest.schema"] = "nf-core"
+        self.lint_obj.nf_config["manifest"]["schema"] = "nf-core"
         results = self.lint_obj.files_exist()
         assert results["failed"] == []
         assert results["ignored"] == []
diff --git a/tests/pipelines/lint/test_modules_json.py b/tests/pipelines/lint/test_modules_json.py
index 0d8333d9a2..6e72930009 100644
--- a/tests/pipelines/lint/test_modules_json.py
+++ b/tests/pipelines/lint/test_modules_json.py
@@ -1,10 +1,74 @@
+import json
+
+from nf_core.modules.modules_json import (
+    ModulesJson,
+    ModulesJsonType,
+)
+
 from ..test_lint import TestLint
 
 
 class TestLintModulesJson(TestLint):
+    def setUp(self) -> None:
+        super().setUp()
+        self._modules_json_object: ModulesJson = ModulesJson(self.pipeline_dir)
+        self._modules_json_object.load()
+        self.modules_json_path = self._modules_json_object.modules_json_path
+        assert self._modules_json_object.modules_json is not None
+        self.modules_json: ModulesJsonType = self._modules_json_object.modules_json
+
+    def _update_modules_json(self, new_modules_json) -> None:
+        # Update modules_json so that it is concordant at all levels of the class
+        self.modules_json = new_modules_json
+        self._modules_json_object.modules_json = new_modules_json
+        with open(self.modules_json_path, "w") as modules_json_file:
+            json.dump(new_modules_json, modules_json_file)
+
     def test_modules_json_pass(self):
         self.lint_obj._load()
         results = self.lint_obj.modules_json()
         assert len(results.get("warned", [])) == 0
         assert len(results.get("failed", [])) == 0
         assert len(results.get("passed", [])) > 0
+
+    def test_modules_json_with_repo_not_starting_with_http_fail(self):
+        # Change the link of the first repo in modules_json to not start with "http"
+        new_modules_json = self.modules_json
+        first_repo = next(iter(new_modules_json["repos"]))
+        new_modules_json["repos"]["incorrect_repo_link"] = new_modules_json["repos"].pop(first_repo)
+
+        self._update_modules_json(new_modules_json)
+
+        # Check linting results
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 1
+        assert len(results.get("passed", [])) == 1  # The repository still contains only installed modules
+
+    def test_modules_json_with_only_subworkflow_entries(self):
+        # Keep only "subworkflows" in the first repo in modules_json
+        new_modules_json = self.modules_json
+        first_repo = next(iter(new_modules_json["repos"]))
+        new_modules_json["repos"][first_repo] = {"subworkflows": new_modules_json["repos"][first_repo]["subworkflows"]}
+
+        self._update_modules_json(new_modules_json)
+
+        # Check linting results
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 0
+        assert len(results.get("passed", [])) == 0  # There is no subworkflow linting so no "passed" is returned
+
+    def test_modules_json_with_repo_with_no_modules_or_subworkflows_fail(self):
+        # Change the first repo in modules_json to have no modules or subworkflows
+        new_modules_json = self.modules_json
+        first_repo = next(iter(new_modules_json["repos"]))
+        new_modules_json["repos"][first_repo] = {}
+
+        self._update_modules_json(new_modules_json)
+
+        # Check linting results
+        results = self.lint_obj.modules_json()
+        assert len(results.get("warned", [])) == 0
+        assert len(results.get("failed", [])) == 1
+        assert len(results.get("passed", [])) == 0
diff --git a/tests/pipelines/lint/test_multiqc_config.py b/tests/pipelines/lint/test_multiqc_config.py
index 5da6e567ec..e3f691508f 100644
--- a/tests/pipelines/lint/test_multiqc_config.py
+++ b/tests/pipelines/lint/test_multiqc_config.py
@@ -104,7 +104,7 @@ def test_multiqc_config_report_comment_release_fail(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj._load()
         # bump version
-        lint_obj.nf_config["manifest.version"] = "1.0"
+        lint_obj.nf_config["manifest"]["version"] = "1.0"
         result = lint_obj.multiqc_config()
         # Reset the file
         with open(self.multiqc_config_yml, "w") as fh:
diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py
index 63c58b149b..493aa49a76 100644
--- a/tests/pipelines/lint/test_nextflow_config.py
+++ b/tests/pipelines/lint/test_nextflow_config.py
@@ -34,7 +34,7 @@ def test_nextflow_config_bad_name_fail(self):
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj.load_pipeline_config()
 
-        lint_obj.nf_config["manifest.name"] = "bad_name"
+        lint_obj.nf_config["manifest"]["name"] = "bad_name"
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) > 0
         assert len(result["warned"]) == 0
@@ -45,7 +45,7 @@ def test_nextflow_config_dev_in_release_mode_failed(self):
         lint_obj.load_pipeline_config()
 
         lint_obj.release_mode = True
-        lint_obj.nf_config["manifest.version"] = "dev_is_bad_name"
+        lint_obj.nf_config["manifest"]["version"] = "dev_is_bad_name"
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) > 0
         assert len(result["warned"]) == 0
@@ -105,9 +105,13 @@ def test_catch_params_assignment_in_main_nf(self):
         lint_obj.load_pipeline_config()
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) == 2
+        assert (
+            result["failed"][0]
+            == "Config `params.custom_config_base` is not set to `https://raw.githubusercontent.com/nf-core/configs/master`"
+        )
         assert (
             result["failed"][1]
-            == "Config default value incorrect: `params.custom_config_base` is set as `https://raw.githubusercontent.com/nf-core/configs/master` in `nextflow_schema.json` but is `null` in `nextflow.config`."
+            == "Default value from the Nextflow schema `params.custom_config_base = `https://raw.githubusercontent.com/nf-core/configs/master`` not found in `nextflow.config`."
         )
 
     def test_allow_params_reference_in_main_nf(self):
diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py
index e888a1d6a1..a2c1babd6a 100644
--- a/tests/pipelines/lint/test_nfcore_yml.py
+++ b/tests/pipelines/lint/test_nfcore_yml.py
@@ -48,6 +48,15 @@ def test_nfcore_yml_fail_nfcore_version(self):
         assert len(results.get("passed", [])) >= 0
         assert len(results.get("ignored", [])) == 0
 
+    def test_nfcore_yml_container_registry_accepted(self):
+        """Lint test: nfcore_yml - PASS - container-registry field is accepted without errors"""
+        self.nf_core_yml["container-registry"] = ["community.wave.seqera.io/library/", "ghcr.io/"]
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
+
+        assert self.lint_obj._load()
+        results = self.lint_obj.nfcore_yml()
+        assert len(results.get("failed", [])) == 0
+
     def test_nfcore_yml_nested_lint_config(self) -> None:
         """Lint test: nfcore_yml with nested lint config - PASS"""
         valid_yaml = """
diff --git a/tests/pipelines/lint/test_version_consistency.py b/tests/pipelines/lint/test_version_consistency.py
index c7f7f28919..d11b3d3369 100644
--- a/tests/pipelines/lint/test_version_consistency.py
+++ b/tests/pipelines/lint/test_version_consistency.py
@@ -35,7 +35,7 @@ def test_version_consistency_pass(self):
         lint_obj.load_pipeline_config()
         lint_obj.nextflow_config()
         # Set the version for the container
-        lint_obj.nf_config["process.container"] = "nfcore/pipeline:1.0.0"
+        lint_obj.nf_config["process"]["container"] = "nfcore/pipeline:1.0.0"
         result = lint_obj.version_consistency()
         assert result["passed"] == [
             "Version tags are consistent: manifest.version = 1.0.0, process.container = 1.0.0, nfcore_yml.version = 1.0.0",
@@ -73,7 +73,7 @@ def test_version_consistency_not_consistent(self):
         lint_obj.load_pipeline_config()
         lint_obj.nextflow_config()
 
-        lint_obj.nf_config["process.container"] = "nfcore/pipeline:0.1"
+        lint_obj.nf_config["process"]["container"] = "nfcore/pipeline:0.1"
         result = lint_obj.version_consistency()
         assert len(result["passed"]) == 0
         assert result["failed"] == [
diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py
index 3f34c18533..85c78e96a1 100644
--- a/tests/pipelines/test_bump_version.py
+++ b/tests/pipelines/test_bump_version.py
@@ -24,7 +24,7 @@ def test_bump_pipeline_version(self):
 
         # Check nextflow.config
         new_pipeline_obj.load_pipeline_config()
-        assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1.0"
+        assert new_pipeline_obj.nf_config["manifest"]["version"].strip("'\"") == "1.1.0"
 
         # Check multiqc_config.yml
         with open(new_pipeline_obj._fp("assets/multiqc_config.yml")) as fh:
@@ -47,7 +47,7 @@ def test_dev_bump_pipeline_version(self):
 
         # Check the pipeline config
         new_pipeline_obj.load_pipeline_config()
-        assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.2dev"
+        assert new_pipeline_obj.nf_config["manifest"]["version"].strip("'\"") == "1.2dev"
 
     def test_bump_nextflow_version(self):
         # Bump the version number to a specific version, preferably one
@@ -58,7 +58,7 @@ def test_bump_nextflow_version(self):
         new_pipeline_obj._load()
 
         # Check nextflow.config
-        assert new_pipeline_obj.nf_config["manifest.nextflowVersion"].strip("'\"") == f"!>={version}"
+        assert new_pipeline_obj.nf_config["manifest"]["nextflowVersion"].strip("'\"") == f"!>={version}"
 
         # Check .github/workflows/nf-test.yml
         with open(new_pipeline_obj._fp(".github/workflows/nf-test.yml")) as fh:
diff --git a/tests/pipelines/test_container_configs.py b/tests/pipelines/test_container_configs.py
index e90b39a021..e879a5f5e1 100644
--- a/tests/pipelines/test_container_configs.py
+++ b/tests/pipelines/test_container_configs.py
@@ -1,14 +1,11 @@
 """Tests for the ContainerConfigs helper used by pipelines."""
 
-from pathlib import Path
-from unittest.mock import patch
+import shutil
 
-import pytest
 import ruamel.yaml
 
 from nf_core.modules.install import ModuleInstall
 from nf_core.pipelines.containers_utils import PLATFORMS, ContainerConfigs
-from nf_core.utils import NF_INSPECT_MIN_NF_VERSION, pretty_nf_version
 
 from ..test_pipelines import TestPipelines
 
@@ -22,30 +19,6 @@ def setUp(self) -> None:
         super().setUp()
         self.container_configs = ContainerConfigs(self.pipeline_dir)
 
-    def test_check_nextflow_version_sufficient_ok(self) -> None:
-        """check_nextflow_version should return silently when version is sufficient."""
-        with patch(
-            "nf_core.pipelines.containers_utils.check_nextflow_version",
-            return_value=True,
-        ) as mocked_check:
-            self.container_configs.check_nextflow_version_sufficient()
-
-        mocked_check.assert_called_once_with(NF_INSPECT_MIN_NF_VERSION, silent=True)
-
-    def test_check_nextflow_version_sufficient_too_low(self) -> None:
-        """check_nextflow_version should raise UserWarning when version is too low."""
-        with (
-            patch(
-                "nf_core.pipelines.containers_utils.check_nextflow_version",
-                return_value=False,
-            ),
-            pytest.raises(UserWarning) as excinfo,
-        ):
-            self.container_configs.check_nextflow_version_sufficient()
-
-        # Error message should mention the minimal required version
-        assert pretty_nf_version(NF_INSPECT_MIN_NF_VERSION) in str(excinfo.value)
-
     def test_generate_all_container_configs(self) -> None:
         """Run generate_all_container_configs in a pipeline."""
         # Install fastqc and multiqc
@@ -67,10 +40,11 @@ def test_generate_all_container_configs(self) -> None:
             with cfg_path.open("r") as fh:
                 content = fh.readlines()
                 value = fastqc_meta_yml["containers"][runtime][arch][protocol]
-                assert f"process {{ withName: 'FASTQC' {{ container = '{value}' }} }}\n" in content
+                key = "conda" if p_name.startswith("conda_lock_") else "container"
+                assert f"process {{ withName: 'FASTQC' {{ {key} = '{value}' }} }}\n" in content
 
-    def test_generate_container_configs_new_module_injected(self) -> None:
-        """new_module_name/path are used when nextflow inspect doesn't yet know about the module."""
+    def test_generate_container_configs_newly_installed_module(self) -> None:
+        """A newly installed module is picked up from disk by the filesystem scan."""
         mods_install = ModuleInstall(
             self.pipeline_dir, prompt=False, force=False, sha="79b36b51048048374b642289bfe9e591ef56fe05"
         )
@@ -79,41 +53,49 @@ def test_generate_container_configs_new_module_injected(self) -> None:
         with open(self.pipeline_dir / "modules" / "nf-core" / "fastqc" / "meta.yml") as fh:
             fastqc_meta_yml = yaml.load(fh)
 
-        with (
-            patch("nf_core.pipelines.containers_utils.check_nextflow_version", return_value=True),
-            patch(
-                "nf_core.pipelines.containers_utils.run_cmd",
-                return_value=(b'{"processes": []}', b""),
-            ),
-        ):
-            self.container_configs.generate_container_configs(
-                new_module_path=Path("modules/nf-core/fastqc"),
-                new_module_name="fastqc",
-            )
+        self.container_configs.generate_container_configs()
 
         conf_dir = self.pipeline_dir / "conf"
         for p_name, (runtime, arch, protocol) in PLATFORMS.items():
             cfg_path = conf_dir / f"containers_{p_name}.config"
             assert cfg_path.exists()
             value = fastqc_meta_yml["containers"][runtime][arch][protocol]
-            assert f"process {{ withName: 'FASTQC' {{ container = '{value}' }} }}\n" in cfg_path.read_text()
+            key = "conda" if p_name.startswith("conda_lock_") else "container"
+            assert f"process {{ withName: 'FASTQC' {{ {key} = '{value}' }} }}\n" in cfg_path.read_text()
 
     def test_generate_container_configs_removes_stale_entries(self) -> None:
-        """Stale config files are deleted when all their modules have been removed."""
+        """Stale entries are not present after regeneration."""
         conf_dir = self.pipeline_dir / "conf"
         stale_line = "process { withName: 'REMOVED_MODULE' { container = 'stale/image:latest' } }\n"
         for p_name in PLATFORMS:
             (conf_dir / f"containers_{p_name}.config").write_text(stale_line)
 
-        with (
-            patch("nf_core.pipelines.containers_utils.check_nextflow_version", return_value=True),
-            patch(
-                "nf_core.pipelines.containers_utils.run_cmd",
-                return_value=(b'{"processes": []}', b""),
-            ),
-        ):
-            self.container_configs.generate_container_configs()
+        self.container_configs.generate_container_configs()
 
         for p_name in PLATFORMS:
             cfg_path = conf_dir / f"containers_{p_name}.config"
-            assert not cfg_path.exists(), f"{cfg_path.name} should be deleted when all modules are removed"
+            if cfg_path.exists():
+                assert stale_line not in cfg_path.read_text(), (
+                    f"{cfg_path.name} still contains stale entry after regeneration"
+                )
+
+    def test_generate_container_configs_no_modules_dir(self) -> None:
+        """Returns an empty set immediately when there is no modules/ directory."""
+        shutil.rmtree(self.pipeline_dir / "modules", ignore_errors=True)
+        result = self.container_configs.generate_container_configs()
+        assert result == set()
+
+    def test_generate_container_configs_skips_meta_without_containers(self) -> None:
+        """meta.yml files without a containers key are silently ignored."""
+        module_dir = self.pipeline_dir / "modules" / "local" / "fake"
+        module_dir.mkdir(parents=True, exist_ok=True)
+        (module_dir / "meta.yml").write_text("name: fake\ndescription: no containers here\n")
+        (module_dir / "main.nf").write_text('process FAKE {\n  script:\n  """\n  echo hello\n  """\n}\n')
+
+        self.container_configs.generate_container_configs()
+
+        conf_dir = self.pipeline_dir / "conf"
+        for p_name in PLATFORMS:
+            cfg_path = conf_dir / f"containers_{p_name}.config"
+            if cfg_path.exists():
+                assert "FAKE" not in cfg_path.read_text(), f"{cfg_path.name} contains entry for FAKE module"
diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py
index e97f2f10b6..419c618ac0 100644
--- a/tests/pipelines/test_launch.py
+++ b/tests/pipelines/test_launch.py
@@ -17,7 +17,7 @@ class TestLaunch(TestPipelines):
     def setUp(self) -> None:
         super().setUp()
         self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json")
-        self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn)
+        self.launcher = nf_core.pipelines.launch.Launch(str(self.pipeline_dir), params_out=self.nf_params_fn)
 
     @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True])
     @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui")
@@ -336,3 +336,15 @@ def test_build_command_params_cl(self):
         self.launcher.schema_obj.input_params.update({"input": "custom_input"})
         self.launcher.build_command()
         assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} --input "custom_input"'
+
+
+def test_launch_params_out_option_is_path():
+    """The --params-out CLI option converts its value to a Path, so params_out never
+    reaches Launch as a str that would crash params_out.exists() (#4299)."""
+    import click
+
+    from nf_core.__main__ import command_pipelines_launch
+
+    param = next(p for p in command_pipelines_launch.params if p.name == "params_out")
+    ctx = click.Context(command_pipelines_launch)
+    assert isinstance(param.type.convert("nf-params.json", param, ctx), Path)
diff --git a/tests/pipelines/test_rocrate.py b/tests/pipelines/test_rocrate.py
index 30df70f821..20ffbafd13 100644
--- a/tests/pipelines/test_rocrate.py
+++ b/tests/pipelines/test_rocrate.py
@@ -278,7 +278,7 @@ def test_parse_manifest_contributors_logs_parse_errors(self):
 
         # Set nf_config directly to avoid running nextflow config -flat on invalid Groovy syntax
         # (unquoted `alice` is valid Groovy but references an undefined variable, causing nextflow to fail)
-        self.rocrate_obj.pipeline_obj.nf_config["manifest.contributors"] = (
+        self.rocrate_obj.pipeline_obj.nf_config["manifest"]["contributors"] = (
             "[[\n    name: 'Alice Example',\n    github: alice\n]]"
         )
 
diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py
index 5965a5c011..bc5600f6e2 100644
--- a/tests/pipelines/test_schema.py
+++ b/tests/pipelines/test_schema.py
@@ -5,6 +5,7 @@
 import shutil
 import tempfile
 import unittest
+from io import StringIO
 from pathlib import Path
 from unittest import mock
 
@@ -130,6 +131,32 @@ def test_schema_docs(self):
             assert definition["title"] in docs
             assert definition["description"] in docs
 
+    @with_temporary_file
+    def test_schema_docs_markdown_linebreak(self, tmp_file):
+        """Check that Markdown docs linebreak only happens in a terminal"""
+        self.schema_obj.schema_filename = self.template_schema
+        self.schema_obj.load_schema()
+
+        with (
+            mock.patch("rich.console.Console.is_terminal", new_callable=mock.PropertyMock, return_value=False),
+            mock.patch("sys.stdout", new_callable=StringIO) as mock_stdout,
+        ):
+            self.schema_obj.print_documentation()
+            docs = mock_stdout.getvalue()
+
+        with (
+            mock.patch("rich.console.Console.is_terminal", new_callable=mock.PropertyMock, return_value=True),
+            mock.patch("sys.stdout", new_callable=StringIO) as mock_stdout,
+        ):
+            self.schema_obj.print_documentation()
+            docs_tty = mock_stdout.getvalue()
+
+        self.schema_obj.print_documentation(output_fn=tmp_file.name, force=True)
+        tmp_file.seek(0)
+
+        assert docs_tty.count("\n") > docs.count("\n")
+        assert tmp_file.read().decode() == docs
+
     @with_temporary_file
     def test_save_schema(self, tmp_file):
         """Try to save a schema"""
diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py
index aa27170f26..5d21b7a086 100644
--- a/tests/pipelines/test_sync.py
+++ b/tests/pipelines/test_sync.py
@@ -143,14 +143,14 @@ def test_get_wf_config_missing_required_config(self):
         """Try getting a workflow config, then make it miss a required config option"""
         # Try to sync, check we halt with the right error
         psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
-        psync.required_config_vars = ["fakethisdoesnotexist"]
+        psync.required_config_vars = {"fakesection": ["fakethisdoesnotexist"]}
         with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info:
             psync.inspect_sync_dir()
             psync.get_wf_config()
         # Check that we did actually get some config back
-        assert psync.wf_config["params.validate_params"] == "true"
+        assert psync.wf_config["params"]["validate_params"] is True
         # Check that we raised because of the missing fake config var
-        assert exc_info.value.args[0] == "Workflow config variable `fakethisdoesnotexist` not found!"
+        assert exc_info.value.args[0] == "Workflow config variable `fakesection.fakethisdoesnotexist` not found!"
 
     def test_checkout_template_branch(self):
         """Try checking out the TEMPLATE branch of the pipeline"""
@@ -403,7 +403,7 @@ def test_push_merge_branch(self):
         psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
         psync.inspect_sync_dir()
         psync.get_wf_config()
-        psync.repo.create_remote("origin", self.remote_path)
+        psync.repo.create_remote("origin", str(self.remote_path))
 
         psync.create_merge_base_branch()
         psync.push_merge_branch()
@@ -415,7 +415,7 @@ def test_push_merge_branch_without_create_branch(self):
         psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
         psync.inspect_sync_dir()
         psync.get_wf_config()
-        psync.repo.create_remote("origin", self.remote_path)
+        psync.repo.create_remote("origin", str(self.remote_path))
 
         with pytest.raises(nf_core.pipelines.sync.PullRequestExceptionError) as exc_info:
             psync.push_merge_branch()
diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py
index 91263d2847..67b007f9d9 100644
--- a/tests/subworkflows/test_install.py
+++ b/tests/subworkflows/test_install.py
@@ -18,6 +18,33 @@
 
 
 class TestSubworkflowsInstall(TestSubworkflows):
+    def test_subworkflow_install_force_skip_deps_does_not_reinstall_deps(self):
+        """`install --force --skip-deps` leaves transitive deps' SHAs pinned."""
+        assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
+        samtools_index_path = Path(self.pipeline_dir, "modules", "nf-core", "samtools", "index")
+        assert samtools_index_path.exists()
+        before_sha = ModulesJson(self.pipeline_dir).get_modules_json()["repos"][
+            "https://github.com/nf-core/modules.git"
+        ]["modules"]["nf-core"]["samtools/index"]["git_sha"]
+
+        force_skip = SubworkflowInstall(self.pipeline_dir, prompt=False, force=True, skip_deps=True)
+        assert force_skip.install("bam_sort_stats_samtools") is not False
+        after_sha = ModulesJson(self.pipeline_dir).get_modules_json()["repos"][
+            "https://github.com/nf-core/modules.git"
+        ]["modules"]["nf-core"]["samtools/index"]["git_sha"]
+        assert before_sha == after_sha
+
+    def test_subworkflow_install_skip_deps_preserves_installed_by_tracking(self):
+        """`install --skip-deps` of a parent records the new dependent in shared subcomponents' installed_by."""
+        # Install the sub-subworkflow first so it's already on disk before we --skip-deps the parent.
+        assert self.subworkflow_install.install("bam_stats_samtools") is not False
+        skip_install = SubworkflowInstall(self.pipeline_dir, prompt=False, force=False, skip_deps=True)
+        assert skip_install.install("bam_sort_stats_samtools") is not False
+        installed_by = ModulesJson(self.pipeline_dir).get_modules_json()["repos"][
+            "https://github.com/nf-core/modules.git"
+        ]["subworkflows"]["nf-core"]["bam_stats_samtools"]["installed_by"]
+        assert sorted(installed_by) == sorted(["subworkflows", "bam_sort_stats_samtools"])
+
     def test_subworkflows_install_bam_sort_stats_samtools(self):
         """Test installing a subworkflow - bam_sort_stats_samtools"""
         assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False
diff --git a/tests/subworkflows/test_patch.py b/tests/subworkflows/test_patch.py
index 884af41e83..62a39b3cb0 100644
--- a/tests/subworkflows/test_patch.py
+++ b/tests/subworkflows/test_patch.py
@@ -196,7 +196,7 @@ def test_create_patch_update_success(self):
         ) == Path("subworkflows", GITLAB_REPO, "bam_sort_stats_samtools", patch_fn)
 
         # Update the subworkflow
-        update_obj = nf_core.subworkflows.update.SubworkflowUpdate(
+        update_obj = nf_core.subworkflows.SubworkflowUpdate(
             self.pipeline_dir,
             sha=OLD_SHA,
             show_diff=False,
@@ -256,7 +256,7 @@ def test_create_patch_update_fail(self):
         with open(swf_path / patch_fn) as fh:
             patch_contents = fh.read()
 
-        update_obj = nf_core.subworkflows.update.SubworkflowUpdate(
+        update_obj = nf_core.subworkflows.SubworkflowUpdate(
             self.pipeline_dir,
             sha=FAIL_SHA,
             show_diff=False,
diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py
index 936b61c782..25a41a1e42 100644
--- a/tests/subworkflows/test_update.py
+++ b/tests/subworkflows/test_update.py
@@ -4,6 +4,7 @@
 from pathlib import Path
 from unittest import mock
 
+import pytest
 import questionary
 import yaml
 
@@ -32,6 +33,66 @@ def test_install_and_update(self):
         assert update_obj.update("bam_stats_samtools") is True
         assert cmp_component(tmpdir, sw_path) is True
 
+    def test_subworkflow_update_skip_deps_skips_linked_components(self):
+        """`--skip-deps` updates the named subworkflow's SHA but leaves transitive deps untouched."""
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+        old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        old_dep_sha = old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][
+            "samtools/flagstat"
+        ]["git_sha"]
+
+        update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, skip_deps=True)
+        assert update_obj.update("fastq_align_bowtie2") is True
+
+        mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
+        # The named subworkflow's SHA moved.
+        assert (
+            mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][
+                "git_sha"
+            ]
+            != old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][
+                "fastq_align_bowtie2"
+            ]["git_sha"]
+        )
+        # A transitively-linked module's SHA did not.
+        assert (
+            mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["samtools/flagstat"]["git_sha"]
+            == old_dep_sha
+        )
+
+    def test_subworkflow_update_skip_deps_save_diff_only_named_component(self):
+        """`--skip-deps --save-diff` writes a diff for only the named subworkflow, no linked components."""
+        assert self.subworkflow_install_old.install("fastq_align_bowtie2")
+        diff_path = Path(tempfile.mkdtemp()) / "skipdeps.diff"
+        update_obj = SubworkflowUpdate(
+            self.pipeline_dir,
+            show_diff=False,
+            save_diff_fn=diff_path,
+            skip_deps=True,
+        )
+        assert update_obj.update("fastq_align_bowtie2") is True
+
+        diff_text = diff_path.read_text()
+        # The named subworkflow's main.nf should be in the diff
+        assert "subworkflows/nf-core/fastq_align_bowtie2/main.nf" in diff_text
+        # Transitively-linked module files (e.g. samtools/*) must not be in the diff
+        for linked in (
+            "modules/nf-core/samtools/flagstat/main.nf",
+            "modules/nf-core/samtools/index/main.nf",
+            "modules/nf-core/samtools/sort/main.nf",
+        ):
+            assert linked not in diff_text, f"unexpected linked component in --skip-deps diff: {linked}"
+
+    def test_subworkflow_update_skip_deps_with_update_deps_errors(self):
+        """`--skip-deps` and `--update-deps` are mutually exclusive."""
+        with pytest.raises(UserWarning, match="mutually exclusive"):
+            SubworkflowUpdate(self.pipeline_dir, skip_deps=True, update_deps=True, show_diff=False)._parameter_checks()
+
+    def test_subworkflow_update_skip_deps_with_all_errors(self):
+        """`--skip-deps` and `--all` are mutually exclusive."""
+        with pytest.raises(UserWarning, match="mutually exclusive"):
+            SubworkflowUpdate(self.pipeline_dir, skip_deps=True, update_all=True, show_diff=False)._parameter_checks()
+
     def test_install_at_hash_and_update(self):
         """Installs an old version of a subworkflow in the pipeline and updates it"""
         assert self.subworkflow_install_old.install("fastq_align_bowtie2")
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 60fd4606f8..312b94cc73 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -106,7 +106,7 @@ def test_cli_launch(self, mock_launcher):
                 "revision": "abcdef",
                 "id": "idgui",
                 "command-only": None,
-                "params-out": "/path/params/out",
+                "params-out": Path("/path/params/out"),
                 "params-in": temp_params_in.name,
                 "save-all": None,
                 "show-hidden": None,
diff --git a/tests/test_modules.py b/tests/test_modules.py
index fce0c848ee..52603d7326 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -14,6 +14,7 @@
 import nf_core.modules.modules_repo
 import nf_core.modules.remove
 from nf_core import __version__
+from nf_core.modules.modules_utils import CondaEntry, ContainerEntry, MetaYmlContainers
 from nf_core.pipelines.lint_utils import run_prettier_on_file
 from nf_core.utils import NFCoreYamlConfig
 
@@ -65,6 +66,20 @@ def create_modules_repo_dummy(tmp_dir):
         meta_yml = yaml.load(fh)
     del meta_yml["tools"][0]["bpipe"]["doi"]
     meta_yml["keywords"] = ["pipelines", "bioinformatics", "run"]
+    docker = ContainerEntry(name="quay.io/biocontainers/bpipe:0.9.13--hdfd78af_0", build_id="", scan_id="")
+    sing = ContainerEntry(
+        name="oras://community.wave.seqera.io/library/bpipe:0.9.13--hdfd78af_0",
+        build_id="",
+        https="https://depot.galaxyproject.org/singularity/bpipe:0.9.13--hdfd78af_0",
+    )
+    conda_amd64 = CondaEntry(lock_file="modules/nf-core/bpipe/test/.conda-lock/linux_amd64-bd-dummy_1.txt")
+    conda_arm64 = CondaEntry(lock_file="modules/nf-core/bpipe/test/.conda-lock/linux_arm64-bd-dummy_1.txt")
+    containers = MetaYmlContainers(
+        docker={"linux/amd64": docker, "linux/arm64": docker},
+        singularity={"linux/amd64": sing, "linux/arm64": sing},
+        conda={"linux/amd64": conda_amd64, "linux/arm64": conda_arm64},
+    )
+    meta_yml["containers"] = containers.dump_for_meta_yml()
     with open(str(meta_yml_path), "w") as fh:
         yaml.dump(meta_yml, fh)
         run_prettier_on_file(fh.name)
@@ -179,3 +194,7 @@ def test_modulesrepo_class(self):
     @pytest.fixture(autouse=True)
     def _use_caplog(self, caplog):
         self.caplog = caplog
+
+    @pytest.fixture(autouse=True)
+    def _tmp_path(self, tmp_path):
+        self.tmp_path = tmp_path
diff --git a/tests/test_utils.py b/tests/test_utils.py
index fe5ff56d8e..aaf6e157bd 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -104,7 +104,7 @@ def test_rich_force_colours_true(self):
     def testload_pipeline_config(self):
         """Load the pipeline Nextflow config"""
         self.pipeline_obj.load_pipeline_config()
-        assert self.pipeline_obj.nf_config["dag.enabled"] == "true"
+        assert self.pipeline_obj.nf_config["dag"]["enabled"] is True
 
     # TODO nf-core: Assess and strip out if no longer required for DSL2
 
@@ -249,10 +249,10 @@ def test_set_wd_revert_on_raise(self):
     @mock.patch("nf_core.utils.run_cmd")
     def test_fetch_wf_config(self, mock_run_cmd):
         """Test the fetch_wf_config() regular expression to read config params."""
-        mock_run_cmd.return_value = (b"params.param1 ? 'a=b' : ''\nparams.param2 = foo", b"mock")
-        config = nf_core.utils.fetch_wf_config(".", False)
-        assert len(config.keys()) == 1
-        assert "params.param2" in list(config.keys())
+        mock_run_cmd.return_value = (b'{"params": {"param2": "foo"}}', b"mock")
+        config = nf_core.utils.fetch_wf_config(Path(), False)
+        assert "params" in config
+        assert config["params"].get("param2") == "foo"
 
     @with_temporary_folder
     def test_get_wf_files(self, tmpdir):
diff --git a/tests/test_version_updater.py b/tests/test_version_updater.py
new file mode 100644
index 0000000000..5d938f5b20
--- /dev/null
+++ b/tests/test_version_updater.py
@@ -0,0 +1,63 @@
+"""Tests for the detached remote-version cache updater."""
+
+import json
+import subprocess
+import sys
+from unittest import mock
+
+import pytest
+from packaging.version import InvalidVersion
+
+import nf_core.utils
+from nf_core.version_updater import refresh_version_cache
+
+
+def test_refresh_version_cache(tmp_path):
+    """A valid remote version is written to the cache atomically."""
+    remote_version_path = tmp_path / "remote_version"
+    remote_version_path.write_text("4.1.0\n")
+    cache_path = tmp_path / "latest_version.json"
+
+    refresh_version_cache(remote_version_path.as_uri(), cache_path)
+
+    cached = json.loads(cache_path.read_text())
+    assert cached["version"] == "4.1.0"
+    assert isinstance(cached["timestamp"], float)
+
+
+def test_refresh_version_cache_rejects_invalid_version(tmp_path):
+    """A malformed response does not replace an existing valid cache."""
+    remote_version_path = tmp_path / "remote_version"
+    remote_version_path.write_text("not a version")
+    cache_path = tmp_path / "latest_version.json"
+    original_cache = '{"version": "4.0.0", "timestamp": 123}'
+    cache_path.write_text(original_cache)
+
+    with pytest.raises(InvalidVersion):
+        refresh_version_cache(remote_version_path.as_uri(), cache_path)
+
+    assert cache_path.read_text() == original_cache
+
+
+def test_spawn_remote_version_refresh_uses_updater_module(tmp_path, monkeypatch):
+    """The parent process launches the updater without embedding Python source."""
+    cache_path = tmp_path / "latest_version.json"
+    monkeypatch.setattr(nf_core.utils, "NFCORE_CACHE_DIR", tmp_path)
+    monkeypatch.setattr(nf_core.utils, "REMOTE_VERSION_CACHE", cache_path)
+
+    with mock.patch("subprocess.Popen") as popen:
+        nf_core.utils._spawn_remote_version_refresh("https://example.com/tools_version?v=4.0.0")
+
+    popen.assert_called_once_with(
+        [
+            sys.executable,
+            "-m",
+            "nf_core.version_updater",
+            "https://example.com/tools_version?v=4.0.0",
+            str(cache_path),
+        ],
+        stdin=subprocess.DEVNULL,
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.DEVNULL,
+        start_new_session=True,
+    )
diff --git a/uv.lock b/uv.lock
index 01b3e9ce76..d36e7988cd 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2,24 +2,33 @@ version = 1
 revision = 3
 requires-python = ">=3.10, <4"
 resolution-markers = [
-    "python_full_version >= '3.15'",
-    "python_full_version >= '3.12' and python_full_version < '3.15'",
-    "python_full_version == '3.11.*'",
+    "python_full_version >= '3.15' and sys_platform == 'win32'",
+    "python_full_version >= '3.15' and sys_platform == 'emscripten'",
+    "python_full_version >= '3.15' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+    "python_full_version == '3.14.*' and sys_platform == 'win32'",
+    "python_full_version == '3.14.*' and sys_platform == 'emscripten'",
+    "python_full_version == '3.14.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+    "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'win32'",
+    "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'emscripten'",
+    "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'emscripten'",
+    "python_full_version == '3.11.*' and sys_platform != 'emscripten' and sys_platform != 'win32'",
     "python_full_version < '3.11'",
 ]
 
 [[package]]
 name = "aiohappyeyeballs"
-version = "2.6.1"
+version = "2.7.1"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/26/30/f84a107a9c4331c14b2b586036f40965c128aa4fee4dda5d3d51cb14ad54/aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558", size = 22760, upload-time = "2025-03-12T01:42:48.764Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/ce/f4/eec0465c2f67b2664688d0240b3212d5196fd89e741df67ddb81f8d35658/aiohappyeyeballs-2.7.1.tar.gz", hash = "sha256:065665c041c42a5938ed220bdcd7230f22527fbec085e1853d2402c8a3615d9d", size = 24757, upload-time = "2026-07-01T17:11:55.501Z" }
 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/71/43/1947f06babed6b3f1d7f38b0c767f52df66bfb2bc10b468c4a7de9eceff2/aiohappyeyeballs-2.7.1-py3-none-any.whl", hash = "sha256:9243213661e29250eb41368e5daa826fc017156c3b8a11440826b2e3ed376472", size = 15038, upload-time = "2026-07-01T17:11:54.055Z" },
 ]
 
 [[package]]
 name = "aiohttp"
-version = "3.13.5"
+version = "3.14.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -29,112 +38,129 @@ dependencies = [
     { name = "frozenlist" },
     { name = "multidict" },
     { name = "propcache" },
+    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
     { name = "yarl" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
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