diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index b290e09017..97c8c97fe3 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,20 +1,20 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 0000000000..a5af98b254
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core/sarek devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 31fc01849c..bff17fd3ff 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -25,9 +25,9 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
@@ -52,6 +52,8 @@ runs:
       with:
         auto-update-conda: true
         conda-solver: libmamba
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
     # Set up secrets
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index ac030fd586..6adb0fff4b 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@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         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/cloudtest.yml b/.github/workflows/cloudtest.yml
index b3a9811c26..2b9045ec65 100644
--- a/.github/workflows/cloudtest.yml
+++ b/.github/workflows/cloudtest.yml
@@ -91,19 +91,19 @@ jobs:
         uses: seqeralabs/action-tower-launch@v2
         with:
           run_name: sarek_${{ matrix.profile }}
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets[matrix.compute_env] }}
+          compute_env: ${{ vars[matrix.compute_env] }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: ${{ secrets[matrix.workdir] }}/work/sarek/work-${{ steps.revision.outputs.revision }}/${{ matrix.profile }}
+          workdir: ${{ vars[matrix.workdir] }}/work/sarek/work-${{ steps.revision.outputs.revision }}/${{ matrix.profile }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "${{ secrets[matrix.workdir] }}/sarek/results-${{ steps.revision.outputs.revision }}/${{ matrix.profile }}/"
+              "outdir": "${{ vars[matrix.workdir] }}/sarek/results-${{ steps.revision.outputs.revision }}/${{ matrix.profile }}/"
             }
           profiles: ${{ matrix.profile }}
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 999bcc3829..45884ff900 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -44,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -57,7 +57,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@dev
+          pip install git+https://github.com/nf-core/tools.git
 
       - name: Make a cache directory for the container images
         run: |
@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index af6f0e07b8..8957338b18 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,7 +47,7 @@ jobs:
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +67,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c368..7a527a3464 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d9df..e6e9bc269c 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml
index 0980509d59..3eefb47cd2 100644
--- a/.github/workflows/nf-test-gpu.yml
+++ b/.github/workflows/nf-test-gpu.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -39,9 +39,10 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           fetch-depth: 0
+
       - name: get number of shards
         id: set-shards
         uses: ./.github/actions/get-shards
@@ -70,19 +71,21 @@ jobs:
         profile: [docker, singularity]
         isMain:
           - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
-        # Exclude singularity on dev
+        # Exclude conda and singularity on dev
         exclude:
+          - isMain: false
+            profile: "conda"
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.04.8"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-gpu-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           fetch-depth: 0
 
@@ -96,6 +99,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
           SENTIEON_AUTH_MECH: "GitHub Actions - token"
           SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
           SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 91bebd86a4..ece325f840 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -39,9 +39,10 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
+
       - name: get number of shards
         id: set-shards
         uses: ./.github/actions/get-shards
@@ -85,7 +86,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -95,6 +96,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
           SENTIEON_AUTH_MECH: "GitHub Actions - token"
           SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
           SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 0f73249562..431d3d4457 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -14,6 +14,10 @@ jobs:
         run: |
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
+      - name: get description
+        id: get_description
+        run: |
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -22,7 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index beb5c77fbe..e8560fc7c9 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.gitignore b/.gitignore
index 9cc2a80834..48fe85bcaa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@ null/
 test-datasets/
 test.tap
 test.xml
+.vscode/mcp.json
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 83599f6339..0000000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
-  - name: Update Nextflow and setup pre-commit
-    command: |
-      pre-commit install --install-hooks
-      nextflow self-update
-
-vscode:
-  extensions:
-    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index 5050076aa4..36063f34e1 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -13,7 +13,7 @@ lint:
   nf_test_content: false
   schema_params: false
   template_strings: false
-nf_core_version: 3.3.2
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: Maxime Garcia, Szilveszter Juhos, Friederike Hanssen
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bb41beec14..d06777a8f7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
diff --git a/.prettierignore b/.prettierignore
index edd29f01ed..dd749d43d9 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,4 +10,7 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a302626c3c..db5e1e5495 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| `multiqc`  | 1.31        | 1.32        |
 
 ### Parameters
 
@@ -44,6 +45,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#2041](https://github.com/nf-core/sarek/pull/2041) - Back to dev
 - [#2043](https://github.com/nf-core/sarek/pull/2043) - Refactor postvariantcalling and split out varlociraptor from other options
 - [#2048](https://github.com/nf-core/sarek/pull/2048) - No null value for snpeff_cache and vep_cache in tests
+- [#2058](https://github.com/nf-core/sarek/pull/2058) - Template update for nf-core/tools v3.5.1
 
 #### Fixed
 
diff --git a/README.md b/README.md
index 64f6606b0c..d82f691b29 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,7 @@
   </picture>
 </h1>
 
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/sarek)
 [![GitHub Actions CI Status](https://github.com/nf-core/sarek/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/sarek/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/sarek/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/sarek/actions/workflows/linting.yml)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results)
@@ -12,7 +13,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/assets/schema_input.json b/assets/schema_input.json
index dac459f9da..3c910dc055 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -34,7 +34,7 @@
                 "enum": [0, 1]
             },
             "lane": {
-                "type": "string",
+                "anyOf": [{ "type": "integer" }, { "type": "string" }],
                 "pattern": "^\\S+$",
                 "description": "Lane identifier used to distinguish between different sequencing runs of the same sample.",
                 "errorMessage": "Lane identifier cannot contain spaces",
diff --git a/conf/base.config b/conf/base.config
index ea597795de..4e184eca9c 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,6 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 8.h    * task.attempt }
 
-    // memory errors which should be retried. otherwise error out
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
@@ -31,6 +30,7 @@ process {
     }
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
     }
     withLabel:process_single {
         cpus   = { 1                   }
diff --git a/docs/usage.md b/docs/usage.md
index 8d8cda63f6..b38bc6d93b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -424,7 +424,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `shifter`
   - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
 - `charliecloud`
-  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+  - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
@@ -457,6 +457,26 @@ Whilst the default requirements set within the pipeline will hopefully work for
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
+### Custom Containers
+
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
+
+To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
+
+### Custom Tool Arguments
+
+A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
+
+To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
+
+### nf-core/configs
+
+In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
+
+See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files.
+
+If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
+
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
@@ -1115,8 +1135,8 @@ Which can then be used this way in Sarek:
 ```bash
 nextflow run nf-core/sarek \
     --igenomes_base s3://my-reference-data/igenomes/ \
-    --snpeff_cache s3://my-reference-data/cache/ensemblvep/ \
-    --vep_cache s3://my-reference-data/cache/snpeff/ \
+    --snpeff_cache s3://my-reference-data/cache/snpeff/ \
+    --vep_cache s3://my-reference-data/cache/ensemblvep/ \
     ...
 ```
 
diff --git a/main.nf b/main.nf
index 787ca6ee7f..7c5a4ddd29 100755
--- a/main.nf
+++ b/main.nf
@@ -272,10 +272,9 @@ workflow NFCORE_SAREK {
         PREPARE_GENOME.out.pon,
         PREPARE_GENOME.out.pon_tbi,
         params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([]),
-         // Set Varlociraptor reference files
-        params.varlociraptor_scenario_germline   ? Channel.fromPath(params.varlociraptor_scenario_germline).map { it -> [[id: it.baseName - '.yte'], it] }.collect()    : Channel.fromPath("${projectDir}/assets/varlociraptor_germline.yte.yaml").collect(),
-        params.varlociraptor_scenario_somatic    ? Channel.fromPath(params.varlociraptor_scenario_somatic).map { it -> [[id: it.baseName - '.yte'], it] }.collect()     : Channel.fromPath("${projectDir}/assets/varlociraptor_somatic.yte.yaml").collect(),
-        params.varlociraptor_scenario_tumor_only ? Channel.fromPath(params.varlociraptor_scenario_tumor_only).map { it -> [[id: it.baseName - '.yte'], it] }.collect()  : Channel.fromPath("${projectDir}/assets/varlociraptor_tumor_only.yte.yaml").collect(),
+        params.varlociraptor_scenario_germline ? Channel.fromPath(params.varlociraptor_scenario_germline).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_germline.yte.yaml").collect(),
+        params.varlociraptor_scenario_somatic ? Channel.fromPath(params.varlociraptor_scenario_somatic).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_somatic.yte.yaml").collect(),
+        params.varlociraptor_scenario_tumor_only ? Channel.fromPath(params.varlociraptor_scenario_tumor_only).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : Channel.fromPath("${projectDir}/assets/varlociraptor_tumor_only.yte.yaml").collect(),
         snpeff_cache,
         params.snpeff_db,
         vep_cache,
@@ -306,6 +305,9 @@ workflow {
         args,
         params.outdir,
         params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden,
     )
 
     //
diff --git a/modules.json b/modules.json
index 1aff8a161c..6c1d954c6f 100644
--- a/modules.json
+++ b/modules.json
@@ -602,17 +602,17 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
                         "installed_by": ["subworkflows"]
                     },
                     "vcf_annotate_ensemblvep": {
diff --git a/nextflow.config b/nextflow.config
index a475616256..437a8beb47 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -141,13 +141,15 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = null
+    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+    // Config options
     config_profile_name        = null
     config_profile_description = null
     custom_config_version      = 'master'
@@ -201,7 +203,18 @@ profiles {
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
     }
-    arm {
+    arm64 {
+        process.arch            = 'arm64'
+        // TODO https://github.com/nf-core/modules/issues/6694
+        // For now if you're using arm64 you have to use wave for the sake of the maintainers
+        // wave profile
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    emulate_amd64 {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
@@ -258,18 +271,6 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    gitpod {
-        executor.name           = 'local'
-        executor.cpus           = 4
-        executor.memory         = 8.GB
-        process {
-            resourceLimits = [
-                memory: 8.GB,
-                cpus  : 4,
-                time  : 1.h
-            ]
-        }
-    }
     gpu {
         docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
         apptainer.runOptions    = '--nv'
@@ -342,6 +343,7 @@ profiles {
 // Load nf-core/sarek custom profiles from different institutions.
 includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
+
 // Load nf-core/sarek custom profiles from different institutions.
 includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/sarek.config" : "/dev/null"
 
@@ -427,115 +429,86 @@ manifest {
         ],
         [
             name: 'Szilveszter Juhos',
-            affiliation: '',
             github: '@szilvajuhos',
             contribution: ['author'],
             orcid: '0000-0001-6280-4643'
         ],
         [
             name: 'Abhinav Sharma',
-            affiliation: '',
             github: '@abhi18av',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Adam Talbot',
             affiliation: 'Seqera',
             github: '@adamrtalbot',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Adrian Lärkeryd',
-            affiliation: '',
             github: '@adrlar',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Àitor Olivares',
-            affiliation: '',
             github: '@AitorPeseta',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Alexander Peltzer',
-            affiliation: '',
             github: '@apeltzer',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Alison Meynert',
-            affiliation: '',
             github: '@ameynert',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Anders Sune Pedersen',
-            affiliation: '',
             github: '@asp8200',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Aron Skaftason',
-            affiliation: '',
             github: '@arontommi',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Barry Digby',
-            affiliation: '',
             github: '@BarryDigby',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Bekir Ergüner',
-            affiliation: '',
             github: '@berguner',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Björn Nystedt',
-            affiliation: '',
             github: '@bjornnystedt',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Christina Chatzipantsiou',
-            affiliation: '',
             github: '@cgpu',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Chela James',
-            affiliation: '',
             github: '@chelauk',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'David Mas-Ponte',
-            affiliation: '',
             github: '@davidmasp',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Edmund Miller',
             affiliation: 'Seqera',
             github: '@edmundmiller',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Famke Bäuerle',
@@ -546,80 +519,59 @@ manifest {
         ],
         [
             name: 'Francesco Lescai',
-            affiliation: '',
             github: '@lescai',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Francisco Martínez',
-            affiliation: '',
             github: '@nevinwu',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Gavin Mackenzie',
-            affiliation: '',
             github: '@GCJMackenzie',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Gisela Gabernet',
-            affiliation: '',
             github: '@ggabernet',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Grant Neilson',
-            affiliation: '',
             github: '@grantn5',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Max Käller',
-            affiliation: '',
             github: '@gulfshores',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Harshil Patel',
             affiliation: 'Seqera',
             github: '@drpatelh',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Hongwei Ye',
-            affiliation: '',
             github: '@YeHW',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'James A. Fellows Yates',
-            affiliation: '',
             github: '@jfy133',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Jesper Eisfeldt',
-            affiliation: '',
             github: '@J35P312',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Johannes Alneberg',
-            affiliation: '',
             github: '@alneberg',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Jonas Kjellin',
@@ -630,157 +582,115 @@ manifest {
         ],
         [
             name: 'José Fernández Navarro',
-            affiliation: '',
             github: '@jfnavarro',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Júlia Mir Pedrol',
-            affiliation: '',
             github: '@mirpedrol',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Ken Brewer',
             affiliation: 'Seqera',
             github: '@kenibrewer',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Lasse Westergaard Folkersen',
-            affiliation: '',
             github: '@lassefolkersen',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Lucia Conde',
-            affiliation: '',
             github: '@lconde-ucl',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Louis Le Nézet',
-            affiliation: '',
             github: '@LouisLeNezet',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Malin Larsson',
-            affiliation: '',
             github: '@malinlarsson',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Marcel Martin',
-            affiliation: '',
             github: '@marcelm',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Nick Smith',
-            affiliation: '',
             github: '@nickhsmith',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Nicolas Schcolnicov',
-            affiliation: '',
             github: '@nschcolnicov',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Nilesh Tawari',
-            affiliation: '',
             github: '@nilesh-tawari',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Nils Homer',
-            affiliation: '',
             github: '@nh13',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Olga Botvinnik',
-            affiliation: '',
             github: '@olgabot',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Oskar Wacker',
-            affiliation: '',
             github: '@WackerO',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Pall Olason',
-            affiliation: '',
             github: '@pallolason',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Paul Cantalupo',
-            affiliation: '',
             github: '@pcantalupo',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Phil Ewels',
             affiliation: 'Seqera',
             github: '@ewels',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Pierre Lindenbaum',
-            affiliation: '',
             github: '@lindenb',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Sabrina Krakau',
-            affiliation: '',
             github: '@skrakau',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Sam Minot',
-            affiliation: '',
             github: '@sminot',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Sebastian DiLorenzo',
-            affiliation: '',
             github: '@Sebastian-D',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Silvia Morini',
-            affiliation: '',
             github: '@silviamorins',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Simon Pearce',
@@ -791,38 +701,28 @@ manifest {
         ],
         [
             name: 'Solenne Correard',
-            affiliation: '',
             github: '@scorreard',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Susanne Jodoin',
-            affiliation: '',
             github: '@SusiJo',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Tobias Koch',
-            affiliation: '',
             github: '@KochTobi',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Winni Kretzschmar',
-            affiliation: '',
             github: '@winni2k',
             contribution: ['contributor'],
-            orcid: ''
         ],
         [
             name: 'Patricie Skaláková',
-            affiliation: '',
             github: '@Patricie34',
             contribution: ['contributor'],
-            orcid: ''
         ]
     ]
     homePage        = 'https://github.com/nf-core/sarek'
@@ -837,49 +737,14 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
     id 'nf-prov@1.2.2'   // Provenance reports for pipeline runs
     id 'nf-fgbio@1.0.0'  // Validation of read structures passed to fgbio consensus generation
 }
 
 validation {
-    defaultIgnoreParams = ["genomes"]
+    defaultIgnoreParams = ["genomes", "freebayes_filter", "vep_cache_version"]
     monochromeLogs = params.monochrome_logs
-    lenientMode = true
-    help {
-        enabled = true
-        command = "nextflow run nf-core/sarek -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
-        showHiddenParameter = "show_hidden"
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;37m      ____\033[0m
-\033[0;37m    .´ _  `.\033[0m
-\033[0;37m   /  \033[0;32m|\\\033[0m`-_ \\\033[0m     \033[0;34m __        __   ___     \033[0m
-\033[0;37m  |   \033[0;32m| \\\033[0m  `-|\033[0m    \033[0;34m|__`  /\\  |__) |__  |__/\033[0m
-\033[0;37m   \\ \033[0;32m|   \\\033[0m  /\033[0m     \033[0;34m.__| /¯¯\\ |  \\ |___ |  \\\033[0m
-\033[0;37m    `\033[0;32m|\033[0m____\033[0;32m\\\033[0m´\033[0m
-
-\033[0;35m  nf-core/sarek ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/nf-core/sarek/blob/master/CITATIONS.md
-"""
-    }
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e4df2e49e3..e33762eae7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1247,6 +1247,18 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
+                },
+                "help": {
+                    "type": ["boolean", "string"],
+                    "description": "Display the help message."
+                },
+                "help_full": {
+                    "type": "boolean",
+                    "description": "Display the full detailed help message."
+                },
+                "show_hidden": {
+                    "type": "boolean",
+                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                 }
             }
         }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 89097d0969..e4a7e7ce20 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-11-05T15:53:37+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-sarek_logo_dark.png\">\n    <img alt=\"nf-core/sarek\" src=\"docs/images/nf-core-sarek_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/sarek/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/sarek/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/sarek/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/sarek/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476425-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/sarek)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23sarek-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/sarek)\n[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)\n[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)\n[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/sarek** is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/sarek/results).\n\nIt's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/nf-core-sarek) and [Dockstore](https://dockstore.org/workflows/github.com/nf-core/sarek).\n\n<p align=\"center\">\n    <img title=\"Sarek Workflow\" src=\"docs/images/sarek_workflow.png\" width=30%>\n</p>\n\n## Pipeline summary\n\nDepending on the options and samples provided, the pipeline can currently perform the following:\n\n- Form consensus reads from UMI sequences (`fgbio`)\n- Sequencing quality control and trimming (enabled by `--trim_fastq`) (`FastQC`, `fastp`)\n- Contamination removal (`BBSplit`, enabled by `--tools bbsplit`)\n- Map Reads to Reference (`BWA-mem`, `BWA-mem2`, `dragmap` or `Sentieon BWA-mem`)\n- Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator` and `GATK ApplyBQSR` or `Sentieon LocusCollector` and `Sentieon Dedup`)\n- _Experimental Feature_: Use GPU-accelerated parabricks implementation as alternative to \"Map Reads to Reference\" + \"Process BAM file\" (`--aligner parabricks`)\n- Summarise alignment statistics (`samtools stats`, `mosdepth`)\n- Variant calling (enabled by `--tools`, see [compatibility](https://nf-co.re/sarek/latest/docs/usage#which-variant-calling-tool-is-implemented-for-which-data-type)):\n  - `ASCAT`\n  - `CNVkit`\n  - `Control-FREEC`\n  - `DeepVariant`\n  - `freebayes`\n  - `GATK HaplotypeCaller`\n  - `GATK Mutect2`\n  - `indexcov`\n  - `Lofreq`\n  - `Manta`\n  - `mpileup`\n  - `MSIsensor2`\n  - `MSIsensor-pro`\n  - `MuSE`\n  - `Sentieon Haplotyper`\n  - `Strelka`\n  - `TIDDIT`\n- Post-variant calling options, one of:\n  - Filtering (`bcftools view` (default: filter by `PASS,.`)), normalisation (`bcftools norm`) and consensus calling (`bcftools isec`, default: called by at least 2 tools `-n+2`) on all vcfs and/or `bcftools concat` for germline vcfs\n  - `Varlociraptor` for all vcfs\n- Variant filtering and annotation (`SnpEff`, `Ensembl VEP`, `BCFtools annotate`)\n- Summarise and represent QC (`MultiQC`)\n\n<p align=\"center\">\n    <img title=\"Sarek Workflow\" src=\"docs/images/sarek_subway.png\" width=60%>\n</p>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\npatient,sample,lane,fastq_1,fastq_2\nID1,S1,L002,ID1_S1_L002_R1_001.fastq.gz,ID1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/sarek \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/sarek/usage) and the [parameter documentation](https://nf-co.re/sarek/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/sarek/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/sarek/output).\n\n## Benchmarking\n\nOn each release, the pipeline is run on 3 full size tests:\n\n- `test_full` runs tumor-normal data for one patient from the SEQ2C consortium\n- `test_full_germline` runs a WGS 30X Genome-in-a-Bottle(NA12878) dataset\n- `test_full_germline_ncbench_agilent` runs two WES samples with 75M and 200M reads (data available [here](https://github.com/ncbench/ncbench-workflow#contributing-callsets)). The results are uploaded to Zenodo, evaluated against a truth dataset, and results are made available via the [NCBench dashboard](https://ncbench.github.io/report/report.html#).\n\n## Credits\n\nSarek was originally written by Maxime U Garcia and Szilveszter Juhos at the [National Genomics Infastructure](https://ngisweden.scilifelab.se) and [National Bioinformatics Infastructure Sweden](https://nbis.se) which are both platforms at [SciLifeLab](https://scilifelab.se), with the support of [The Swedish Childhood Tumor Biobank (Barntum\u00f6rbanken)](https://ki.se/forskning/barntumorbanken).\nFriederike Hanssen and Gisela Gabernet at [QBiC](https://www.qbic.uni-tuebingen.de/) later joined and helped with further development.\n\nThe Nextflow DSL2 conversion of the pipeline was lead by Friederike Hanssen and Maxime U Garcia.\n\nMaintenance is now lead by Friederike Hanssen and Maxime U Garcia (now at [Seqera](https://seqera.io))\n\nMain developers:\n\n- [Maxime U Garcia](https://github.com/maxulysse)\n- [Friederike Hanssen](https://github.com/FriederikeHanssen)\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Abhinav Sharma](https://github.com/abhi18av)\n- [Adam Talbot](https://github.com/adamrtalbot)\n- [Adrian L\u00e4rkeryd](https://github.com/adrlar)\n- [\u00c0itor Olivares](https://github.com/AitorPeseta)\n- [Alexander Peltzer](https://github.com/apeltzer)\n- [Alison Meynert](https://github.com/ameynert)\n- [Anders Sune Pedersen](https://github.com/asp8200)\n- [arontommi](https://github.com/arontommi)\n- [BarryDigby](https://github.com/BarryDigby)\n- [Bekir Erg\u00fcner](https://github.com/berguner)\n- [bjornnystedt](https://github.com/bjornnystedt)\n- [cgpu](https://github.com/cgpu)\n- [Chela James](https://github.com/chelauk)\n- [David Mas-Ponte](https://github.com/davidmasp)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Famke B\u00e4uerle](https://github.com/famosab)\n- [Francesco Lescai](https://github.com/lescai)\n- [Francisco Mart\u00ednez](https://github.com/nevinwu)\n- [Gavin Mackenzie](https://github.com/GCJMackenzie)\n- [Gisela Gabernet](https://github.com/ggabernet)\n- [Grant Neilson](https://github.com/grantn5)\n- [gulfshores](https://github.com/gulfshores)\n- [Harshil Patel](https://github.com/drpatelh)\n- [Hongwei Ye](https://github.com/YeHW)\n- [James A. Fellows Yates](https://github.com/jfy133)\n- [Jesper Eisfeldt](https://github.com/J35P312)\n- [Johannes Alneberg](https://github.com/alneberg)\n- [Jonas Kjellin](https://github.com/kjellinjonas)\n- [Jos\u00e9 Fern\u00e1ndez Navarro](https://github.com/jfnavarro)\n- [J\u00falia Mir Pedrol](https://github.com/mirpedrol)\n- [Ken Brewer](https://github.com/kenibrewer)\n- [Lasse Westergaard Folkersen](https://github.com/lassefolkersen)\n- [Lucia Conde](https://github.com/lconde-ucl)\n- [Louis Le N\u00e9zet](https://github.com/LouisLeNezet)\n- [Malin Larsson](https://github.com/malinlarsson)\n- [Marcel Martin](https://github.com/marcelm)\n- [Nick Smith](https://github.com/nickhsmith)\n- [Nicolas Schcolnicov](https://github.com/nschcolnicov)\n- [Nilesh Tawari](https://github.com/nilesh-tawari)\n- [Nils Homer](https://github.com/nh13)\n- [Olga Botvinnik](https://github.com/olgabot)\n- [Oskar Wacker](https://github.com/WackerO)\n- [pallolason](https://github.com/pallolason)\n- [Paul Cantalupo](https://github.com/pcantalupo)\n- [Phil Ewels](https://github.com/ewels)\n- [Pierre Lindenbaum](https://github.com/lindenb)\n- [Sabrina Krakau](https://github.com/skrakau)\n- [Sam Minot](https://github.com/sminot)\n- [Sebastian-D](https://github.com/Sebastian-D)\n- [Silvia Morini](https://github.com/silviamorins)\n- [Simon Pearce](https://github.com/SPPearce)\n- [Solenne Correard](https://github.com/scorreard)\n- [Susanne Jodoin](https://github.com/SusiJo)\n- [Szilveszter Juhos](https://github.com/szilvajuhos)\n- [Tobias Koch](https://github.com/KochTobi)\n- [Winni Kretzschmar](https://github.com/winni2k)\n- [Patricie Skal\u00e1kov\u00e1](https://github.com/Patricie34)\n\n## Acknowledgements\n\n|      [![Barntum\u00f6rbanken](docs/images/BTB_logo.png)](https://ki.se/forskning/barntumorbanken)      |            [![SciLifeLab](docs/images/SciLifeLab_logo.png)](https://scilifelab.se)             |\n| :-----------------------------------------------------------------------------------------------: | :--------------------------------------------------------------------------------------------: |\n| [![National Genomics Infrastructure](docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/) | [![National Bioinformatics Infrastructure Sweden](docs/images/NBIS_logo.png)](https://nbis.se) |\n|              [![QBiC](docs/images/QBiC_logo.png)](https://www.qbic.uni-tuebingen.de)              |                   [![GHGA](docs/images/GHGA_logo.png)](https://www.ghga.de/)                   |\n|                     [![DNGC](docs/images/DNGC_logo.png)](https://eng.ngc.dk/)                     |                                                                                                |\n\n## Contributions & Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#sarek` channel](https://nfcore.slack.com/channels/sarek) (you can join with [this invite](https://nf-co.re/join/slack)), or contact us: [Maxime U Garcia](mailto:maxime.garcia@seqera.io?subject=[GitHub]%20nf-core/sarek), [Friederike Hanssen](mailto:friederike.hanssen@qbic.uni-tuebingen.de?subject=[GitHub]%20nf-core/sarek)\n\n## Citations\n\nIf you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:\n\n> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031).\n\n> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).\n\nYou can cite the sarek zenodo record for a specific version using the following [doi: 10.5281/zenodo.3476425](https://doi.org/10.5281/zenodo.3476425)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\n## CHANGELOG\n\n- [CHANGELOG](CHANGELOG.md)\n",
+            "datePublished": "2025-11-19T15:39:16+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-sarek_logo_dark.png\">\n    <img alt=\"nf-core/sarek\" src=\"docs/images/nf-core-sarek_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/sarek)\n[![GitHub Actions CI Status](https://github.com/nf-core/sarek/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/sarek/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/sarek/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/sarek/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476425-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/sarek)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23sarek-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/sarek)\n[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)\n[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)\n[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/sarek** is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/sarek/results).\n\nIt's listed on [Elixir - Tools and Data Services Registry](https://bio.tools/nf-core-sarek) and [Dockstore](https://dockstore.org/workflows/github.com/nf-core/sarek).\n\n<p align=\"center\">\n    <img title=\"Sarek Workflow\" src=\"docs/images/sarek_workflow.png\" width=30%>\n</p>\n\n## Pipeline summary\n\nDepending on the options and samples provided, the pipeline can currently perform the following:\n\n- Form consensus reads from UMI sequences (`fgbio`)\n- Sequencing quality control and trimming (enabled by `--trim_fastq`) (`FastQC`, `fastp`)\n- Contamination removal (`BBSplit`, enabled by `--tools bbsplit`)\n- Map Reads to Reference (`BWA-mem`, `BWA-mem2`, `dragmap` or `Sentieon BWA-mem`)\n- Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator` and `GATK ApplyBQSR` or `Sentieon LocusCollector` and `Sentieon Dedup`)\n- _Experimental Feature_: Use GPU-accelerated parabricks implementation as alternative to \"Map Reads to Reference\" + \"Process BAM file\" (`--aligner parabricks`)\n- Summarise alignment statistics (`samtools stats`, `mosdepth`)\n- Variant calling (enabled by `--tools`, see [compatibility](https://nf-co.re/sarek/latest/docs/usage#which-variant-calling-tool-is-implemented-for-which-data-type)):\n  - `ASCAT`\n  - `CNVkit`\n  - `Control-FREEC`\n  - `DeepVariant`\n  - `freebayes`\n  - `GATK HaplotypeCaller`\n  - `GATK Mutect2`\n  - `indexcov`\n  - `Lofreq`\n  - `Manta`\n  - `mpileup`\n  - `MSIsensor2`\n  - `MSIsensor-pro`\n  - `MuSE`\n  - `Sentieon Haplotyper`\n  - `Strelka`\n  - `TIDDIT`\n- Post-variant calling options, one of:\n  - `BCFtools concat` for germline vcfs and/or `BCFtools view` (default: filter by `PASS`), `BCFtools norm` for all vcfs\n  - `Varlociraptor` for all vcfs\n- Variant filtering and annotation (`SnpEff`, `Ensembl VEP`, `BCFtools annotate`)\n- Summarise and represent QC (`MultiQC`)\n\n<p align=\"center\">\n    <img title=\"Sarek Workflow\" src=\"docs/images/sarek_subway.png\" width=60%>\n</p>\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\npatient,sample,lane,fastq_1,fastq_2\nID1,S1,L002,ID1_S1_L002_R1_001.fastq.gz,ID1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/sarek \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/sarek/usage) and the [parameter documentation](https://nf-co.re/sarek/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/sarek/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/sarek/output).\n\n## Benchmarking\n\nOn each release, the pipeline is run on 3 full size tests:\n\n- `test_full` runs tumor-normal data for one patient from the SEQ2C consortium\n- `test_full_germline` runs a WGS 30X Genome-in-a-Bottle(NA12878) dataset\n- `test_full_germline_ncbench_agilent` runs two WES samples with 75M and 200M reads (data available [here](https://github.com/ncbench/ncbench-workflow#contributing-callsets)). The results are uploaded to Zenodo, evaluated against a truth dataset, and results are made available via the [NCBench dashboard](https://ncbench.github.io/report/report.html#).\n\n## Credits\n\nSarek was originally written by Maxime U Garcia and Szilveszter Juhos at the [National Genomics Infastructure](https://ngisweden.scilifelab.se) and [National Bioinformatics Infastructure Sweden](https://nbis.se) which are both platforms at [SciLifeLab](https://scilifelab.se), with the support of [The Swedish Childhood Tumor Biobank (Barntum\u00f6rbanken)](https://ki.se/forskning/barntumorbanken).\nFriederike Hanssen and Gisela Gabernet at [QBiC](https://www.qbic.uni-tuebingen.de/) later joined and helped with further development.\n\nThe Nextflow DSL2 conversion of the pipeline was lead by Friederike Hanssen and Maxime U Garcia.\n\nMaintenance is now lead by Friederike Hanssen and Maxime U Garcia (now at [Seqera](https://seqera.io))\n\nMain developers:\n\n- [Maxime U Garcia](https://github.com/maxulysse)\n- [Friederike Hanssen](https://github.com/FriederikeHanssen)\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Abhinav Sharma](https://github.com/abhi18av)\n- [Adam Talbot](https://github.com/adamrtalbot)\n- [Adrian L\u00e4rkeryd](https://github.com/adrlar)\n- [\u00c0itor Olivares](https://github.com/AitorPeseta)\n- [Alexander Peltzer](https://github.com/apeltzer)\n- [Alison Meynert](https://github.com/ameynert)\n- [Anders Sune Pedersen](https://github.com/asp8200)\n- [arontommi](https://github.com/arontommi)\n- [BarryDigby](https://github.com/BarryDigby)\n- [Bekir Erg\u00fcner](https://github.com/berguner)\n- [bjornnystedt](https://github.com/bjornnystedt)\n- [cgpu](https://github.com/cgpu)\n- [Chela James](https://github.com/chelauk)\n- [David Mas-Ponte](https://github.com/davidmasp)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Famke B\u00e4uerle](https://github.com/famosab)\n- [Francesco Lescai](https://github.com/lescai)\n- [Francisco Mart\u00ednez](https://github.com/nevinwu)\n- [Gavin Mackenzie](https://github.com/GCJMackenzie)\n- [Gisela Gabernet](https://github.com/ggabernet)\n- [Grant Neilson](https://github.com/grantn5)\n- [gulfshores](https://github.com/gulfshores)\n- [Harshil Patel](https://github.com/drpatelh)\n- [Hongwei Ye](https://github.com/YeHW)\n- [James A. Fellows Yates](https://github.com/jfy133)\n- [Jesper Eisfeldt](https://github.com/J35P312)\n- [Johannes Alneberg](https://github.com/alneberg)\n- [Jonas Kjellin](https://github.com/kjellinjonas)\n- [Jos\u00e9 Fern\u00e1ndez Navarro](https://github.com/jfnavarro)\n- [J\u00falia Mir Pedrol](https://github.com/mirpedrol)\n- [Ken Brewer](https://github.com/kenibrewer)\n- [Lasse Westergaard Folkersen](https://github.com/lassefolkersen)\n- [Lucia Conde](https://github.com/lconde-ucl)\n- [Louis Le N\u00e9zet](https://github.com/LouisLeNezet)\n- [Malin Larsson](https://github.com/malinlarsson)\n- [Marcel Martin](https://github.com/marcelm)\n- [Nick Smith](https://github.com/nickhsmith)\n- [Nicolas Schcolnicov](https://github.com/nschcolnicov)\n- [Nilesh Tawari](https://github.com/nilesh-tawari)\n- [Nils Homer](https://github.com/nh13)\n- [Olga Botvinnik](https://github.com/olgabot)\n- [Oskar Wacker](https://github.com/WackerO)\n- [pallolason](https://github.com/pallolason)\n- [Paul Cantalupo](https://github.com/pcantalupo)\n- [Phil Ewels](https://github.com/ewels)\n- [Pierre Lindenbaum](https://github.com/lindenb)\n- [Sabrina Krakau](https://github.com/skrakau)\n- [Sam Minot](https://github.com/sminot)\n- [Sebastian-D](https://github.com/Sebastian-D)\n- [Silvia Morini](https://github.com/silviamorins)\n- [Simon Pearce](https://github.com/SPPearce)\n- [Solenne Correard](https://github.com/scorreard)\n- [Susanne Jodoin](https://github.com/SusiJo)\n- [Szilveszter Juhos](https://github.com/szilvajuhos)\n- [Tobias Koch](https://github.com/KochTobi)\n- [Winni Kretzschmar](https://github.com/winni2k)\n- [Patricie Skal\u00e1kov\u00e1](https://github.com/Patricie34)\n\n## Acknowledgements\n\n|      [![Barntum\u00f6rbanken](docs/images/BTB_logo.png)](https://ki.se/forskning/barntumorbanken)      |            [![SciLifeLab](docs/images/SciLifeLab_logo.png)](https://scilifelab.se)             |\n| :-----------------------------------------------------------------------------------------------: | :--------------------------------------------------------------------------------------------: |\n| [![National Genomics Infrastructure](docs/images/NGI_logo.png)](https://ngisweden.scilifelab.se/) | [![National Bioinformatics Infrastructure Sweden](docs/images/NBIS_logo.png)](https://nbis.se) |\n|              [![QBiC](docs/images/QBiC_logo.png)](https://www.qbic.uni-tuebingen.de)              |                   [![GHGA](docs/images/GHGA_logo.png)](https://www.ghga.de/)                   |\n|                     [![DNGC](docs/images/DNGC_logo.png)](https://eng.ngc.dk/)                     |                                                                                                |\n\n## Contributions & Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#sarek` channel](https://nfcore.slack.com/channels/sarek) (you can join with [this invite](https://nf-co.re/join/slack)), or contact us: [Maxime U Garcia](mailto:maxime.garcia@seqera.io?subject=[GitHub]%20nf-core/sarek), [Friederike Hanssen](mailto:friederike.hanssen@qbic.uni-tuebingen.de?subject=[GitHub]%20nf-core/sarek)\n\n## Citations\n\nIf you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:\n\n> Friederike Hanssen, Maxime U Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Oskar Wacker, Nicholas Smith, nf-core community, Gisela Gabernet, Sven Nahnsen **Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery** _NAR Genomics and Bioinformatics_ Volume 6, Issue 2, June 2024, lqae031, [doi: 10.1093/nargab/lqae031](https://doi.org/10.1093/nargab/lqae031).\n\n> Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]** _F1000Research_ 2020, 9:63 [doi: 10.12688/f1000research.16665.2](http://dx.doi.org/10.12688/f1000research.16665.2).\n\nYou can cite the sarek zenodo record for a specific version using the following [doi: 10.5281/zenodo.3476425](https://doi.org/10.5281/zenodo.3476425)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\n## CHANGELOG\n\n- [CHANGELOG](CHANGELOG.md)\n",
             "hasPart": [
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@@ -105,7 +105,7 @@
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+                    "@id": "#06f831fd-7306-45b0-934e-7b328b9f362d"
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             "name": "nf-core/sarek"
@@ -132,79 +132,8 @@
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-            ],
             "dateCreated": "",
-            "dateModified": "2025-11-05T16:53:37Z",
+            "dateModified": "2025-11-19T16:39:16Z",
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             "keywords": [
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@@ -224,53 +153,6 @@
             "license": [
                 "MIT"
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-                {
-                    "@id": "#jc.fernandez.navarro@gmail.com"
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@@ -301,11 +183,11 @@
             "version": "!>=25.04.8"
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+            "@id": "#06f831fd-7306-45b0-934e-7b328b9f362d",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#606291c7-4c19-4d6f-b498-b8cc8ddb4e2e"
+                    "@id": "#9c2e81df-ab11-4ead-b9f5-bc8369300646"
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@@ -314,7 +196,7 @@
             "name": "Test suite for nf-core/sarek"
         },
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-            "@id": "#606291c7-4c19-4d6f-b498-b8cc8ddb4e2e",
+            "@id": "#9c2e81df-ab11-4ead-b9f5-bc8369300646",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/sarek",
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@@ -451,132 +333,6 @@
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\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
index a7a0d3d8e8..a06e31388b 100644
--- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
@@ -9,6 +9,7 @@
 include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap        } from 'plugin/nf-schema'
 include { samplesheetToList       } from 'plugin/nf-schema'
+include { paramsHelp              } from 'plugin/nf-schema'
 include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification          } from '../../nf-core/utils_nfcore_pipeline'
@@ -24,15 +25,18 @@ include { SAMPLESHEET_TO_CHANNEL  } from '../samplesheet_to_channel'
 
 workflow PIPELINE_INITIALISATION {
     take:
-    version           // boolean: Display version and exit
-    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
+    version // boolean: Display version and exit
+    validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
     nextflow_cli_args //   array: List of positional nextflow CLI args
-    outdir            //  string: The output directory where the results will be saved
-    input             //  string: Path to input samplesheet
+    outdir //  string: The output directory where the results will be saved
+    input //  string: Path to input samplesheet
+    help // boolean: Display help message and exit
+    help_full // boolean: Show the full help message
+    show_hidden // boolean: Show hidden parameters in the help message
 
     main:
 
-    versions = Channel.empty()
+    versions = channel.empty()
 
     // Print version and exit if required and dump pipeline parameters to JSON file
     UTILS_NEXTFLOW_PIPELINE(
@@ -43,10 +47,43 @@ workflow PIPELINE_INITIALISATION {
     )
 
     // Validate parameters and generate parameter summary to stdout
+    //
+    def before_text = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;37m      ____\033[0m
+\033[0;37m    .´ _  `.\033[0m
+\033[0;37m   /  \033[0;32m|\\\033[0m`-_ \\\033[0m     \033[0;34m __        __   ___     \033[0m
+\033[0;37m  |   \033[0;32m| \\\033[0m  `-|\033[0m    \033[0;34m|__`  /\\  |__) |__  |__/\033[0m
+\033[0;37m   \\ \033[0;32m|   \\\033[0m  /\033[0m     \033[0;34m.__| /¯¯\\ |  \\ |___ |  \\\033[0m
+\033[0;37m    `\033[0;32m|\033[0m____\033[0;32m\\\033[0m´\033[0m
+
+\033[0;35m  nf-core/sarek ${workflow.manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+    def after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/nf-core/sarek/blob/master/CITATIONS.md
+"""
+    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+
     UTILS_NFSCHEMA_PLUGIN(
         workflow,
         validate_params,
         null,
+        help,
+        help_full,
+        show_hidden,
+        before_text,
+        after_text,
+        command,
     )
 
     // Check config provided to the pipeline
@@ -109,10 +146,10 @@ workflow PIPELINE_INITIALISATION {
     params.input_restart = retrieveInput((!params.build_only_index && !input), params.step, params.outdir)
 
     ch_from_samplesheet = params.build_only_index
-        ? Channel.empty()
+        ? channel.empty()
         : input
-            ? Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
-            : Channel.fromList(samplesheetToList(params.input_restart, "${projectDir}/assets/schema_input.json"))
+            ? channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
+            : channel.fromList(samplesheetToList(params.input_restart, "${projectDir}/assets/schema_input.json"))
 
     SAMPLESHEET_TO_CHANNEL(
         ch_from_samplesheet,
@@ -165,13 +202,13 @@ workflow PIPELINE_INITIALISATION {
 
 workflow PIPELINE_COMPLETION {
     take:
-    email           //  string: email address
-    email_on_fail   //  string: email address sent on pipeline failure
+    email //  string: email address
+    email_on_fail //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-    outdir          //    path: Path to output directory where results will be published
+    outdir //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url        //  string: hook URL for notifications
-    multiqc_report  //  string: Path to MultiQC report
+    hook_url //  string: hook URL for notifications
+    multiqc_report //  string: Path to MultiQC report
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index bfd258760d..2f30e9a463 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -98,7 +98,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML()))
 }
 
 //
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 4994303ea0..ee4738c8d1 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -4,6 +4,7 @@
 
 include { paramsSummaryLog   } from 'plugin/nf-schema'
 include { validateParameters } from 'plugin/nf-schema'
+include { paramsHelp         } from 'plugin/nf-schema'
 
 workflow UTILS_NFSCHEMA_PLUGIN {
 
@@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN {
                         //           when this input is empty it will automatically use the configured schema or
                         //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
                         //           for meta pipelines
+    help                // boolean:  show help message
+    help_full           // boolean:  show full help message
+    show_hidden         // boolean:  show hidden parameters in help message
+    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
 
     main:
 
+    if(help || help_full) {
+        help_options = [
+            beforeText: before_text,
+            afterText: after_text,
+            command: command,
+            showHidden: show_hidden,
+            fullHelp: help_full,
+        ]
+        if(parameters_schema) {
+            help_options << [parametersSchema: parameters_schema]
+        }
+        log.info paramsHelp(
+            help_options,
+            params.help instanceof String ? params.help : "",
+        )
+        exit 0
+    }
+
     //
     // Print parameter summary to stdout. This will display the parameters
     // that differ from the default given in the JSON schema
     //
+
+    summary_options = [:]
     if(parameters_schema) {
-        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
-    } else {
-        log.info paramsSummaryLog(input_workflow)
+        summary_options << [parametersSchema: parameters_schema]
     }
+    log.info before_text
+    log.info paramsSummaryLog(summary_options, input_workflow)
+    log.info after_text
 
     //
     // Validate the parameters using nextflow_schema.json or the schema
     // given via the validation.parametersSchema configuration option
     //
     if(validate_params) {
+        validateOptions = [:]
         if(parameters_schema) {
-            validateParameters(parameters_schema:parameters_schema)
-        } else {
-            validateParameters()
+            validateOptions << [parametersSchema: parameters_schema]
         }
+        validateParameters(validateOptions)
     }
 
     emit:
diff --git a/tests/nextflow.config b/tests/nextflow.config
index a8329dd09f..d643dc7e12 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -9,8 +9,7 @@ params {
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
 }
 
-// Should resolve issue with accessing s3 from the runners
-aws.client.anonymous = true
+aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
 
 process {
     withName: 'SENTIEON_VARCAL_SNP' {
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
index f110391707..d18020a6fc 100644
--- a/workflows/sarek/main.nf
+++ b/workflows/sarek/main.nf
@@ -122,9 +122,9 @@ workflow SAREK {
 
     main:
     // To gather all QC reports for MultiQC
-    ch_multiqc_files = Channel.empty()
-    multiqc_report   = Channel.empty()
-    reports          = Channel.empty()
+    ch_multiqc_files = channel.empty()
+    multiqc_report = channel.empty()
+    reports = channel.empty()
 
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -136,8 +136,8 @@ workflow SAREK {
     if (step == 'mapping') {
         // Figure out if input is bam, fastq, or spring
         input_sample_type = input_sample.branch {
-            bam:                 it[0].data_type == "bam"
-            fastq_gz:            it[0].data_type == "fastq_gz"
+            bam: it[0].data_type == "bam"
+            fastq_gz: it[0].data_type == "fastq_gz"
             one_fastq_gz_spring: it[0].data_type == "one_fastq_gz_spring"
             two_fastq_gz_spring: it[0].data_type == "two_fastq_gz_spring"
         }
@@ -202,7 +202,7 @@ workflow SAREK {
         }
     }
     else {
-        input_fastq = Channel.empty().mix(input_sample)
+        input_fastq = channel.empty().mix(input_sample)
     }
 
     if (step in ['mapping', 'markduplicates', 'prepare_recalibration', 'recalibrate']) {
@@ -215,11 +215,11 @@ workflow SAREK {
                 index_alignment,
                 intervals_bed_combined,
                 known_sites_indels,
-                Channel.value("cram"),
+                channel.value("cram"),
             )
 
             // Gather preprocessing output
-            cram_variant_calling = Channel.empty()
+            cram_variant_calling = channel.empty()
             cram_variant_calling = cram_variant_calling.mix(FASTQ_PREPROCESS_PARABRICKS.out.cram)
 
             // Gather used softwares versions
@@ -243,7 +243,7 @@ workflow SAREK {
             )
 
             // Gather preprocessing output
-            cram_variant_calling = Channel.empty()
+            cram_variant_calling = channel.empty()
             cram_variant_calling = cram_variant_calling.mix(FASTQ_PREPROCESS_GATK.out.cram_variant_calling)
 
             // Gather used softwares versions
@@ -254,12 +254,12 @@ workflow SAREK {
 
     if (step == 'variant_calling') {
 
-        cram_variant_calling = Channel.empty().mix(input_sample)
+        cram_variant_calling = channel.empty().mix(input_sample)
     }
 
     if (step == 'annotate') {
 
-        cram_variant_calling = Channel.empty()
+        cram_variant_calling = channel.empty()
     }
 
     // RUN CRAM QC on the recalibrated CRAM files or when starting from step variant calling. NGSCheckmate should be run also on non-recalibrated CRAM files
@@ -276,7 +276,7 @@ workflow SAREK {
 
     if (tools) {
 
-        bam_variant_calling = Channel.empty()
+        bam_variant_calling = channel.empty()
 
         //  For cnvkit, msisensor2 and muse we need to use bam input and not cram
         if (tools.split(',').contains('cnvkit') || tools.split(',').contains('msisensor2') || tools.split(',').contains('muse')) {
@@ -368,11 +368,11 @@ workflow SAREK {
             .map { normal, tumor ->
                 def meta = [:]
 
-                meta.id            = "${tumor[1].sample}_vs_${normal[1].sample}".toString()
-                meta.normal_id     = normal[1].sample
-                meta.patient       = normal[0]
-                meta.sex           = normal[1].sex
-                meta.tumor_id      = tumor[1].sample
+                meta.id = "${tumor[1].sample}_vs_${normal[1].sample}".toString()
+                meta.normal_id = normal[1].sample
+                meta.patient = normal[0]
+                meta.sex = normal[1].sex
+                meta.tumor_id = tumor[1].sample
                 meta.contamination = tumor[1].contamination
 
                 [meta, normal[2], normal[3], tumor[2], tumor[3]]
@@ -382,11 +382,11 @@ workflow SAREK {
             .map { normal, tumor ->
                 def meta = [:]
 
-                meta.id        = "${tumor[1].sample}_vs_${normal[1].sample}".toString()
+                meta.id = "${tumor[1].sample}_vs_${normal[1].sample}".toString()
                 meta.normal_id = normal[1].sample
-                meta.patient   = normal[0]
-                meta.sex       = normal[1].sex
-                meta.tumor_id  = tumor[1].sample
+                meta.patient = normal[0]
+                meta.sex = normal[1].sex
+                meta.tumor_id = tumor[1].sample
 
                 [meta, normal[2], normal[3], tumor[2], tumor[3]]
             }
@@ -498,10 +498,10 @@ workflow SAREK {
         )
 
         // QC on raw variant calls
-        VCF_QC_BCFTOOLS_VCFTOOLS(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_all
-                                .mix(BAM_VARIANT_CALLING_TUMOR_ONLY_ALL.out.vcf_all)
-                                .mix(BAM_VARIANT_CALLING_SOMATIC_ALL.out.vcf_all),
-                                intervals_bed_combined)
+        VCF_QC_BCFTOOLS_VCFTOOLS(
+            BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_all.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_ALL.out.vcf_all).mix(BAM_VARIANT_CALLING_SOMATIC_ALL.out.vcf_all),
+            intervals_bed_combined,
+        )
 
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.bcftools_stats.collect { _meta, stats -> [stats] })
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_counts.collect { _meta, counts -> [counts] })
@@ -582,7 +582,7 @@ workflow SAREK {
     //
     // Collate and save software versions
     //
-    version_yaml = Channel.empty()
+    version_yaml = channel.empty()
     if (!(skip_tools.split(',').contains('versions'))) {
         version_yaml = softwareVersionsToYAML(versions).collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_' + 'sarek_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true)
     }
@@ -591,15 +591,15 @@ workflow SAREK {
     // MODULE: MultiQC
     //
     if (!(skip_tools.split(',').contains('multiqc'))) {
-        ch_multiqc_config = Channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
-        ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-        ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+        ch_multiqc_config = channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
+        ch_multiqc_custom_config = params.multiqc_config ? channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty()
+        ch_multiqc_logo = params.multiqc_logo ? channel.fromPath(params.multiqc_logo, checkIfExists: true) : channel.empty()
 
         summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-        ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+        ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
-        ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+        ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
 
         ch_multiqc_files = ch_multiqc_files.mix(version_yaml)
         ch_multiqc_files = ch_multiqc_files.mix(reports)
@@ -618,7 +618,7 @@ workflow SAREK {
 
     emit:
     multiqc_report // channel: /path/to/multiqc_report.html
-    versions       // channel: [ path(versions.yml) ]
+    versions // channel: [ path(versions.yml) ]
 }
 
 /*