diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 97c8c97f..237c9ed0 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore",
     "image": "nfcore/devcontainer:latest",
 
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
deleted file mode 100644
index cefff7d3..00000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,118 +0,0 @@
-# `IntGenomicsLab/lrsomatic`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving IntGenomicsLab/lrsomatic.
-
-We try to manage the required tasks for IntGenomicsLab/lrsomatic using GitHub issues, you probably came to this page when creating one.
-Please use the pre-filled template to save time.
-
-However, don't be put off by this template - other more general issues and suggestions are welcome!
-Contributions to the code are even more welcome ;)
-
-## Contribution workflow
-
-If you'd like to write some code for IntGenomicsLab/lrsomatic, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [IntGenomicsLab/lrsomatic issues](https://github.com/IntGenomicsLab/lrsomatic/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [IntGenomicsLab/lrsomatic repository](https://github.com/IntGenomicsLab/lrsomatic) to your GitHub account
-3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
-5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
-
-If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
-
-## Tests
-
-You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
-
-```bash
-nf-test test --profile debug,test,docker --verbose
-```
-
-When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
-Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
-
-There are typically two types of tests that run:
-
-### Lint tests
-
-`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
-
-If any failures or warnings are encountered, please follow the listed URL for more documentation.
-
-### Pipeline tests
-
-Each `nf-core` pipeline should be set up with a minimal set of test-data.
-`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
-If there are any failures then the automated tests fail.
-These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
-
-## Patch
-
-:warning: Only in the unlikely and regretful event of a release happening with a bug.
-
-- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
-- Fix the bug, and bump version (X.Y.Z+1).
-- Open a pull-request from `patch` to `main`/`master` with the changes.
-
-## Pipeline contribution conventions
-
-To make the `IntGenomicsLab/lrsomatic` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
-
-### Adding a new step
-
-If you wish to contribute a new step, please use the following coding standards:
-
-1. Define the corresponding input channel into your new process from the expected previous process channel.
-2. Write the process block (see below).
-3. Define the output channel if needed (see below).
-4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
-6. Add sanity checks and validation for all relevant parameters.
-7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test in the `tests` directory.
-9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
-10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
-
-### Default values
-
-Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
-
-Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
-
-### Default processes resource requirements
-
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
-
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
-
-### Naming schemes
-
-Please use the following naming schemes, to make it easy to understand what is going where.
-
-- initial process channel: `ch_output_from_<process>`
-- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
-
-### Nextflow version bumping
-
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
-
-### Images and figures
-
-For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
-
-## GitHub Codespaces
-
-This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
-
-To get started:
-
-- Open the repo in [Codespaces](https://github.com/IntGenomicsLab/lrsomatic/codespaces)
-- Tools installed
-  - nf-core
-  - Nextflow
-
-Devcontainer specs:
-
-- [DevContainer config](.devcontainer/devcontainer.json)
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 00000000..7f210a1e
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,7 @@
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #lrsomatic channel"
+    url: https://nfcore.slack.com/channels/lrsomatic
+    about: Discussion about the IntGenomicsLab/lrsomatic pipeline
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 41961fd1..1e0906c0 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/IntGenomicsLab/lrsomatic/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/IntGenomicsLab/lrsomatic/tree/main/docs/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/IntGenomicsLab/lrsomatic/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/IntGenomicsLab/lrsomatic/tree/main/docs/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 34085279..e2833ee9 100644
--- a/.github/actions/get-shards/action.yml
+++ b/.github/actions/get-shards/action.yml
@@ -21,7 +21,7 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 3b9724c7..ad686e8e 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -20,24 +20,24 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
         python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,7 +48,7 @@ runs:
 
     - name: Conda setup
       if: contains(inputs.profile, 'conda')
-      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
         auto-update-conda: true
         conda-solver: libmamba
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 0e125373..6e8e5cd2 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 6adb0fff..172de6f3 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@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
+      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # 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/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 45884ff9..5b6592c1 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -39,12 +39,12 @@ jobs:
     needs: configure
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
@@ -54,10 +54,16 @@ jobs:
         with:
           apptainer-version: 1.3.4
 
+      - name: Read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Make a cache directory for the container images
         run: |
@@ -127,7 +133,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index b9b23241..2b6d1142 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -31,22 +31,18 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
+      # Install and run prek
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -54,7 +50,7 @@ jobs:
 
       - name: Commit & push changes
         id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a34..8738ffc9 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,33 +11,31 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
@@ -45,12 +43,10 @@ jobs:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -58,7 +54,7 @@ jobs:
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc26..5b0c24f7 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
+        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index a22a97fc..3a48a15b 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: "0.9.3"
+  NFT_VER: "0.9.4"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -39,7 +39,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -76,19 +76,17 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.4"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index e8560fc7..ea30827e 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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
@@ -29,7 +29,7 @@ jobs:
         run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with:
@@ -42,5 +42,5 @@ jobs:
             > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
             > Please update your pipeline to the latest version.
             >
-            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
           #
diff --git a/.gitignore b/.gitignore
index c5c144e3..cc2b1a77 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,4 @@ testing/
 testing*
 *.pyc
 null/
-.nf-test
-.nf-test.log
-out/
+.lineage/
diff --git a/.nf-core.yml b/.nf-core.yml
index 07124956..c5e9c752 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -26,8 +26,7 @@ lint:
     - validation.help.afterText
     - validation.summary.beforeText
     - validation.summary.afterText
-  schema_params: false
-nf_core_version: 3.5.2
+nf_core_version: 4.0.1
 repository_type: pipeline
 template:
   author: Jonas Demeulemeester
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d06777a8..f51e1a28 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.6.2
+          - prettier@3.8.3
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -13,15 +13,21 @@ repos:
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
       - id: end-of-file-fixer
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
+        args: ["-output", "json"]
diff --git a/.prettierignore b/.prettierignore
index dd749d43..63cde500 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/
diff --git a/README.md b/README.md
index dd8d110e..c958ca02 100644
--- a/README.md
+++ b/README.md
@@ -3,11 +3,10 @@
 [![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/IntGenomicsLab/lrsomatic)
 [![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)
-[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)
 [![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%A525.04.0-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-3.5.1-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)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-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-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)
 [![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/)
@@ -97,7 +96,7 @@ nextflow run IntGenomicsLab/lrsomatic \
 More detail is given in our [usage documentation](/docs/usage.md)
 
 > [!WARNING]
-> 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).
+> 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/running/run-pipelines#using-parameter-files).
 
 ## Credits
 
@@ -161,7 +160,7 @@ more detail is given in our [output documentation](/docs/output.md)
 
 ## Contributions and Support
 
-If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).
 
 ## Citations
 
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
deleted file mode 100644
index a7f7c25d..00000000
--- a/assets/adaptivecard.json
+++ /dev/null
@@ -1,67 +0,0 @@
-{
-    "type": "message",
-    "attachments": [
-        {
-            "contentType": "application/vnd.microsoft.card.adaptive",
-            "contentUrl": null,
-            "content": {
-                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
-                "msteams": {
-                    "width": "Full"
-                },
-                "type": "AdaptiveCard",
-                "version": "1.2",
-                "body": [
-                    {
-                        "type": "TextBlock",
-                        "size": "Large",
-                        "weight": "Bolder",
-                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "IntGenomicsLab/lrsomatic v${version} - ${runName}",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "spacing": "None",
-                        "text": "Completed at ${dateComplete} (duration: ${duration})",
-                        "isSubtle": true,
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "The command used to launch the workflow was as follows:",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "${commandLine}",
-                        "isSubtle": true,
-                        "wrap": true
-                    }
-                ],
-                "actions": [
-                    {
-                        "type": "Action.ShowCard",
-                        "title": "Pipeline Configuration",
-                        "card": {
-                            "type": "AdaptiveCard",
-                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
-                            "body": [
-                                {
-                                    "type": "FactSet",
-                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
-                                    ]
-                                }
-                            ]
-                        }
-                    }
-                ]
-            }
-        }
-    ]
-}
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index e8425ad8..00000000
--- a/assets/slackreport.json
+++ /dev/null
@@ -1,34 +0,0 @@
-{
-    "attachments": [
-        {
-            "fallback": "Plain-text summary of the attachment.",
-            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "IntGenomicsLab/lrsomatic ${version} - ${runName}",
-            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
-            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
-            "fields": [
-                {
-                    "title": "Command used to launch the workflow",
-                    "value": "```${commandLine}```",
-                    "short": false
-                }
-                <%
-                    if (!success) { %>
-                    ,
-                    {
-                        "title": "Full error message",
-                        "value": "```${errorReport}```",
-                        "short": false
-                    },
-                    {
-                        "title": "Pipeline configuration",
-                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
-                        "short": false
-                    }
-                    <% }
-                %>
-            ],
-            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
-        }
-    ]
-}
diff --git a/conf/base.config b/conf/base.config
index df70b052..ed600007 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
@@ -87,4 +87,8 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withLabel: process_gpu {
+        ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
+    }
 }
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
new file mode 100644
index 00000000..f487ba40
--- /dev/null
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
new file mode 100644
index 00000000..e9a3fedc
--- /dev/null
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
new file mode 100644
index 00000000..01b59df5
--- /dev/null
+++ b/conf/containers_docker_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
new file mode 100644
index 00000000..7785cb13
--- /dev/null
+++ b/conf/containers_docker_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
new file mode 100644
index 00000000..754821b3
--- /dev/null
+++ b/conf/containers_singularity_https_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
new file mode 100644
index 00000000..93071de8
--- /dev/null
+++ b/conf/containers_singularity_https_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
new file mode 100644
index 00000000..952881d8
--- /dev/null
+++ b/conf/containers_singularity_oras_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
new file mode 100644
index 00000000..498ec506
--- /dev/null
+++ b/conf/containers_singularity_oras_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
new file mode 100644
index 00000000..37ecd1f3
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,165 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `IntGenomicsLab/lrsomatic`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving IntGenomicsLab/lrsomatic.
+
+This page describes the recommended nf-core way to contribute to both IntGenomicsLab/lrsomatic and nf-core pipelines in general, including:
+
+- [General contribution guidelines](#general-contribution-guidelines): common procedures or guides across all nf-core pipelines.
+- [Pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines): procedures or guides specific to the development conventions of IntGenomicsLab/lrsomatic.
+
+## General contribution guidelines
+
+### Contribution quick start
+
+To contribute code to any nf-core pipeline:
+
+- [ ] Ensure you have Nextflow, nf-core tools, and nf-test installed. See the [nf-core/tools repository](https://github.com/nf-core/tools) for instructions.
+- [ ] Check whether a GitHub [issue](https://github.com/IntGenomicsLab/lrsomatic/issues) about your idea already exists. If an issue does not exist, create one so that others are aware you are working on it.
+- [ ] [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [IntGenomicsLab/lrsomatic repository](https://github.com/IntGenomicsLab/lrsomatic) to your GitHub account.
+- [ ] Create a branch on your forked repository and make your changes following [pipeline conventions](#pipeline-contribution-conventions) (if applicable).
+- [ ] To fix major bugs, name your branch `patch` and follow the [patch release](#patch-release) process.
+- [ ] Update relevant documentation within the `docs/` folder, use nf-core/tools to update `nextflow_schema.json`, and update `CITATIONS.md`.
+- [ ] Run and/or update tests. See [Testing](#testing) for more information.
+- [ ] [Lint](#lint-tests) your code with nf-core/tools.
+- [ ] Submit a pull request (PR) against the `dev` branch and request a review.
+
+If you are not used to this workflow with Git, see the [GitHub documentation](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or [Git resources](https://try.github.io/) for more information.
+
+### GitHub Codespaces
+
+You can contribute to IntGenomicsLab/lrsomatic without installing a local development environment on your machine by using [GitHub Codespaces](https://github.com/codespaces).
+
+[GitHub Codespaces](https://github.com/codespaces) is an online developer environment that runs in your browser, complete with VS Code and a terminal.
+Most nf-core repositories include a devcontainer configuration, which creates a GitHub Codespaces environment specifically for Nextflow development.
+The environment includes pre-installed nf-core tools, Nextflow, and a few other helpful utilities via a Docker container.
+
+To get started, open the repository in [Codespaces](https://github.com/IntGenomicsLab/lrsomatic/codespaces).
+
+### Testing
+
+Once you have made your changes, run the pipeline with nf-test to test them locally.
+For additional information, use the `--verbose` flag to view the Nextflow console log output.
+
+```bash
+nf-test test --tag test --profile +docker --verbose
+```
+
+If you have added new functionality, ensure you update the test assertions in the `.nf.test` files in the `tests/` directory.
+Update the snapshots with the following command:
+
+```bash
+nf-test test --tag test --profile +docker --verbose --update-snapshots
+```
+
+When you create a pull request with changes, GitHub Actions will run automatic tests.
+Pull requests are typically reviewed when these tests are passing.
+
+Two types of tests are typically run:
+
+#### Lint tests
+
+nf-core has a [set of guidelines](https://nf-co.re/docs/specifications/overview) which all pipelines must follow.
+To enforce these, run linting with nf-core/tools:
+
+```bash
+nf-core pipelines lint <pipeline_directory>
+```
+
+If you encounter failures or warnings, follow the linked documentation printed to screen.
+For more information about linting tests, see [nf-core/tools API documentation](https://nf-co.re/docs/nf-core-tools/api_reference/latest/pipeline_lint_tests/actions_awsfulltest).
+
+#### Pipeline tests
+
+Each nf-core pipeline should be set up with a minimal set of test data.
+GitHub Actions runs the pipeline on this data to ensure it runs through and exits successfully.
+If there are any failures then the automated tests fail.
+These tests are run with the latest available version of Nextflow and the minimum required version specified in the pipeline code.
+
+### Patch release
+
+> [!WARNING]
+> Only in the unlikely event of a release that contains a critical bug.
+
+- [ ] Create a new branch `patch` on your fork based on `upstream/main` or `upstream/master`.
+- [ ] Fix the bug and use nf-core/tools to bump the version to the next semantic version, for example, `1.2.3` → `1.2.4`.
+- [ ] Open a Pull Request from `patch` directly to `main`/`master` with the changes.
+
+### Pipeline contribution conventions
+
+nf-core semi-standardises how you write code and other contributions to make the IntGenomicsLab/lrsomatic code and processing logic more understandable for new contributors and to ensure quality.
+
+#### Add a new pipeline step
+
+To contribute a new step to the pipeline, follow the general nf-core coding procedure.
+Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines):
+
+- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel.
+- [ ] Install a module with nf-core/tools, or write a local module (see [default processes resource requirements](#default-processes-resource-requirements)), and add it to the target `<workflow>.nf`.
+- [ ] Define the output channel if needed. Mix the version output channel into `ch_versions` and relevant files into `ch_multiqc`.
+- [ ] Add new or updated parameters to `nextflow.config` with a [default value](#default-parameter-values).
+- [ ] Add new or updated parameters and relevant help text to `nextflow_schema.json` with [nf-core/tools](#default-parameter-values).
+- [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow.
+- [ ] Perform local tests to validate that the new code works as expected.
+  - [ ] If applicable, add a new test in the `tests` directory.
+- [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate.
+- [ ] [Lint](lint) the code with nf-core/tools.
+- [ ] Update any diagrams or pipeline images as necessary.
+- [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order.
+- [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module.
+- [ ] Add a description of the output files and, if relevant, images from the MultiQC report to `docs/output.md`.
+
+To update the minimum required Nextflow version, see the [Nextflow version bumping](#nextflow-version-bumping) section below. For more information about pipeline contributions, see [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines).
+
+#### Channel naming schemes
+
+Use the following naming schemes for channels to make the channel flow easier to understand:
+
+- Initial process channel: `ch_output_from_<process>`
+- Intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+
+#### Default parameter values
+
+Parameters should be initialised and defined with default values within the `params` scope in `nextflow.config`.
+They should also be documented in the pipeline JSON schema.
+
+To update `nextflow_schema.json`, run:
+
+```bash
+nf-core pipelines schema build
+```
+
+The schema builder interface that loads in your browser should automatically update the defaults in the parameter documentation.
+
+#### Default processes resource requirements
+
+If you write a local module, specify a default set of resource requirements for the process.
+
+Sensible defaults for process resource requirements (CPUs, memory, time) should be defined in `conf/base.config`.
+Specify these with generic `withLabel:` selectors, so they can be shared across multiple processes and steps of the pipeline.
+
+nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
+These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements.
+
+Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+
+#### Nextflow version bumping
+
+If you use a new feature from core Nextflow, bump the minimum required Nextflow version in the pipeline with:
+
+```bash
+nf-core pipelines bump-version --nextflow . <min_nf_version>
+```
+
+#### Images and figures guidelines
+
+If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics).
+
+## Pipeline specific contribution guidelines
+
+<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->
diff --git a/docs/usage.md b/docs/usage.md
index a6447322..660fd595 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -78,7 +78,7 @@ work                # Directory containing the nextflow working files
 ```
 
 > [!WARNING]
-> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -328,19 +328,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
-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.
+To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-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.
+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/running/configuration/nextflow-for-your-system#update-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.
+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/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website.
 
 ### nf-core/configs
 
diff --git a/main.nf b/main.nf
index a6011fff..5fc4266e 100644
--- a/main.nf
+++ b/main.nf
@@ -81,7 +81,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         INTGENOMICSLAB_LRSOMATIC.out.multiqc_report
     )
 }
diff --git a/modules.json b/modules.json
index e7597448..cdaf6853 100644
--- a/modules.json
+++ b/modules.json
@@ -114,7 +114,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     },
                     "nanoplot": {
@@ -206,12 +206,12 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "65f5e638d901a51534c68fd5c1c19e8112fb4df1",
+                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
new file mode 100644
index 00000000..76190304
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
@@ -0,0 +1,1552 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
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+- libgomp >=7.5.0
+constrains:
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+license: BSD-3-Clause
+license_family: BSD
+size: 28948
+timestamp: 1770939786096
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+md5: aaa2a381ccc56eac91d63b6c1240312f
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+- python-gil
+license: MIT
+license_family: MIT
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
new file mode 100644
index 00000000..a55a4d49
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
@@ -0,0 +1,126 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
new file mode 100644
index 00000000..a58231a0
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
new file mode 100644
index 00000000..f787dbe1
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
@@ -0,0 +1,125 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-aarch64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958
+https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6
+https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1
+https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc
+https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f
+https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.5-hfae3067_0.conda#05d1e0b30acd816a192c03dc6e164f4d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda#2f364feefb6a7c00423e80dcb12db62a
+https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda#76298a9e6d71ee6e832a8d0d7373b261
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+https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5
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+https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda#25d896c331481145720a21e5145fad65
+https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda#071cf7b0ce333c81718b054066c15102
+https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.5-hfae3067_0.conda#d2bb0c889d94f2fdc5856392c3002976
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
+https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda#f51503ac45a4888bce71af9027a2ecc9
+https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype6-2.14.3-hdae7a39_0.conda#b99ed99e42dafb27889483b3098cace7
+https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype-2.14.3-h8af1aa0_0.conda#a229e22d4d8814a07702b0919d8e6701
+https://conda.anaconda.org/conda-forge/linux-aarch64/fontconfig-2.17.1-hba86a56_0.conda#0fed1ff55f4938a65907f3ecf62609db
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681
+https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e
+https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac
+https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda#164fc43f0b53b6e3a7bc7dce5e4f1dc9
+https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda#daddf757c3ecd6067b9af1df1f25d89e
+https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda#fb7130c190f9b4ec91219840a05ba3ac
+https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda#e1c36c6121a7c9c76f2f148f1e83b983
+https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda#080594bf4493e6bae2607e65390c520a
+https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda#e5de3c36dd548b35ff2a8aa49208dcb3
+https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda#04558c96691bed63104678757beb4f8d
+https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-0.30.0-py314h02b7a91_0.conda#e7f6ed9e60043bb5cbcc527764897f0d
+https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda#870293df500ca7e18bedefa5838a22ab
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda#439cd0f567d697b20a8f45cb70a1005a
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda#ada41c863af263cc4c5fcbaff7c3e4dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda#4feebd0fbf61075a1a9c2e9b3936c257
+https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2#7b08314a6867a9d5648a1c3265e9eb8e
+https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda#6dd4f07147774bf720075a210f8026b9
+https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552
+https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.0-he8854b5_0.conda#ad8164bdeece883b825c50639c0c4725
+https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2#4f0d284f5d11e04277b552eb1c172c7f
+https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda#a85ba48648f6868016f2741fd9170250
+https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171
+https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda#a9138815598fe6b91a1d6782ca657b0c
+https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda#24e92d0942c799db387f5c9d7b81f1af
+https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda#8c6fd84f9c87ac00636007c6131e457d
+https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c
+https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2
+https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2
+https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3
+https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351
+https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964
+https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8
+https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c
+https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b
+https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684
+https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98
+https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910
+https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372
+https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7
+https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88
+https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58
+https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240
+https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6
+https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98
+https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c
+https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2
+https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac
+https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130
+https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59
+https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0
+https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66
+https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9
+https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a
+https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864
+https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6
+https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206
+https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b
+https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873
+https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f
+https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 009874d4..37e7612d 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.33
+  - bioconda::multiqc=1.34
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 5376aea1..e80e8cd8 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,9 +3,9 @@ process MULTIQC {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data'
-        : 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b'}"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
+        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ef434a9a..2facc627 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -110,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
     linux/arm64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
   docker:
     linux/amd64:
-      build_id: bd-ee7739d47738383b_1
-      name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b
-      scanId: sc-6ddec592dcadd583_4
+      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
+      build_id: bd-db7c73dae76bc9e6_1
+      scan_id: sc-66fc7138dbf1cf48_1
     linux/arm64:
-      build_id: bd-58d7dee710ab3aa8_1
-      name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8
-      scanId: sc-a04c42273e34c55c_2
+      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
+      build_id: bd-d167b8012595a136_1
+      scan_id: sc-ac701dfa631a2af9_1
   singularity:
     linux/amd64:
-      build_id: bd-e3576ddf588fa00d_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
+      build_id: bd-4fc8657c816047c0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
     linux/arm64:
-      build_id: bd-2537ca5f8445e3c2_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
+      build_id: bd-7fbd82d945c06726_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index 0e422eaa..4cbdb95d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -29,13 +29,26 @@ nextflow_process {
 
         then {
             assert process.success
-            assertAll(
-                { assert snapshot(
-                    file(process.out.report[0][1]).name,
-                    file(process.out.data[0][1]).name,
-                    process.out.findAll { key, val -> key.startsWith("versions")
-                }).match() }
-            )
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
         }
     }
 
@@ -59,13 +72,26 @@ nextflow_process {
 
         then {
             assert process.success
-            assertAll(
-                { assert snapshot(
-                    file(process.out.report[0][1]).name,
-                    file(process.out.data[0][1]).name,
-                    process.out.findAll { key, val -> key.startsWith("versions")
-                }).match() }
-            )
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
         }
     }
 
@@ -77,7 +103,7 @@ nextflow_process {
                 input[0] = channel.of([
                     [ id: 'FASTQC' ],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
-                    file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true),
+                    file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true),
                     [],
                     [],
                     []
@@ -88,14 +114,26 @@ nextflow_process {
 
         then {
             assert process.success
-            assertAll(
-                { assert snapshot(
-                    file(process.out.report[0][1]).name,
-                    file(process.out.data[0][1]).name,
-                    file(process.out.plots[0][1]).name,
-                    process.out.findAll { key, val -> key.startsWith("versions")
-                }).match() }
-            )
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
         }
     }
 
@@ -108,8 +146,8 @@ nextflow_process {
                     [ id: 'FASTQC' ],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
                     [
-                        file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true),
-                        file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)
+                        file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true),
+                        file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true)
                     ],
                     [],
                     [],
@@ -121,14 +159,26 @@ nextflow_process {
 
         then {
             assert process.success
-            assertAll(
-                { assert snapshot(
-                    file(process.out.report[0][1]).name,
-                    file(process.out.data[0][1]).name,
-                    file(process.out.plots[0][1]).name,
-                    process.out.findAll { key, val -> key.startsWith("versions")
-                }).match() }
-            )
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
         }
     }
 
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index c022701f..7c2f370f 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,44 +1,190 @@
 {
     "sarscov2 single-end [fastqc] [multiple configs]": {
         "content": [
-            "multiqc_report.html",
-            "multiqc_data",
-            "multiqc_plots",
             {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "multiqc_report.html",
                 "versions": [
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-03-17T16:15:42.577775492",
         "meta": {
-            "nf-test": "0.9.3",
+            "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-26T20:21:35.851707"
+        }
     },
     "sarscov2 single-end [fastqc]": {
         "content": [
-            "multiqc_report.html",
-            "multiqc_data",
             {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_software_versions.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "multiqc_report.html",
                 "versions": [
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-03-17T16:21:17.072841555",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-26T15:10:36.019680076"
+        }
     },
     "sarscov2 single-end [fastqc] - stub": {
         "content": [
@@ -75,56 +221,202 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-02-26T15:14:39.789193051",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-26T15:14:39.789193051"
+        }
     },
     "sarscov2 single-end [fastqc] [config]": {
         "content": [
-            "multiqc_report.html",
-            "multiqc_data",
-            "multiqc_plots",
             {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "multiqc_report.html",
                 "versions": [
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-03-17T16:15:30.372239611",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-26T15:21:29.116129274"
+        }
     },
     "sarscov2 single-end [fastqc] - custom prefix": {
         "content": [
-            "custom_prefix.html",
-            "custom_prefix_data",
             {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_software_versions.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "custom_prefix.html",
                 "versions": [
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-03-17T16:15:18.189023981",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-02-26T15:10:43.419877592"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
index c537a6a3..374dfef2 100644
--- a/modules/nf-core/multiqc/tests/nextflow.config
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -1,5 +1,6 @@
 process {
     withName: 'MULTIQC' {
         ext.prefix = null
+        ext.args = '-p'
     }
 }
diff --git a/nextflow.config b/nextflow.config
index 84c9f487..fff0dcc7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -104,31 +104,16 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
     version                      = false
-    outdir                      = null
-    publish_dir_mode            = 'copy'
-    email                       = null
-    email_on_fail               = null
-    plaintext_email             = false
-    monochrome_logs             = false
-    hook_url                    = null
-    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
-    config_profile_name        = null
-    config_profile_description = null
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
-    config_profile_name         = null
-    config_profile_description  = null
+    config_profile_name          = null
+    config_profile_description   = null
 
     custom_config_version       = 'master'
     custom_config_base          = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
@@ -139,6 +124,10 @@ params {
     validate_params             = true
 }
 
+// Backwards compatibility for publishDir syntax
+outputDir = params.outdir
+workflow.output.mode = params.publish_dir_mode
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -380,7 +369,7 @@ manifest {
     description     = """Workflow for somatic variant calling of long read data"""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=25.04.0'
+    nextflowVersion = '!>=25.10.4'
     version         = '1.1.0dev'
     doi             = ''
 }
@@ -394,6 +383,5 @@ validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
 }
-
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a7cc1495..6de5a18d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -68,22 +68,24 @@
             "type": "object",
             "properties": {
                 "germline_var_keep": {
-                    "type": "array",
+                    "type": ["string", "array"],
                     "description": "List of germline variant callers to use. Must include at least one of [deepvariant, clair].",
                     "items": {
                         "type": "string",
                         "enum": ["deepvariant", "clair"]
                     },
-                    "minItems": 1
+                    "minItems": 1,
+                    "default": "['deepvariant', 'clair']"
                 },
                 "somatic_var_keep": {
-                    "type": "array",
+                    "type": ["string", "array"],
                     "description": "List of somatic variant callers to use. Must include at least one of [deepsomatic, clair].",
                     "items": {
                         "type": "string",
                         "enum": ["deepsomatic", "clair"]
                     },
-                    "minItems": 1
+                    "minItems": 1,
+                    "default": "['deepsomatic', 'clair']"
                 },
                 "germline_var_combine": {
                     "type": "string",
@@ -108,6 +110,9 @@
                     "description": "When both somatic callers are used, specifies which caller's format to use for variants called by both. Must be [deepsomatic, clair].",
                     "default": "deepsomatic",
                     "enum": ["deepsomatic", "clair"]
+                },
+                "generate_gvcf": {
+                    "type": "boolean"
                 }
             }
         },
@@ -126,7 +131,6 @@
                 },
                 "igenomes_ignore": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Do not load the iGenomes reference config.",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
@@ -202,7 +206,6 @@
                 },
                 "download_vep_cache": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Download the VEP cache if not already present"
                 },
                 "vep_custom": {
@@ -283,7 +286,6 @@
                 },
                 "ascat_pdf_plots": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Boolean for ASCAT production of pdf plots (entered as string)"
                 }
             }
@@ -307,73 +309,58 @@
             "properties": {
                 "skip_qc": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips all QC steps"
                 },
                 "skip_cramino": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips Cramino"
                 },
                 "skip_mosdepth": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips Mosdepth"
                 },
                 "skip_bamstats": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips samtools flagstat, stats, and idxstats"
                 },
                 "skip_wakhan": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips wakhan"
                 },
                 "skip_fiber": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip Fibertools steps"
                 },
                 "skip_ascat": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip ASCAT"
                 },
                 "skip_m6a": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip m6a calling by Fibertools"
                 },
                 "skip_vep": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip VEP annotation"
                 },
                 "skip_normalfiber": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip Fibertools steps for the normal sample"
                 },
                 "skip_nanoplot": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip Nanoplot"
                 },
                 "skip_whatshapstats": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip WhatsHap stats"
                 },
                 "skip_modcall": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip modification calling"
                 },
-                "use_gpu": {
-                    "type": "boolean",
-                    "default": false,
-                    "description": "Use GPU for supported tools (e.g. DeepVariant, DeepSomatic, Clair3)"
+                "skip_modkit": {
+                    "type": "boolean"
                 }
             }
         },
@@ -434,7 +421,6 @@
             "properties": {
                 "version": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
@@ -458,7 +444,6 @@
                 },
                 "plaintext_email": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Send plain-text email instead of HTML.",
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
@@ -473,18 +458,10 @@
                 },
                 "monochrome_logs": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
-                "hook_url": {
-                    "type": "string",
-                    "description": "Incoming hook URL for messaging service",
-                    "fa_icon": "fas fa-people-group",
-                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
-                    "hidden": true
-                },
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
@@ -524,19 +501,20 @@
                     "hidden": true
                 },
                 "help": {
-                    "type": "boolean",
-                    "default": false,
+                    "type": ["boolean", "string"],
                     "description": "Display the help message."
                 },
                 "help_full": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display the full detailed help message."
                 },
                 "show_hidden": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
+                },
+                "use_gpu": {
+                    "type": "boolean",
+                    "description": "Use GPU for supported tools (e.g. DeepVariant, DeepSomatic, Clair3)"
                 }
             }
         }
diff --git a/nf-test.config b/nf-test.config
index 3a1fff59..f7aaeb4a 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,21 +1,35 @@
 config {
     // location for all nf-test tests
-    testsDir "."
+    testsDir = "."
 
     // nf-test directory including temporary files for each test
-    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "tests/nextflow.config"
+    configFile = "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
+    ignore = [
+        'modules/nf-core/**/tests/*',
+        'subworkflows/nf-core/**/tests/*',
+    ]
 
     // run all test with defined profile(s) from the main nextflow.config
-    profile "test"
+    profile = "test"
 
     // list of filenames or patterns that should be trigger a full test run
-    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+    triggers = [
+        '.github/actions/nf-test/action.yml',
+        '.github/workflows/nf-test.yml',
+        'assets/schema_input.json',
+        'bin/*',
+        'conf/test.config',
+        'nextflow.config',
+        'nextflow_schema.json',
+        'nf-test.config',
+        'tests/.nftignore',
+        'tests/nextflow.config',
+    ]
 
     // load the necessary plugins
     plugins {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index e0ca7d28..93231d05 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -1,6 +1,6 @@
 {
     "@context": [
-        "https://w3id.org/ro/crate/1.1/context",
+        "https://w3id.org/ro/crate/1.2/context",
         {
             "GithubService": "https://w3id.org/ro/terms/test#GithubService",
             "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-12-23T12:58:53+00:00",
-            "description": "# IntGenomicsLab/lrsomatic\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/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\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%A525.04.0-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/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow \u2014 **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\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```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row represents a sample. The bam files should always be unaligned bam files. All fields except for `bam_normal` are required. If `bam_normal` is empty, the pipeline will run in tumour only mode. `platform` should be either `ont` or `pb` for Oxford Nanopore Sequencing or PacBio sequencing, respectively. `sex` refers to the biological sex of the sample and should be either `female` or `male`. Finally, `fiber` specifies whether your sample is Fiber-seq data or not and should have either `y` for Yes or `n` for No.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\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\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Alexandra Pan\u010d\u00edkov\u00e1, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThis pipeline produces a series of different output files. The main output is an aligned and phased tumour bam file. This bam file can be used by any typical downstream tool that uses bam files as input. Furthermore, we have sample-specific QC outputs from `cramino` (fastq), `cramino` (bam), `mosdepth`, `samtools` (stats/flagstat/idxstats), and optionally `fibertools`. Finally, we have a `multiqc` report from that combines the output from `mosdepth` and `samtools` into one html report.\n\nBesides QC and the aligned and phased bam file, we have output from (structural) variant and copy number callers, of which some are optional. The output from these variant callers can be found in their respective folders. For small and structural variant callers (`clairS`, `clairS-TO`, and `severus`) these will contain, among others, `vcf` files with called variants. For `ascat` these contain files with final copy number information and plots of the copy number profiles.\n\nExample output directory structure:\n\n```\n\u251c\u2500\u2500 Sample 1\n\u2502    \u251c\u2500\u2500 ascat\n\u2502    \u251c\u2500\u2500 bamfiles\n\u2502    \u251c\u2500\u2500 qc\n\u2502    \u2502    \u251c\u2500\u2500 tumor\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_aln\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_ubam\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 fibertoolsrs\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 mosdepth\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 samtools\n\u2502    \u251c\u2500\u2500 variants\n\u2502    \u2502   \u251c\u2500\u2500clairS-TO\n\u2502    \u2502   \u251c\u2500\u2500severus\n\u2502    \u251c\u2500\u2500 vep\n\u2502    \u2502   \u251c\u2500\u2500 germline\n\u2502    \u2502   \u251c\u2500\u2500 somatic\n\u2502    \u2502   \u251c\u2500\u2500 SVs\n\u2502\n\u251c\u2500\u2500 Sample 2\n\u2502    \u251c\u2500\u2500 ascat\n\u2502    \u251c\u2500\u2500 bamfiles\n\u2502    \u251c\u2500\u2500 qc\n\u2502    \u2502    \u251c\u2500\u2500 tumor\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_aln\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_ubam\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 fibertoolsrs\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 mosdepth\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 samtools\n\u2502    \u2502    \u251c\u2500\u2500 normal\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_aln\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_ubam\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 fibertoolsrs\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 mosdepth\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 samtools\n\u2502    \u251c\u2500\u2500 variants\n\u2502    \u2502   \u251c\u2500\u2500 clair3\n\u2502    \u2502   \u251c\u2500\u2500 clairS\n\u2502    \u2502   \u251c\u2500\u2500 severus\n\u2502    \u251c\u2500\u2500 vep\n\u2502    \u2502   \u251c\u2500\u2500 germline\n\u2502    \u2502   \u251c\u2500\u2500 somatic\n\u2502    \u2502   \u251c\u2500\u2500 SVs\n\u251c\u2500\u2500 pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Luc\u00eda Rocha Iraiz\u00f3s, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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",
+            "datePublished": "2026-04-29T11:16:38+00:00",
+            "description": "# IntGenomicsLab/lrsomatic\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/IntGenomicsLab/lrsomatic)\n[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)\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%A525.10.4-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-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)\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/IntGenomicsLab/lrsomatic)\n\n## Introduction\n\n**IntGenomicsLab/lrsomatic** is a robust bioinformatics pipeline designed for processing and analyzing **somatic DNA sequencing** data for long-read sequencing technologies from **Oxford Nanopore** and **PacBio**. It supports both canonical base DNA and modified base calling, including specialized applications such as **Fiber-seq**.\n\nThis **end-to-end pipeline** handles the entire workflow \u2014 **from raw read processing and alignment, to comprehensive somatic variant calling**, including single nucleotide variants, indels, structural variants, copy number alterations, and modified bases.\n\nIt can be run in both **matched tumour-normal** and **tumour-only mode**, offering flexibility depending on the users study design.\n\nDeveloped using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.\n\nFor more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).\n\n## Pipeline summary\n\n![image](./assets/lrsomatic_1.0.png)\n\n**1) Pre-processing:**\n\na. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))\n\nb. Alignment to the reference genome ([`minimap2`](https://github.com/lh3/minimap2))\n\nc. Post alignment QC ([`cramino`](https://github.com/wdecoster/cramino), [`samtools idxstats`](https://github.com/samtools/samtools), [`samtools flagstats`](https://github.com/samtools/samtools), [`samtools stats`](https://github.com/samtools/samtools))\n\nd. Specific for calling modified base calling ([`Modkit`](https://github.com/nanoporetech/modkit), [`Fibertools`](https://github.com/fiberseq/fibertools-rs))\n\n**2i) Matched mode: small variant calling:**\n\na. Calling Germline SNPs ([`Clair3`](https://github.com/HKU-BAL/Clair3))\n\nb. Phasing and Haplotagging the SNPs in the normal and tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\nc. Calling somatic SNVs ([`ClairS`](https://github.com/HKU-BAL/ClairS))\n\n**2ii) Tumour only mode: small variant calling:**\n\na. Calling Germline SNPs and somatic SNVs ([`ClairS-TO`](https://github.com/HKU-BAL/ClairS-TO))\n\nb. Phasing and Haplotagging germline SNPs in tumour BAM ([`LongPhase`](https://github.com/twolinin/longphase))\n\n**3) Large variant calling:**\n\na. Somatic structural variant calling ([`Severus`](https://github.com/KolmogorovLab/Severus))\n\nb. Copy number alterion calling; long read version of ([`ASCAT`](https://github.com/VanLoo-lab/ascat))\n\n**4) Annotation:**\n\na. Small variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\nb. Structural variant annotation ([`VEP`](https://github.com/Ensembl/ensembl-vep))\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\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```csv\nsample,bam_tumor,bam_normal,platform,sex,fiber\nsample1,tumour.bam,normal.bam,ont,female,n\nsample2,tumour.bam,,ont,female,y\nsample3,tumour.bam,,pb,male,n\nsample4,tumour.bam,normal.bam,pb,male,y\n```\n\nEach row represents a sample. The bam files should always be unaligned bam files. All fields except for `bam_normal` are required. If `bam_normal` is empty, the pipeline will run in tumour only mode. `platform` should be either `ont` or `pb` for Oxford Nanopore Sequencing or PacBio sequencing, respectively. `sex` refers to the biological sex of the sample and should be either `female` or `male`. Finally, `fiber` specifies whether your sample is Fiber-seq data or not and should have either `y` for Yes or `n` for No.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run IntGenomicsLab/lrsomatic \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\nMore detail is given in our [usage documentation](/docs/usage.md)\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/running/run-pipelines#using-parameter-files).\n\n## Credits\n\nIntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth, Alexandra Pan\u010d\u00edkov\u00e1, Marios Eftychiou, Ruben Cools, Laurens Lambrechts, and Jonas Demeulemeester.\n\n## Pipeline output\n\nThis pipeline produces a series of different output files. The main output is an aligned and phased tumour bam file. This bam file can be used by any typical downstream tool that uses bam files as input. Furthermore, we have sample-specific QC outputs from `cramino` (fastq), `cramino` (bam), `mosdepth`, `samtools` (stats/flagstat/idxstats), and optionally `fibertools`. Finally, we have a `multiqc` report from that combines the output from `mosdepth` and `samtools` into one html report.\n\nBesides QC and the aligned and phased bam file, we have output from (structural) variant and copy number callers, of which some are optional. The output from these variant callers can be found in their respective folders. For small and structural variant callers (`clairS`, `clairS-TO`, and `severus`) these will contain, among others, `vcf` files with called variants. For `ascat` these contain files with final copy number information and plots of the copy number profiles.\n\nExample output directory structure:\n\n```\n\u251c\u2500\u2500 Sample 1\n\u2502    \u251c\u2500\u2500 ascat\n\u2502    \u251c\u2500\u2500 bamfiles\n\u2502    \u251c\u2500\u2500 qc\n\u2502    \u2502    \u251c\u2500\u2500 tumor\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_aln\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_ubam\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 fibertoolsrs\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 mosdepth\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 samtools\n\u2502    \u251c\u2500\u2500 variants\n\u2502    \u2502   \u251c\u2500\u2500clairS-TO\n\u2502    \u2502   \u251c\u2500\u2500severus\n\u2502    \u251c\u2500\u2500 vep\n\u2502    \u2502   \u251c\u2500\u2500 germline\n\u2502    \u2502   \u251c\u2500\u2500 somatic\n\u2502    \u2502   \u251c\u2500\u2500 SVs\n\u2502\n\u251c\u2500\u2500 Sample 2\n\u2502    \u251c\u2500\u2500 ascat\n\u2502    \u251c\u2500\u2500 bamfiles\n\u2502    \u251c\u2500\u2500 qc\n\u2502    \u2502    \u251c\u2500\u2500 tumor\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_aln\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_ubam\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 fibertoolsrs\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 mosdepth\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 samtools\n\u2502    \u2502    \u251c\u2500\u2500 normal\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_aln\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 cramino_ubam\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 fibertoolsrs\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 mosdepth\n\u2502    \u2502    \u2502   \u251c\u2500\u2500 samtools\n\u2502    \u251c\u2500\u2500 variants\n\u2502    \u2502   \u251c\u2500\u2500 clair3\n\u2502    \u2502   \u251c\u2500\u2500 clairS\n\u2502    \u2502   \u251c\u2500\u2500 severus\n\u2502    \u251c\u2500\u2500 vep\n\u2502    \u2502   \u251c\u2500\u2500 germline\n\u2502    \u2502   \u251c\u2500\u2500 somatic\n\u2502    \u2502   \u251c\u2500\u2500 SVs\n\u251c\u2500\u2500 pipeline_info\n```\n\nmore detail is given in our [output documentation](/docs/output.md)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\n## Citations\n\nIf you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:\n\n> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data\n>\n> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Luc\u00eda Rocha Iraiz\u00f3s, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester\n>\n> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -109,7 +109,7 @@
             },
             "conformsTo": [
                 {
-                    "@id": "https://w3id.org/ro/crate/1.1"
+                    "@id": "https://w3id.org/ro/crate/1.2"
                 },
                 {
                     "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
@@ -123,8 +123,13 @@
                 "SoftwareSourceCode",
                 "ComputationalWorkflow"
             ],
+            "contributor": [
+                {
+                    "@id": "https://orcid.org/0000-0002-2660-2478"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-12-23T13:58:53Z",
+            "dateModified": "2026-04-29T13:16:38Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,7 +165,7 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.04.0"
+            "version": "!>=25.10.4"
         },
         {
             "@id": "#37ea2685-1622-4ca2-a059-c12365c26c03",
@@ -298,6 +303,11 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "https://orcid.org/0000-0002-2660-2478",
+            "@type": "Person",
+            "name": "Jonas Demeulemeester"
         }
     ]
 }
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf
index 34db6e1f..78387c60 100644
--- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf
@@ -14,7 +14,6 @@ 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'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -182,7 +181,6 @@ workflow PIPELINE_COMPLETION {
     plaintext_email // boolean: Send plain-text email instead of HTML
     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
 
     main:
@@ -206,9 +204,6 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
     }
 
     workflow.onError {
diff --git a/subworkflows/nf-core/deepvariant/tests/deepvariant-workflow-and-process-equality-tester.nf b/subworkflows/nf-core/deepvariant/tests/deepvariant-workflow-and-process-equality-tester.nf
deleted file mode 100644
index 83a16d55..00000000
--- a/subworkflows/nf-core/deepvariant/tests/deepvariant-workflow-and-process-equality-tester.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-include { DEEPVARIANT_RUNDEEPVARIANT      } from '../../../../modules/nf-core/deepvariant/rundeepvariant/main'
-include { DEEPVARIANT                     } from '../main'
-
-workflow DEEPVARIANT_WORKFLOW_AND_PROCESS_EQUALITY_TESTER {
-    take:
-    ch_input   // channel: [ val(meta), path(input), path(index), path(intervals)]
-    ch_fasta   // channel: [ val(meta2), path(fasta) ]
-    ch_fai     // channel: [ val(meta3), path(fail) ]
-    ch_gzi     // channel: [ val(meta4), path(gzi) ]
-    ch_par_bed // channel: [ val(meta5), path(par_bed) ]
-
-    main:
-
-    DEEPVARIANT(ch_input, ch_fasta, ch_fai, ch_gzi, ch_par_bed)
-    DEEPVARIANT_RUNDEEPVARIANT(ch_input, ch_fasta, ch_fai, ch_gzi, ch_par_bed)
-
-    emit:
-    wf_vcf = DEEPVARIANT.out.vcf
-    pc_vcf = DEEPVARIANT_RUNDEEPVARIANT.out.vcf
-    wf_gvcf = DEEPVARIANT.out.gvcf
-    pc_gvcf = DEEPVARIANT_RUNDEEPVARIANT.out.gvcf
-}
diff --git a/subworkflows/nf-core/deepvariant/tests/equality.nf.test b/subworkflows/nf-core/deepvariant/tests/equality.nf.test
deleted file mode 100644
index c4a2276e..00000000
--- a/subworkflows/nf-core/deepvariant/tests/equality.nf.test
+++ /dev/null
@@ -1,63 +0,0 @@
-
-nextflow_workflow {
-
-    name "Compare subworkflow DEEPVARIANT to the process DEEPVARIANT_RUNDEEPVARIANT"
-    script "./deepvariant-workflow-and-process-equality-tester.nf"
-    config "./nextflow.config"
-    workflow "DEEPVARIANT_WORKFLOW_AND_PROCESS_EQUALITY_TESTER"
-
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "subworkflows/deepvariant"
-
-    tag "deepvariant"
-    tag "deepvariant/makeexamples"
-    tag "deepvariant/callvariants"
-    tag "deepvariant/postprocessvariants"
-    tag "deepvariant/rundeepvariant"
-
-    test("ensure that the subworkflow and DEEPVARIANT_RUNDEEPVARIANT have the same output") {
-        when {
-            workflow {
-                """
-                input[0] = Channel.of(
-                [
-                    [ id:'test', single_end:false ], // meta map
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
-                ],
-                [
-                    [ id:'test2', single_end:false ], // meta map
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true),
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
-                ]
-                )
-                input[1] = [
-                    [ id:'genome'],
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
-                    ]
-                input[2] = [
-                    [ id:'genome'],
-                      file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]
-                input[3] = [
-                    [],[]
-                ]
-                input[4] = [
-                    [],[]
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert path(workflow.out.wf_vcf[0][1]).vcf.variantsMD5 == path(workflow.out.pc_vcf[0][1]).vcf.variantsMD5 },
-                { assert path(workflow.out.wf_gvcf[0][1]).vcf.variantsMD5 == path(workflow.out.pc_gvcf[0][1]).vcf.variantsMD5 },
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 2f30e9a4..afca5439 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE {
     checkProfileProvided(nextflow_cli_args)
 
     emit:
-    valid_config
+    valid_config = valid_config
 }
 
 /*
@@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) {
         log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
-
-//
-// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
-//
-def imNotification(summary_params, hook_url) {
-    def summary = [:]
-    summary_params
-        .keySet()
-        .sort()
-        .each { group ->
-            summary << summary_params[group]
-        }
-
-    def misc_fields = [:]
-    misc_fields['start']          = workflow.start
-    misc_fields['complete']       = workflow.complete
-    misc_fields['scriptfile']     = workflow.scriptFile
-    misc_fields['scriptid']       = workflow.scriptId
-    if (workflow.repository) {
-        misc_fields['repository'] = workflow.repository
-    }
-    if (workflow.commitId) {
-        misc_fields['commitid']   = workflow.commitId
-    }
-    if (workflow.revision) {
-        misc_fields['revision']   = workflow.revision
-    }
-    misc_fields['nxf_version']    = workflow.nextflow.version
-    misc_fields['nxf_build']      = workflow.nextflow.build
-    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
-
-    def msg_fields = [:]
-    msg_fields['version']      = getWorkflowVersion()
-    msg_fields['runName']      = workflow.runName
-    msg_fields['success']      = workflow.success
-    msg_fields['dateComplete'] = workflow.complete
-    msg_fields['duration']     = workflow.duration
-    msg_fields['exitStatus']   = workflow.exitStatus
-    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-    msg_fields['projectDir']   = workflow.projectDir
-    msg_fields['summary']      = summary << misc_fields
-
-    // Render the JSON template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    // Different JSON depending on the service provider
-    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
-    def json_template = engine.createTemplate(hf).make(msg_fields)
-    def json_message  = json_template.toString()
-
-    // POST
-    def post = new URL(hook_url).openConnection()
-    post.setRequestMethod("POST")
-    post.setDoOutput(true)
-    post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"))
-    def postRC = post.getResponseCode()
-    if (!postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText())
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
new file mode 100644
index 00000000..8940d32d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap
new file mode 100644
index 00000000..859d1030
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index acb39724..1df8b76f 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
         }
         log.info paramsHelp(
             help_options,
-            params.help instanceof String ? params.help : "",
+            (params.help instanceof String && params.help != "true") ? params.help : "",
         )
         exit 0
     }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 8d8c7371..f6537cc3 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.5.1"
+    id "nf-schema@2.6.1"
 }
 
 validation {