From e4d5a899368a8c57746802d6eac2687cde0cf966 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 28 Apr 2026 11:21:19 +0000
Subject: [PATCH 01/14] Template update for nf-core/tools version 4.0.0

---
 .devcontainer/devcontainer.json               |    1 +
 .github/CONTRIBUTING.md                       |  125 --
 .github/PULL_REQUEST_TEMPLATE.md              |    4 +-
 .github/actions/get-shards/action.yml         |    2 +-
 .github/actions/nf-test/action.yml            |   10 +-
 .github/workflows/awsfulltest.yml             |   25 +-
 .github/workflows/awstest.yml                 |    4 +-
 .github/workflows/branch.yml                  |    2 +-
 .github/workflows/clean-up.yml                |    2 +-
 .github/workflows/download_pipeline.yml       |   14 +-
 .github/workflows/fix_linting.yml             |   22 +-
 .github/workflows/linting.yml                 |   34 +-
 .github/workflows/linting_comment.yml         |    4 +-
 .github/workflows/nf-test.yml                 |    8 +-
 .github/workflows/release-announcements.yml   |    4 +-
 .../workflows/template-version-comment.yml    |    6 +-
 .gitignore                                    |    1 +
 .nf-core.yml                                  |    4 +-
 .pre-commit-config.yaml                       |   16 +-
 .prettierignore                               |    2 -
 CHANGELOG.md                                  |    2 +-
 README.md                                     |   12 +-
 assets/adaptivecard.json                      |   67 -
 assets/multiqc_config.yml                     |    4 +-
 assets/slackreport.json                       |   34 -
 conf/base.config                              |    2 +-
 conf/containers_conda_lock_files_amd64.config |    2 +
 conf/containers_conda_lock_files_arm64.config |    2 +
 conf/containers_docker_amd64.config           |    2 +
 conf/containers_docker_arm64.config           |    2 +
 .../containers_singularity_https_amd64.config |    2 +
 .../containers_singularity_https_arm64.config |    2 +
 conf/containers_singularity_oras_amd64.config |    2 +
 conf/containers_singularity_oras_arm64.config |    2 +
 docs/CONTRIBUTING.md                          |  185 ++
 docs/usage.md                                 |    8 +-
 main.nf                                       |    7 +-
 modules.json                                  |    8 +-
 .../linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt     |  822 +++++++++
 .../linux_arm64-bd-e455e32f745abe68_1.txt     |  769 ++++++++
 modules/nf-core/fastqc/main.nf                |   43 +-
 modules/nf-core/fastqc/meta.yml               |   51 +-
 modules/nf-core/fastqc/tests/main.nf.test     |   12 +-
 .../nf-core/fastqc/tests/main.nf.test.snap    |  228 ++-
 .../linux_amd64-bd-c1f4a7982b743963_1.txt     | 1552 +++++++++++++++++
 .../linux_amd64-bd-db7c73dae76bc9e6_1.txt     |  126 ++
 .../linux_arm64-bd-40bf3b435e89dc22_1.txt     | 1502 ++++++++++++++++
 .../linux_arm64-bd-d167b8012595a136_1.txt     |  125 ++
 modules/nf-core/multiqc/environment.yml       |    2 +-
 modules/nf-core/multiqc/main.nf               |   51 +-
 modules/nf-core/multiqc/meta.yml              |  165 +-
 .../multiqc/tests/custom_prefix.config        |    5 +
 modules/nf-core/multiqc/tests/main.nf.test    |  191 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |  435 ++++-
 modules/nf-core/multiqc/tests/nextflow.config |    1 +
 nextflow.config                               |   10 +-
 nextflow_schema.json                          |    7 -
 nf-test.config                                |   26 +-
 ro-crate-metadata.json                        |   36 +-
 .../main.nf                                   |   17 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |   66 +-
 .../utils_nfcore_pipeline/tests/main.nf.test  |   29 +
 .../tests/main.nf.test.snap                   |   19 +
 .../nf-core/utils_nfschema_plugin/main.nf     |    3 +-
 .../tests/nextflow.config                     |    2 +-
 tests/default.nf.test                         |   14 +-
 tests/nextflow.config                         |    2 +-
 workflows/variantbenchmarking.nf              |   84 +-
 68 files changed, 6284 insertions(+), 746 deletions(-)
 delete mode 100644 .github/CONTRIBUTING.md
 delete mode 100644 assets/adaptivecard.json
 delete mode 100644 assets/slackreport.json
 create mode 100644 conf/containers_conda_lock_files_amd64.config
 create mode 100644 conf/containers_conda_lock_files_arm64.config
 create mode 100644 conf/containers_docker_amd64.config
 create mode 100644 conf/containers_docker_arm64.config
 create mode 100644 conf/containers_singularity_https_amd64.config
 create mode 100644 conf/containers_singularity_https_arm64.config
 create mode 100644 conf/containers_singularity_oras_amd64.config
 create mode 100644 conf/containers_singularity_oras_arm64.config
 create mode 100644 docs/CONTRIBUTING.md
 create mode 100644 modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
 create mode 100644 modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
 create mode 100644 modules/nf-core/multiqc/tests/custom_prefix.config
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap

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 c7696f86..00000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,125 +0,0 @@
-# `nf-core/variantbenchmarking`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving nf-core/variantbenchmarking.
-
-We try to manage the required tasks for nf-core/variantbenchmarking 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 ;)
-
-> [!NOTE]
-> If you need help using or modifying nf-core/variantbenchmarking then the best place to ask is on the nf-core Slack [#variantbenchmarking](https://nfcore.slack.com/channels/variantbenchmarking) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Contribution workflow
-
-If you'd like to write some code for nf-core/variantbenchmarking, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [nf-core/variantbenchmarking issues](https://github.com/nf-core/variantbenchmarking/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 [nf-core/variantbenchmarking repository](https://github.com/nf-core/variantbenchmarking) 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.
-
-## Getting help
-
-For further information/help, please consult the [nf-core/variantbenchmarking documentation](https://nf-co.re/variantbenchmarking/usage) and don't hesitate to get in touch on the nf-core Slack [#variantbenchmarking](https://nfcore.slack.com/channels/variantbenchmarking) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Pipeline contribution conventions
-
-To make the `nf-core/variantbenchmarking` 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/nf-core/variantbenchmarking/codespaces)
-- Tools installed
-  - nf-core
-  - Nextflow
-
-Devcontainer specs:
-
-- [DevContainer config](.devcontainer/devcontainer.json)
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index e510d3e9..591a0040 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/nf-core/variantbenchmarking/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/variantbenchmarking/tree/master/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/nf-core/variantbenchmarking/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/variantbenchmarking/tree/master/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/variantbenchmarking _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile 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/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 39da3227..57c1d5c8 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -23,7 +23,7 @@ jobs:
           echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
@@ -33,14 +33,33 @@ jobs:
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
           workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/variantbenchmarking/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'variantbenchmarking'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *variantbenchmarking/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *variantbenchmarking/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/variantbenchmarking/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 010f8d35..9abec849 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Seqera Platform CLI tool action
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 9d2c4e66..efb28a85 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 11a48fc7..e3149282 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@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # 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..bfe46c98 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@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # 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: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc26..2bc3c07f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(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 c98d76ec..efd72d65 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
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ 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
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 431d3d44..78d5dbe0 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@master
+      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)
@@ -34,7 +34,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
+      - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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: ${{ steps.read_yml.outputs['nf_core_version'] }}.
             > Please update your pipeline to the latest version.
             >
-            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
           #
diff --git a/.gitignore b/.gitignore
index a42ce016..cc2b1a77 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.lineage/
diff --git a/.nf-core.yml b/.nf-core.yml
index ce77d299..e63cdaba 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,7 +3,7 @@ lint:
     - .gitignore
     - docs/images/nf-core-variantbenchmarking_logo_dark.png
     - docs/images/nf-core-variantbenchmarking_logo_light.png
-nf_core_version: 3.5.1
+nf_core_version: 4.0.0
 repository_type: pipeline
 template:
   author: kuebra.narci@dkfz-heidelberg.de
@@ -13,4 +13,4 @@ template:
   name: variantbenchmarking
   org: nf-core
   outdir: .
-  version: 1.3.0
+  version: 1.6.0dev
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d06777a8..f51e1a28 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.6.2
+          - prettier@3.8.3
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -13,15 +13,21 @@ repos:
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              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/CHANGELOG.md b/CHANGELOG.md
index 31e9f614..0d4af2e0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.3.0 - [date]
+## v1.6.0dev - [date]
 
 Initial release of nf-core/variantbenchmarking, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/README.md b/README.md
index 1e6bd6bf..4b9325c6 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,8 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![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-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)
 [![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/)
@@ -30,13 +30,13 @@
 -->
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
 > [!NOTE]
-> 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.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -66,7 +66,7 @@ nextflow run nf-core/variantbenchmarking \
 ```
 
 > [!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).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).
 
@@ -86,7 +86,7 @@ We thank the following people for their extensive assistance in the development
 
 ## 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).
 
 For further information or help, don't hesitate to get in touch on the [Slack `#variantbenchmarking` channel](https://nfcore.slack.com/channels/variantbenchmarking) (you can join with [this invite](https://nf-co.re/join/slack)).
 
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
deleted file mode 100644
index 4b5f7c53..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": "nf-core/variantbenchmarking 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/multiqc_config.yml b/assets/multiqc_config.yml
index a3b84028..9b0ed731 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/variantbenchmarking/releases/tag/1.3.0" target="_blank">nf-core/variantbenchmarking</a>
+  This report has been generated by the <a href="https://github.com/nf-core/variantbenchmarking/tree/dev" target="_blank">nf-core/variantbenchmarking</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/variantbenchmarking/1.3.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/variantbenchmarking/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-variantbenchmarking-methods-description":
     order: -1000
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index 9e94a79c..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": "nf-core/variantbenchmarking ${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 b970bb48..5628e8d7 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'
 
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
new file mode 100644
index 00000000..d3ee1b4e
--- /dev/null
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
+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..2b90ac4f
--- /dev/null
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
+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..65f1814a
--- /dev/null
+++ b/conf/containers_docker_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
+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..6c845ba4
--- /dev/null
+++ b/conf/containers_docker_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } }
+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..838f2484
--- /dev/null
+++ b/conf/containers_singularity_https_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
+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..090173be
--- /dev/null
+++ b/conf/containers_singularity_https_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } }
+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..773f3698
--- /dev/null
+++ b/conf/containers_singularity_oras_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
+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..798cc638
--- /dev/null
+++ b/conf/containers_singularity_oras_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } }
+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..8260ad3f
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,185 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `nf-core/variantbenchmarking`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving nf-core/variantbenchmarking.
+
+This page describes the recommended nf-core way to contribute to both nf-core/variantbenchmarking 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 nf-core/variantbenchmarking.
+
+> [!NOTE]
+> If you need help using or modifying nf-core/variantbenchmarking, ask on the nf-core Slack [#variantbenchmarking](https://nfcore.slack.com/channels/variantbenchmarking) channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+## 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/nf-core/variantbenchmarking/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 [nf-core/variantbenchmarking repository](https://github.com/nf-core/variantbenchmarking) 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.
+
+## Use of AI and LLMs
+
+The nf-core stance on the use of AI and LLMs is that humans are still ultimately responsible for their submitted code, regardless of the tools they use.
+
+If you’re using AI tools, try to stick by these guidelines:
+
+- Keep PRs as small and focussed as possible
+- Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR)
+- Review all generated code yourself before opening a PR, and ensure that you understand it
+- Engage with the community review process and expect to make revisions
+
+For more detail, see the the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
+
+### Getting help
+
+For further information and help, see the [nf-core/variantbenchmarking documentation](https://nf-co.re/variantbenchmarking/usage) or ask on the nf-core [#variantbenchmarking](https://nfcore.slack.com/channels/variantbenchmarking) Slack channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+### GitHub Codespaces
+
+You can contribute to nf-core/variantbenchmarking 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/nf-core/variantbenchmarking/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 nf-core/variantbenchmarking 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 00abef14..667e1cd6 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -76,7 +76,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
 > [!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:
 
@@ -173,19 +173,19 @@ 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 70c16fd0..6c895d6f 100644
--- a/main.nf
+++ b/main.nf
@@ -51,7 +51,11 @@ workflow NFCORE_VARIANTBENCHMARKING {
     // WORKFLOW: Run pipeline
     //
     VARIANTBENCHMARKING (
-        samplesheet
+        samplesheet,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
     )
     emit:
     multiqc_report = VARIANTBENCHMARKING.out.multiqc_report // channel: /path/to/multiqc_report.html
@@ -95,7 +99,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         NFCORE_VARIANTBENCHMARKING.out.multiqc_report
     )
 }
diff --git a/modules.json b/modules.json
index 0cc9c96d..3e04aca2 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     }
                 }
@@ -26,12 +26,12 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
new file mode 100644
index 00000000..7770ccd5
--- /dev/null
+++ b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
@@ -0,0 +1,822 @@
+
+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/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/fastqc-0.12.1-hdfd78af_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
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diff --git a/modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
new file mode 100644
index 00000000..cdc434ca
--- /dev/null
+++ b/modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 23e16634..10851264 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,37 +1,40 @@
 process FASTQC {
     tag "${meta.id}"
-    label 'process_medium'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
-        'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0'
+        : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads, stageAs: '?/*')
 
     output:
     tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
+    tuple val(meta), path("*.zip"), emit: zip
+    tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args          = task.ext.args ?: ''
-    def prefix        = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to     = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
-    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
+    // Dividing the task.memory by task.cpus allows to stick to requested amount of RAM in the label
+    def memory_in_mb = task.memory
+        ? (task.memory.toUnit('MB') / task.cpus).intValue()
+        : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+    def fastqc_memory_arg = fastqc_memory ? "--memory ${fastqc_memory}" : ''
 
     """
     printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
@@ -41,13 +44,8 @@ process FASTQC {
     fastqc \\
         ${args} \\
         --threads ${task.cpus} \\
-        --memory ${fastqc_memory} \\
+        ${fastqc_memory_arg} \\
         ${renamed_files}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 
     stub:
@@ -55,10 +53,5 @@ process FASTQC {
     """
     touch ${prefix}.html
     touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index c8d9d025..2f6cfef6 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -53,13 +53,28 @@ output:
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
           ontologies: []
+  versions_fastqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@drpatelh"
   - "@grst"
@@ -70,3 +85,27 @@ maintainers:
   - "@grst"
   - "@ewels"
   - "@FelixKrueger"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68
+      build_id: bd-e455e32f745abe68_1
+      scan_id: sc-f102f736465af88c_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2
+      build_id: bd-5cb1a2fa2f18c7c2_1
+      scan_id: sc-0c0466326b6b77d2_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd
+      build_id: bd-5c4bd442468d75dd_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035
+      build_id: bd-127a87fc06499035_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index e9d79a07..66c44da9 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -58,7 +58,7 @@ nextflow_process {
                 { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
                 { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
                 { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -82,7 +82,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -106,7 +106,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -142,7 +142,7 @@ nextflow_process {
                 { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
                 { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
                 { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -166,7 +166,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index d5db3092..c8ee120f 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,15 +1,21 @@
 {
     "sarscov2 custom_prefix": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:16.374038"
+        "timestamp": "2025-10-28T16:39:14.518503"
     },
     "sarscov2 single-end [fastq] - stub": {
         "content": [
@@ -33,7 +39,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -44,8 +54,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -59,10 +73,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:24.993809"
+        "timestamp": "2025-10-28T16:39:19.309008"
     },
     "sarscov2 custom_prefix - stub": {
         "content": [
@@ -86,7 +100,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -97,8 +115,12 @@
                         "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -112,58 +134,82 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:03:10.93942"
+        "timestamp": "2025-10-28T16:39:44.94888"
     },
     "sarscov2 interleaved [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:42.355718"
+        "timestamp": "2025-10-28T16:38:45.168496"
     },
     "sarscov2 paired-end [bam]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:53.276274"
+        "timestamp": "2025-10-28T16:38:53.268919"
     },
     "sarscov2 multiple [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:05.527626"
+        "timestamp": "2025-10-28T16:39:05.050305"
     },
     "sarscov2 paired-end [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:31.188871"
+        "timestamp": "2025-10-28T16:38:37.2373"
     },
     "sarscov2 paired-end [fastq] - stub": {
         "content": [
@@ -187,7 +233,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -198,8 +248,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -213,10 +267,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:34.273566"
+        "timestamp": "2025-10-28T16:39:24.450398"
     },
     "sarscov2 multiple [fastq] - stub": {
         "content": [
@@ -240,7 +294,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -251,8 +309,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -266,22 +328,28 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:03:02.304411"
+        "timestamp": "2025-10-28T16:39:39.758762"
     },
     "sarscov2 single-end [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:19.095607"
+        "timestamp": "2025-10-28T16:38:29.555068"
     },
     "sarscov2 interleaved [fastq] - stub": {
         "content": [
@@ -305,7 +373,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -316,8 +388,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -331,10 +407,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:44.640184"
+        "timestamp": "2025-10-28T16:39:29.193136"
     },
     "sarscov2 paired-end [bam] - stub": {
         "content": [
@@ -358,7 +434,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -369,8 +449,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -384,9 +468,9 @@
             }
         ],
         "meta": {
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         },
-        "timestamp": "2024-07-22T11:02:53.550742"
+        "timestamp": "2025-10-28T16:39:34.144919"
     }
 }
\ No newline at end of file
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
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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
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda#49f570f3bc4c874a06ea69b7225753af
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb
+https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda#2c21e66f50753a083cbe6b80f38268fa
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda#1b08cd684f34175e4514474793d44bcb
+https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda#c80d8a3b84358cb967fa81e7075fbc8a
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-hf4e2dac_0.conda#810d83373448da85c3f673fbcb7ad3a3
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
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+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
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new file mode 100644
index 00000000..a58231a0
--- /dev/null
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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
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+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
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+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
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+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 d02016a0..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=1.32
+  - bioconda::multiqc=1.34
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index c1158fb0..e80e8cd8 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,24 +1,21 @@
 process MULTIQC {
+    tag "${meta.id}"
     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/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
-        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
+    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:
-    path  multiqc_files, stageAs: "?/*"
-    path(multiqc_config)
-    path(extra_multiqc_config)
-    path(multiqc_logo)
-    path(replace_names)
-    path(sample_names)
+    tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
 
     output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
+    tuple val(meta), path("*.html"), emit: report
+    tuple val(meta), path("*_data"), emit: data
+    tuple val(meta), path("*_plots"), emit: plots, optional: true
+    // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,38 +23,28 @@ process MULTIQC {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
-    def config = multiqc_config ? "--config $multiqc_config" : ''
-    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : ""
     def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
     def replace = replace_names ? "--replace-names ${replace_names}" : ''
     def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
-        $args \\
-        $config \\
-        $prefix \\
-        $extra_config \\
-        $logo \\
-        $replace \\
-        $samples \\
+        ${args} \\
+        ${config} \\
+        ${prefix} \\
+        ${logo} \\
+        ${replace} \\
+        ${samples} \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir multiqc_data
+    touch multiqc_data/.stub
     mkdir multiqc_plots
+    touch multiqc_plots/.stub
     touch multiqc_report.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ce30eb73..2facc627 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,6 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into
-  a single report
+description: Aggregate results from bioinformatics analyses across many samples
+  into a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,74 +12,91 @@ tools:
         It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
-      licence: ["GPL-3.0-or-later"]
+      licence:
+        - "GPL-3.0-or-later"
       identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-      ontologies: []
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-      ontologies:
-        - edam: http://edamontology.org/format_3750 # YAML
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections
-        in multiqc_config.
-      pattern: "*.{yml,yaml}"
-      ontologies:
-        - edam: http://edamontology.org/format_3750 # YAML
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-      ontologies: []
-  - replace_names:
-      type: file
-      description: |
-        Optional two-column sample renaming file. First column a set of
-        patterns, second column a set of corresponding replacements. Passed via
-        MultiQC's `--replace-names` option.
-      pattern: "*.{tsv}"
-      ontologies:
-        - edam: http://edamontology.org/format_3475 # TSV
-  - sample_names:
-      type: file
-      description: |
-        Optional TSV file with headers, passed to the MultiQC --sample_names
-        argument.
-      pattern: "*.{tsv}"
-      ontologies:
-        - edam: http://edamontology.org/format_3475 # TSV
-output:
-  report:
-    - "*multiqc_report.html":
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'sample1', single_end:false ]
+    - multiqc_files:
         type: file
-        description: MultiQC report file
-        pattern: "multiqc_report.html"
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
         ontologies: []
-  data:
-    - "*_data":
-        type: directory
-        description: MultiQC data dir
-        pattern: "multiqc_data"
-  plots:
-    - "*_plots":
+    - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+    - multiqc_logo:
         type: file
-        description: Plots created by MultiQC
-        pattern: "*_data"
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
         ontologies: []
-  versions:
-    - versions.yml:
+    - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+    - sample_names:
         type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3475
+output:
+  report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.html":
+          type: file
+          description: MultiQC report file
+          pattern: ".html"
+          ontologies: []
+  data:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
+  plots:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_plots"
+          ontologies: []
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - multiqc:
+          type: string
+          description: The tool name
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@abhi18av"
   - "@bunop"
@@ -90,3 +107,27 @@ maintainers:
   - "@bunop"
   - "@drpatelh"
   - "@jfy133"
+containers:
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
+      build_id: bd-db7c73dae76bc9e6_1
+      scan_id: sc-66fc7138dbf1cf48_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
+      build_id: bd-d167b8012595a136_1
+      scan_id: sc-ac701dfa631a2af9_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
+      build_id: bd-4fc8657c816047c0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
+      build_id: bd-7fbd82d945c06726_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config
new file mode 100644
index 00000000..b30b1358
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/custom_prefix.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = "custom_prefix"
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index 33316a7d..4cbdb95d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -15,25 +15,84 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    []
+                ])
                 """
             }
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
-                { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
-            )
+            assert process.success
+            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()
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - custom prefix") {
+        config "./custom_prefix.config"
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    []
+                ])
+                """
+            }
         }
 
+        then {
+            assert process.success
+            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()
+        }
     }
 
     test("sarscov2 single-end [fastqc] [config]") {
@@ -41,23 +100,85 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true),
+                    [],
+                    [],
+                    []
+                ])
                 """
             }
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
-                { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
-            )
+            assert process.success
+            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("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] [multiple configs]") {
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [
+                        file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true),
+                        file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true)
+                    ],
+                    [],
+                    [],
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${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()
         }
     }
 
@@ -68,25 +189,23 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    []
+                ])
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.report.collect { file(it).getName() } +
-                                process.out.data.collect { file(it).getName() } +
-                                process.out.plots.collect { file(it).getName() } +
-                                process.out.versions ).match("multiqc_stub") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index a88bafd6..7c2f370f 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,41 +1,422 @@
 {
-    "multiqc_versions_single": {
+    "sarscov2 single-end [fastqc] [multiple configs]": {
         "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "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",
+                        "1.34"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-17T16:15:42.577775492",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:33:24.356715"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
-    "multiqc_stub": {
+    "sarscov2 single-end [fastqc]": {
         "content": [
-            [
-                "multiqc_report.html",
-                "multiqc_data",
-                "multiqc_plots",
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "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",
+                        "1.34"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-17T16:21:17.072841555",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:34:11.103619"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
-    "multiqc_versions_config": {
+    "sarscov2 single-end [fastqc] - stub": {
         "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "data": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        [
+                            ".stub:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        [
+                            ".stub:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.34"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-02-26T15:14:39.789193051",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:34:04.615233"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 single-end [fastqc] [config]": {
+        "content": [
+            {
+                "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",
+                        "1.34"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-17T16:15:30.372239611",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 single-end [fastqc] - custom prefix": {
+        "content": [
+            {
+                "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",
+                        "1.34"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-17T16:15:18.189023981",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ 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 ae585ad0..0a0a906d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,7 +32,6 @@ 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
@@ -53,6 +52,10 @@ 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'
 
@@ -251,8 +254,8 @@ manifest {
     description     = """Variant Benchmarking pipeline for germline and somatic variant callers """
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=25.04.0'
-    version         = '1.3.0'
+    nextflowVersion = '!>=25.10.4'
+    version         = '1.6.0dev'
     doi             = ''
 }
 
@@ -265,6 +268,5 @@ 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 9a177833..3f5b11b2 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -180,13 +180,6 @@
                     "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",
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 f5db563d..11971bd0 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",
@@ -21,9 +21,9 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-11-20T09:32:24+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-variantbenchmarking_logo_dark.png\">\n    <img alt=\"nf-core/variantbenchmarking\" src=\"docs/images/nf-core-variantbenchmarking_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/variantbenchmarking)\n[![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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/nf-core/variantbenchmarking)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantbenchmarking-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/variantbenchmarking** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\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<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/variantbenchmarking \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/variantbenchmarking/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/variantbenchmarking/output).\n\n## Credits\n\nnf-core/variantbenchmarking was originally written by kuebra.narci@dkfz-heidelberg.de.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#variantbenchmarking` channel](https://nfcore.slack.com/channels/variantbenchmarking) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/variantbenchmarking for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2026-04-28T11:21:12+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-variantbenchmarking_logo_dark.png\">\n    <img alt=\"nf-core/variantbenchmarking\" src=\"docs/images/nf-core-variantbenchmarking_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/variantbenchmarking)\n[![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/variantbenchmarking)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantbenchmarking-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/variantbenchmarking** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/variantbenchmarking \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/variantbenchmarking/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/variantbenchmarking/output).\n\n## Credits\n\nnf-core/variantbenchmarking was originally written by kuebra.narci@dkfz-heidelberg.de.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#variantbenchmarking` channel](https://nfcore.slack.com/channels/variantbenchmarking) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/variantbenchmarking for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#3471111a-4754-483d-ad9c-2b92cbbc02da"
+                    "@id": "#306c4f18-fa5d-4edc-b42d-a14b7de74b7c"
                 }
             ],
             "name": "nf-core/variantbenchmarking"
@@ -112,7 +112,7 @@
             },
             "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"
@@ -122,8 +122,13 @@
         {
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "contributor": [
+                {
+                    "@id": "#79f54a56-4f5c-473e-b09a-df4a2c64b9c7"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-11-20T09:32:24Z",
+            "dateModified": "2026-04-28T11:21:12Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -141,8 +146,8 @@
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/variantbenchmarking", "https://nf-co.re/variantbenchmarking/1.3.0/"],
-            "version": ["1.3.0"]
+            "url": ["https://github.com/nf-core/variantbenchmarking", "https://nf-co.re/variantbenchmarking/dev/"],
+            "version": ["1.6.0dev"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -154,14 +159,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.04.0"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "#3471111a-4754-483d-ad9c-2b92cbbc02da",
+            "@id": "#306c4f18-fa5d-4edc-b42d-a14b7de74b7c",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#0c3604cd-a616-4645-8219-f569fc03cc1e"
+                    "@id": "#c48d6e85-f79c-40f5-97e5-faa8144265f0"
                 }
             ],
             "mainEntity": {
@@ -170,7 +175,7 @@
             "name": "Test suite for nf-core/variantbenchmarking"
         },
         {
-            "@id": "#0c3604cd-a616-4645-8219-f569fc03cc1e",
+            "@id": "#c48d6e85-f79c-40f5-97e5-faa8144265f0",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/variantbenchmarking",
             "resource": "repos/nf-core/variantbenchmarking/actions/workflows/nf-test.yml",
@@ -297,6 +302,11 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#79f54a56-4f5c-473e-b09a-df4a2c64b9c7",
+            "@type": "Person",
+            "name": "kuebra.narci@dkfz-heidelberg.de"
         }
     ]
 }
diff --git a/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf b/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf
index cfa1119c..6d77620d 100644
--- a/subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_variantbenchmarking_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'
 
@@ -54,6 +53,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+
+    def before_text = ""
+    def after_text = ""
     before_text = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -71,6 +73,10 @@ workflow PIPELINE_INITIALISATION {
 * Software dependencies
     https://github.com/nf-core/variantbenchmarking/blob/master/CITATIONS.md
 """
+    if (monochrome_logs) {
+        before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '')
+    }
+
     command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
     UTILS_NFSCHEMA_PLUGIN (
@@ -102,7 +108,7 @@ workflow PIPELINE_INITIALISATION {
     //
 
     channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -140,7 +146,6 @@ 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:
@@ -164,13 +169,11 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
+
     }
 
     workflow.onError {
-        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+        log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting"
     }
 }
 
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 ee4738c8..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
     }
@@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     emit:
     dummy_emit = true
 }
-
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 {
diff --git a/tests/default.nf.test b/tests/default.nf.test
index a54fade1..21998911 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -13,19 +13,19 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 8ce368c8..cbe782e8 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -8,7 +8,7 @@
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/variantbenchmarking'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/variantbenchmarking/'
 }
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
diff --git a/workflows/variantbenchmarking.nf b/workflows/variantbenchmarking.nf
index 2afa3495..26187063 100644
--- a/workflows/variantbenchmarking.nf
+++ b/workflows/variantbenchmarking.nf
@@ -20,23 +20,25 @@ workflow VARIANTBENCHMARKING {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
+    multiqc_config
+    multiqc_logo
+    multiqc_methods_description
+    outdir
+
     main:
 
-    ch_versions = channel.empty()
-    ch_multiqc_files = channel.empty()
+    def ch_versions = channel.empty()
+    def ch_multiqc_files = channel.empty()
     //
     // MODULE: Run FastQC
     //
-    FASTQC (
-        ch_samplesheet
-    )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    FASTQC(ch_samplesheet)
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.map{ _meta, file -> file })
 
     //
     // Collate and save software versions
     //
-    def topic_versions = Channel.topic("versions")
+    def topic_versions = channel.topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path
@@ -53,59 +55,43 @@ workflow VARIANTBENCHMARKING {
             "${process}:\n${tool_versions.join('\n')}"
         }
 
-    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+    def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
         .mix(topic_versions_string)
         .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
+            storeDir: "${outdir}/pipeline_info",
             name: 'nf_core_'  +  'variantbenchmarking_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
-        ).set { ch_collated_versions }
-
+        )
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = channel.fromPath(
-        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config = params.multiqc_config ?
-        channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        channel.empty()
-    ch_multiqc_logo          = params.multiqc_logo ?
-        channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        channel.empty()
-
-    summary_params      = paramsSummaryMap(
-        workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
-        file(params.multiqc_methods_description, checkIfExists: true) :
-        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = channel.value(
-        methodsDescriptionText(ch_multiqc_custom_methods_description))
-
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_methods_description.collectFile(
-            name: 'methods_description_mqc.yaml',
-            sort: true
-        )
-    )
-
-    MULTIQC (
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList(),
-        [],
-        []
+    def ch_summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def ch_workflow_summary = channel.value(paramsSummaryMultiqc(ch_summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    def ch_multiqc_custom_methods_description = multiqc_methods_description
+        ? file(multiqc_methods_description, checkIfExists: true)
+        : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
+    MULTIQC(
+        ch_multiqc_files.flatten().collect().map { files ->
+            [
+                [id: 'variantbenchmarking'],
+                files,
+                multiqc_config
+                    ? file(multiqc_config, checkIfExists: true)
+                    : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true),
+                multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [],
+                [],
+                [],
+            ]
+        }
     )
-
-    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
-
 }
 
 /*

From adc9484bed79fa00c6381b96ef97e14e8768f9fd Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 30 Apr 2026 13:33:33 +0000
Subject: [PATCH 02/14] Template update for nf-core/tools version 4.0.2

---
 .github/workflows/download_pipeline.yml |  8 +++++---
 .github/workflows/fix_linting.yml       |  2 +-
 .github/workflows/linting.yml           |  2 +-
 .github/workflows/linting_comment.yml   |  2 +-
 .nf-core.yml                            |  2 +-
 README.md                               |  2 +-
 nextflow_schema.json                    |  1 -
 ro-crate-metadata.json                  | 18 +++++++++---------
 8 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 5b6592c1..a7bf4fc2 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -38,6 +38,9 @@ jobs:
     runs-on: ubuntu-latest
     needs: configure
     steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
@@ -55,10 +58,9 @@ jobs:
           apptainer-version: 1.3.4
 
       - name: Read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
-        with:
-          config: ${{ github.workspace }}/.nf-core.yml
+        run: |
+          echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT"
 
       - name: Install dependencies
         run: |
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index e3149282..d78af776 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -37,7 +37,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index bfe46c98..8738ffc9 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -17,7 +17,7 @@ jobs:
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Run prek
-        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 2bc3c07f..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@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.nf-core.yml b/.nf-core.yml
index e63cdaba..37b634ff 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -3,7 +3,7 @@ lint:
     - .gitignore
     - docs/images/nf-core-variantbenchmarking_logo_dark.png
     - docs/images/nf-core-variantbenchmarking_logo_light.png
-nf_core_version: 4.0.0
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: kuebra.narci@dkfz-heidelberg.de
diff --git a/README.md b/README.md
index 4b9325c6..fb31fc3c 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-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-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3f5b11b2..30a5a7f2 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -74,7 +74,6 @@
                 },
                 "igenomes_base": {
                     "type": "string",
-                    "format": "directory-path",
                     "description": "The base path to the igenomes reference files",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 11971bd0..85cc07c0 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2026-04-28T11:21:12+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-variantbenchmarking_logo_dark.png\">\n    <img alt=\"nf-core/variantbenchmarking\" src=\"docs/images/nf-core-variantbenchmarking_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/variantbenchmarking)\n[![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/variantbenchmarking)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantbenchmarking-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/variantbenchmarking** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/variantbenchmarking \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/variantbenchmarking/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/variantbenchmarking/output).\n\n## Credits\n\nnf-core/variantbenchmarking was originally written by kuebra.narci@dkfz-heidelberg.de.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#variantbenchmarking` channel](https://nfcore.slack.com/channels/variantbenchmarking) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/variantbenchmarking for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-04-30T13:33:25+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-variantbenchmarking_logo_dark.png\">\n    <img alt=\"nf-core/variantbenchmarking\" src=\"docs/images/nf-core-variantbenchmarking_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/variantbenchmarking)\n[![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/variantbenchmarking)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantbenchmarking-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/variantbenchmarking** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/variantbenchmarking \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/variantbenchmarking/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/variantbenchmarking/output).\n\n## Credits\n\nnf-core/variantbenchmarking was originally written by kuebra.narci@dkfz-heidelberg.de.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#variantbenchmarking` channel](https://nfcore.slack.com/channels/variantbenchmarking) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/variantbenchmarking for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#306c4f18-fa5d-4edc-b42d-a14b7de74b7c"
+                    "@id": "#ddac9ff4-c8bd-47a3-90ce-06951c5bbb32"
                 }
             ],
             "name": "nf-core/variantbenchmarking"
@@ -124,11 +124,11 @@
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "contributor": [
                 {
-                    "@id": "#79f54a56-4f5c-473e-b09a-df4a2c64b9c7"
+                    "@id": "#2551c24b-07be-42af-a808-93ceadbf357d"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-04-28T11:21:12Z",
+            "dateModified": "2026-04-30T13:33:25Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -162,11 +162,11 @@
             "version": "!>=25.10.4"
         },
         {
-            "@id": "#306c4f18-fa5d-4edc-b42d-a14b7de74b7c",
+            "@id": "#ddac9ff4-c8bd-47a3-90ce-06951c5bbb32",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#c48d6e85-f79c-40f5-97e5-faa8144265f0"
+                    "@id": "#7aec460b-6e2e-42ca-8cb5-3169d8430b30"
                 }
             ],
             "mainEntity": {
@@ -175,7 +175,7 @@
             "name": "Test suite for nf-core/variantbenchmarking"
         },
         {
-            "@id": "#c48d6e85-f79c-40f5-97e5-faa8144265f0",
+            "@id": "#7aec460b-6e2e-42ca-8cb5-3169d8430b30",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/variantbenchmarking",
             "resource": "repos/nf-core/variantbenchmarking/actions/workflows/nf-test.yml",
@@ -304,7 +304,7 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "#79f54a56-4f5c-473e-b09a-df4a2c64b9c7",
+            "@id": "#2551c24b-07be-42af-a808-93ceadbf357d",
             "@type": "Person",
             "name": "kuebra.narci@dkfz-heidelberg.de"
         }

From ff78a0703d1fb1b54aaababdf509932320fc565d Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Wed, 20 May 2026 13:36:07 +0200
Subject: [PATCH 03/14] snaps

---
 conf/containers_conda_lock_files_amd64.config |   3 +-
 conf/containers_conda_lock_files_arm64.config |   3 +-
 conf/containers_docker_amd64.config           |   3 +-
 conf/containers_docker_arm64.config           |   3 +-
 .../containers_singularity_https_amd64.config |   3 +-
 .../containers_singularity_https_arm64.config |   3 +-
 conf/containers_singularity_oras_amd64.config |   3 +-
 conf/containers_singularity_oras_arm64.config |   3 +-
 .../linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt     | 822 ------------------
 .../linux_arm64-bd-e455e32f745abe68_1.txt     | 769 ----------------
 ... => linux_amd64-bd-839587b417d23042_1.txt} | 767 ++++++++--------
 .../linux_amd64-bd-db7c73dae76bc9e6_1.txt     | 126 ---
 ... => linux_arm64-bd-3e45d17b40a576b4_1.txt} | 766 ++++++++--------
 .../linux_arm64-bd-d167b8012595a136_1.txt     | 125 ---
 modules/nf-core/multiqc/environment.yml       |   2 +-
 modules/nf-core/multiqc/main.nf               |   4 +-
 modules/nf-core/multiqc/meta.yml              |  28 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |  10 +-
 subworkflows/local/prepare_vcfs_test/main.nf  |   4 +-
 .../local/report_benchmark_statistics/main.nf |   4 +-
 subworkflows/local/sv_vcf_conversion/main.nf  |  12 +-
 subworkflows/local/wittyer_benchmark/main.nf  |   2 +-
 tests/default.nf.test.snap                    |  46 +-
 tests/germline_small.nf.test                  |  28 +-
 tests/germline_small.nf.test.snap             |  10 +-
 tests/somatic_snv.nf.test                     |  28 +-
 tests/somatic_snv.nf.test.snap                |  10 +-
 tests/somatic_sv.nf.test                      |  14 +-
 tests/somatic_sv.nf.test.snap                 |  36 +-
 29 files changed, 885 insertions(+), 2752 deletions(-)
 delete mode 100644 modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
 delete mode 100644 modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
 rename modules/nf-core/multiqc/.conda-lock/{linux_amd64-bd-c1f4a7982b743963_1.txt => linux_amd64-bd-839587b417d23042_1.txt} (75%)
 delete mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
 rename modules/nf-core/multiqc/.conda-lock/{linux_arm64-bd-40bf3b435e89dc22_1.txt => linux_arm64-bd-3e45d17b40a576b4_1.txt} (75%)
 delete mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt

diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index d3ee1b4e..a05393e6 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index 2b90ac4f..7b7f2b66 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
index 65f1814a..66a4c027 100644
--- a/conf/containers_docker_amd64.config
+++ b/conf/containers_docker_amd64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
index 6c845ba4..209188f0 100644
--- a/conf/containers_docker_arm64.config
+++ b/conf/containers_docker_arm64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } }
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
index 838f2484..2465ec54 100644
--- a/conf/containers_singularity_https_amd64.config
+++ b/conf/containers_singularity_https_amd64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
index 090173be..80ca27ed 100644
--- a/conf/containers_singularity_https_arm64.config
+++ b/conf/containers_singularity_https_arm64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } }
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
index 773f3698..19753cfe 100644
--- a/conf/containers_singularity_oras_amd64.config
+++ b/conf/containers_singularity_oras_amd64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
index 798cc638..e5439f67 100644
--- a/conf/containers_singularity_oras_arm64.config
+++ b/conf/containers_singularity_oras_arm64.config
@@ -1,2 +1 @@
-process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } }
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0' } }
diff --git a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
deleted file mode 100644
index 7770ccd5..00000000
--- a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
+++ /dev/null
@@ -1,822 +0,0 @@
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index cdc434ca..00000000
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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-839587b417d23042_1.txt
similarity index 75%
rename from modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
rename to modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
index 76190304..33a1c692 100644
--- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
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 license_family: MIT
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 timestamp: 1773935801332
-- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
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 noarch: generic
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 license_family: MIT
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 license_family: MIT
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 license_family: Apache
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-- libcblas   3.11.0   5*_openblas
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 license_family: BSD
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-- blas 2.305   openblas
-- liblapack  3.11.0   5*_openblas
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 constrains:
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 license_family: MIT
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-- libgomp 15.2.0 he0feb66_18
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-- libxcb >=1.17.0,<2.0a0
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 license: HPND
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 md5: 3e9427ee186846052e81fadde8ebe96a
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 license_family: MIT
 size: 5251872
 timestamp: 1772628857717
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 depends:
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 constrains:
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-- polars-runtime-compat ==1.39.3
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-- libstdcxx >=14
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-- __glibc >=2.17,<3.0.a0
-- _python_abi3_support 1.*
-- cpython >=3.10
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 license: MIT
 license_family: MIT
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 noarch: python
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 depends:
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 license: MIT
 license_family: MIT
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 md5: f2c23a77b25efcad57d377b34bd84941
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 license_family: MIT
 size: 14645
 timestamp: 1736766960536
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 depends:
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-- typing-extensions >=4.6.1
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-- pydantic-core ==2.41.5
+- pydantic-core ==2.46.4
 - python
 license: MIT
 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py314h2e6c369_1.conda
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 depends:
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 license: MIT
 license_family: MIT
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 depends:
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 license: BSD-2-Clause
 license_family: BSD
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 md5: 461219d1a5bd61342293efa2c0c90eac
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 license_family: BSD
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
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-- libexpat >=2.7.3,<3.0a0
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-- libsqlite >=3.51.2,<4.0a0
-- libuuid >=2.41.3,<3.0a0
-- libzlib >=1.3.1,<2.0a0
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 - ncurses >=6.5,<7.0a0
-- openssl >=3.5.5,<4.0a0
+- openssl >=3.5.6,<4.0a0
 - python_abi 3.14.* *_cp314
 - readline >=8.3,<9.0a0
 - tk >=8.6.13,<8.7.0a0
 - tzdata
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 license: Python-2.0
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 python_site_packages_path: lib/python3.14/site-packages
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 license_family: BSD
 size: 27848
 timestamp: 1772388605021
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
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 depends:
-- cpython 3.14.3.*
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 - python_abi * *_cp314
 license: Python-2.0
-size: 50062
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 md5: 310259a5b03ff02289d7705f39e2b1d2
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 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.2.28-py314h5bd0f2a_0.conda
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-md5: 3c8b6a8c4d0ff5a264e9831eac4941f4
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 depends:
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 license: Apache-2.0 AND CNRI-Python
 license_family: PSF
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-- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda
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 depends:
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-- certifi >=2017.4.17
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 license: Apache-2.0
 license_family: APACHE
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 depends:
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 license: MIT
 license_family: MIT
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 md5: 0c20a8ebcddb24a45da89d5e917e6cb9
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 license_family: MIT
 size: 22284
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.52.0-h04a0ce9_0.conda
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-- icu >=78.2,<79.0a0
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-- libsqlite 3.52.0 hf4e2dac_0
-- libzlib >=1.3.1,<2.0a0
-- ncurses >=6.5,<7.0a0
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 md5: d705f9d8a1185a2b01cced191177a028
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 license: MPL-2.0 and MIT
 size: 94132
 timestamp: 1770153424136
-- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda
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-- python >=3.10
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 license: MIT
 license_family: MIT
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 license_family: PSF
 size: 91383
 timestamp: 1756220668932
-- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda
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 license_family: MIT
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 license: LicenseRef-Public-Domain
 size: 119135
 timestamp: 1767016325805
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
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 license_family: MIT
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 timestamp: 1753484064210
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
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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
deleted file mode 100644
index a55a4d49..00000000
--- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+++ /dev/null
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-
-# 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-3e45d17b40a576b4_1.txt
similarity index 75%
rename from modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
rename to modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
index a58231a0..492ce480 100644
--- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
@@ -14,17 +14,17 @@ linux-aarch64:
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 - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
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@@ -173,15 +170,15 @@ license: MIT
 license_family: MIT
 size: 64927
 timestamp: 1773935801332
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 license: BSD-3-Clause AND MIT AND EPL-2.0
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@@ -206,42 +203,41 @@ license: bzip2-1.0.6
 license_family: BSD
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 noarch: generic
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 license_family: MIT
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 license_family: Apache
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 license_family: BSD
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 constrains:
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-- liblapacke 3.11.0   5*_openblas
-- blas 2.305   openblas
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 constrains:
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 depends:
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 constrains:
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 md5: 7b9813e885482e3ccb1fa212b86d7fd0
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 license_family: BSD
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 constrains:
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 license_family: GPL
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-- python >=3.8,!=3.14.1
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 license_family: MIT
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 timestamp: 1770905275632
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 license: X11 AND BSD-3-Clause
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 md5: a2c1eeadae7a309daed9d62c96012a2b
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 license_family: MOZILLA
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 timestamp: 1763490303490
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-- libblas >=3.9.0,<4.0a0
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 constrains:
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 license: BSD-3-Clause
 license_family: BSD
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 md5: cea962410e327262346d48d01f05936c
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 license_family: BSD
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 license: Apache-2.0
 license_family: Apache
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-- libfreetype >=2.14.1
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 license: HPND
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 md5: 3e9427ee186846052e81fadde8ebe96a
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 license_family: MIT
 size: 5251872
 timestamp: 1772628857717
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 depends:
-- polars-runtime-32 ==1.39.3
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 constrains:
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-- polars-runtime-64 ==1.39.3
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 license: MIT
 license_family: MIT
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 noarch: python
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 constrains:
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 license: MIT
 license_family: MIT
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 md5: ab7288cc39545556d1bc5e71ab2df9a9
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 license_family: MIT
 size: 14645
 timestamp: 1736766960536
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-md5: c3946ed24acdb28db1b5d63321dbca7d
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-- pydantic-core ==2.41.5
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 license: MIT
 license_family: MIT
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 depends:
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 license: MIT
 license_family: MIT
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 depends:
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 license: BSD-2-Clause
 license_family: BSD
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 sha256: ba3b032fa52709ce0d9fd388f63d330a026754587a2f461117cac9ab73d8d0d8
 md5: 461219d1a5bd61342293efa2c0c90eac
@@ -1153,31 +1111,31 @@ license: BSD-3-Clause
 license_family: BSD
 size: 21085
 timestamp: 1733217331982
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.3-hb06a95a_101_cp314.conda
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-sha256: 87e9dff5646aba87cecfbc08789634c855871a7325169299d749040b0923a356
-md5: 205011b36899ff0edf41b3db0eda5a44
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda
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 depends:
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 - ld_impl_linux-aarch64 >=2.36.1
-- libexpat >=2.7.3,<3.0a0
+- libexpat >=2.7.5,<3.0a0
 - libffi >=3.5.2,<3.6.0a0
 - libgcc >=14
 - liblzma >=5.8.2,<6.0a0
 - libmpdec >=4.0.0,<5.0a0
-- libsqlite >=3.51.2,<4.0a0
-- libuuid >=2.41.3,<3.0a0
-- libzlib >=1.3.1,<2.0a0
+- libsqlite >=3.52.0,<4.0a0
+- libuuid >=2.42,<3.0a0
+- libzlib >=1.3.2,<2.0a0
 - ncurses >=6.5,<7.0a0
-- openssl >=3.5.5,<4.0a0
+- openssl >=3.5.6,<4.0a0
 - python_abi 3.14.* *_cp314
 - readline >=8.3,<9.0a0
 - tk >=8.6.13,<8.7.0a0
 - tzdata
 - zstd >=1.5.7,<1.6.0a0
 license: Python-2.0
-size: 37305578
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 python_site_packages_path: lib/python3.14/site-packages
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
 sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5
@@ -1188,15 +1146,15 @@ license: BSD-3-Clause
 license_family: BSD
 size: 27848
 timestamp: 1772388605021
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
-sha256: 233aebd94c704ac112afefbb29cf4170b7bc606e22958906f2672081bc50638a
-md5: 235765e4ea0d0301c75965985163b5a1
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda
+sha256: 36ff7984e4565c85149e64f8206303d412a0652e55cf806dcb856903fa056314
+md5: e4e60721757979d01d3964122f674959
 depends:
-- cpython 3.14.3.*
+- cpython 3.14.4.*
 - python_abi * *_cp314
 license: Python-2.0
-size: 50062
-timestamp: 1770674497152
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 - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2
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 md5: 310259a5b03ff02289d7705f39e2b1d2
@@ -1253,9 +1211,9 @@ license: MIT
 license_family: MIT
 size: 51788
 timestamp: 1760379115194
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.2.28-py314h51f160d_0.conda
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-md5: 818aa2c9f6b3c808da5e7be22a9a424c
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.5.9-py314h51f160d_0.conda
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 depends:
 - libgcc >=14
 - python >=3.14,<3.15.0a0
@@ -1263,27 +1221,27 @@ depends:
 - python_abi 3.14.* *_cp314
 license: Apache-2.0 AND CNRI-Python
 license_family: PSF
-size: 408097
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-- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda
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 depends:
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-- certifi >=2017.4.17
+- certifi >=2023.5.7
 - charset-normalizer >=2,<4
 - idna >=2.5,<4
-- urllib3 >=1.21.1,<3
+- urllib3 >=1.26,<3
 - python
 constrains:
-- chardet >=3.0.2,<6
+- chardet >=3.0.2,<8
 license: Apache-2.0
 license_family: APACHE
-size: 63602
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-- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
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 depends:
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 - pygments >=2.13.0,<3.0.0
@@ -1292,8 +1250,8 @@ depends:
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 license: MIT
 license_family: MIT
-size: 208472
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+size: 208577
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 md5: 0c20a8ebcddb24a45da89d5e917e6cb9
@@ -1331,19 +1289,18 @@ license: MIT
 license_family: MIT
 size: 22284
 timestamp: 1735770589188
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.52.0-hf1c7be2_0.conda
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-md5: d9634079df93a65ee045b3c75f35cae1
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.1-he8854b5_0.conda
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 depends:
-- icu >=78.2,<79.0a0
 - libgcc >=14
-- libsqlite 3.52.0 h10b116e_0
-- libzlib >=1.3.1,<2.0a0
-- ncurses >=6.5,<7.0a0
+- libsqlite 3.53.1 h022381a_0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
 - readline >=8.3,<9.0a0
 license: blessing
-size: 209416
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 md5: 55bf7b559202236157b14323b40f19e6
@@ -1382,20 +1339,20 @@ depends:
 license: MPL-2.0 and MIT
 size: 94132
 timestamp: 1770153424136
-- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda
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-md5: 260af1b0a94f719de76b4e14094e9a3b
+- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda
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 depends:
-- importlib-metadata >=3.6
-- python >=3.10
-- typing-extensions >=4.10.0
 - typing_extensions >=4.14.0
+- python >=3.10
+- importlib-metadata >=3.6
+- python
 constrains:
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 license: MIT
 license_family: MIT
-size: 36838
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
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 md5: edd329d7d3a4ab45dcf905899a7a6115
@@ -1405,16 +1362,17 @@ license: PSF-2.0
 license_family: PSF
 size: 91383
 timestamp: 1756220668932
-- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda
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-md5: a0a4a3035667fc34f29bfbd5c190baa6
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda
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 license_family: MIT
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 license: LicenseRef-Public-Domain
 size: 119135
 timestamp: 1767016325805
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
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-md5: 9272daa869e03efe68833e3dc7a02130
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 license: MIT
 license_family: MIT
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 md5: 1c246e1105000c3660558459e2fd6d43
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 license_family: MIT
 size: 88088
 timestamp: 1753484092643
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
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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
deleted file mode 100644
index f787dbe1..00000000
--- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+++ /dev/null
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-
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-aarch64
-@EXPLICIT
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-https://conda.anaconda.org/conda-forge/linux-aarch64/libblas-3.11.0-6_haddc8a3_openblas.conda#652bb20bb4618cacd11e17ae070f47ce
-https://conda.anaconda.org/conda-forge/linux-aarch64/libcblas-3.11.0-6_hd72aa62_openblas.conda#939e300b110db241a96a1bed438c315b
-https://conda.anaconda.org/conda-forge/linux-aarch64/liblapack-3.11.0-6_h88aeb00_openblas.conda#e23a27b52fb320687239e2c5ae4d7540
-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 37e7612d..7a970e2b 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=1.34
+  - bioconda::multiqc=1.35
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index e80e8cd8..4c593a97 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -4,8 +4,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
-        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data'
+        : 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042'}"
 
     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 2facc627..b85d0e35 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: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
   docker:
     linux/amd64:
-      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
-      build_id: bd-db7c73dae76bc9e6_1
-      scan_id: sc-66fc7138dbf1cf48_1
+      name: community.wave.seqera.io/library/multiqc:1.35--839587b417d23042
+      build_id: bd-839587b417d23042_1
+      scan_id: sc-f87d7a31551c029f_1
     linux/arm64:
-      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
-      build_id: bd-d167b8012595a136_1
-      scan_id: sc-ac701dfa631a2af9_1
+      name: community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4
+      build_id: bd-3e45d17b40a576b4_1
+      scan_id: sc-1d0cf4ed1a4b61e0_1
   singularity:
     linux/amd64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
-      build_id: bd-4fc8657c816047c0_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393
+      build_id: bd-cb7458fda84d6393_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
-      build_id: bd-7fbd82d945c06726_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0
+      build_id: bd-f79e87603d312ac0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7c2f370f..44899216 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -81,7 +81,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -175,7 +175,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -221,7 +221,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -314,7 +314,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -408,7 +408,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
diff --git a/subworkflows/local/prepare_vcfs_test/main.nf b/subworkflows/local/prepare_vcfs_test/main.nf
index 36754884..61ce76a1 100644
--- a/subworkflows/local/prepare_vcfs_test/main.nf
+++ b/subworkflows/local/prepare_vcfs_test/main.nf
@@ -161,7 +161,7 @@ workflow PREPARE_VCFS_TEST {
 
      // branch out test samples with missing GT field (e.g. strelka) to add GT field using gawk
     vcf_ch
-        .branch { meta, vcf, tbi ->
+        .branch { meta, _vcf, _tbi ->
             def is_rtg = params.method?.contains("rtgtools")
             def is_strelka_manta = ['strelka', 'manta'].contains(meta.caller.toLowerCase())
             def is_somatic = params.analysis == "somatic"
@@ -172,7 +172,7 @@ workflow PREPARE_VCFS_TEST {
 
     // Add GT field using
     ADD_GT_STRELKA(
-        ch_branched_vcf.needs_gt.map{ meta, vcf, _tbi -> tuple(meta, vcf) },
+        ch_branched_vcf.needs_gt.map{ meta, file, _tbi -> tuple(meta, file) },
         [],
         false
     )
diff --git a/subworkflows/local/report_benchmark_statistics/main.nf b/subworkflows/local/report_benchmark_statistics/main.nf
index 25a1eb8b..6545c67d 100644
--- a/subworkflows/local/report_benchmark_statistics/main.nf
+++ b/subworkflows/local/report_benchmark_statistics/main.nf
@@ -30,7 +30,7 @@ workflow REPORT_BENCHMARK_STATISTICS {
         PLOTS_METRICS(
             MERGE_REPORTS.out.summary
         )
-        ch_plots = ch_plots.mix(PLOTS_METRICS.out.plots.flatten())
+        ch_plots = ch_plots.mix(PLOTS_METRICS.out.plots)
     }
 
     if (params.variant_type != "snv" && !params.skip_plots.contains("svlength")){
@@ -64,6 +64,6 @@ workflow REPORT_BENCHMARK_STATISTICS {
     )
 
     emit:
-    ch_plots        // channel: [ meta, plots.png ]
+    ch_plots        // channel: [ plots.png ]
     merged_reports  // channel: [ meta, summary.csv]
 }
diff --git a/subworkflows/local/sv_vcf_conversion/main.nf b/subworkflows/local/sv_vcf_conversion/main.nf
index d0dd7a14..c0ee1cee 100644
--- a/subworkflows/local/sv_vcf_conversion/main.nf
+++ b/subworkflows/local/sv_vcf_conversion/main.nf
@@ -35,7 +35,7 @@ workflow SV_VCF_CONVERSIONS {
 
     if (params.sv_standardization.contains("svtk")){
 
-        out_vcf_ch = Channel.empty()
+        out_vcf_ch = channel.empty()
 
         supported_callers2 = ["delly", "melt", "manta", "wham", "dragen", "lumpy", "scrable", "smoove"]
         input_ch
@@ -78,8 +78,8 @@ workflow SV_VCF_CONVERSIONS {
     }
 
     input_ch
-        .branch { input ->
-            compressed:   input[1].getName().endsWith('.gz')
+        .branch { files ->
+            compressed:   files[1].getName().endsWith('.gz')
             uncompressed: true
         }
         .set { ch_inputs }
@@ -127,9 +127,9 @@ workflow SV_VCF_CONVERSIONS {
                 SVYNC.out.vcf,
                 input.other
             )
-            .map{ input ->
-                def meta = input[0]
-                def vcf = input[1]
+            .map{ file ->
+                def meta = file[0]
+                def vcf = file[1]
                 [ meta, vcf ]
             }
             .set { vcf_ch }
diff --git a/subworkflows/local/wittyer_benchmark/main.nf b/subworkflows/local/wittyer_benchmark/main.nf
index 118d9ded..06ff25e2 100644
--- a/subworkflows/local/wittyer_benchmark/main.nf
+++ b/subworkflows/local/wittyer_benchmark/main.nf
@@ -33,7 +33,7 @@ workflow WITTYER_BENCHMARK {
         TABIX_BGZIP_QUERY.out.output
             .join(TABIX_BGZIP_TRUTH.out.output, failOnDuplicate:true, failOnMismatch:true)
             .join(bed, failOnDuplicate:true, failOnMismatch:true)
-            .map{ meta, vcf, truth_vcf, bed -> [meta, vcf, truth_vcf, bed, []] }
+            .map{ meta, vcf, truth_vcf, bed_file -> [meta, vcf, truth_vcf, bed_file, []] }
     )
 
     WITTYER.out.report
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index a4a0db16..2aa38086 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -88,6 +88,11 @@
                 "structural/HG002/stats/survivor/HG002_mqc.stats",
                 "structural/multiqc",
                 "structural/multiqc/multiqc_data",
+                "structural/multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
                 "structural/multiqc/multiqc_data/llms-full.txt",
                 "structural/multiqc/multiqc_data/multiqc.log",
                 "structural/multiqc/multiqc_data/multiqc.parquet",
@@ -101,14 +106,32 @@
                 "structural/multiqc/multiqc_data/multiqc_variant_calling_summary.txt",
                 "structural/multiqc/multiqc_plots",
                 "structural/multiqc/multiqc_plots/pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
                 "structural/multiqc/multiqc_plots/pdf/survivor-cnt.pdf",
                 "structural/multiqc/multiqc_plots/pdf/survivor-pct.pdf",
                 "structural/multiqc/multiqc_plots/pdf/variant_calling_summary.pdf",
                 "structural/multiqc/multiqc_plots/png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-cnt.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-log.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
                 "structural/multiqc/multiqc_plots/png/survivor-cnt.png",
                 "structural/multiqc/multiqc_plots/png/survivor-pct.png",
                 "structural/multiqc/multiqc_plots/png/variant_calling_summary.png",
                 "structural/multiqc/multiqc_plots/svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-cnt.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-log.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg",
                 "structural/multiqc/multiqc_plots/svg/survivor-cnt.svg",
                 "structural/multiqc/multiqc_plots/svg/survivor-pct.svg",
                 "structural/multiqc/multiqc_plots/svg/variant_calling_summary.svg",
@@ -199,8 +222,13 @@
             [
                 "HG002.bcftools_stats.txt:md5,184d672828c019a6f0cf732bcd3eae40",
                 "HG002_mqc.stats:md5,1640b71d7317b5f7be31a8712e876e10",
+                "bcftools_stats_indel-lengths.txt:md5,642235d2bfca7a9cfb7bed765455196d",
+                "bcftools_stats_vqc_Count_Indels.txt:md5,e00010736baafe749c8edf8014fe6376",
+                "bcftools_stats_vqc_Count_SNP.txt:md5,39aa806aa38207206d46aa691b86af08",
+                "bcftools_stats_vqc_Count_Transitions.txt:md5,39aa806aa38207206d46aa691b86af08",
+                "bcftools_stats_vqc_Count_Transversions.txt:md5,39aa806aa38207206d46aa691b86af08",
                 "multiqc_bcftools_stats.txt:md5,3d782febc5ec3109b56ba4bce2d6fdb1",
-                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b",
                 "multiqc_survivor.txt:md5,959dc53884368cf2f85d18be5c627b99",
                 "multiqc_variant_calling_summary.txt:md5,8fdcd482b04882572cee4f68ad9baf99",
                 "test1.delly.bcftools_stats.txt:md5,9847ff08b49e4a10d865d61ef2cbe375",
@@ -211,10 +239,10 @@
                 "test3.manta_mqc.stats:md5,c6d5b9f40c4aa8c7b30155464eb52e3c"
             ]
         ],
-        "timestamp": "2026-04-22T12:18:17.150470471",
+        "timestamp": "2026-05-20T13:11:27.985179706",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     },
     "-stub": {
@@ -306,7 +334,9 @@
                 "structural/HG002/stats/survivor/HG002_mqc.stats",
                 "structural/multiqc",
                 "structural/multiqc/multiqc_data",
+                "structural/multiqc/multiqc_data/.stub",
                 "structural/multiqc/multiqc_plots",
+                "structural/multiqc/multiqc_plots/.stub",
                 "structural/multiqc/multiqc_report.html",
                 "structural/summary",
                 "structural/summary/comparisons",
@@ -399,6 +429,8 @@
             [
                 "HG002.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "HG002_mqc.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test1.delly.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test1.delly_mqc.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test2.lumpy.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -407,10 +439,10 @@
                 "test3.manta_mqc.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-04-22T12:20:04.299430777",
+        "timestamp": "2026-05-20T13:12:32.273840803",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/germline_small.nf.test b/tests/germline_small.nf.test
index 9f03371d..86785e5f 100644
--- a/tests/germline_small.nf.test
+++ b/tests/germline_small.nf.test
@@ -18,21 +18,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success },
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -50,21 +50,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success },
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
index f4b39202..c0f805c4 100644
--- a/tests/germline_small.nf.test.snap
+++ b/tests/germline_small.nf.test.snap
@@ -111,7 +111,9 @@
                 "small/HG002/stats/bcftools/HG002.bcftools_stats.txt",
                 "small/multiqc",
                 "small/multiqc/multiqc_data",
+                "small/multiqc/multiqc_data/.stub",
                 "small/multiqc/multiqc_plots",
+                "small/multiqc/multiqc_plots/.stub",
                 "small/multiqc/multiqc_report.html",
                 "small/summary",
                 "small/summary/comparisons",
@@ -258,6 +260,8 @@
             [
                 "genome.sdf:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "HG002.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test6.HG002.strelka.extended.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test6.HG002.strelka.roc.Locations.INDEL.PASS.csv.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "test6.HG002.strelka.roc.Locations.INDEL.csv.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
@@ -280,10 +284,10 @@
                 "test7.bcftools.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-04-22T12:26:29.644786845",
+        "timestamp": "2026-05-20T13:18:29.304813192",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     },
     "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": {
diff --git a/tests/somatic_snv.nf.test b/tests/somatic_snv.nf.test
index 91966d2b..99681731 100644
--- a/tests/somatic_snv.nf.test
+++ b/tests/somatic_snv.nf.test
@@ -18,21 +18,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success },
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -50,21 +50,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success },
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap
index a502cfd1..828c0d37 100644
--- a/tests/somatic_snv.nf.test.snap
+++ b/tests/somatic_snv.nf.test.snap
@@ -474,7 +474,9 @@
                 "snv/SEQC2/stats/bcftools/SEQC2.bcftools_stats.txt",
                 "snv/multiqc",
                 "snv/multiqc/multiqc_data",
+                "snv/multiqc/multiqc_data/.stub",
                 "snv/multiqc/multiqc_plots",
+                "snv/multiqc/multiqc_plots/.stub",
                 "snv/multiqc/multiqc_report.html",
                 "snv/summary",
                 "snv/summary/comparisons",
@@ -622,6 +624,8 @@
             [
                 "genome.sdf:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "SEQC2.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test10.SEQC2.strelka.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test10.SEQC2.strelka.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test10.strelka.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -633,10 +637,10 @@
                 "test9.mutect2.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-04-22T12:32:38.567210453",
+        "timestamp": "2026-05-20T13:25:37.679632604",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/somatic_sv.nf.test b/tests/somatic_sv.nf.test
index 4d7717b9..8199b1ba 100644
--- a/tests/somatic_sv.nf.test
+++ b/tests/somatic_sv.nf.test
@@ -17,21 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success },
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_variantbenchmarking_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap
index ce31f46d..9343a18d 100644
--- a/tests/somatic_sv.nf.test.snap
+++ b/tests/somatic_sv.nf.test.snap
@@ -86,6 +86,11 @@
                 "structural/SEQC2/stats/survivor/SEQC2_mqc.stats",
                 "structural/multiqc",
                 "structural/multiqc/multiqc_data",
+                "structural/multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
+                "structural/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
                 "structural/multiqc/multiqc_data/llms-full.txt",
                 "structural/multiqc/multiqc_data/multiqc.log",
                 "structural/multiqc/multiqc_data/multiqc.parquet",
@@ -105,6 +110,12 @@
                 "structural/multiqc/multiqc_data/truvari-bench-pre-rec-plot.txt",
                 "structural/multiqc/multiqc_plots",
                 "structural/multiqc/multiqc_plots/pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
+                "structural/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
                 "structural/multiqc/multiqc_plots/pdf/survivor-cnt.pdf",
                 "structural/multiqc/multiqc_plots/pdf/survivor-pct.pdf",
                 "structural/multiqc/multiqc_plots/pdf/truvari-bench-classifications-plot_Base-cnt.pdf",
@@ -118,6 +129,12 @@
                 "structural/multiqc/multiqc_plots/pdf/truvari-bench-pre-rec-plot.pdf",
                 "structural/multiqc/multiqc_plots/pdf/variant_calling_summary.pdf",
                 "structural/multiqc/multiqc_plots/png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-cnt.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-log.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
+                "structural/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
                 "structural/multiqc/multiqc_plots/png/survivor-cnt.png",
                 "structural/multiqc/multiqc_plots/png/survivor-pct.png",
                 "structural/multiqc/multiqc_plots/png/truvari-bench-classifications-plot_Base-cnt.png",
@@ -131,6 +148,12 @@
                 "structural/multiqc/multiqc_plots/png/truvari-bench-pre-rec-plot.png",
                 "structural/multiqc/multiqc_plots/png/variant_calling_summary.png",
                 "structural/multiqc/multiqc_plots/svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-cnt.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-log.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg",
+                "structural/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg",
                 "structural/multiqc/multiqc_plots/svg/survivor-cnt.svg",
                 "structural/multiqc/multiqc_plots/svg/survivor-pct.svg",
                 "structural/multiqc/multiqc_plots/svg/truvari-bench-classifications-plot_Base-cnt.svg",
@@ -222,8 +245,13 @@
             [
                 "SEQC2.bcftools_stats.txt:md5,83f0ebd019579c2f90e82bf4e3e6d3e0",
                 "SEQC2_mqc.stats:md5,75fd7f87d3534ab64b95b5490317b11f",
+                "bcftools_stats_indel-lengths.txt:md5,17ba6b0ab26cf8f1032fad4b6d4fd913",
+                "bcftools_stats_vqc_Count_Indels.txt:md5,2baad19f17a829584ba2a14a3cd46802",
+                "bcftools_stats_vqc_Count_SNP.txt:md5,9237c2c4b23e992e58fd74ca0e5b1c14",
+                "bcftools_stats_vqc_Count_Transitions.txt:md5,9237c2c4b23e992e58fd74ca0e5b1c14",
+                "bcftools_stats_vqc_Count_Transversions.txt:md5,9237c2c4b23e992e58fd74ca0e5b1c14",
                 "multiqc_bcftools_stats.txt:md5,c7b07be149ee5eb2c86d6d5a9e8267d7",
-                "multiqc_citations.txt:md5,38f633e1381fe6da4bcbec213cd00061",
+                "multiqc_citations.txt:md5,e7e57ff8b7ef2a5e4452481812e26169",
                 "multiqc_survivor.txt:md5,dac25d5e28bd8fa745bd11fb8ef456da",
                 "multiqc_variant_calling_summary.txt:md5,b40fdc152b64968b6959098e7d4efba7",
                 "test11.manta.bcftools_stats.txt:md5,f5ce9394427a2458852ae6b6d840d315",
@@ -232,10 +260,10 @@
                 "test12.tiddit_mqc.stats:md5,950514053b461a3868a12fd5ced0a3d8"
             ]
         ],
-        "timestamp": "2026-04-22T12:35:34.355188874",
+        "timestamp": "2026-05-20T13:29:11.961442327",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     }
 }
\ No newline at end of file

From 7e6768ffafbd423682c04663393433e0de0a0550 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 20 May 2026 11:39:23 +0000
Subject: [PATCH 04/14] [automated] Fix code linting

---
 workflows/variantbenchmarking.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/variantbenchmarking.nf b/workflows/variantbenchmarking.nf
index a9450f62..3fa41162 100644
--- a/workflows/variantbenchmarking.nf
+++ b/workflows/variantbenchmarking.nf
@@ -409,7 +409,7 @@ workflow VARIANTBENCHMARKING {
     def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
 
-    
+
     MULTIQC(
         ch_multiqc_files.flatten().collect().map { files ->
             [

From 594764f3f79edab80655c01ccedd86eae3369637 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Wed, 20 May 2026 13:52:44 +0200
Subject: [PATCH 05/14] fix monochrome_logs

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 7b6f0d48..4e950524 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -72,7 +72,6 @@ params {
     email                        = null
     email_on_fail                = null
     plaintext_email              = false
-    monochromeLogs               = false
     monochrome_logs              = false
     help                         = false
     help_full                    = false

From 4a6ecb0017deee37a659a7c727a204cf86203360 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Wed, 20 May 2026 14:02:30 +0200
Subject: [PATCH 06/14] improve volume in nf-test

---
 .github/workflows/nf-test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 8f100f1a..eec4076e 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -30,6 +30,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
+      - volume=60gb
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
       total_shards: ${{ steps.set-shards.outputs.total_shards }}
@@ -64,6 +65,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
+      - volume=60gb
     strategy:
       fail-fast: false
       matrix:

From bc606fd3c5946a1deed799bc12aa413e4119526b Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Thu, 21 May 2026 12:48:22 +0200
Subject: [PATCH 07/14] fix nf-test error for report_benchmarking_statistics

---
 conf/modules.config                           |  5 +--
 nextflow.config                               |  2 +-
 subworkflows/local/ensemble_test_vcfs/main.nf |  2 +-
 .../local/report_benchmark_statistics/main.nf | 31 ++++++++++++++-----
 .../tests/main.nf.test                        |  3 +-
 .../tests/main.nf.test.snap                   | 12 +++----
 6 files changed, 36 insertions(+), 19 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 3e35fa19..efeeed12 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -656,8 +656,9 @@ process {
     }
 
     withName: 'CREATE_DATAVZRD_INPUT' {
-        ext.prefix = { "${meta.id}.datavzrd.yaml" }
-        ext.args = { "> /dev/null ; sed \"s|CSVPATH|${meta.csv}|g\"" }
+        ext.prefix = { "${meta.id}.datavzrd" }
+        ext.suffix = "yaml"
+        ext.args2  = { " '{ gsub(/CSVPATH/, \"${meta.csv}\"); print }' " }
         publishDir = [
             enabled: false
         ]
diff --git a/nextflow.config b/nextflow.config
index 4e950524..ca022708 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -39,7 +39,7 @@ params {
     //  Preprocess spesific parameters
     preprocess                 = ""
     sv_standardization         = ""
-    skip_plots                 = ""
+    skip_plots                 = []
 
     // Filtering parameters
     min_sv_size                = 0
diff --git a/subworkflows/local/ensemble_test_vcfs/main.nf b/subworkflows/local/ensemble_test_vcfs/main.nf
index f975f392..eda86a0b 100644
--- a/subworkflows/local/ensemble_test_vcfs/main.nf
+++ b/subworkflows/local/ensemble_test_vcfs/main.nf
@@ -100,7 +100,7 @@ workflow ENSEMBLE_TEST_VCFS {
             .set{vcf_ch}
 
         // drop meta information from vcf test samples
-        ch_test_vcfs = vcf_ch.map { meta, vcf ->
+        ch_test_vcfs = vcf_ch.map { _meta, vcf ->
             [ [id: 'truth'], vcf ]
         }
 
diff --git a/subworkflows/local/report_benchmark_statistics/main.nf b/subworkflows/local/report_benchmark_statistics/main.nf
index 6545c67d..a3162967 100644
--- a/subworkflows/local/report_benchmark_statistics/main.nf
+++ b/subworkflows/local/report_benchmark_statistics/main.nf
@@ -6,7 +6,7 @@ include { MERGE_REPORTS         } from '../../../modules/local/custom/merge_repo
 include { PLOTS_METRICS         } from '../../../modules/local/plots/metrics'
 include { DATAVZRD              } from '../../../modules/nf-core/datavzrd'
 include { PLOTS_SVLEN_DIST      } from '../../../modules/local/plots/svlen_dist'
-include { CAT_CAT as CREATE_DATAVZRD_INPUT } from '../../../modules/nf-core/cat/cat'
+include { GAWK as CREATE_DATAVZRD_INPUT } from '../../../modules/nf-core/gawk'
 
 workflow REPORT_BENCHMARK_STATISTICS {
     take:
@@ -30,15 +30,22 @@ workflow REPORT_BENCHMARK_STATISTICS {
         PLOTS_METRICS(
             MERGE_REPORTS.out.summary
         )
-        ch_plots = ch_plots.mix(PLOTS_METRICS.out.plots)
+        ch_plots = ch_plots.mix(PLOTS_METRICS.out.plots.flatten())
     }
 
     if (params.variant_type != "snv" && !params.skip_plots.contains("svlength")){
         // plot INDEL/SV distribution plots
-        PLOTS_SVLEN_DIST(
-            evaluations.map { item -> tuple(item[0], item[1]) }.groupTuple()
-                .mix(evaluations_csv.map { item -> tuple(item[0], item[1]) }.groupTuple())
+        evaluations.map { item -> 
+            tuple(item[0], item[1]) 
+        }.groupTuple()
+        .mix(
+            evaluations_csv.map { item -> 
+                tuple(item[0], item[1]) 
+            }.groupTuple()
         )
+        .set { svlen_input }
+        
+        PLOTS_SVLEN_DIST(svlen_input)
         ch_plots = ch_plots.mix(PLOTS_SVLEN_DIST.out.plot)
     }
 
@@ -56,12 +63,22 @@ workflow REPORT_BENCHMARK_STATISTICS {
         .set { template_ch }
 
     CREATE_DATAVZRD_INPUT (
-        template_ch
+        template_ch,
+        [],
+        false
     )
+  
+    CREATE_DATAVZRD_INPUT.out.output
+        .map { meta, yaml_file ->
+            def clean_meta = meta.findAll { it.key != 'csv' }
+            [ clean_meta, yaml_file ]
+        }
+        .set { clean_datavzrd_input_ch }
 
     DATAVZRD (
-        CREATE_DATAVZRD_INPUT.out.file_out.join(template_ch)
+        clean_datavzrd_input_ch.join(summary)
     )
+    ch_plots.view()
 
     emit:
     ch_plots        // channel: [ plots.png ]
diff --git a/subworkflows/local/report_benchmark_statistics/tests/main.nf.test b/subworkflows/local/report_benchmark_statistics/tests/main.nf.test
index 4cbfc41c..f9117656 100644
--- a/subworkflows/local/report_benchmark_statistics/tests/main.nf.test
+++ b/subworkflows/local/report_benchmark_statistics/tests/main.nf.test
@@ -8,8 +8,7 @@ nextflow_workflow {
     tag "subworkflows_report_benchmark_statistics"
     tag "subworkflows/report_benchmark_statistics"
     tag "datavzrd"
-    tag "cat"
-    tag "cat/cat"
+    tag "gawk"
     tag "merge_reports"
 
     test("report benchmark statistics - structural variants") {
diff --git a/subworkflows/local/report_benchmark_statistics/tests/main.nf.test.snap b/subworkflows/local/report_benchmark_statistics/tests/main.nf.test.snap
index 8d15da4b..d01f189a 100644
--- a/subworkflows/local/report_benchmark_statistics/tests/main.nf.test.snap
+++ b/subworkflows/local/report_benchmark_statistics/tests/main.nf.test.snap
@@ -38,10 +38,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-26T09:41:53.268420415",
+        "timestamp": "2026-05-21T12:46:51.20184711",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     },
     "report benchmark statistics - structural variants": {
@@ -68,10 +68,10 @@
                 
             }
         ],
-        "timestamp": "2026-03-26T09:41:32.589910959",
+        "timestamp": "2026-05-21T12:46:36.09150481",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     }
 }
\ No newline at end of file

From f082beb6b8a02f9b3ac6155bf3866b04442ecbdd Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Thu, 21 May 2026 13:56:37 +0200
Subject: [PATCH 08/14] renew tests

---
 .../local/report_benchmark_statistics/main.nf |   1 -
 tests/default.nf.test.snap                    |   8 +-
 tests/germline_small.nf.test.snap             |  12 +-
 tests/somatic_snv.nf.test                     |   2 +-
 tests/somatic_snv.nf.test.snap                | 428 +++++++++---------
 tests/somatic_sv.nf.test.snap                 |   4 +-
 6 files changed, 227 insertions(+), 228 deletions(-)

diff --git a/subworkflows/local/report_benchmark_statistics/main.nf b/subworkflows/local/report_benchmark_statistics/main.nf
index a3162967..9f344f71 100644
--- a/subworkflows/local/report_benchmark_statistics/main.nf
+++ b/subworkflows/local/report_benchmark_statistics/main.nf
@@ -78,7 +78,6 @@ workflow REPORT_BENCHMARK_STATISTICS {
     DATAVZRD (
         clean_datavzrd_input_ch.join(summary)
     )
-    ch_plots.view()
 
     emit:
     ch_plots        // channel: [ plots.png ]
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 2aa38086..e1a8875a 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -28,7 +28,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -239,7 +239,7 @@
                 "test3.manta_mqc.stats:md5,c6d5b9f40c4aa8c7b30155464eb52e3c"
             ]
         ],
-        "timestamp": "2026-05-20T13:11:27.985179706",
+        "timestamp": "2026-05-21T13:02:07.308551843",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.1"
@@ -274,7 +274,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -439,7 +439,7 @@
                 "test3.manta_mqc.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-05-20T13:12:32.273840803",
+        "timestamp": "2026-05-21T13:03:05.643745178",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.1"
diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap
index c0f805c4..1d5a813b 100644
--- a/tests/germline_small.nf.test.snap
+++ b/tests/germline_small.nf.test.snap
@@ -52,7 +52,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -284,7 +284,7 @@
                 "test7.bcftools.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-05-20T13:18:29.304813192",
+        "timestamp": "2026-05-21T13:28:29.467299363",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.1"
@@ -343,7 +343,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -676,10 +676,10 @@
                 "test7.bcftools.bcftools_stats.txt:md5,ccc59737c476e1f77dcef59c50d0e56a"
             ]
         ],
-        "timestamp": "2026-04-22T12:24:10.486402795",
+        "timestamp": "2026-05-21T13:06:12.568495589",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/somatic_snv.nf.test b/tests/somatic_snv.nf.test
index 99681731..8fe56040 100644
--- a/tests/somatic_snv.nf.test
+++ b/tests/somatic_snv.nf.test
@@ -7,7 +7,7 @@ nextflow_pipeline {
     tag "snv"
     config "../conf/tests/somatic_snv.config"
 
-    test("Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy'") {
+    test("Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy,rtgtools'") {
 
         when {
             params {
diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap
index 828c0d37..87d1509a 100644
--- a/tests/somatic_snv.nf.test.snap
+++ b/tests/somatic_snv.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy'": {
+    "-stub": {
         "content": [
             89,
             {
@@ -37,7 +37,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -90,27 +90,6 @@
                 "references",
                 "references/rtgtools",
                 "references/rtgtools/genome.sdf",
-                "references/rtgtools/genome.sdf/done",
-                "references/rtgtools/genome.sdf/format.log",
-                "references/rtgtools/genome.sdf/mainIndex",
-                "references/rtgtools/genome.sdf/nameIndex0",
-                "references/rtgtools/genome.sdf/namedata0",
-                "references/rtgtools/genome.sdf/namepointer0",
-                "references/rtgtools/genome.sdf/progress",
-                "references/rtgtools/genome.sdf/reference.txt",
-                "references/rtgtools/genome.sdf/seqdata0",
-                "references/rtgtools/genome.sdf/seqdata1",
-                "references/rtgtools/genome.sdf/seqdata2",
-                "references/rtgtools/genome.sdf/seqdata3",
-                "references/rtgtools/genome.sdf/seqpointer0",
-                "references/rtgtools/genome.sdf/seqpointer1",
-                "references/rtgtools/genome.sdf/seqpointer2",
-                "references/rtgtools/genome.sdf/seqpointer3",
-                "references/rtgtools/genome.sdf/sequenceIndex0",
-                "references/rtgtools/genome.sdf/suffixIndex0",
-                "references/rtgtools/genome.sdf/suffixdata0",
-                "references/rtgtools/genome.sdf/suffixpointer0",
-                "references/rtgtools/genome.sdf/summary.txt",
                 "snv",
                 "snv/SEQC2",
                 "snv/SEQC2/preprocess",
@@ -121,72 +100,9 @@
                 "snv/SEQC2/stats/bcftools/SEQC2.bcftools_stats.txt",
                 "snv/multiqc",
                 "snv/multiqc/multiqc_data",
-                "snv/multiqc/multiqc_data/bcftools-stats-subtypes.txt",
-                "snv/multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
-                "snv/multiqc/multiqc_data/bcftools_stats_variant_depths.txt",
-                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
-                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
-                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
-                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
-                "snv/multiqc/multiqc_data/llms-full.txt",
-                "snv/multiqc/multiqc_data/multiqc.log",
-                "snv/multiqc/multiqc_data/multiqc.parquet",
-                "snv/multiqc/multiqc_data/multiqc_bcftools_stats.txt",
-                "snv/multiqc/multiqc_data/multiqc_citations.txt",
-                "snv/multiqc/multiqc_data/multiqc_data.json",
-                "snv/multiqc/multiqc_data/multiqc_general_stats.txt",
-                "snv/multiqc/multiqc_data/multiqc_software_versions.txt",
-                "snv/multiqc/multiqc_data/multiqc_sompy_combined_data.txt",
-                "snv/multiqc/multiqc_data/multiqc_sompy_indel_data.txt",
-                "snv/multiqc/multiqc_data/multiqc_sompy_snv_data.txt",
-                "snv/multiqc/multiqc_data/multiqc_sources.txt",
-                "snv/multiqc/multiqc_data/multiqc_variant_calling_summary.txt",
-                "snv/multiqc/multiqc_data/sompy_combined_plot.txt",
-                "snv/multiqc/multiqc_data/sompy_indel_plot.txt",
-                "snv/multiqc/multiqc_data/sompy_snv_plot.txt",
+                "snv/multiqc/multiqc_data/.stub",
                 "snv/multiqc/multiqc_plots",
-                "snv/multiqc/multiqc_plots/pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
-                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
-                "snv/multiqc/multiqc_plots/pdf/sompy_combined_plot.pdf",
-                "snv/multiqc/multiqc_plots/pdf/sompy_indel_plot.pdf",
-                "snv/multiqc/multiqc_plots/pdf/sompy_snv_plot.pdf",
-                "snv/multiqc/multiqc_plots/pdf/variant_calling_summary.pdf",
-                "snv/multiqc/multiqc_plots/png",
-                "snv/multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png",
-                "snv/multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-cnt.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-log.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
-                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
-                "snv/multiqc/multiqc_plots/png/sompy_combined_plot.png",
-                "snv/multiqc/multiqc_plots/png/sompy_indel_plot.png",
-                "snv/multiqc/multiqc_plots/png/sompy_snv_plot.png",
-                "snv/multiqc/multiqc_plots/png/variant_calling_summary.png",
-                "snv/multiqc/multiqc_plots/svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-cnt.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-log.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg",
-                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg",
-                "snv/multiqc/multiqc_plots/svg/sompy_combined_plot.svg",
-                "snv/multiqc/multiqc_plots/svg/sompy_indel_plot.svg",
-                "snv/multiqc/multiqc_plots/svg/sompy_snv_plot.svg",
-                "snv/multiqc/multiqc_plots/svg/variant_calling_summary.svg",
+                "snv/multiqc/multiqc_plots/.stub",
                 "snv/multiqc/multiqc_report.html",
                 "snv/summary",
                 "snv/summary/comparisons",
@@ -196,49 +112,58 @@
                 "snv/summary/comparisons/rtgtools/rtgtools.TP_base.csv",
                 "snv/summary/comparisons/rtgtools/rtgtools.TP_comp.csv",
                 "snv/summary/comparisons/sompy",
-                "snv/summary/comparisons/sompy/sompy.FN.csv",
-                "snv/summary/comparisons/sompy/sompy.FP.csv",
-                "snv/summary/comparisons/sompy/sompy.TP_comp.csv",
+                "snv/summary/comparisons/sompy/sompy.FN.summary.csv",
+                "snv/summary/comparisons/sompy/sompy.FP.summary.csv",
+                "snv/summary/comparisons/sompy/sompy.TP_comp.summary.csv",
                 "snv/summary/datavzrd",
                 "snv/summary/datavzrd/rtgtools",
                 "snv/summary/datavzrd/rtgtools/index.html",
+                "snv/summary/datavzrd/rtgtools/network",
+                "snv/summary/datavzrd/rtgtools/network/config.js",
+                "snv/summary/datavzrd/rtgtools/network/data",
+                "snv/summary/datavzrd/rtgtools/network/data/data_1.js",
+                "snv/summary/datavzrd/rtgtools/network/functions.js",
+                "snv/summary/datavzrd/rtgtools/network/heatmap.js",
+                "snv/summary/datavzrd/rtgtools/network/index_1.html",
+                "snv/summary/datavzrd/rtgtools/network/plots",
+                "snv/summary/datavzrd/rtgtools/network/plots/plot_0.js",
                 "snv/summary/datavzrd/rtgtools/static",
+                "snv/summary/datavzrd/rtgtools/static/bootstrap-select.min.css",
+                "snv/summary/datavzrd/rtgtools/static/bootstrap-table-fixed-columns.min.css",
+                "snv/summary/datavzrd/rtgtools/static/bootstrap-table.min.css",
+                "snv/summary/datavzrd/rtgtools/static/bootstrap.min.css",
                 "snv/summary/datavzrd/rtgtools/static/bundle.js",
-                "snv/summary/datavzrd/rtgtools/test",
-                "snv/summary/datavzrd/rtgtools/test/config.js",
-                "snv/summary/datavzrd/rtgtools/test/data",
-                "snv/summary/datavzrd/rtgtools/test/data/data_1.js",
-                "snv/summary/datavzrd/rtgtools/test/functions.js",
-                "snv/summary/datavzrd/rtgtools/test/index_1.html",
-                "snv/summary/datavzrd/rtgtools/test/plots",
-                "snv/summary/datavzrd/rtgtools/test/plots/plots.js",
+                "snv/summary/datavzrd/rtgtools/static/datavzrd.css",
                 "snv/summary/datavzrd/sompy",
                 "snv/summary/datavzrd/sompy/index.html",
+                "snv/summary/datavzrd/sompy/network",
+                "snv/summary/datavzrd/sompy/network/config.js",
+                "snv/summary/datavzrd/sompy/network/data",
+                "snv/summary/datavzrd/sompy/network/data/data_1.js",
+                "snv/summary/datavzrd/sompy/network/functions.js",
+                "snv/summary/datavzrd/sompy/network/heatmap.js",
+                "snv/summary/datavzrd/sompy/network/index_1.html",
+                "snv/summary/datavzrd/sompy/network/plots",
+                "snv/summary/datavzrd/sompy/network/plots/plot_0.js",
                 "snv/summary/datavzrd/sompy/static",
+                "snv/summary/datavzrd/sompy/static/bootstrap-select.min.css",
+                "snv/summary/datavzrd/sompy/static/bootstrap-table-fixed-columns.min.css",
+                "snv/summary/datavzrd/sompy/static/bootstrap-table.min.css",
+                "snv/summary/datavzrd/sompy/static/bootstrap.min.css",
                 "snv/summary/datavzrd/sompy/static/bundle.js",
-                "snv/summary/datavzrd/sompy/test",
-                "snv/summary/datavzrd/sompy/test/config.js",
-                "snv/summary/datavzrd/sompy/test/data",
-                "snv/summary/datavzrd/sompy/test/data/data_1.js",
-                "snv/summary/datavzrd/sompy/test/functions.js",
-                "snv/summary/datavzrd/sompy/test/index_1.html",
-                "snv/summary/datavzrd/sompy/test/plots",
-                "snv/summary/datavzrd/sompy/test/plots/plots.js",
+                "snv/summary/datavzrd/sompy/static/datavzrd.css",
                 "snv/summary/plots",
                 "snv/summary/plots/rtgtools",
-                "snv/summary/plots/rtgtools/f1_by_tool_rtgtools_mqc.png",
-                "snv/summary/plots/rtgtools/pr_recall_by_tool_rtgtools_mqc.png",
-                "snv/summary/plots/rtgtools/upset_rtgtools_tp_fn_mqc.png",
-                "snv/summary/plots/rtgtools/upset_rtgtools_tp_fp_mqc.png",
+                "snv/summary/plots/rtgtools/metric_by_tool_rtgtools_mqc.png",
+                "snv/summary/plots/rtgtools/upset_rtgtools.upset.mqc.png",
                 "snv/summary/plots/rtgtools/variants_by_tool_rtgtools_mqc.png",
                 "snv/summary/plots/sompy",
-                "snv/summary/plots/sompy/f1_by_tool_sompy_mqc.png",
-                "snv/summary/plots/sompy/pr_recall_by_tool_sompy_mqc.png",
-                "snv/summary/plots/sompy/upset_sompy_tp_fn_mqc.png",
-                "snv/summary/plots/sompy/upset_sompy_tp_fp_mqc.png",
+                "snv/summary/plots/sompy/metric_by_tool_sompy_mqc.png",
+                "snv/summary/plots/sompy/upset_sompy.upset.mqc.png",
                 "snv/summary/plots/sompy/variants_by_tool_sompy_mqc.png",
                 "snv/summary/tables",
                 "snv/summary/tables/rtgtools",
+                "snv/summary/tables/rtgtools/rtgtools.regions.csv",
                 "snv/summary/tables/rtgtools/rtgtools.summary.csv",
                 "snv/summary/tables/sompy",
                 "snv/summary/tables/sompy/sompy.regions.csv",
@@ -323,57 +248,28 @@
                 "snv/test9/stats/bcftools/test9.mutect2.bcftools_stats.txt"
             ],
             [
-                "nameIndex0:md5,720ad6dfad3d1ee07a3a2bc3ed953395",
-                "namedata0:md5,758c4a60948aed6c6a4c78323aa73ab3",
-                "namepointer0:md5,319f9f665b338f0e218677e036637e94",
-                "reference.txt:md5,c9f7ef637449eb0f006d90080a130e30",
-                "seqdata0:md5,ea8728adf43db158305ba188de66e838",
-                "seqdata1:md5,d3470516d52b20e9477323d051846c3f",
-                "seqdata2:md5,1fd1a98f39b966aac0b696b122a1c6d5",
-                "seqdata3:md5,49ba3e2d1b4ada1d7ed2c29079833491",
-                "seqpointer0:md5,77ad13d617e120eadad10bdec41cc00f",
-                "seqpointer1:md5,fce3fdba9b237ec51f3c356086d0f8b9",
-                "seqpointer2:md5,3d99bc0313f17f491a0a2903d6585b14",
-                "seqpointer3:md5,2a69114e099aa0752e78f417cc8fe7bb",
-                "sequenceIndex0:md5,18c7d37abf02d389fda5d9945b16b614",
-                "suffixIndex0:md5,b7bb2ba061ab54c0bf07c0a941d0277a",
-                "suffixdata0:md5,f2876dd730673cd49c4de191001f634e",
-                "suffixpointer0:md5,468281ffb10d7dd934289af762a03781",
-                "SEQC2.bcftools_stats.txt:md5,689717d58bc2faefb1701a5ee983c593",
-                "bcftools-stats-subtypes.txt:md5,bba32c82e906895f9740f84e11216252",
-                "bcftools_stats_indel-lengths.txt:md5,bd2e91c35c8442abd21e80763d575afc",
-                "bcftools_stats_variant_depths.txt:md5,e37a8bb9b62c27cae98870b0342ac37a",
-                "bcftools_stats_vqc_Count_Indels.txt:md5,c9f26ff78232b4ca262e16b558959fdd",
-                "bcftools_stats_vqc_Count_SNP.txt:md5,0c07768ed6f2942f49becee0b55d3983",
-                "bcftools_stats_vqc_Count_Transitions.txt:md5,e27493661d676f42e5833eb0b81f986f",
-                "bcftools_stats_vqc_Count_Transversions.txt:md5,392e38613596b1aade889f4334a55608",
-                "multiqc_bcftools_stats.txt:md5,e8890d56756d5aa88b4d7345bd6b2142",
-                "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b",
-                "multiqc_sompy_combined_data.txt:md5,cece722dcd3167773629b51c14893dc3",
-                "multiqc_sompy_indel_data.txt:md5,3c0893e35edb7c5e13c530dd14918a90",
-                "multiqc_sompy_snv_data.txt:md5,aa167ee42b48bfb26e722621c0e2dbc6",
-                "multiqc_variant_calling_summary.txt:md5,0bf9a12183da95be49778c2c65f5078e",
-                "sompy_combined_plot.txt:md5,182d53f013558ea07d967eda2aa3bfae",
-                "sompy_indel_plot.txt:md5,072e830d52939faeae5795e6f1cbaed8",
-                "sompy_snv_plot.txt:md5,c7076da1af66fc4e50538d669aa0f1c2",
-                "test10.SEQC2.strelka.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6",
-                "test10.SEQC2.strelka.summary.txt:md5,1e5258e7deb239a9cf5f5d9cf4efc373",
-                "test10.strelka.bcftools_stats.txt:md5,0064a9f57d02f1e8154f5d81eaf2dfe9",
-                "test8.SEQC2.freebayes.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6",
-                "test8.SEQC2.freebayes.summary.txt:md5,2918d0852abdbfd92f324cbfe3fc496b",
-                "test8.freebayes.bcftools_stats.txt:md5,98e3627e2d15d7f31661bd56c021447e",
-                "test9.SEQC2.mutect2.phasing.txt:md5,6d29664d5d20e216220ae051a677eec5",
-                "test9.SEQC2.mutect2.summary.txt:md5,8b0b6501a6290ce013d6e3fe316a7b69",
-                "test9.mutect2.bcftools_stats.txt:md5,13f07551d60c681e81499dbd189b4537"
+                "genome.sdf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "SEQC2.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test10.SEQC2.strelka.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test10.SEQC2.strelka.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test10.strelka.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test8.SEQC2.freebayes.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test8.SEQC2.freebayes.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test8.freebayes.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test9.SEQC2.mutect2.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test9.SEQC2.mutect2.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test9.mutect2.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-04-22T12:30:49.638777486",
+        "timestamp": "2026-05-21T13:56:19.595825455",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.1"
         }
     },
-    "-stub": {
+    "Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy,rtgtools'": {
         "content": [
             89,
             {
@@ -411,7 +307,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -464,6 +360,27 @@
                 "references",
                 "references/rtgtools",
                 "references/rtgtools/genome.sdf",
+                "references/rtgtools/genome.sdf/done",
+                "references/rtgtools/genome.sdf/format.log",
+                "references/rtgtools/genome.sdf/mainIndex",
+                "references/rtgtools/genome.sdf/nameIndex0",
+                "references/rtgtools/genome.sdf/namedata0",
+                "references/rtgtools/genome.sdf/namepointer0",
+                "references/rtgtools/genome.sdf/progress",
+                "references/rtgtools/genome.sdf/reference.txt",
+                "references/rtgtools/genome.sdf/seqdata0",
+                "references/rtgtools/genome.sdf/seqdata1",
+                "references/rtgtools/genome.sdf/seqdata2",
+                "references/rtgtools/genome.sdf/seqdata3",
+                "references/rtgtools/genome.sdf/seqpointer0",
+                "references/rtgtools/genome.sdf/seqpointer1",
+                "references/rtgtools/genome.sdf/seqpointer2",
+                "references/rtgtools/genome.sdf/seqpointer3",
+                "references/rtgtools/genome.sdf/sequenceIndex0",
+                "references/rtgtools/genome.sdf/suffixIndex0",
+                "references/rtgtools/genome.sdf/suffixdata0",
+                "references/rtgtools/genome.sdf/suffixpointer0",
+                "references/rtgtools/genome.sdf/summary.txt",
                 "snv",
                 "snv/SEQC2",
                 "snv/SEQC2/preprocess",
@@ -474,9 +391,72 @@
                 "snv/SEQC2/stats/bcftools/SEQC2.bcftools_stats.txt",
                 "snv/multiqc",
                 "snv/multiqc/multiqc_data",
-                "snv/multiqc/multiqc_data/.stub",
+                "snv/multiqc/multiqc_data/bcftools-stats-subtypes.txt",
+                "snv/multiqc/multiqc_data/bcftools_stats_indel-lengths.txt",
+                "snv/multiqc/multiqc_data/bcftools_stats_variant_depths.txt",
+                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt",
+                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt",
+                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt",
+                "snv/multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt",
+                "snv/multiqc/multiqc_data/llms-full.txt",
+                "snv/multiqc/multiqc_data/multiqc.log",
+                "snv/multiqc/multiqc_data/multiqc.parquet",
+                "snv/multiqc/multiqc_data/multiqc_bcftools_stats.txt",
+                "snv/multiqc/multiqc_data/multiqc_citations.txt",
+                "snv/multiqc/multiqc_data/multiqc_data.json",
+                "snv/multiqc/multiqc_data/multiqc_general_stats.txt",
+                "snv/multiqc/multiqc_data/multiqc_software_versions.txt",
+                "snv/multiqc/multiqc_data/multiqc_sompy_combined_data.txt",
+                "snv/multiqc/multiqc_data/multiqc_sompy_indel_data.txt",
+                "snv/multiqc/multiqc_data/multiqc_sompy_snv_data.txt",
+                "snv/multiqc/multiqc_data/multiqc_sources.txt",
+                "snv/multiqc/multiqc_data/multiqc_variant_calling_summary.txt",
+                "snv/multiqc/multiqc_data/sompy_combined_plot.txt",
+                "snv/multiqc/multiqc_data/sompy_indel_plot.txt",
+                "snv/multiqc/multiqc_data/sompy_snv_plot.txt",
                 "snv/multiqc/multiqc_plots",
-                "snv/multiqc/multiqc_plots/.stub",
+                "snv/multiqc/multiqc_plots/pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-cnt.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths-log.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf",
+                "snv/multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf",
+                "snv/multiqc/multiqc_plots/pdf/sompy_combined_plot.pdf",
+                "snv/multiqc/multiqc_plots/pdf/sompy_indel_plot.pdf",
+                "snv/multiqc/multiqc_plots/pdf/sompy_snv_plot.pdf",
+                "snv/multiqc/multiqc_plots/pdf/variant_calling_summary.pdf",
+                "snv/multiqc/multiqc_plots/png",
+                "snv/multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png",
+                "snv/multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-cnt.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_indel-lengths-log.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png",
+                "snv/multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png",
+                "snv/multiqc/multiqc_plots/png/sompy_combined_plot.png",
+                "snv/multiqc/multiqc_plots/png/sompy_indel_plot.png",
+                "snv/multiqc/multiqc_plots/png/sompy_snv_plot.png",
+                "snv/multiqc/multiqc_plots/png/variant_calling_summary.png",
+                "snv/multiqc/multiqc_plots/svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-cnt.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths-log.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg",
+                "snv/multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg",
+                "snv/multiqc/multiqc_plots/svg/sompy_combined_plot.svg",
+                "snv/multiqc/multiqc_plots/svg/sompy_indel_plot.svg",
+                "snv/multiqc/multiqc_plots/svg/sompy_snv_plot.svg",
+                "snv/multiqc/multiqc_plots/svg/variant_calling_summary.svg",
                 "snv/multiqc/multiqc_report.html",
                 "snv/summary",
                 "snv/summary/comparisons",
@@ -486,58 +466,49 @@
                 "snv/summary/comparisons/rtgtools/rtgtools.TP_base.csv",
                 "snv/summary/comparisons/rtgtools/rtgtools.TP_comp.csv",
                 "snv/summary/comparisons/sompy",
-                "snv/summary/comparisons/sompy/sompy.FN.summary.csv",
-                "snv/summary/comparisons/sompy/sompy.FP.summary.csv",
-                "snv/summary/comparisons/sompy/sompy.TP_comp.summary.csv",
+                "snv/summary/comparisons/sompy/sompy.FN.csv",
+                "snv/summary/comparisons/sompy/sompy.FP.csv",
+                "snv/summary/comparisons/sompy/sompy.TP_comp.csv",
                 "snv/summary/datavzrd",
                 "snv/summary/datavzrd/rtgtools",
                 "snv/summary/datavzrd/rtgtools/index.html",
-                "snv/summary/datavzrd/rtgtools/network",
-                "snv/summary/datavzrd/rtgtools/network/config.js",
-                "snv/summary/datavzrd/rtgtools/network/data",
-                "snv/summary/datavzrd/rtgtools/network/data/data_1.js",
-                "snv/summary/datavzrd/rtgtools/network/functions.js",
-                "snv/summary/datavzrd/rtgtools/network/heatmap.js",
-                "snv/summary/datavzrd/rtgtools/network/index_1.html",
-                "snv/summary/datavzrd/rtgtools/network/plots",
-                "snv/summary/datavzrd/rtgtools/network/plots/plot_0.js",
                 "snv/summary/datavzrd/rtgtools/static",
-                "snv/summary/datavzrd/rtgtools/static/bootstrap-select.min.css",
-                "snv/summary/datavzrd/rtgtools/static/bootstrap-table-fixed-columns.min.css",
-                "snv/summary/datavzrd/rtgtools/static/bootstrap-table.min.css",
-                "snv/summary/datavzrd/rtgtools/static/bootstrap.min.css",
                 "snv/summary/datavzrd/rtgtools/static/bundle.js",
-                "snv/summary/datavzrd/rtgtools/static/datavzrd.css",
+                "snv/summary/datavzrd/rtgtools/test",
+                "snv/summary/datavzrd/rtgtools/test/config.js",
+                "snv/summary/datavzrd/rtgtools/test/data",
+                "snv/summary/datavzrd/rtgtools/test/data/data_1.js",
+                "snv/summary/datavzrd/rtgtools/test/functions.js",
+                "snv/summary/datavzrd/rtgtools/test/index_1.html",
+                "snv/summary/datavzrd/rtgtools/test/plots",
+                "snv/summary/datavzrd/rtgtools/test/plots/plots.js",
                 "snv/summary/datavzrd/sompy",
                 "snv/summary/datavzrd/sompy/index.html",
-                "snv/summary/datavzrd/sompy/network",
-                "snv/summary/datavzrd/sompy/network/config.js",
-                "snv/summary/datavzrd/sompy/network/data",
-                "snv/summary/datavzrd/sompy/network/data/data_1.js",
-                "snv/summary/datavzrd/sompy/network/functions.js",
-                "snv/summary/datavzrd/sompy/network/heatmap.js",
-                "snv/summary/datavzrd/sompy/network/index_1.html",
-                "snv/summary/datavzrd/sompy/network/plots",
-                "snv/summary/datavzrd/sompy/network/plots/plot_0.js",
                 "snv/summary/datavzrd/sompy/static",
-                "snv/summary/datavzrd/sompy/static/bootstrap-select.min.css",
-                "snv/summary/datavzrd/sompy/static/bootstrap-table-fixed-columns.min.css",
-                "snv/summary/datavzrd/sompy/static/bootstrap-table.min.css",
-                "snv/summary/datavzrd/sompy/static/bootstrap.min.css",
                 "snv/summary/datavzrd/sompy/static/bundle.js",
-                "snv/summary/datavzrd/sompy/static/datavzrd.css",
+                "snv/summary/datavzrd/sompy/test",
+                "snv/summary/datavzrd/sompy/test/config.js",
+                "snv/summary/datavzrd/sompy/test/data",
+                "snv/summary/datavzrd/sompy/test/data/data_1.js",
+                "snv/summary/datavzrd/sompy/test/functions.js",
+                "snv/summary/datavzrd/sompy/test/index_1.html",
+                "snv/summary/datavzrd/sompy/test/plots",
+                "snv/summary/datavzrd/sompy/test/plots/plots.js",
                 "snv/summary/plots",
                 "snv/summary/plots/rtgtools",
-                "snv/summary/plots/rtgtools/metric_by_tool_rtgtools_mqc.png",
-                "snv/summary/plots/rtgtools/upset_rtgtools.upset.mqc.png",
+                "snv/summary/plots/rtgtools/f1_by_tool_rtgtools_mqc.png",
+                "snv/summary/plots/rtgtools/pr_recall_by_tool_rtgtools_mqc.png",
+                "snv/summary/plots/rtgtools/upset_rtgtools_tp_fn_mqc.png",
+                "snv/summary/plots/rtgtools/upset_rtgtools_tp_fp_mqc.png",
                 "snv/summary/plots/rtgtools/variants_by_tool_rtgtools_mqc.png",
                 "snv/summary/plots/sompy",
-                "snv/summary/plots/sompy/metric_by_tool_sompy_mqc.png",
-                "snv/summary/plots/sompy/upset_sompy.upset.mqc.png",
+                "snv/summary/plots/sompy/f1_by_tool_sompy_mqc.png",
+                "snv/summary/plots/sompy/pr_recall_by_tool_sompy_mqc.png",
+                "snv/summary/plots/sompy/upset_sompy_tp_fn_mqc.png",
+                "snv/summary/plots/sompy/upset_sompy_tp_fp_mqc.png",
                 "snv/summary/plots/sompy/variants_by_tool_sompy_mqc.png",
                 "snv/summary/tables",
                 "snv/summary/tables/rtgtools",
-                "snv/summary/tables/rtgtools/rtgtools.regions.csv",
                 "snv/summary/tables/rtgtools/rtgtools.summary.csv",
                 "snv/summary/tables/sompy",
                 "snv/summary/tables/sompy/sompy.regions.csv",
@@ -622,22 +593,51 @@
                 "snv/test9/stats/bcftools/test9.mutect2.bcftools_stats.txt"
             ],
             [
-                "genome.sdf:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "SEQC2.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
-                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test10.SEQC2.strelka.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test10.SEQC2.strelka.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test10.strelka.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test8.SEQC2.freebayes.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test8.SEQC2.freebayes.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test8.freebayes.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test9.SEQC2.mutect2.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test9.SEQC2.mutect2.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test9.mutect2.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "nameIndex0:md5,720ad6dfad3d1ee07a3a2bc3ed953395",
+                "namedata0:md5,758c4a60948aed6c6a4c78323aa73ab3",
+                "namepointer0:md5,319f9f665b338f0e218677e036637e94",
+                "reference.txt:md5,c9f7ef637449eb0f006d90080a130e30",
+                "seqdata0:md5,ea8728adf43db158305ba188de66e838",
+                "seqdata1:md5,d3470516d52b20e9477323d051846c3f",
+                "seqdata2:md5,1fd1a98f39b966aac0b696b122a1c6d5",
+                "seqdata3:md5,49ba3e2d1b4ada1d7ed2c29079833491",
+                "seqpointer0:md5,77ad13d617e120eadad10bdec41cc00f",
+                "seqpointer1:md5,fce3fdba9b237ec51f3c356086d0f8b9",
+                "seqpointer2:md5,3d99bc0313f17f491a0a2903d6585b14",
+                "seqpointer3:md5,2a69114e099aa0752e78f417cc8fe7bb",
+                "sequenceIndex0:md5,18c7d37abf02d389fda5d9945b16b614",
+                "suffixIndex0:md5,b7bb2ba061ab54c0bf07c0a941d0277a",
+                "suffixdata0:md5,f2876dd730673cd49c4de191001f634e",
+                "suffixpointer0:md5,468281ffb10d7dd934289af762a03781",
+                "SEQC2.bcftools_stats.txt:md5,689717d58bc2faefb1701a5ee983c593",
+                "bcftools-stats-subtypes.txt:md5,bba32c82e906895f9740f84e11216252",
+                "bcftools_stats_indel-lengths.txt:md5,bd2e91c35c8442abd21e80763d575afc",
+                "bcftools_stats_variant_depths.txt:md5,e37a8bb9b62c27cae98870b0342ac37a",
+                "bcftools_stats_vqc_Count_Indels.txt:md5,c9f26ff78232b4ca262e16b558959fdd",
+                "bcftools_stats_vqc_Count_SNP.txt:md5,0c07768ed6f2942f49becee0b55d3983",
+                "bcftools_stats_vqc_Count_Transitions.txt:md5,e27493661d676f42e5833eb0b81f986f",
+                "bcftools_stats_vqc_Count_Transversions.txt:md5,392e38613596b1aade889f4334a55608",
+                "multiqc_bcftools_stats.txt:md5,e8890d56756d5aa88b4d7345bd6b2142",
+                "multiqc_citations.txt:md5,5cbab4ecbe14049d965fd97bd61d252b",
+                "multiqc_sompy_combined_data.txt:md5,cece722dcd3167773629b51c14893dc3",
+                "multiqc_sompy_indel_data.txt:md5,3c0893e35edb7c5e13c530dd14918a90",
+                "multiqc_sompy_snv_data.txt:md5,aa167ee42b48bfb26e722621c0e2dbc6",
+                "multiqc_variant_calling_summary.txt:md5,0bf9a12183da95be49778c2c65f5078e",
+                "sompy_combined_plot.txt:md5,182d53f013558ea07d967eda2aa3bfae",
+                "sompy_indel_plot.txt:md5,072e830d52939faeae5795e6f1cbaed8",
+                "sompy_snv_plot.txt:md5,c7076da1af66fc4e50538d669aa0f1c2",
+                "test10.SEQC2.strelka.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6",
+                "test10.SEQC2.strelka.summary.txt:md5,1e5258e7deb239a9cf5f5d9cf4efc373",
+                "test10.strelka.bcftools_stats.txt:md5,0064a9f57d02f1e8154f5d81eaf2dfe9",
+                "test8.SEQC2.freebayes.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6",
+                "test8.SEQC2.freebayes.summary.txt:md5,2918d0852abdbfd92f324cbfe3fc496b",
+                "test8.freebayes.bcftools_stats.txt:md5,98e3627e2d15d7f31661bd56c021447e",
+                "test9.SEQC2.mutect2.phasing.txt:md5,6d29664d5d20e216220ae051a677eec5",
+                "test9.SEQC2.mutect2.summary.txt:md5,8b0b6501a6290ce013d6e3fe316a7b69",
+                "test9.mutect2.bcftools_stats.txt:md5,13f07551d60c681e81499dbd189b4537"
             ]
         ],
-        "timestamp": "2026-05-20T13:25:37.679632604",
+        "timestamp": "2026-05-21T13:55:17.095891839",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.1"
diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap
index 9343a18d..0dc72540 100644
--- a/tests/somatic_sv.nf.test.snap
+++ b/tests/somatic_sv.nf.test.snap
@@ -22,7 +22,7 @@
                     "bcftools": 1.22
                 },
                 "CREATE_DATAVZRD_INPUT": {
-                    "pigz": 2.8
+                    "gawk": "5.3.0"
                 },
                 "DATAVZRD": {
                     "datavzrd": "2.63.3"
@@ -260,7 +260,7 @@
                 "test12.tiddit_mqc.stats:md5,950514053b461a3868a12fd5ced0a3d8"
             ]
         ],
-        "timestamp": "2026-05-20T13:29:11.961442327",
+        "timestamp": "2026-05-21T13:13:27.598845797",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.1"

From 986847672e212e4a14fe6f548079b2b06d8c0e83 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 21 May 2026 11:59:20 +0000
Subject: [PATCH 09/14] [automated] Fix code linting

---
 .../local/report_benchmark_statistics/main.nf        | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/subworkflows/local/report_benchmark_statistics/main.nf b/subworkflows/local/report_benchmark_statistics/main.nf
index 9f344f71..71bb43be 100644
--- a/subworkflows/local/report_benchmark_statistics/main.nf
+++ b/subworkflows/local/report_benchmark_statistics/main.nf
@@ -35,16 +35,16 @@ workflow REPORT_BENCHMARK_STATISTICS {
 
     if (params.variant_type != "snv" && !params.skip_plots.contains("svlength")){
         // plot INDEL/SV distribution plots
-        evaluations.map { item -> 
-            tuple(item[0], item[1]) 
+        evaluations.map { item ->
+            tuple(item[0], item[1])
         }.groupTuple()
         .mix(
-            evaluations_csv.map { item -> 
-                tuple(item[0], item[1]) 
+            evaluations_csv.map { item ->
+                tuple(item[0], item[1])
             }.groupTuple()
         )
         .set { svlen_input }
-        
+
         PLOTS_SVLEN_DIST(svlen_input)
         ch_plots = ch_plots.mix(PLOTS_SVLEN_DIST.out.plot)
     }
@@ -67,7 +67,7 @@ workflow REPORT_BENCHMARK_STATISTICS {
         [],
         false
     )
-  
+
     CREATE_DATAVZRD_INPUT.out.output
         .map { meta, yaml_file ->
             def clean_meta = meta.findAll { it.key != 'csv' }

From 2fb60e4bb1e63b0acfdc9d35cd0b37371d070377 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Thu, 21 May 2026 14:16:53 +0200
Subject: [PATCH 10/14] add changelog

---
 CHANGELOG.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a8a4d846..cc213909 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- Template update for nf-core/tools v4.0.2 + a few fixes around [#305](https://github.com/nf-core/variantbenchmarking/issues/305)
+
 ### `Fixed`
 
 ### `Dependencies`
+| Dependency     | Old version | New version |
+| -------------- | ----------- | ----------- |
+| pigz           | 2.8         | depreciated |
+| nf-core        | 3.5.1       | 4.0.2       |
+| prettier       | 3.6.2       | 3.8.3       |
+
 
 ## 1.5.0
 

From 3d28ec83881c9097a6240f21be8a3da85c1963db Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 21 May 2026 12:29:14 +0000
Subject: [PATCH 11/14] [automated] Fix code linting

---
 CHANGELOG.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cc213909..2b9fa47e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,12 +12,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 ### `Dependencies`
-| Dependency     | Old version | New version |
-| -------------- | ----------- | ----------- |
-| pigz           | 2.8         | depreciated |
-| nf-core        | 3.5.1       | 4.0.2       |
-| prettier       | 3.6.2       | 3.8.3       |
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| pigz       | 2.8         | depreciated |
+| nf-core    | 3.5.1       | 4.0.2       |
+| prettier   | 3.6.2       | 3.8.3       |
 
 ## 1.5.0
 

From 4e6f7804e16a74a22db7faf268f8539a1c06f544 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Thu, 21 May 2026 15:30:15 +0200
Subject: [PATCH 12/14] Update conf/containers_conda_lock_files_amd64.config
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 conf/containers_conda_lock_files_amd64.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index a05393e6..92ef6eeb 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }

From 0d6903c04d9bafac6e1925bbcd1e02cabcb9abfc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Thu, 21 May 2026 15:30:28 +0200
Subject: [PATCH 13/14] Update conf/containers_conda_lock_files_arm64.config
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 conf/containers_conda_lock_files_arm64.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index 7b7f2b66..6b975ee0 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }

From 31ee55f585023cf1a5826c0893a08aae52d82935 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Thu, 21 May 2026 15:45:13 +0200
Subject: [PATCH 14/14] take conda back

---
 conf/containers_conda_lock_files_amd64.config | 2 +-
 conf/containers_conda_lock_files_arm64.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index 92ef6eeb..a05393e6 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index 6b975ee0..7b7f2b66 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }