diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 97c8c97..237c9ed 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 4948d40..0000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,125 +0,0 @@
-# `nf-core/proteinannotator`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving nf-core/proteinannotator.
-
-We try to manage the required tasks for nf-core/proteinannotator 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/proteinannotator then the best place to ask is on the nf-core Slack [#proteinannotator](https://nfcore.slack.com/channels/proteinannotator) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Contribution workflow
-
-If you'd like to write some code for nf-core/proteinannotator, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [nf-core/proteinannotator issues](https://github.com/nf-core/proteinannotator/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/proteinannotator repository](https://github.com/nf-core/proteinannotator) 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/proteinannotator documentation](https://nf-co.re/proteinannotator/usage) and don't hesitate to get in touch on the nf-core Slack [#proteinannotator](https://nfcore.slack.com/channels/proteinannotator) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Pipeline contribution conventions
-
-To make the `nf-core/proteinannotator` 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/proteinannotator/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 5d0e8d4..2211da8 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/proteinannotator/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/proteinannotator/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/proteinannotator/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/proteinannotator/tree/master/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/proteinannotator _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 (e.g. `nf-test test */local --profile=~test,docker` for all new local tests).
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 3408527..e2833ee 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: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index efe8e86..f6104bd 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -32,24 +32,24 @@ runs:
         path: ./subworkflows
         depth: 10
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ 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')
@@ -60,7 +60,7 @@ 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 562018e..bb23b1a 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -23,21 +23,40 @@ jobs:
           echo "revision={%- raw -%}${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
           workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/proteinannotator/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'proteinannotator'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *proteinannotator/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *proteinannotator/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/proteinannotator/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 50644cc..0507133 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 1243a2d..ef68e64 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 6adb0ff..172de6f 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 45884ff..a7bf4fc 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -38,13 +38,16 @@ 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@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 +57,15 @@ jobs:
         with:
           apptainer-version: 1.3.4
 
+      - name: Read .nf-core.yml
+        id: read_yml
+        run: |
+          echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT"
+
       - 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 +135,7 @@ 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 e18e27a..3d6fa6c 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -31,22 +31,18 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
+      # Install and run prek
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -54,7 +50,7 @@ jobs:
 
       - name: Commit & push changes
         id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a3..8738ffc 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,33 +11,31 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
@@ -45,12 +43,10 @@ jobs:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -58,7 +54,7 @@ jobs:
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc2..5b0c24f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
+        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index fd742d1..efd72d6 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:
-          - "25.10.0"
+          - "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 431d3d4..78d5dbe 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 e8560fc..ea30827 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 1989f4d..34d6bb2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,7 +7,7 @@ testing/
 testing*
 *.pyc
 null/
-
+.lineage/
 # Nextflow nf-tests output
 .nf-test.log
 .nf-test/tests
diff --git a/.nf-core.yml b/.nf-core.yml
index 50507a8..290610a 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,17 +8,17 @@ lint:
     - docs/images/nf-core-proteinannotator_logo_light.png
     - docs/images/nf-core-proteinannotator_logo_dark.png
     - .github/PULL_REQUEST_TEMPLATE.md
-nf_core_version: 3.5.1
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: Olga Botvinnik, Evangelos Karatzas
   description: Generation of sequence-level annotations for amino acid sequences
-  version: 1.0.0
-  force: true
+  force: false
+  is_nfcore: true
+  name: proteinannotator
+  org: nf-core
   outdir: .
   skip_features:
     - fastqc
     - igenomes
-  is_nfcore: true
-  name: proteinannotator
-  org: nf-core
+  version: 1.1.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d06777a..f51e1a2 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 8e669dc..d49d403 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 6c034ab..096796b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,26 @@
 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).
 
+## v1.1.0 - [2026/05/05]
+
+### `Added`
+
+- [#90](https://github.com/nf-core/proteinannotator/pull/90) - Added the option to download and use the latest `metagRoot` HMM library (or use path to an existing one) for domain annotation. (by @angelphanth)
+- [#87](https://github.com/nf-core/proteinannotator/pull/87) - Added the option to download and use the latest `NMPFams` HMM library (or use path to an existing one) for domain annotation. (by @npechl)
+- [#85](https://github.com/nf-core/proteinannotator/pull/85) - Added zenodo doi in `nextflow.config`. (by @vagkaratzas)
+
+### `Changed`
+
+- [#93](https://github.com/nf-core/proteinfamilies/pull/93) - nf-core tools template update to 4.0.2. (by @vagkaratzas)
+- [#85](https://github.com/nf-core/proteinannotator/pull/85) - `test_full.config` input samplesheet path is now set properly. (by @vagkaratzas)
+
+### `Dependencies`
+
+| Tool    | Previous version | New version |
+| ------- | ---------------- | ----------- |
+| aria2   | 1.36.0           | 1.37.0      |
+| multiqc | 1.33             | 1.34        |
+
 ## v1.0.0 - Yellow Saiga - [2026/02/09]
 
 Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template.
diff --git a/README.md b/README.md
index 2eef432..55e9344 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,8 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/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/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)
 [![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%A525.10.0-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-4.0.2-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/)
@@ -37,7 +37,7 @@ Generate input amino acid sequence statistics with ([`SeqFu`](https://github.com
 ### Annotate sequences
 
 1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases
-   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/) and [FunFam](https://download.cathdb.info/cath/releases/all-releases/)
+   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)
 2. Functional annotation:
    - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.
 3. Predict secondary structure compositional features such as α-helices, β-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))
@@ -46,7 +46,7 @@ Generate input amino acid sequence statistics with ([`SeqFu`](https://github.com
 ## 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.
 
 First, prepare a samplesheet with your input data that looks as follows:
 
@@ -70,7 +70,7 @@ nextflow run nf-core/proteinannotator \
 ```
 
 > [!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/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/parameters).
 
@@ -93,7 +93,7 @@ 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 `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (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 9b61f5d..0000000
--- 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/proteinannotator 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 e9ddc17..5b3abbb 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/proteinannotator/releases/tag/1.0.0" target="_blank">nf-core/proteinannotator</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/proteinannotator/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/proteinannotator/releases/tag/1.1.0" target="_blank">nf-core/proteinannotator</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/proteinannotator/1.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-proteinannotator-methods-description":
     order: -1000
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index 8642c46..0000000
--- 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/proteinannotator ${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 bbc7b33..7212d70 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 0000000..f487ba4
--- /dev/null
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
new file mode 100644
index 0000000..e9a3fed
--- /dev/null
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
new file mode 100644
index 0000000..01b59df
--- /dev/null
+++ b/conf/containers_docker_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
new file mode 100644
index 0000000..7785cb1
--- /dev/null
+++ b/conf/containers_docker_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
new file mode 100644
index 0000000..754821b
--- /dev/null
+++ b/conf/containers_singularity_https_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
new file mode 100644
index 0000000..93071de
--- /dev/null
+++ b/conf/containers_singularity_https_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
new file mode 100644
index 0000000..952881d
--- /dev/null
+++ b/conf/containers_singularity_oras_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
new file mode 100644
index 0000000..498ec50
--- /dev/null
+++ b/conf/containers_singularity_oras_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
diff --git a/conf/modules.config b/conf/modules.config
index ec1428c..b325242 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -90,6 +90,22 @@ process {
         ]
     }
 
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:ARIA2_NMPFAMS' {
+        publishDir = [
+            path: { "${params.outdir}/downloaded_dbs/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:ARIA2_METAGROOT' {
+        publishDir = [
+            path: { "${params.outdir}/downloaded_dbs/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:HMMSEARCH_PFAM' {
         ext.args   = { "-E ${params.hmmsearch_evalue_cutoff}" }
         publishDir = [
@@ -110,6 +126,26 @@ process {
         ]
     }
 
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:HMMSEARCH_NMPFAMS' {
+        ext.args   = { "-E ${params.hmmsearch_evalue_cutoff}" }
+        publishDir = [
+            path: { "${params.outdir}/domain_annotation/nmpfams/" },
+            mode: params.publish_dir_mode,
+            pattern: "*.domtbl.gz",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:DOMAIN_ANNOTATION:HMMSEARCH_METAGROOT' {
+        ext.args   = { "-E ${params.hmmsearch_evalue_cutoff}" }
+        publishDir = [
+            path: { "${params.outdir}/domain_annotation/metagroot/" },
+            mode: params.publish_dir_mode,
+            pattern: "*.domtbl.gz",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:FUNCTIONAL_ANNOTATION:ARIA2' {
         publishDir = [
             path: { "${params.outdir}/downloaded_dbs/" },
diff --git a/conf/test.config b/conf/test.config
index 252ec87..23f4a82 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -25,8 +25,10 @@ params {
     // Input data
     input = params.pipelines_testdata_base_path + 'proteinannotator/samplesheet/samplesheet.csv'
     // Domain annotation
-    pfam_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
-    funfam_latest_link = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'
+    pfam_latest_link        = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
+    funfam_latest_link      = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'
+    nmpfams_latest_link     = params.pipelines_testdata_base_path + 'proteinannotator/testdata/nmpfams/nmpfamsdb_test.hmm.gz'
+    metagroot_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/metagroot/metagroot_test.hmm.gz'
     // Functional annotation
     interproscan_db_url       = params.pipelines_testdata_base_path + 'proteinannotator/testdata/interproscan/interproscan_test.tar.gz'
     interproscan_applications = 'Hamap,TIGRFAM,sfld'
diff --git a/conf/test_full.config b/conf/test_full.config
index bfb05f7..dbcca1e 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,11 +15,13 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = params.pipelines_testdata_base_path + 'proteinannotator/testdata/samplesheet.csv'
+    input = params.pipelines_testdata_base_path + 'proteinannotator/samplesheet/samplesheet.csv'
     // Domain annotation
-    pfam_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
-    funfam_latest_link = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'
+    pfam_latest_link        = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
+    funfam_latest_link      = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'
+    nmpfams_latest_link     = params.pipelines_testdata_base_path + 'proteinannotator/testdata/nmpfams/nmpfamsdb_test.hmm.gz'
+    metagroot_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/metagroot/metagroot_test.hmm.gz'
     // Functional annotation
-    interproscan_db_url       = params.pipelines_testdata_base_path + 'proteinannotator/testdata/interproscan_test.tar.gz'
+    interproscan_db_url       = params.pipelines_testdata_base_path + 'proteinannotator/testdata/interproscan/interproscan_test.tar.gz'
     interproscan_applications = 'Hamap,TIGRFAM,sfld'
 }
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
new file mode 100644
index 0000000..9be0942
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,186 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `nf-core/proteinannotator`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving nf-core/proteinannotator.
+
+This page describes the recommended nf-core way to contribute to both nf-core/proteinannotator 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/proteinannotator.
+
+> [!NOTE]
+> If you need help using or modifying nf-core/proteinannotator, ask on the nf-core Slack [#proteinannotator](https://nfcore.slack.com/channels/proteinannotator) 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/proteinannotator/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/proteinannotator repository](https://github.com/nf-core/proteinannotator) 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/proteinannotator documentation](https://nf-co.re/proteinannotator/usage) or ask on the nf-core [#proteinannotator](https://nfcore.slack.com/channels/proteinannotator) Slack channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+### GitHub Codespaces
+
+You can contribute to nf-core/proteinannotator 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/proteinannotator/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/proteinannotator 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
+
+- When adding or modifying annotation tools, ensure that the reference database paths are parameterised in `nextflow.config` and documented in `nextflow_schema.json` — hardcoded paths are a common source of portability issues.
+- Protein annotation steps can be computationally expensive; always set sensible `withLabel:` resource defaults in `conf/base.config` and test locally with a small FASTA subset before opening a PR.
diff --git a/docs/output.md b/docs/output.md
index fcd3159..71db3de 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,9 +14,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [SeqFu](#seqfu) for input amino acid sequences quality control (QC)
   - [SeqKit](#seqkit) for preprocessing input amino acid sequences (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences)
 - [Database download](#database-download) Optionally download selected databases for annotation.
-  - [aria2](#aria2) - To optionally download the Pfam, FunFam, and/or InterProScan databases through the pipeline.
+  - [aria2](#aria2) - To optionally download the Pfam, FunFam, NMPFams, metagRoot and/or InterProScan databases through the pipeline.
 - [Domain annotation](#domain-annotation) Annotate proteins with domains from established repositories.
-  - [hmmer](#hmmer) - To optionally match the input sequence to known Pfam and/or FunFam domains through `hmmer/hmmsearch`
+  - [hmmer](#hmmer) - To optionally match the input sequence to known Pfam, FunFam, NMPFams and/or metagRoot domains through `hmmer/hmmsearch`
 - [Functional annotation](#functional-annotation) Annotate proteins with functional domains
   - [InterProScan](#Interproscan) - Search the InterProScan database for functional domains
 - [s4pred](#s4pred) - Predict secondary structures of sequences, producing amino acid level probabilities of forming an α-helix, a β-strand or a coil.
@@ -72,10 +72,12 @@ The `seqkit` module is used for initial preprocessing (i.e., gap removal, conver
   - `Pfam-A*.hmm.gz`: (optional) The latest full, or a minimal test, Pfam-A HMM database that can be downloaded through the pipeline.
   - `interproscan_test.tar.gz`: (optional) the downloaded InterProScan archive of member databases according to the optional user-provided url
   - `funfam-hmm3-v4_3_0*.lib.gz`: (optional) The latest (v4_3_0) full, or a minimal test, FunFam HMM database that can be downloaded through the pipeline.
+  - `nmpfamsdb.hmm.gz`: (optional) The latest full, or a minimal test, NMPFams HMM database that can be downloaded through the pipeline.
+  - `metagroot.hmm.gz`: (optional) The latest full, or a minimal test, metagRoot HMM database that can be downloaded through the pipeline.
 
 </details>
 
-If the `skip_*` flags (e.g., `skip_pfam`, `skip_funfam`, `skip_interproscan`) for each annotation database is set to `true`, or the `*_db` parameter paths (e.g., `pfam_db`, `funfam_db`, `interproscan_db`) are set (i.e., not `null`), or the run is resumed after a successful database download, then the respective database will not be (re)downloaded. The full database links can be found in the main `nextflow.config` file, while minimal test versions can be found in the `test` and `test_full` profiles (i.e., `conf/test.config`, `conf/test_full.config`).
+If the `skip_*` flags (e.g., `skip_pfam`, `skip_funfam`, `skip_nmpfams`, `skip_metagroot`, `skip_interproscan`) for each annotation database is set to `true`, or the `*_db` parameter paths (e.g., `pfam_db`, `funfam_db`, `nmpfams_db`, `metagroot_db`, `interproscan_db`) are set (i.e., not `null`), or the run is resumed after a successful database download, then the respective database will not be (re)downloaded. The full database links can be found in the main `nextflow.config` file, while minimal test versions can be found in the `test` and `test_full` profiles (i.e., `conf/test.config`, `conf/test_full.config`).
 
 [aria2](https://github.com/aria2/aria2/) is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.
 
@@ -91,12 +93,16 @@ If the `skip_*` flags (e.g., `skip_pfam`, `skip_funfam`, `skip_interproscan`) fo
     - `<samplename>.domtbl.gz`: `hmmer/hmmsearch` results along parameters info.
   - `funfam/`
     - `<samplename>.domtbl.gz`: `hmmer/hmmsearch` results along parameters info.
+  - `nmpfams/`
+    - `<samplename>.domtbl.gz`: `hmmer/hmmsearch` results along parameters info.
+  - `metagroot/`
+    - `<samplename>.domtbl.gz`: `hmmer/hmmsearch` results along parameters info.
 
 </details>
 
-Each of the `domain_annotation/` subfolders (e.g., `pfam`, `funfam`) contain a `.domtbl.gz` annotation file per input sample, depending on which domain annotation databases were used in the pipeline execution.
+Each of the `domain_annotation/` subfolders (e.g., `pfam`, `funfam`, `nmpfams`, `metagroot`) contain a `.domtbl.gz` annotation file per input sample, depending on which domain annotation databases were used in the pipeline execution.
 
-[hmmer](https://github.com/EddyRivasLab/hmmer) is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.
+[hmmer](https://github.com/EddyRivasLab/hmmer) (HMMER) is a sequence search tool that uses profile hidden Markov models (profile HMMs) to identify homologous sequences against curated databases such as Pfam, FunFam, NMPFams and metagRoot.
 
 ### Functional annotation
 
@@ -108,7 +114,7 @@ Each of the `domain_annotation/` subfolders (e.g., `pfam`, `funfam`) contain a `
 - `functional_annotation/`
   - `interproscan/`
     - `<samplename>/`
-      - `<samplename>.gff`: general feature format (GFF) file
+      - `<samplename>.gff3`: general feature format (GFF) file
       - `<samplename>.json`: javascript object notation (JSON) file
       - `<samplename>.tsv`: tab-separated variable (TSV) file
       - `<samplename>.xml`: eXtensible markup language (XML) file
@@ -383,18 +389,6 @@ The `s4pred` module is used to predict secondary structures of amino acid sequen
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
-### SeqKit stats
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `seqkit/`
-  - `{prefix}.tsv`: output of `seqkit stats` command on `{prefix}.fasta` input file, in tab-delimited text format.
-
-</details>
-
-[SeqKit stats](https://bioinf.shenwei.me/seqkit/usage/#stats) generates simple statistics for protein FASTA files, such as number of residues, minimal sequence length, average sequence length, and maximal sequence length.
-
 ### Pipeline information
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index 3ac3aa4..15daf94 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -6,11 +6,13 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
+**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics and generates sequence-level annotations for amino acid sequences.
+It takes a protein FASTA file as input and performs conserved domain annotation (using Pfam, FunFam, NMPFams and metagRoot HMM databases), functional annotation (using InterProScan), and secondary structure prediction (using s4pred).
+Optionally, paths to pre-downloaded databases can be provided to skip the automatic download steps and speed up repeated runs.
 
 ## Samplesheet input
 
-You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 2 columns, and a header row as shown in the examples below.
 
 ```bash
 --input '[path to samplesheet file]'
@@ -58,7 +60,7 @@ 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:
 
@@ -82,9 +84,8 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
 
 [InterProScan](https://github.com/ebi-pf-team/interproscan) is used to provide more information about the proteins annotated on the contigs. By default, turning on this subworkflow without `--skip_interproscan` will download and unzip the InterPro database. The database will then be saved in the output directory `<output_directory>/downloaded_dbs/interproscan_db/`. We recommend keeping a copy of this directory for future reuse in case the results folder is deleted.
 
-:::note
-The large database download (5.5GB) can take up to 4 hours depending on the bandwidth.
-:::
+> [!NOTE]
+> The large database download (5.5GB) can take up to 4 hours depending on the bandwidth.
 
 A local version of the database can be supplied to the pipeline by passing the InterProScan database directory to `--interproscan_db <path/to/downloaded-untarred-interproscan_db-dir/>`. The directory can be created by running (e.g. for database version 5.72-103.0):
 
@@ -199,19 +200,19 @@ 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 98d7d67..a676182 100644
--- a/main.nf
+++ b/main.nf
@@ -39,6 +39,10 @@ workflow NFCORE_PROTEINANNOTATOR {
     //
     PROTEINANNOTATOR (
         samplesheet,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
         params.skip_preprocessing,
         params.skip_pfam,
         params.pfam_db,
@@ -46,6 +50,12 @@ workflow NFCORE_PROTEINANNOTATOR {
         params.skip_funfam,
         params.funfam_db,
         params.funfam_latest_link,
+        params.skip_nmpfams,
+        params.nmpfams_db,
+        params.nmpfams_latest_link,
+        params.skip_metagroot,
+        params.metagroot_db,
+        params.metagroot_latest_link,
         params.skip_interproscan,
         params.interproscan_db_url,
         params.interproscan_db,
@@ -93,7 +103,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         NFCORE_PROTEINANNOTATOR.out.multiqc_report
     )
 }
diff --git a/modules.json b/modules.json
index 37ba5b8..64dec58 100644
--- a/modules.json
+++ b/modules.json
@@ -7,57 +7,52 @@
                 "nf-core": {
                     "aria2": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "a971f6723149313787b278969dcbe0fb4411bb4a",
                         "installed_by": ["modules"]
                     },
                     "interproscan": {
                         "branch": "master",
-                        "git_sha": "50ab4e0a9616556589152fef559b50a6e86c326b",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     },
                     "s4pred/runmodel": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "seqfu/stats": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/replace": {
                         "branch": "master",
-                        "git_sha": "2eccc519c7d25e24c8ef2a5a94062630b8383daf",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/rmdup": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
                     "seqkit/seq": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["faa_seqfu_seqkit"]
                     },
-                    "seqkit/stats": {
-                        "branch": "master",
-                        "git_sha": "28935b89b7e1f19e835f8c6e4c8322d4b505dded",
-                        "installed_by": ["modules"]
-                    },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     }
                 }
@@ -66,22 +61,22 @@
                 "nf-core": {
                     "faa_seqfu_seqkit": {
                         "branch": "master",
-                        "git_sha": "2eccc519c7d25e24c8ef2a5a94062630b8383daf",
+                        "git_sha": "bf70cbf44b42ff4a81afcb673fcef604f5ef3a85",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "65f5e638d901a51534c68fd5c1c19e8112fb4df1",
+                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
+                        "git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/aria2/environment.yml b/modules/nf-core/aria2/environment.yml
index 4536048..77fb37b 100644
--- a/modules/nf-core/aria2/environment.yml
+++ b/modules/nf-core/aria2/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::aria2=1.36.0
+  - conda-forge::aria2=1.37.0
diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf
index f3ec399..889fc35 100644
--- a/modules/nf-core/aria2/main.nf
+++ b/modules/nf-core/aria2/main.nf
@@ -3,16 +3,16 @@ process ARIA2 {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/aria2:1.36.0' :
-        'biocontainers/aria2:1.36.0' }"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/95/95c0d3d867f5bc805b926b08ee761a993b24062739743eb82cc56363e0f7817d/data' :
+        'community.wave.seqera.io/library/aria2:1.37.0--3a9ec328469995dd' }"
 
     input:
     tuple val(meta), val(source_url)
 
     output:
     tuple val(meta), path("$downloaded_file"), emit: downloaded_file
-    path "versions.yml"                      , emit: versions
+    tuple val("${task.process}"), val("aria2"), eval("aria2c --version 2>&1 | sed -n 's/^aria2 version \\([^ ]*\\).*/\\1/p'"), emit: versions_aria2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,22 +26,15 @@ process ARIA2 {
         --check-certificate=false \\
         ${args} \\
         ${source_url}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ')
-    END_VERSIONS
     """
 
     stub:
+    def args = task.ext.args ?: ''
     downloaded_file = source_url.split("/")[-1]
 
     """
-    touch ${downloaded_file}
+    echo ${args}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ')
-    END_VERSIONS
+    touch ${downloaded_file}
     """
 }
diff --git a/modules/nf-core/aria2/meta.yml b/modules/nf-core/aria2/meta.yml
index 9dc7289..87f6c50 100644
--- a/modules/nf-core/aria2/meta.yml
+++ b/modules/nf-core/aria2/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "aria2"
 description: CLI Download utility
 keywords:
@@ -13,7 +12,8 @@ tools:
       homepage: "https://aria2.github.io/"
       documentation: "https://aria2.github.io/manual/en/html/index.html"
       tool_dev_url: "https://github.com/aria2/aria2/"
-      licence: ["GPL v2"]
+      licence:
+        - "GPL v2"
       identifier: ""
 input:
   - - meta:
@@ -39,13 +39,27 @@ output:
           description: Downloaded file from source
           pattern: "*.*"
           ontologies: []
+  versions_aria2:
+    - - ${task.process}:
+          type: string
+          description: Process name
+      - aria2:
+          type: string
+          description: Tool name
+      - aria2c --version 2>&1 | sed -n 's/^aria2 version \([^ ]*\).*/\1/p':
+          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: Process name
+      - aria2:
+          type: string
+          description: Tool name
+      - aria2c --version 2>&1 | sed -n 's/^aria2 version \([^ ]*\).*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@JoseEspinosa"
   - "@leoisl"
diff --git a/modules/nf-core/aria2/tests/main.nf.test b/modules/nf-core/aria2/tests/main.nf.test
index ba03351..641b136 100644
--- a/modules/nf-core/aria2/tests/main.nf.test
+++ b/modules/nf-core/aria2/tests/main.nf.test
@@ -10,16 +10,17 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test' ], // meta map
-                             params.test_data['sarscov2']['illumina']['test_single_end_bam']  // https URL
-                           ]
+                input[0] = [
+                    [ id:'test' ],
+                    params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam'
+                ]
                 """
             }
         }
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -29,16 +30,17 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test' ], // meta map
-                             params.test_data['sarscov2']['illumina']['test_single_end_bam']  // https URL
-                           ]
+                input[0] = [
+                    [ id:'test' ],
+                    params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam'
+                ]
                 """
             }
         }
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/aria2/tests/main.nf.test.snap b/modules/nf-core/aria2/tests/main.nf.test.snap
index 96911f6..137c207 100644
--- a/modules/nf-core/aria2/tests/main.nf.test.snap
+++ b/modules/nf-core/aria2/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 Illumina single end [bam] - stub": {
         "content": [
             {
-                "0": [
+                "downloaded_file": [
                     [
                         {
                             "id": "test"
@@ -10,28 +10,25 @@
                         "test.single_end.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,1d3d763f0ff390b632205a498112b076"
-                ],
-                "downloaded_file": [
+                "versions_aria2": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.single_end.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "ARIA2",
+                        "aria2",
+                        "1.37.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,1d3d763f0ff390b632205a498112b076"
                 ]
             }
         ],
-        "timestamp": "2023-12-14T17:34:30.569759"
+        "timestamp": "2026-03-11T13:35:36.793301",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2 Illumina single end [bam]": {
         "content": [
             {
-                "0": [
+                "downloaded_file": [
                     [
                         {
                             "id": "test"
@@ -39,22 +36,19 @@
                         "test.single_end.bam:md5,21afed4c3e007de5e007cc5cbaebede7"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,1d3d763f0ff390b632205a498112b076"
-                ],
-                "downloaded_file": [
+                "versions_aria2": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.single_end.bam:md5,21afed4c3e007de5e007cc5cbaebede7"
+                        "ARIA2",
+                        "aria2",
+                        "1.37.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,1d3d763f0ff390b632205a498112b076"
                 ]
             }
         ],
-        "timestamp": "2023-12-14T17:34:22.216677"
+        "timestamp": "2026-03-11T11:59:51.569292",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf
index 603a865..1ac7640 100644
--- a/modules/nf-core/hmmer/hmmsearch/main.nf
+++ b/modules/nf-core/hmmer/hmmsearch/main.nf
@@ -3,9 +3,9 @@ process HMMER_HMMSEARCH {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmmer:3.4--hdbdd923_1' :
-        'biocontainers/hmmer:3.4--hdbdd923_1' }"
+        'quay.io/biocontainers/hmmer:3.4--hdbdd923_1' }"
 
     input:
     tuple val(meta), path(hmmfile), path(seqdb), val(write_align), val(write_target), val(write_domain)
@@ -15,7 +15,7 @@ process HMMER_HMMSEARCH {
     tuple val(meta), path('*.sto.gz')   , emit: alignments    , optional: true
     tuple val(meta), path('*.tbl.gz')   , emit: target_summary, optional: true
     tuple val(meta), path('*.domtbl.gz'), emit: domain_summary, optional: true
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('hmmer'), eval("hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'"), emit: versions_hmmer, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,11 +42,6 @@ process HMMER_HMMSEARCH {
         ${write_align ? '*.sto' : ''} \\
         ${write_target ? '*.tbl' : ''} \\
         ${write_domain ? '*.domtbl' : ''}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmmer: \$(hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
-    END_VERSIONS
     """
 
     stub:
@@ -61,10 +56,5 @@ process HMMER_HMMSEARCH {
         ${write_align ? '*.sto' : ''} \\
         ${write_target ? '*.tbl' : ''} \\
         ${write_domain ? '*.domtbl' : ''}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmmer: \$(hmmsearch -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/hmmer/hmmsearch/meta.yml b/modules/nf-core/hmmer/hmmsearch/meta.yml
index 97daa54..0bfc5ca 100644
--- a/modules/nf-core/hmmer/hmmsearch/meta.yml
+++ b/modules/nf-core/hmmer/hmmsearch/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: hmmer_hmmsearch
 description: search profile(s) against a sequence database
 keywords:
@@ -12,7 +13,8 @@ tools:
       documentation: http://hmmer.org/documentation.html
       tool_dev_url: https://github.com/EddyRivasLab/hmmer
       doi: "10.1371/journal.pcbi.1002195"
-      licence: ["BSD"]
+      licence:
+        - "BSD"
       identifier: ""
 input:
   - - meta:
@@ -32,16 +34,16 @@ input:
         ontologies: []
     - write_align:
         type: boolean
-        description: Flag to save optional alignment output. Specify with 'true' to
-          save.
+        description: Flag to save optional alignment output. Specify with 'true'
+          to save.
     - write_target:
         type: boolean
-        description: Flag to save optional per target summary. Specify with 'true' to
-          save.
+        description: Flag to save optional per target summary. Specify with 'true'
+          to save.
     - write_domain:
         type: boolean
-        description: Flag to save optional per domain summary. Specify with 'true' to
-          save.
+        description: Flag to save optional per domain summary. Specify with 'true'
+          to save.
 output:
   output:
     - - meta:
@@ -62,7 +64,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.sto.gz":
           type: file
-          description: Optional multiple sequence alignment (MSA) in Stockholm format
+          description: Optional multiple sequence alignment (MSA) in Stockholm
+            format
           pattern: "*.{sto.gz}"
           ontologies: []
   target_summary:
@@ -73,7 +76,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.tbl.gz":
           type: file
-          description: Optional tabular (space-delimited) summary of per-target output
+          description: Optional tabular (space-delimited) summary of per-target
+            output
           pattern: "*.{tbl.gz}"
           ontologies: []
   domain_summary:
@@ -84,16 +88,31 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.domtbl.gz":
           type: file
-          description: Optional tabular (space-delimited) summary of per-domain output
+          description: Optional tabular (space-delimited) summary of per-domain
+            output
           pattern: "*.{domtbl.gz}"
           ontologies: []
+  versions_hmmer:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hmmer:
+          type: string
+          description: The name of the tool
+      - hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//':
+          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 name of the process
+      - hmmer:
+          type: string
+          description: The name of the tool
+      - hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@Midnighter"
 maintainers:
diff --git a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test
index f1b59e9..14d0a7e 100644
--- a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test
+++ b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.output[0][1]).linesGzip.toString().contains('[ok]') },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
             )
         }
 
@@ -60,7 +60,7 @@ nextflow_process {
                 { assert path(process.out.target_summary.get(0).get(1)).linesGzip.toString().contains('[ok]') },
                 { assert snapshot(
                     process.out.alignments +
-                    process.out.versions
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
diff --git a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap
index e6b2277..a789c38 100644
--- a/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap
+++ b/modules/nf-core/hmmer/hmmsearch/tests/main.nf.test.snap
@@ -1,15 +1,21 @@
 {
     "hmmer/hmmsearch": {
         "content": [
-            [
-                "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f"
-            ]
+            {
+                "versions_hmmer": [
+                    [
+                        "HMMER_HMMSEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-05-07T12:11:28.12628",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-28T12:18:47.293093635"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "hmmer/hmmsearch - stub": {
         "content": [
@@ -33,7 +39,11 @@
                     
                 ],
                 "4": [
-                    "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f"
+                    [
+                        "HMMER_HMMSEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
                 ],
                 "alignments": [
                     
@@ -53,16 +63,20 @@
                 "target_summary": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f"
+                "versions_hmmer": [
+                    [
+                        "HMMER_HMMSEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-07T12:11:36.304424",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-28T12:18:57.862047944"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "hmmer/hmmsearch - optional - stub": {
         "content": [
@@ -104,7 +118,11 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f"
+                    [
+                        "HMMER_HMMSEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
                 ],
                 "alignments": [
                     [
@@ -142,16 +160,20 @@
                         "test.tbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f"
+                "versions_hmmer": [
+                    [
+                        "HMMER_HMMSEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-07T12:11:40.288705",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-28T12:19:03.49192788"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "hmmer/hmmsearch - optional": {
         "content": [
@@ -163,13 +185,21 @@
                     },
                     "test.sto.gz:md5,5c44c289b9e36aa1f7f3afae2005fbb7"
                 ],
-                "versions.yml:md5,37393b1da5a14113d3290ab8b3b4c40f"
+                {
+                    "versions_hmmer": [
+                        [
+                            "HMMER_HMMSEARCH",
+                            "hmmer",
+                            "3.4"
+                        ]
+                    ]
+                }
             ]
         ],
+        "timestamp": "2026-05-07T12:11:32.272907",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-28T12:18:52.725638562"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/interproscan/main.nf b/modules/nf-core/interproscan/main.nf
index a1779f3..0afeb91 100644
--- a/modules/nf-core/interproscan/main.nf
+++ b/modules/nf-core/interproscan/main.nf
@@ -4,9 +4,9 @@ process INTERPROSCAN {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/interproscan:5.59_91.0--hec16e2b_1' :
-        'biocontainers/interproscan:5.59_91.0--hec16e2b_1' }"
+        'quay.io/biocontainers/interproscan:5.59_91.0--hec16e2b_1' }"
 
     input:
     tuple val(meta), path(fasta)
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 0000000..7619030
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
@@ -0,0 +1,1552 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/kaleido-core-0.2.1-h3644ca4_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.1.0-hdb68285_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-5_h4a7cf45_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.2-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.55-h421ea60_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-hf4e2dac_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py314h67df5f8_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/mathjax-2.7.7-ha770c72_3.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/nspr-4.38-h29cc59b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/nss-3.118-h445c969_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.1.1-py314h8ec4b1a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.39.3-pyh58ad624_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.39.3-py310hffdcd12_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-compat-1.39.3-py310hbcd5346_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py314h2e6c369_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pyyaml-6.0.3-py314h67df5f8_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.2.28-py314h5bd0f2a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.30.0-py314h2e6c369_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.52.0-h04a0ce9_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/tiktoken-0.12.0-py314h67fec18_3.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda
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+md5: 30cd29cb87d819caead4d55184c1d115
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 24194
+timestamp: 1764460141901
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda
+sha256: ea4e50c465d70236408cb0bfe0115609fd14db1adcd8bd30d8918e0291f8a75f
+md5: 2aadb0d17215603a82a2a6b0afd9a4cb
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+- __glibc >=2.17,<3.0.a0
+- libgcc >=14
+- libstdcxx >=14
+license: Zlib
+license_family: Other
+size: 122618
+timestamp: 1770167931827
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
+md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
+depends:
+- __glibc >=2.17,<3.0.a0
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 601375
+timestamp: 1764777111296
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 0000000..a55a4d4
--- /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
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
new file mode 100644
index 0000000..a58231a
--- /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 0000000..f787dbe
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
@@ -0,0 +1,125 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-aarch64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958
+https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6
+https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1
+https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc
+https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f
+https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.5-hfae3067_0.conda#05d1e0b30acd816a192c03dc6e164f4d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda#2f364feefb6a7c00423e80dcb12db62a
+https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda#76298a9e6d71ee6e832a8d0d7373b261
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+https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5
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+https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552
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+https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171
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+https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c
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+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
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+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 009874d..37e7612 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.33
+  - bioconda::multiqc=1.34
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 3b0e975..e80e8cd 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,25 +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/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' :
-        'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
+        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
 
     input:
-    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 "*.html"      , emit: report
-    path "*_data"      , emit: data
-    path "*_plots"     , optional:true, emit: plots
-    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
+    tuple val(meta), path("*.html"), emit: report
+    tuple val(meta), path("*_data"), emit: data
+    tuple val(meta), path("*_plots"), emit: plots, optional: true
     // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,8 +23,7 @@ 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}" : ''
@@ -38,7 +33,6 @@ process MULTIQC {
         ${args} \\
         ${config} \\
         ${prefix} \\
-        ${extra_config} \\
         ${logo} \\
         ${replace} \\
         ${samples} \\
@@ -50,6 +44,7 @@ process MULTIQC {
     mkdir multiqc_data
     touch multiqc_data/.stub
     mkdir multiqc_plots
+    touch multiqc_plots/.stub
     touch multiqc_report.html
     """
 }
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 861cd7f..2facc62 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
@@ -12,67 +12,81 @@ 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:
-    - "*.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: ".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: Plots created by MultiQC
-        pattern: "*_data"
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+    - 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
+    - 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
+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
@@ -96,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
     linux/arm64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
   docker:
     linux/amd64:
-      build_id: bd-ee7739d47738383b_1
-      name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b
-      scanId: sc-6ddec592dcadd583_4
+      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
+      build_id: bd-db7c73dae76bc9e6_1
+      scan_id: sc-66fc7138dbf1cf48_1
     linux/arm64:
-      build_id: bd-58d7dee710ab3aa8_1
-      name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8
-      scanId: sc-a04c42273e34c55c_2
+      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
+      build_id: bd-d167b8012595a136_1
+      scan_id: sc-ac701dfa631a2af9_1
   singularity:
     linux/amd64:
-      build_id: bd-e3576ddf588fa00d_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
+      build_id: bd-4fc8657c816047c0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
     linux/arm64:
-      build_id: bd-2537ca5f8445e3c2_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
+      build_id: bd-7fbd82d945c06726_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index d1ae8b0..4cbdb95 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -15,25 +15,41 @@ 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.findAll { key, val -> key.startsWith("versions")}).match() }
-            )
+            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") {
@@ -42,24 +58,41 @@ 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] ==~ ".*/custom_prefix.html" },
-                { assert process.out.data[0] ==~ ".*/custom_prefix_data" }
-            )
+            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]") {
@@ -67,23 +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.findAll { key, val -> key.startsWith("versions")}).match() }
-            )
+            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()
         }
     }
 
@@ -94,25 +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.findAll { key, val -> key.startsWith("versions")} ).match() }
+                { 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 d72d35b..7c2f370 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,61 +1,422 @@
 {
+    "sarscov2 single-end [fastqc] [multiple configs]": {
+        "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": "2026-03-17T16:15:42.577775492",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
     "sarscov2 single-end [fastqc]": {
         "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": "multiqc_report.html",
                 "versions": [
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-03-17T16:21:17.072841555",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-09T10:10:43.020315838"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2 single-end [fastqc] - stub": {
         "content": [
-            [
-                "multiqc_report.html",
-                "multiqc_data",
-                "multiqc_plots",
-                {
-                    "versions": [
+            {
+                "data": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        [
+                            ".stub:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
                         [
-                            "MULTIQC",
-                            "multiqc",
-                            "1.33"
+                            ".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": "25.10.2"
-        },
-        "timestamp": "2025-12-09T10:11:14.131950776"
+            "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",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
         ],
+        "timestamp": "2026-03-17T16:15:18.189023981",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-09T10:11:07.15692209"
+            "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 c537a6a..374dfef 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/modules/nf-core/s4pred/runmodel/main.nf b/modules/nf-core/s4pred/runmodel/main.nf
index d96ea5b..697f24a 100644
--- a/modules/nf-core/s4pred/runmodel/main.nf
+++ b/modules/nf-core/s4pred/runmodel/main.nf
@@ -3,9 +3,9 @@ process S4PRED_RUNMODEL {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/s4pred:1.2.1--pyhdfd78af_1':
-        'biocontainers/s4pred:1.2.1--pyhdfd78af_1' }"
+        'quay.io/biocontainers/s4pred:1.2.1--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf
index ced2451..5872e04 100644
--- a/modules/nf-core/seqfu/stats/main.nf
+++ b/modules/nf-core/seqfu/stats/main.nf
@@ -1,20 +1,20 @@
 process SEQFU_STATS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hfd12232_2':
-        'biocontainers/seqfu:1.22.3--hfd12232_2' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hfd12232_2'
+        : 'quay.io/biocontainers/seqfu:1.22.3--hfd12232_2'}"
 
     input:
     // stats can get one or more fasta or fastq files
     tuple val(meta), path(files)
 
     output:
-    tuple val(meta), path("*.tsv")    , emit: stats
+    tuple val(meta), path("*.tsv"), emit: stats
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('seqfu'), eval('seqfu version'), emit: versions_seqfu, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,28 +25,18 @@ process SEQFU_STATS {
     """
     seqfu \\
         stats \\
-        $args \\
+        ${args} \\
         --multiqc ${prefix}_mqc.txt \\
-        $files > ${prefix}.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqfu: \$(seqfu version)
-    END_VERSIONS
+        ${files} > ${prefix}.tsv
     """
 
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    echo $args
+    echo ${args}
 
     touch ${prefix}.tsv
     touch ${prefix}_mqc.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqfu: \$(seqfu version)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml
index 573498c..856e6f7 100644
--- a/modules/nf-core/seqfu/stats/meta.yml
+++ b/modules/nf-core/seqfu/stats/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "seqfu_stats"
 description: Statistics for FASTA or FASTQ files
 keywords:
@@ -13,11 +12,10 @@ tools:
       documentation: "https://telatin.github.io/seqfu2/"
       tool_dev_url: "https://github.com/telatin/seqfu2"
       doi: "10.3390/bioengineering8050059"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:seqfu
-
 input:
-  # Only when we have meta
   - - meta:
         type: map
         description: |
@@ -28,9 +26,8 @@ input:
         description: One or more FASTA or FASTQ files
         pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}"
         ontologies:
-          - edam: http://edamontology.org/format_1930 # FASTQ
+          - edam: http://edamontology.org/format_1930
 output:
-  #Only when we have meta
   stats:
     - - meta:
           type: map
@@ -42,7 +39,7 @@ output:
           description: Tab-separated output file with basic sequence statistics.
           pattern: "*.{tsv}"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
   multiqc:
     - - meta:
           type: map
@@ -54,13 +51,27 @@ output:
           description: MultiQC ready table
           pattern: "*.{_mqc.txt}"
           ontologies: []
+  versions_seqfu:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqfu:
+          type: string
+          description: The name of the tool
+      - seqfu version:
+          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 name of the process
+      - seqfu:
+          type: string
+          description: The name of the tool
+      - seqfu version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@telatin"
 maintainers:
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test b/modules/nf-core/seqfu/stats/tests/main.nf.test
index 3d13b05..c52781c 100644
--- a/modules/nf-core/seqfu/stats/tests/main.nf.test
+++ b/modules/nf-core/seqfu/stats/tests/main.nf.test
@@ -9,8 +9,8 @@ nextflow_process {
     tag "seqfu"
     tag "seqfu/stats"
 
+    // test with 1 FAA file (with  multiple sequences of different length)
     test("seqfu stats - faa") {
-        // test with 1 FAA file (with  multiple sequences of different length)
         when {
             process {
                 """
@@ -25,26 +25,25 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
+    // test feeding a mix of files including compressed
     test("seqfu stats - multiple files") {
-        // test feeding a mix of files including compressed
         when {
             process {
                 """
                 input[0] = [
-                            [ id:'test_multiple' ],
-                            [
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
-                            ]
-                        ]
+                    [ id:'test_multiple' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                ]
                 """
             }
         }
@@ -52,10 +51,9 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 
     test("seqfu stats - faa - stub") {
@@ -76,13 +74,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success},
-                { assert snapshot(
-                    process.out,
-                    process.out.versions.collect{ path(it).yaml }
-                ).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
index 30b1699..e6ac1e3 100644
--- a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap
@@ -2,25 +2,6 @@
     "seqfu stats - faa - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ],
                 "multiqc": [
                     [
                         {
@@ -37,46 +18,24 @@
                         "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                "versions_seqfu": [
+                    [
+                        "SEQFU_STATS",
+                        "seqfu",
+                        "1.22.3"
+                    ]
                 ]
-            },
-            [
-                {
-                    "SEQFU_STATS": {
-                        "seqfu": "1.22.3"
-                    }
-                }
-            ]
+            }
         ],
+        "timestamp": "2026-02-20T11:32:51.572529816",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-24T12:51:50.35812127"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "seqfu stats - faa": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ],
                 "multiqc": [
                     [
                         {
@@ -93,39 +52,24 @@
                         "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                "versions_seqfu": [
+                    [
+                        "SEQFU_STATS",
+                        "seqfu",
+                        "1.22.3"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-02-20T11:32:28.645841762",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-24T12:52:03.19664223"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "seqfu stats - multiple files": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test_multiple"
-                        },
-                        "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_multiple"
-                        },
-                        "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
-                ],
                 "multiqc": [
                     [
                         {
@@ -142,15 +86,19 @@
                         "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689"
+                "versions_seqfu": [
+                    [
+                        "SEQFU_STATS",
+                        "seqfu",
+                        "1.22.3"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-02-20T11:32:36.800156393",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-24T12:52:11.315174611"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
index dd03dac..6abbd14 100644
--- a/modules/nf-core/seqkit/replace/main.nf
+++ b/modules/nf-core/seqkit/replace/main.nf
@@ -3,16 +3,16 @@ process SEQKIT_REPLACE {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
-        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
+        : 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(fastx)
 
     output:
     tuple val(meta), path("*.fast*"), emit: fastx
-    tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/seqkit v//'"), emit: versions_seqkit, topic: versions
+    tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/^.*v//'"), emit: versions_seqkit, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml
index 1592787..ed1e818 100644
--- a/modules/nf-core/seqkit/replace/meta.yml
+++ b/modules/nf-core/seqkit/replace/meta.yml
@@ -47,7 +47,7 @@ output:
       - seqkit:
           type: string
           description: The name of the tool
-      - "seqkit version | sed 's/seqkit v//'":
+      - seqkit version | sed 's/^.*v//':
           type: eval
           description: The expression to obtain the version of seqkit
 
@@ -59,7 +59,7 @@ topics:
       - seqkit:
           type: string
           description: The name of the tool
-      - "seqkit version | sed 's/seqkit v//'":
+      - seqkit version | sed 's/^.*v//':
           type: eval
           description: The expression to obtain the version of seqkit
 
diff --git a/modules/nf-core/seqkit/rmdup/main.nf b/modules/nf-core/seqkit/rmdup/main.nf
index 4c83add..22f3b1a 100644
--- a/modules/nf-core/seqkit/rmdup/main.nf
+++ b/modules/nf-core/seqkit/rmdup/main.nf
@@ -4,9 +4,9 @@ process SEQKIT_RMDUP {
     // File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
-        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
+        'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
@@ -14,7 +14,7 @@ process SEQKIT_RMDUP {
     output:
     tuple val(meta), path("${prefix}.${extension}") , emit: fastx
     tuple val(meta), path("*.log")                  , emit: log
-    path "versions.yml"                             , emit: versions
+    tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/^.*v//'"), emit: versions_seqkit, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,11 +37,6 @@ process SEQKIT_RMDUP {
         $fastx \\
         -o ${prefix}.${extension} \\
         2>| >(tee ${prefix}.log >&2)
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$(seqkit version | cut -d' ' -f2)
-    END_VERSIONS
     """
 
     stub:
@@ -57,10 +52,5 @@ process SEQKIT_RMDUP {
     echo \\
         '[INFO] 0 duplicated records removed' \\
         > ${prefix}.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$(seqkit version | cut -d' ' -f2)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/seqkit/rmdup/meta.yml b/modules/nf-core/seqkit/rmdup/meta.yml
index 62baa3a..e8dd3f0 100644
--- a/modules/nf-core/seqkit/rmdup/meta.yml
+++ b/modules/nf-core/seqkit/rmdup/meta.yml
@@ -53,13 +53,27 @@ output:
           description: Log containing information regarding removed duplicates
           pattern: "*.log"
           ontologies: []
+  versions_seqkit:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqkit:
+          type: string
+          description: The name of the tool
+      - seqkit version | sed '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 name of the process
+      - seqkit:
+          type: string
+          description: The name of the tool
+      - seqkit version | sed 's/^.*v//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@GallVp"
 maintainers:
diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
index 4b2858d..764cd09 100644
--- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
@@ -19,7 +19,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -37,16 +41,20 @@
                         "test.log:md5,cf833211befdf890bb6b2a3cd0b91853"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:08:29.041177508",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:12:04.249165"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
@@ -68,7 +76,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -86,16 +98,20 @@
                         "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:08:15.046237092",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:11:57.07272"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-genome_fasta": {
         "content": [
@@ -117,7 +133,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -135,16 +155,20 @@
                         "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:07:53.771340434",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:11:44.13147"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "repeated-fasta": {
         "content": [
@@ -166,7 +190,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -184,16 +212,20 @@
                         "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:08:00.578741348",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:11:48.203975"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-genome_fasta_gz": {
         "content": [
@@ -215,7 +247,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -233,15 +269,19 @@
                         "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_RMDUP",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:08:07.836784907",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:11:52.657459"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/seq/main.nf b/modules/nf-core/seqkit/seq/main.nf
index c3b6cb5..d78040a 100644
--- a/modules/nf-core/seqkit/seq/main.nf
+++ b/modules/nf-core/seqkit/seq/main.nf
@@ -4,16 +4,16 @@ process SEQKIT_SEQ {
     // File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
-        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
+        : 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(fastx)
 
     output:
     tuple val(meta), path("${prefix}.*"), emit: fastx
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/^.*v//'"), emit: versions_seqkit, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -39,11 +39,6 @@ process SEQKIT_SEQ {
         ${fastx} \\
         ${call_gzip} \\
         > ${prefix}.${extension}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$(seqkit version | cut -d' ' -f2)
-    END_VERSIONS
     """
 
     stub:
@@ -58,10 +53,5 @@ process SEQKIT_SEQ {
     }
     """
     touch ${prefix}.${extension}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        seqkit: \$(seqkit version | cut -d' ' -f2)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/seqkit/seq/meta.yml b/modules/nf-core/seqkit/seq/meta.yml
index b1bca11..df93e0c 100644
--- a/modules/nf-core/seqkit/seq/meta.yml
+++ b/modules/nf-core/seqkit/seq/meta.yml
@@ -44,13 +44,27 @@ output:
           pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}"
           ontologies:
             - edam: http://edamontology.org/format_1930 # FASTQ
+  versions_seqkit:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - seqkit:
+          type: string
+          description: The name of the tool
+      - seqkit version | sed '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 name of the process
+      - seqkit:
+          type: string
+          description: The name of the tool
+      - seqkit version | sed 's/^.*v//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@GallVp"
 maintainers:
diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
index 6817193..bbcc995 100644
--- a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -21,16 +25,20 @@
                         "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:09:25.839048434",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:13:34.513457"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
@@ -44,7 +52,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -54,16 +66,20 @@
                         "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:09:12.72324007",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:13:27.316329"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-genome_fasta": {
         "content": [
@@ -77,7 +93,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -87,16 +107,20 @@
                         "test.fasta:md5,483f4a5dfe60171c86ee9b7e6dff908b"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:08:58.152442646",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:13:18.463038"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-genome_fasta_gz": {
         "content": [
@@ -110,7 +134,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ],
                 "fastx": [
                     [
@@ -120,15 +148,19 @@
                         "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
+                "versions_seqkit": [
+                    [
+                        "SEQKIT_SEQ",
+                        "seqkit",
+                        "2.9.0"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-12T13:09:05.344232955",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-01-15T15:13:22.960973"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/stats/environment.yml b/modules/nf-core/seqkit/stats/environment.yml
deleted file mode 100644
index b26fb1e..0000000
--- a/modules/nf-core/seqkit/stats/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf
deleted file mode 100644
index 540aa88..0000000
--- a/modules/nf-core/seqkit/stats/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-process SEQKIT_STATS {
-    tag "${meta.id}"
-    label 'process_low'
-
-    conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
-        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.tsv"), emit: stats
-    tuple val("${task.process}"), val('seqkit'), eval("seqkit version | sed 's/seqkit v//'"), emit: versions_seqkit, topic: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: '--all'
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    seqkit stats \\
-        --tabular \\
-        --threads ${task.cpus} \\
-        ${args} \\
-        ${reads} > '${prefix}.tsv'
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.tsv
-    """
-}
diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml
deleted file mode 100644
index 1d51b05..0000000
--- a/modules/nf-core/seqkit/stats/meta.yml
+++ /dev/null
@@ -1,72 +0,0 @@
-name: "seqkit_stats"
-description: simple statistics of FASTA/Q files
-keywords:
-  - seqkit
-  - fasta
-  - stats
-tools:
-  - "seqkit":
-      description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation,
-        written by Wei Shen.
-      homepage: https://bioinf.shenwei.me/seqkit/usage/
-      documentation: https://bioinf.shenwei.me/seqkit/usage/
-      tool_dev_url: https://github.com/shenwei356/seqkit/
-      doi: "10.1371/journal.pone.0163962"
-      licence: ["MIT"]
-      identifier: biotools:seqkit
-input:
-  - - meta:
-        type: map
-        description: >
-          Groovy Map containing sample information e.g. [ id:'test', single_end:false
-          ]
-    - reads:
-        type: file
-        description: >
-          Either FASTA or FASTQ files.
-        pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]"
-        ontologies:
-          - edam: http://edamontology.org/format_1930 # FASTQ
-output:
-  stats:
-    - - meta:
-          type: map
-          description: >
-            Groovy Map containing sample information e.g. [ id:'test', single_end:false
-            ]
-      - "*.tsv":
-          type: file
-          description: >
-            Tab-separated output file with basic sequence statistics.
-          pattern: "*.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
-  versions_seqkit:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - seqkit:
-          type: string
-          description: The name of the tool
-      - "seqkit version | sed 's/seqkit v//'":
-          type: eval
-          description: The expression to obtain the version of seqkit
-
-topics:
-  versions:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - seqkit:
-          type: string
-          description: The name of the tool
-      - "seqkit version | sed 's/seqkit v//'":
-          type: eval
-          description: The expression to obtain the version of seqkit
-
-authors:
-  - "@Midnighter"
-  - "@heuermh"
-maintainers:
-  - "@Midnighter"
-  - "@heuermh"
diff --git a/modules/nf-core/seqkit/stats/tests/main.nf.test b/modules/nf-core/seqkit/stats/tests/main.nf.test
deleted file mode 100644
index 2cd4eb4..0000000
--- a/modules/nf-core/seqkit/stats/tests/main.nf.test
+++ /dev/null
@@ -1,141 +0,0 @@
-nextflow_process {
-
-    name "Test Process SEQKIT_STATS"
-    script "../main.nf"
-    process "SEQKIT_STATS"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "seqkit"
-    tag "seqkit/stats"
-
-    test("single_end") {
-
-        when {
-            process {
-                """
-                input[0] = [[ id:'test', single_end:true ], // meta map
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("paired_end") {
-
-        when {
-            process {
-                """
-                input[0] = [[ id:'test', single_end:false ], // meta map
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("nanopore") {
-
-        when {
-            process {
-                """
-                input[0] = [[ id:'test', single_end:true ], // meta map
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("genome_fasta") {
-
-        when {
-            process {
-                """
-                input[0] = [[ id:'test', single_end:false ], // meta map
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("transcriptome_fasta") {
-
-        when {
-            process {
-                """
-                input[0] = [[ id:'test', single_end:false ], // meta map
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("single_end - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [[ id:'test', single_end:true ], // meta map
-                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/seqkit/stats/tests/main.nf.test.snap b/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
deleted file mode 100644
index b83e6a6..0000000
--- a/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
+++ /dev/null
@@ -1,260 +0,0 @@
-{
-    "nanopore": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.tsv:md5,14f97a9e0414998854ead651e0e69449"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.tsv:md5,14f97a9e0414998854ead651e0e69449"
-                    ]
-                ],
-                "versions_seqkit": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T13:29:39.937621054"
-    },
-    "genome_fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,82b33df8ec2515560b80c3d0bc64c898"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,82b33df8ec2515560b80c3d0bc64c898"
-                    ]
-                ],
-                "versions_seqkit": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T13:29:45.268086738"
-    },
-    "transcriptome_fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,eef67c2e2f225391836d59d5b0d6c3b7"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,eef67c2e2f225391836d59d5b0d6c3b7"
-                    ]
-                ],
-                "versions_seqkit": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T13:29:50.657274211"
-    },
-    "single_end": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
-                    ]
-                ],
-                "versions_seqkit": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T13:29:29.264287187"
-    },
-    "paired_end": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
-                    ]
-                ],
-                "versions_seqkit": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T13:29:34.665600897"
-    },
-    "single_end - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ],
-                "stats": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions_seqkit": [
-                    [
-                        "SEQKIT_STATS",
-                        "seqkit",
-                        "2.9.0"
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T13:29:55.952952629"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index b9c324d..bf2c056 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -3,7 +3,7 @@ process UNTAR {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
         ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
         : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
diff --git a/nextflow.config b/nextflow.config
index e56f91f..c55ff22 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -25,6 +25,12 @@ params {
     skip_funfam             = false
     funfam_db               = null
     funfam_latest_link      = "https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz"
+    skip_nmpfams            = false
+    nmpfams_db              = null
+    nmpfams_latest_link     = "https://pavlopoulos-lab.org/envofams/databases/hmmer/nmpfamsdb.hmm.gz"
+    skip_metagroot          = false
+    metagroot_db            = null
+    metagroot_latest_link   = "https://pavlopoulos-lab.org/envofams/databases/hmmer/metagroot.hmm.gz"
     hmmsearch_evalue_cutoff = 0.001
 
     // Functional annotation
@@ -52,7 +58,6 @@ 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
@@ -74,6 +79,10 @@ 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'
 
@@ -285,9 +294,9 @@ manifest {
     description     = """Generation of sequence-level annotations for amino acid sequences"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=25.10.0'
-    version         = '1.0.0'
-    doi             = ''
+    nextflowVersion = '!>=25.10.4'
+    version         = '1.1.0'
+    doi             = '10.5281/zenodo.18547735'
 }
 
 // Nextflow plugins
@@ -299,6 +308,5 @@ 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 b7ad6d8..25cabc4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -141,13 +141,6 @@
                     "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",
@@ -276,6 +269,40 @@
                     "default": "https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz",
                     "description": "CATH hosted link to the latest available (v4_3_0) FunFam HMM database file."
                 },
+                "skip_nmpfams": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-ban",
+                    "description": "Skip the domain annotation with the NMPFams database.",
+                    "help": "Skips the domain annotation of input sequence against a NMPFams database."
+                },
+                "nmpfams_db": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "Path to an already installed NMPFams HMM database.",
+                    "help_text": "If left null and skip_nmpfams is false, the pipeline will start downloading the latest NMPFams HMM library."
+                },
+                "nmpfams_latest_link": {
+                    "type": "string",
+                    "default": "https://pavlopoulos-lab.org/envofams/databases/hmmer/nmpfamsdb.hmm.gz",
+                    "description": "NMPFams hosted link to the latest NMPFams HMM database file."
+                },
+                "skip_metagroot": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-ban",
+                    "description": "Skip the domain annotation with the metagRoot database.",
+                    "help": "Skips the domain annotation of input sequence against a metagRoot database."
+                },
+                "metagroot_db": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "Path to an already installed metagRoot HMM database (.hmm.gz).",
+                    "help_text": "If left null and skip_metagroot is false, the pipeline will start downloading the latest metagRoot HMM library."
+                },
+                "metagroot_latest_link": {
+                    "type": "string",
+                    "default": "https://pavlopoulos-lab.org/envofams/databases/hmmer/metagroot.hmm.gz",
+                    "description": "metagRoot hosted link to the latest available metagRoot HMM database file."
+                },
                 "hmmsearch_evalue_cutoff": {
                     "type": "number",
                     "default": 0.001,
@@ -291,8 +318,7 @@
             "properties": {
                 "skip_interproscan": {
                     "type": "boolean",
-                    "description": "Run InterProScan",
-                    "default": false
+                    "description": "Skip the functional annotation with InterProScan."
                 },
                 "interproscan_db_url": {
                     "type": "string",
@@ -317,7 +343,7 @@
                 },
                 "interproscan_enableprecalc": {
                     "type": "boolean",
-                    "help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `---diasable-precalc`",
+                    "help_text": "This increases the speed of functional annotation with InterProScan by pre-calculating matches found in the UniProtKB, thereby identifying unique matches in the query sequences for faster annotation. By default this is turned off.\n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--disable-precalc`",
                     "description": "Pre-calculates residue mutual matches.",
                     "fa_icon": "fas fa-clock"
                 }
@@ -362,7 +388,6 @@
         {
             "$ref": "#/$defs/domain_annotation_params"
         },
-
         {
             "$ref": "#/$defs/functional_annotation_options"
         },
diff --git a/nf-test.config b/nf-test.config
index 3a1fff5..f7aaeb4 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 8058a02..2362767 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-02-09T10:42:29+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_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/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/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/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\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%A525.10.0-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/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![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/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n<p>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/proteinannotator_metromap_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/proteinannotator_metromap_light.png\">\n  </picture>\n</p>\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/) and [FunFam](https://download.cathdb.info/cath/releases/all-releases/)\n2. Functional annotation:\n   - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\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/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/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/proteinannotator/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/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\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 `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\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": "2026-05-05T11:29:10+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_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/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/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/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\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/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![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/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n<p>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/proteinannotator_metromap_dark.png\">\n    <img alt=\"nf-core/proteinannotator\" src=\"docs/images/proteinannotator_metromap_light.png\">\n  </picture>\n</p>\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n   such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)\n2. Functional annotation:\n   - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\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/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/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/proteinannotator/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/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\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 `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\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": "#aff5d966-2a2a-4cbf-bf15-44cdd5058ceb"
+                    "@id": "#add10720-d931-4d57-b223-4f80652e48ef"
                 }
             ],
             "name": "nf-core/proteinannotator"
@@ -126,13 +126,18 @@
                 "SoftwareSourceCode",
                 "ComputationalWorkflow"
             ],
-            "creator": [
+            "author": [
                 {
                     "@id": "https://orcid.org/0000-0003-4412-7970"
                 }
             ],
+            "contributor": [
+                {
+                    "@id": "https://orcid.org/0000-0002-9052-6000"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2026-02-09T10:42:29Z",
+            "dateModified": "2026-05-05T12:29:10Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -145,7 +150,7 @@
             ],
             "maintainer": [
                 {
-                    "@id": "https://orcid.org/0000-0003-4412-7970"
+                    "@id": "https://orcid.org/0000-0001-9132-8981"
                 }
             ],
             "name": [
@@ -159,10 +164,10 @@
             },
             "url": [
                 "https://github.com/nf-core/proteinannotator",
-                "https://nf-co.re/proteinannotator/1.0.0/"
+                "https://nf-co.re/proteinannotator/1.1.0/"
             ],
             "version": [
-                "1.0.0"
+                "1.1.0"
             ]
         },
         {
@@ -175,14 +180,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.10.0"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "#aff5d966-2a2a-4cbf-bf15-44cdd5058ceb",
+            "@id": "#add10720-d931-4d57-b223-4f80652e48ef",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#5d20d507-f40f-4fcc-854d-5d27a47f2941"
+                    "@id": "#e8ae9185-b672-49e3-bd1b-e3c44f4175a5"
                 }
             ],
             "mainEntity": {
@@ -191,7 +196,7 @@
             "name": "Test suite for nf-core/proteinannotator"
         },
         {
-            "@id": "#5d20d507-f40f-4fcc-854d-5d27a47f2941",
+            "@id": "#e8ae9185-b672-49e3-bd1b-e3c44f4175a5",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/proteinannotator",
             "resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml",
@@ -322,8 +327,26 @@
         {
             "@id": "https://orcid.org/0000-0003-4412-7970",
             "@type": "Person",
-            "email": "olga.botvinnik@gmail.com",
-            "name": "Olga Botvinnik"
+            "affiliation": "Seanome, San Francisco, CA, USA",
+            "email": "olga@seanome.org",
+            "name": "Olga Botvinnik",
+            "url": "https://github.com/olgabot"
+        },
+        {
+            "@id": "https://orcid.org/0000-0002-9052-6000",
+            "@type": "Person",
+            "affiliation": "Network.bio, New York, NY, USA",
+            "email": "heuermh@acm.org",
+            "name": "Michael L Heuer",
+            "url": "https://github.com/heuermh"
+        },
+        {
+            "@id": "https://orcid.org/0000-0001-9132-8981",
+            "@type": "Person",
+            "affiliation": "EMBL-EBI",
+            "email": "vangelis@ebi.ac.uk",
+            "name": "Evangelos Karatzas",
+            "url": "https://github.com/vagkaratzas"
         }
     ]
 }
\ No newline at end of file
diff --git a/subworkflows/local/domain_annotation/main.nf b/subworkflows/local/domain_annotation/main.nf
index 1ec8289..130a237 100644
--- a/subworkflows/local/domain_annotation/main.nf
+++ b/subworkflows/local/domain_annotation/main.nf
@@ -1,30 +1,41 @@
-include { ARIA2 as ARIA2_PFAM                 } from '../../../modules/nf-core/aria2/main'
-include { ARIA2 as ARIA2_FUNFAM               } from '../../../modules/nf-core/aria2/main'
-include { HMMER_HMMSEARCH as HMMSEARCH_PFAM   } from '../../../modules/nf-core/hmmer/hmmsearch/main'
-include { HMMER_HMMSEARCH as HMMSEARCH_FUNFAM } from '../../../modules/nf-core/hmmer/hmmsearch/main'
+include { ARIA2 as ARIA2_PFAM                       } from '../../../modules/nf-core/aria2/main'
+include { ARIA2 as ARIA2_FUNFAM                     } from '../../../modules/nf-core/aria2/main'
+include { ARIA2 as ARIA2_NMPFAMS                    } from '../../../modules/nf-core/aria2/main'
+include { ARIA2 as ARIA2_METAGROOT                  } from '../../../modules/nf-core/aria2/main'
+include { HMMER_HMMSEARCH as HMMSEARCH_PFAM         } from '../../../modules/nf-core/hmmer/hmmsearch/main'
+include { HMMER_HMMSEARCH as HMMSEARCH_FUNFAM       } from '../../../modules/nf-core/hmmer/hmmsearch/main'
+include { HMMER_HMMSEARCH as HMMSEARCH_NMPFAMS      } from '../../../modules/nf-core/hmmer/hmmsearch/main'
+include { HMMER_HMMSEARCH as HMMSEARCH_METAGROOT    } from '../../../modules/nf-core/hmmer/hmmsearch/main'
 
 workflow DOMAIN_ANNOTATION {
     take:
-    ch_fasta            // channel: [ val(meta), [ fasta ] ]
-    skip_pfam           // boolean
-    pfam_db             // string, path to the pfam HMM database, if already exists
-    pfam_latest_link    // string, path to the latest pfam HMM database, to download
-    skip_funfam         // boolean
-    funfam_db           // string, path to the funfam HMM database, if already exists
-    funfam_latest_link  // string, path to the latest funfam HMM database, to download
+    ch_fasta               // channel: [ val(meta), [ fasta ] ]
+    skip_pfam              // boolean
+    pfam_db                // string, path to the pfam HMM database, if already exists
+    pfam_latest_link       // string, path to the latest pfam HMM database, to download
+    skip_funfam            // boolean
+    funfam_db              // string, path to the funfam HMM database, if already exists
+    funfam_latest_link     // string, path to the latest funfam HMM database, to download
+    skip_nmpfams           // boolean
+    nmpfams_db             // string
+    nmpfams_latest_link    // string
+    skip_metagroot         // boolean
+    metagroot_db           // string, path to the metagroot HMM database, if already exists
+    metagroot_latest_link  // string, path to the latest metagroot HMM database, to download
 
     main:
 
-    ch_versions       = channel.empty()
-    ch_pfam_domains   = channel.empty()
-    ch_funfam_domains = channel.empty()
+    ch_versions             = channel.empty()
+    ch_pfam_domains         = channel.empty()
+    ch_funfam_domains       = channel.empty()
+    ch_nmpfams_domains      = channel.empty()
+    ch_metagroot_domains    = channel.empty()
 
     if (!skip_pfam) {
         if (!pfam_db) {
             ch_pfam_link = channel.of([ [ id: 'pfam' ], pfam_latest_link ])
 
             ARIA2_PFAM( ch_pfam_link )
-            ch_versions = ch_versions.mix( ARIA2_PFAM.out.versions )
             ch_pfam_db = ARIA2_PFAM.out.downloaded_file
         } else {
             ch_pfam_db = channel.of([ [ id: 'pfam' ], pfam_db ])
@@ -35,7 +46,6 @@ workflow DOMAIN_ANNOTATION {
             .map{ meta, seqs, _meta2, models -> [meta, models, seqs, false, false, true] }
 
         HMMSEARCH_PFAM( ch_input_for_hmmsearch_pfam )
-        ch_versions = ch_versions.mix( HMMSEARCH_PFAM.out.versions.first() )
         ch_pfam_domains = HMMSEARCH_PFAM.out.domain_summary
     }
 
@@ -44,7 +54,6 @@ workflow DOMAIN_ANNOTATION {
             ch_funfam_link = channel.of([ [ id: 'funfam' ], funfam_latest_link ])
 
             ARIA2_FUNFAM( ch_funfam_link )
-            ch_versions = ch_versions.mix( ARIA2_FUNFAM.out.versions )
             ch_funfam_db = ARIA2_FUNFAM.out.downloaded_file
         } else {
             ch_funfam_db = channel.of([ [ id: 'funfam' ], funfam_db ])
@@ -55,12 +64,49 @@ workflow DOMAIN_ANNOTATION {
             .map{ meta, seqs, _meta2, models -> [meta, models, seqs, false, false, true] }
 
         HMMSEARCH_FUNFAM( ch_input_for_hmmsearch_funfam )
-        ch_versions = ch_versions.mix( HMMSEARCH_FUNFAM.out.versions.first() )
         ch_funfam_domains = HMMSEARCH_FUNFAM.out.domain_summary
     }
 
+    if (!skip_nmpfams) {
+        if (!nmpfams_db) {
+            ch_nmpfams_link = channel.of([ [ id: 'nmpfams' ], nmpfams_latest_link ])
+
+            ARIA2_NMPFAMS( ch_nmpfams_link )
+            ch_nmpfams_db = ARIA2_NMPFAMS.out.downloaded_file
+        } else {
+            ch_nmpfams_db = channel.of([ [ id: 'nmpfams' ], nmpfams_db ])
+        }
+
+        ch_input_for_hmmsearch_nmpfams = ch_fasta
+            .combine(ch_nmpfams_db)
+            .map{ meta, seqs, _meta2, models -> [meta, models, seqs, false, false, true] }
+
+        HMMSEARCH_NMPFAMS( ch_input_for_hmmsearch_nmpfams )
+        ch_nmpfams_domains = HMMSEARCH_NMPFAMS.out.domain_summary
+    }
+
+    if (!skip_metagroot) {
+        if (!metagroot_db) {
+            ch_metagroot_link = channel.of([ [ id: 'metagroot' ], metagroot_latest_link ])
+
+            ARIA2_METAGROOT( ch_metagroot_link )
+            ch_metagroot_db = ARIA2_METAGROOT.out.downloaded_file
+        } else {
+            ch_metagroot_db = channel.of([ [ id: 'metagroot' ], metagroot_db ])
+        }
+
+        ch_input_for_hmmsearch_metagroot = ch_fasta
+            .combine(ch_metagroot_db)
+            .map{ meta, seqs, _meta2, models -> [meta, models, seqs, false, false, true] }
+
+        HMMSEARCH_METAGROOT( ch_input_for_hmmsearch_metagroot )
+        ch_metagroot_domains = HMMSEARCH_METAGROOT.out.domain_summary
+    }
+
     emit:
-    pfam_domains   = ch_pfam_domains
-    funfam_domains = ch_funfam_domains
-    versions       = ch_versions
+    pfam_domains        = ch_pfam_domains
+    funfam_domains      = ch_funfam_domains
+    nmpfams_domains     = ch_nmpfams_domains
+    metagroot_domains   = ch_metagroot_domains
+    versions            = ch_versions
 }
diff --git a/subworkflows/local/domain_annotation/meta.yml b/subworkflows/local/domain_annotation/meta.yml
index e04e241..630237b 100644
--- a/subworkflows/local/domain_annotation/meta.yml
+++ b/subworkflows/local/domain_annotation/meta.yml
@@ -42,6 +42,30 @@ input:
       type: string
       description: |
         Path to the latest FunFam HMM database, to download
+  - skip_nmpfams:
+      type: boolean
+      description: |
+        Skip domain annotation with nmpfamsDB
+  - nmpfams_db:
+      type: string
+      description: |
+        Path to an existing HMM NPMFamDB library on the system. If provided, the ARIA2_nmpfams db download will be skipped.
+  - nmpfams_latest_link:
+      type: string
+      description: |
+        Path to the latest nmpfamsDB HMM database, to download
+  - skip_metagroot:
+      type: boolean
+      description: |
+        Skip domain annotation with metagRoot
+  - metagroot_db:
+      type: string
+      description: |
+        Path to an existing HMM metagRoot library on the system. If provided, the ARIA2_METAGROOT db download will be skipped.
+  - metagroot_latest_link:
+      type: string
+      description: |
+        Path to the latest metagRoot HMM database, to download
 output:
   - pfam_domains:
       type: file
@@ -51,6 +75,14 @@ output:
       type: file
       description: |
         domtbl.gz files with funfam domain annotation for input amino acid sequences
+  - nmpfams_domains:
+      type: file
+      description: |
+        domtbl.gz files with nmpfams domain annotation for input amino acid sequences
+  - metagroot_domains:
+      type: file
+      description: |
+        domtbl.gz files with metagroot domain annotation for input amino acid sequences
   - versions:
       type: file
       description: |
diff --git a/subworkflows/local/domain_annotation/tests/main.nf.test b/subworkflows/local/domain_annotation/tests/main.nf.test
index c713051..0dc2598 100644
--- a/subworkflows/local/domain_annotation/tests/main.nf.test
+++ b/subworkflows/local/domain_annotation/tests/main.nf.test
@@ -19,6 +19,12 @@ nextflow_workflow {
                 input[4] = false                                                                                   // skip_funfam
                 input[5] = null                                                                                    // funfam_db
                 input[6] = params.pipelines_testdata_base_path + '/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz' // funfam_latest_link
+                input[7] = true                                                                                    // skip_nmpfams
+                input[8] = null                                                                                    // nmpfams_db
+                input[9] = params.pipelines_testdata_base_path + '/testdata/nmpfams/nmpfamsdb_test.hmm.gz'         // nmpfams_latest_link
+                input[10] = true                                                                                   // skip_metagroot
+                input[11] = null                                                                                   // metagroot_db
+                input[12] = params.pipelines_testdata_base_path + '/testdata/metagroot/metagroot_test.hmm.gz'      // metagroot_latest_link
                 """
             }
         }
@@ -50,6 +56,12 @@ nextflow_workflow {
                 input[4] = true                                                                                    // skip_funfam
                 input[5] = null                                                                                    // funfam_db
                 input[6] = params.pipelines_testdata_base_path + '/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz' // funfam_latest_link
+                input[7] = true                                                                                    // skip_nmpfams
+                input[8] = null                                                                                    // nmpfams_db
+                input[9] = params.pipelines_testdata_base_path + '/testdata/nmpfams/nmpfamsdb_test.hmm.gz'         // nmpfams_latest_link
+                input[10] = true                                                                                   // skip_metagroot
+                input[11] = null                                                                                   // metagroot_db
+                input[12] = params.pipelines_testdata_base_path + '/testdata/metagroot/metagroot_test.hmm.gz'      // metagroot_latest_link
                 """
             }
         }
@@ -65,6 +77,78 @@ nextflow_workflow {
         }
     }
 
+    test("faa - nmpfams") {
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id: 'test' ],
+                    file(params.pipelines_testdata_base_path + '/testdata/sequences/test_proteins.faa', checkIfExists: true)
+                ])
+                input[1] = true                                                                                    // skip_pfam
+                input[2] = params.pipelines_testdata_base_path + '/testdata/pfam/Pfam-A_test.hmm.gz'               // pfam_db
+                input[3] = params.pipelines_testdata_base_path + '/testdata/pfam/Pfam-A_test.hmm.gz'               // pfam_latest_link
+                input[4] = true                                                                                    // skip_funfam
+                input[5] = null                                                                                    // funfam_db
+                input[6] = params.pipelines_testdata_base_path + '/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz' // funfam_latest_link
+                input[7] = false                                                                                   // skip_nmpfams
+                input[8] = null                                                                                    // nmpfams_db
+                input[9] = params.pipelines_testdata_base_path + '/testdata/nmpfams/nmpfamsdb_test.hmm.gz'         // nmpfams_latest_link
+                input[10] = true                                                                                   // skip_metagroot
+                input[11] = null                                                                                   // metagroot_db
+                input[12] = params.pipelines_testdata_base_path + '/testdata/metagroot/metagroot_test.hmm.gz'      // metagroot_latest_link
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    path(workflow.out.nmpfams_domains[0][1]).linesGzip[0..7],
+                    workflow.out.versions.collect { path(it).yaml }.unique()
+                    ).match()}
+            )
+        }
+    }
+
+    test("faa - metagroot") {
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id: 'test' ],
+                    file(params.pipelines_testdata_base_path + '/testdata/sequences/test_proteins.faa', checkIfExists: true)
+                ])
+                input[1] = true                                                                                    // skip_pfam
+                input[2] = null                                                                                    // pfam_db
+                input[3] = params.pipelines_testdata_base_path + '/testdata/pfam/Pfam-A_test.hmm.gz'               // pfam_latest_link
+                input[4] = true                                                                                    // skip_funfam
+                input[5] = null                                                                                    // funfam_db
+                input[6] = params.pipelines_testdata_base_path + '/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz' // funfam_latest_link
+                input[7] = true                                                                                    // skip_nmpfams
+                input[8] = null                                                                                    // nmpfams_db
+                input[9] = params.pipelines_testdata_base_path + '/testdata/nmpfams/nmpfamsdb_test.hmm.gz'         // nmpfams_latest_link
+                input[10] = false                                                                                  // skip_metagroot
+                input[11] = null                                                                                   // metagroot_db
+                input[12] = params.pipelines_testdata_base_path + '/testdata/metagroot/metagroot_test.hmm.gz'      // metagroot_latest_link
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    path(workflow.out.metagroot_domains[0][1]).linesGzip[0..7],
+                    workflow.out.versions.collect { path(it).yaml }.unique()
+                    ).match()}
+            )
+        }
+    }
+
     test("faa - domain annotation - stub") {
 
         options "-stub"
@@ -82,6 +166,12 @@ nextflow_workflow {
                 input[4] = false                                                                                   // skip_funfam
                 input[5] = null                                                                                    // funfam_db
                 input[6] = params.pipelines_testdata_base_path + '/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz' // funfam_latest_link
+                input[7] = false                                                                                   // skip_nmpfams
+                input[8] = null                                                                                    // nmpfams_db
+                input[9] = params.pipelines_testdata_base_path + '/testdata/nmpfams/nmpfamsdb_test.hmm.gz'         // nmpfams_latest_link
+                input[10] = false                                                                                  // skip_metagroot
+                input[11] = null                                                                                   // metagroot_db
+                input[12] = params.pipelines_testdata_base_path + '/testdata/metagroot/metagroot_test.hmm.gz'      // metagroot_latest_link
                 """
             }
         }
diff --git a/subworkflows/local/domain_annotation/tests/main.nf.test.snap b/subworkflows/local/domain_annotation/tests/main.nf.test.snap
index f1c925c..d5c4ad9 100644
--- a/subworkflows/local/domain_annotation/tests/main.nf.test.snap
+++ b/subworkflows/local/domain_annotation/tests/main.nf.test.snap
@@ -1,4 +1,26 @@
 {
+    "faa - metagroot": {
+        "content": [
+            [
+                "#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord",
+                "# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target",
+                "#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------",
+                "T1024                -            408 F101326              -            425   9.3e-13   34.9  26.2   1   1   1.8e-12   3.6e-12   33.0  26.2    13   351    18   340    12   407 0.74 LmrP, , 408 residues|",
+                "T1024                -            408 F226054              -            421   1.3e-13   37.4  26.4   1   1   8.6e-14   1.7e-13   37.0  26.4     2   404     2   404     1   408 0.73 LmrP, , 408 residues|",
+                "T1024                -            408 F240027              -            384   8.4e-10   25.0   5.2   1   1     8e-10   1.6e-09   24.1   5.2    26   163    26   160     6   178 0.88 LmrP, , 408 residues|",
+                "T1024                -            408 F287588              -            413     2e-10   26.9  23.3   1   1   1.6e-10   3.1e-10   26.3  23.3    48   363    42   370    30   406 0.74 LmrP, , 408 residues|",
+                "T1024                -            408 F294204              -            387   3.8e-06   12.8  25.9   1   1   2.8e-06   5.6e-06   12.3  25.9    16   372    41   406    30   408 0.76 LmrP, , 408 residues|"
+            ],
+            [
+                
+            ]
+        ],
+        "timestamp": "2026-05-07T13:34:53.191301436",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
     "faa - domain annotation": {
         "content": [
             [
@@ -22,33 +44,36 @@
                 "#"
             ],
             [
-                {
-                    "DOMAIN_ANNOTATION:HMMSEARCH_FUNFAM": {
-                        "hmmer": 3.4
-                    }
-                },
-                {
-                    "DOMAIN_ANNOTATION:ARIA2_FUNFAM": {
-                        "aria2": "1.36.0"
-                    }
-                },
-                {
-                    "DOMAIN_ANNOTATION:ARIA2_PFAM": {
-                        "aria2": "1.36.0"
-                    }
-                },
-                {
-                    "DOMAIN_ANNOTATION:HMMSEARCH_PFAM": {
-                        "hmmer": 3.4
-                    }
-                }
+                
             ]
         ],
+        "timestamp": "2026-05-07T13:34:20.834406599",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-05T08:44:26.478981734"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "faa - nmpfams": {
+        "content": [
+            [
+                "#                                                                            --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord",
+                "# target name        accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target",
+                "#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------",
+                "T1026                -            172 F049289              -             90     1e-05   12.9   0.0   1   1   9.8e-06     2e-05   12.0   0.0    34    76    43    85    33    88 0.93 FBNSV, , 172 residues|",
+                "T1024                -            408 F075270              -             57   1.5e-06   15.3   2.4   1   3   0.00095    0.0019    5.3   0.0     6    25    72    91    68    98 0.85 LmrP, , 408 residues|",
+                "T1024                -            408 F075270              -             57   1.5e-06   15.3   2.4   2   3      0.36      0.71   -2.9   0.0    42    49   148   155   135   162 0.68 LmrP, , 408 residues|",
+                "T1024                -            408 F075270              -             57   1.5e-06   15.3   2.4   3   3   0.00017   0.00033    7.8   0.4    10    48   266   304   257   311 0.89 LmrP, , 408 residues|",
+                "T1024                -            408 F093539              -             93   3.1e-05   11.0   0.1   1   4   1.6e-05   3.1e-05   11.0   0.1    57    75    50    68     6    75 0.82 LmrP, , 408 residues|"
+            ],
+            [
+                
+            ]
+        ],
+        "timestamp": "2026-05-07T13:34:41.751903369",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "faa - pfam_db - skip_funfam": {
         "content": [
@@ -63,18 +88,14 @@
                 "#"
             ],
             [
-                {
-                    "DOMAIN_ANNOTATION:HMMSEARCH_PFAM": {
-                        "hmmer": 3.4
-                    }
-                }
+                
             ]
         ],
+        "timestamp": "2026-05-07T13:34:32.093410935",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-05T10:10:22.057426358"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "faa - domain annotation - stub": {
         "content": [
@@ -96,10 +117,23 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,160d4c5a5001cfb4ff57b94fc52b67d9",
-                    "versions.yml:md5,35e41735706132967dd94bb636833a4a",
-                    "versions.yml:md5,a74a0c8fcb741e59bc14424f612b8d09",
-                    "versions.yml:md5,f1d8a406d3dcb97a7c15e9c810926de1"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.domtbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.domtbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
                 ],
                 "funfam_domains": [
                     [
@@ -109,6 +143,22 @@
                         "test.domtbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "metagroot_domains": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.domtbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "nmpfams_domains": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.domtbl.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "pfam_domains": [
                     [
                         {
@@ -118,17 +168,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,160d4c5a5001cfb4ff57b94fc52b67d9",
-                    "versions.yml:md5,35e41735706132967dd94bb636833a4a",
-                    "versions.yml:md5,a74a0c8fcb741e59bc14424f612b8d09",
-                    "versions.yml:md5,f1d8a406d3dcb97a7c15e9c810926de1"
+                    
                 ]
             }
         ],
+        "timestamp": "2026-05-07T13:35:05.627943668",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-05T08:44:37.015452047"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/functional_annotation/main.nf b/subworkflows/local/functional_annotation/main.nf
index 240c504..5bc5086 100644
--- a/subworkflows/local/functional_annotation/main.nf
+++ b/subworkflows/local/functional_annotation/main.nf
@@ -11,7 +11,6 @@ workflow FUNCTIONAL_ANNOTATION {
 
     main:
     ch_interproscan_tsv = channel.empty()
-    ch_versions         = channel.empty()
 
     if (!skip_interproscan) {
         if (interproscan_db) {
@@ -19,7 +18,6 @@ workflow FUNCTIONAL_ANNOTATION {
         }
         else {
             ARIA2( [ [ id:'interproscan_db' ], interproscan_db_url ] )
-            ch_versions = ch_versions.mix(ARIA2.out.versions.first())
 
             UNTAR( ARIA2.out.downloaded_file )
             ch_interproscan_db = UNTAR.out.untar.map{ f -> f[1] }
@@ -31,5 +29,4 @@ workflow FUNCTIONAL_ANNOTATION {
 
     emit:
     interproscan_tsv = ch_interproscan_tsv
-    versions         = ch_versions         // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
new file mode 100644
index 0000000..6871810
--- /dev/null
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -0,0 +1,62 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: functional_annotation
+description: |
+  Performs functional annotation of protein sequences using InterProScan.
+  Optionally downloads and extracts the InterProScan database via ARIA2 and UNTAR,
+  or uses a pre-existing local database. The annotation step can be skipped entirely.
+keywords:
+  - annotation
+  - functional
+  - interproscan
+  - proteins
+  - fasta
+
+components:
+  - aria2
+  - untar
+  - interproscan
+
+input:
+  - ch_fasta:
+      type: file
+      description: |
+        Channel containing FASTA files with protein sequences to annotate.
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.{fa,fasta,faa}"
+  - skip_interproscan:
+      type: boolean
+      description: |
+        If true, the entire InterProScan annotation step is skipped and no
+        output TSV is produced.
+  - interproscan_db_url:
+      type: string
+      description: |
+        URL to download the InterProScan database archive (tar.gz). Used when
+        interproscan_db is not provided and skip_interproscan is false.
+  - interproscan_db:
+      type: string
+      description: |
+        Path to a pre-existing local InterProScan database directory. When
+        provided, the download and extraction steps are skipped.
+
+output:
+  - interproscan_tsv:
+      type: file
+      description: |
+        TSV file containing InterProScan functional annotation results.
+        Optional — only produced when skip_interproscan is false.
+        Structure: [ val(meta), path(tsv) ]
+      pattern: "*.tsv"
+  - versions:
+      type: file
+      description: |
+        File containing software versions for all tools used in the subworkflow.
+        Only populated when skip_interproscan is false (ARIA2 versions collected).
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+
+authors:
+  - "@vagkaratzas"
+  - "@Muskan-2464"
+maintainers:
+  - "@vagkaratzas"
diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
new file mode 100644
index 0000000..8ea5d3d
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -0,0 +1,63 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FUNCTIONAL_ANNOTATION"
+    script "../main.nf"
+    workflow "FUNCTIONAL_ANNOTATION"
+
+    tag "subworkflows"
+    tag "subworkflows_local"
+    tag "functional_annotation"
+
+    test("l_asparaginase - faa - functional annotation") {
+        config "./nextflow.config"
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'proteomics/interproscan/l_arginase.faa', checkIfExists: true)
+                ])
+                input[1] = false
+                input[2] = params.pipelines_testdata_base_path + '/testdata/interproscan/interproscan_test.tar.gz'
+                input[3] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    path(workflow.out.interproscan_tsv[0][1]).readLines()[0]
+                        .contains("GI|225038609|EFDID|719595|FULL	079fff43a0270e432d339ea71b6f0acf	350	SFLD	SFLDS00057	Glutaminase/Asparaginase	17	347	0.0	T")
+                ).match()}
+            )
+        }
+    }
+
+    test("faa - functional annotation - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = channel.of([
+                    [ id:'test_sample' ],
+                    file(params.pipelines_testdata_base_path + '/testdata/sequences/test_proteins.faa', checkIfExists: true)
+                ])
+                input[1] = true
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assertAll(
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test.snap b/subworkflows/local/functional_annotation/tests/main.nf.test.snap
new file mode 100644
index 0000000..87d1994
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test.snap
@@ -0,0 +1,29 @@
+{
+    "l_asparaginase - faa - functional annotation": {
+        "content": [
+            true
+        ],
+        "timestamp": "2026-05-05T11:45:58.77732872",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "faa - functional annotation - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "interproscan_tsv": [
+                    
+                ]
+            }
+        ],
+        "timestamp": "2026-05-05T11:38:15.575589861",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/functional_annotation/tests/nextflow.config b/subworkflows/local/functional_annotation/tests/nextflow.config
new file mode 100644
index 0000000..bc8c773
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+    withName: INTERPROSCAN {
+        ext.args = '--applications Hamap,TIGRFAM,sfld --disable-precalc'
+        memory = 12.GB
+        cpus = 1
+    }
+}
diff --git a/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf b/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf
index 1ba3ccc..542f1bb 100644
--- a/subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_proteinannotator_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'
 
@@ -28,7 +27,7 @@ workflow PIPELINE_INITIALISATION {
     take:
     version           // boolean: Display version and exit
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
-    _monochrome_logs  // boolean: Do not use coloured log outputs
+    monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
     input             //  string: Path to input samplesheet
@@ -53,6 +52,9 @@ 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
@@ -70,6 +72,10 @@ workflow PIPELINE_INITIALISATION {
 * Software dependencies
     https://github.com/nf-core/proteinannotator/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 (
@@ -81,7 +87,8 @@ workflow PIPELINE_INITIALISATION {
         show_hidden,
         before_text,
         after_text,
-        command
+        command,
+        null
     )
 
     //
@@ -122,8 +129,7 @@ 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
+    multiqc_report  //  string: Path to MultiQC report
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
@@ -146,13 +152,11 @@ 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"
     }
 }
 
@@ -180,7 +184,7 @@ def toolCitationText() {
         params.skip_preprocessing ? "" : "Input sequences were preprocessed with SeqKit (gap trimming, length filtering, validation, duplicate removal) (Shen et al. 2024)."
     ].join(' ').trim()
 
-    def domain_annotation_text = (params.skip_pfam && params.skip_funfam) ? "" : "Domains were annotated with hmmer/hmmsearch (Eddy et al. 2011)."
+    def domain_annotation_text = (params.skip_pfam && params.skip_funfam && params.skip_nmpfams && params.skip_metagroot) ? "" : "Domains were annotated with hmmer/hmmsearch (Eddy et al. 2011)."
 
     def prediction_text = params.skip_s4pred ? "" : "Secondary structures were predicted via the s4pred software (Moffat et al. 2021)."
 
@@ -202,7 +206,7 @@ def toolBibliographyText() {
         params.skip_preprocessing ? '' : '<li>Shen, W., Sipos, B., & Zhao, L. (2024). SeqKit2: A Swiss army knife for sequence and alignment processing. Imeta, 3(3), e191. doi: <a href="https://doi.org/10.1002/imt2.191">10.1002/imt2.191</a></li>'
     ].join(' ').trim()
 
-    def domain_annotation_text = (params.skip_pfam && params.skip_funfam) ? '' : '<li>Eddy, S. R. (2011). Accelerated profile HMM searches. PLoS computational biology, 7(10), e1002195. doi: <a href="https://doi.org/10.1371/journal.pcbi.1002195">10.1371/journal.pcbi.1002195</a></li>'
+    def domain_annotation_text = (params.skip_pfam && params.skip_funfam && params.skip_nmpfams && params.skip_metagroot) ? '' : '<li>Eddy, S. R. (2011). Accelerated profile HMM searches. PLoS computational biology, 7(10), e1002195. doi: <a href="https://doi.org/10.1371/journal.pcbi.1002195">10.1371/journal.pcbi.1002195</a></li>'
 
     def prediction_text = params.skip_s4pred ? '' : '<li>Moffat, L., & Jones, D. T. (2021). Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. Bioinformatics, 37(21), 3744-3751. doi: <a href="https://doi.org/10.1093/bioinformatics/btab491">10.1093/bioinformatics/btab491</a></li>'
 
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
index 068e658..bd5b177 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/main.nf
@@ -1,40 +1,33 @@
-include { SEQFU_STATS as SEQFU_STATS_BEFORE } from '../../../modules/nf-core/seqfu/stats/main'
-include { SEQKIT_SEQ                        } from '../../../modules/nf-core/seqkit/seq/main'
-include { SEQKIT_RMDUP                      } from '../../../modules/nf-core/seqkit/rmdup/main'
-include { SEQKIT_REPLACE                    } from '../../../modules/nf-core/seqkit/replace/main'
-include { SEQFU_STATS as SEQFU_STATS_AFTER  } from '../../../modules/nf-core/seqfu/stats/main'
+include { SEQFU_STATS as SEQFU_STATS_AFTER  } from '../../../modules/nf-core/seqfu/stats'
+include { SEQFU_STATS as SEQFU_STATS_BEFORE } from '../../../modules/nf-core/seqfu/stats'
+include { SEQKIT_REPLACE                    } from '../../../modules/nf-core/seqkit/replace'
+include { SEQKIT_RMDUP                      } from '../../../modules/nf-core/seqkit/rmdup'
+include { SEQKIT_SEQ                        } from '../../../modules/nf-core/seqkit/seq'
 
 workflow FAA_SEQFU_SEQKIT {
-
     take:
-    ch_fasta           // tuple val(meta), path(fasta)
+    ch_fasta // tuple val(meta), path(fasta)
     skip_preprocessing // boolean
 
     main:
     ch_multiqc_files = channel.empty()
-    ch_versions      = channel.empty()
 
-    SEQFU_STATS_BEFORE( ch_fasta )
-    ch_multiqc_files = ch_multiqc_files.mix( SEQFU_STATS_BEFORE.out.multiqc )
-    ch_versions      = ch_versions.mix( SEQFU_STATS_BEFORE.out.versions )
+    SEQFU_STATS_BEFORE(ch_fasta)
+    ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS_BEFORE.out.multiqc)
 
     if (!skip_preprocessing) {
-        SEQKIT_SEQ( ch_fasta )
-        ch_versions = ch_versions.mix( SEQKIT_SEQ.out.versions )
+        SEQKIT_SEQ(ch_fasta)
 
-        SEQKIT_REPLACE( SEQKIT_SEQ.out.fastx )
+        SEQKIT_REPLACE(SEQKIT_SEQ.out.fastx)
 
-        SEQKIT_RMDUP( SEQKIT_REPLACE.out.fastx )
-        ch_fasta    = SEQKIT_RMDUP.out.fastx
-        ch_versions = ch_versions.mix( SEQKIT_RMDUP.out.versions )
+        SEQKIT_RMDUP(SEQKIT_REPLACE.out.fastx)
+        ch_fasta = SEQKIT_RMDUP.out.fastx
 
-        SEQFU_STATS_AFTER( SEQKIT_RMDUP.out.fastx )
-        ch_multiqc_files = ch_multiqc_files.mix( SEQFU_STATS_AFTER.out.multiqc )
-        ch_versions      = ch_versions.mix( SEQFU_STATS_AFTER.out.versions )
+        SEQFU_STATS_AFTER(SEQKIT_RMDUP.out.fastx)
+        ch_multiqc_files = ch_multiqc_files.mix(SEQFU_STATS_AFTER.out.multiqc)
     }
 
     emit:
     fasta         = ch_fasta
     multiqc_files = ch_multiqc_files
-    versions      = ch_versions
 }
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test
index 1fb2d9a..7a18903 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success},
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(sanitizeOutput(workflow.out)).match() }
             )
         }
     }
@@ -54,12 +54,8 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(
-                    workflow.out,
-                    workflow.out.versions.collect{ path(it).yaml }.unique()
-                ).match() }
+                { assert snapshot(sanitizeOutput(workflow.out)).match() }
             )
         }
     }
-
 }
diff --git a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
index b3559a3..c09fb56 100644
--- a/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/faa_seqfu_seqkit/tests/main.nf.test.snap
@@ -2,34 +2,6 @@
     "faa - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub_after_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ],
-                    [
-                        {
-                            "id": "test_stub"
-                        },
-                        "test_stub_before_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,4a72093d798cac55be5088015708d471",
-                    "versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
-                    "versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
-                    "versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
-                ],
                 "fasta": [
                     [
                         {
@@ -51,74 +23,18 @@
                         },
                         "test_stub_before_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4a72093d798cac55be5088015708d471",
-                    "versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
-                    "versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
-                    "versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
                 ]
-            },
-            [
-                {
-                    "FAA_SEQFU_SEQKIT:SEQFU_STATS_AFTER": {
-                        "seqfu": "1.22.3"
-                    }
-                },
-                {
-                    "FAA_SEQFU_SEQKIT:SEQKIT_SEQ": {
-                        "seqkit": "v2.9.0"
-                    }
-                },
-                {
-                    "FAA_SEQFU_SEQKIT:SEQFU_STATS_BEFORE": {
-                        "seqfu": "1.22.3"
-                    }
-                },
-                {
-                    "FAA_SEQFU_SEQKIT:SEQKIT_RMDUP": {
-                        "seqkit": "v2.9.0"
-                    }
-                }
-            ]
+            }
         ],
+        "timestamp": "2026-03-12T14:44:03.010426069",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T14:51:50.251419053"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "faa": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa.fasta:md5,242b2a540b013689b51f8814fab92817"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa_after_mqc.txt:md5,e18db7ac9791039ca747e1bb45f73054"
-                    ],
-                    [
-                        {
-                            "id": "test_faa"
-                        },
-                        "test_faa_before_mqc.txt:md5,45fdb76a36d40a331779d7591f523ed9"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,4a72093d798cac55be5088015708d471",
-                    "versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
-                    "versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
-                    "versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
-                ],
                 "fasta": [
                     [
                         {
@@ -140,19 +56,13 @@
                         },
                         "test_faa_before_mqc.txt:md5,45fdb76a36d40a331779d7591f523ed9"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4a72093d798cac55be5088015708d471",
-                    "versions.yml:md5,8412ce0c46c747dbf5a92d26ecc091ad",
-                    "versions.yml:md5,ae6438038b16e6e6e730325116ed2944",
-                    "versions.yml:md5,bca759d787b0ca55b454a6b0aa55f9ee"
                 ]
             }
         ],
+        "timestamp": "2026-03-12T14:43:53.509896933",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-03T14:51:43.056425196"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index d6e593e..37939ac 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -73,11 +73,23 @@ def getWorkflowVersion() {
 def dumpParametersToJSON(outdir) {
     def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
     def filename  = "params_${timestamp}.json"
-    def temp_pf   = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr   = groovy.json.JsonOutput.toJson(params)
+    def temp_pf       = workflow.launchDir.resolve(".${filename}")
+    def jsonGenerator = new groovy.json.JsonGenerator.Options()
+        .excludeNulls()
+        .addConverter(Path) { Path path -> path.toUriString() }
+        .addConverter(Duration) { Duration duration -> duration.toMillis() }
+        .addConverter(MemoryUnit) { MemoryUnit memory -> memory.toBytes() }
+        .addConverter(nextflow.script.types.VersionNumber) { nextflow.script.types.VersionNumber version -> version.toString() }
+        .build()
+    def jsonStr   = jsonGenerator.toJson(params)
     temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
-
-    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    if (outdir instanceof Path) {
+        temp_pf.copyTo(outdir.resolve("pipeline_info/${filename}"))
+    } else if (outdir instanceof String) {
+        temp_pf.copyTo("${outdir}/pipeline_info/params_${timestamp}.json")
+    } else {
+        log.warn("Could not determine type of outdir, parameters JSON file will not be copied to output directory!")
+    }
     temp_pf.delete()
 }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 2f30e9a..afca543 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 0000000..8940d32
--- /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 0000000..859d103
--- /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 1df8b76..0d9d4e0 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     before_text         // string:   text to show before the help message and parameters summary
     after_text          // string:   text to show after the help message and parameters summary
     command             // string:   an example command of the pipeline
+    cli_typecast        // boolean:  whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour
 
     main:
 
@@ -38,7 +39,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
         }
         log.info paramsHelp(
             help_options,
-            (params.help instanceof String && params.help != "true") ? params.help : "",
+            (help instanceof String && help != "true") ? help : "",
         )
         exit 0
     }
@@ -65,6 +66,9 @@ workflow UTILS_NFSCHEMA_PLUGIN {
         if(parameters_schema) {
             validateOptions << [parametersSchema: parameters_schema]
         }
+        if(cli_typecast != null) {
+            validateOptions << [cliTypecast: cli_typecast]
+        }
         validateParameters(validateOptions)
     }
 
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
index f7d9f02..1d8c75a 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -25,6 +25,30 @@ input:
         option. When this input is empty it will automatically use the configured schema or
         "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
         for meta pipelines.
+  - help:
+      type: boolean, string
+      description: |
+        Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message.
+  - help_full:
+      type: boolean
+      description: Show the full help message and exit.
+  - show_hidden:
+      type: boolean
+      description: Show hidden parameters in the help message.
+  - before_text:
+      type: string
+      description: Text to show before the parameters summary and help message.
+  - after_text:
+      type: string
+      description: Text to show after the parameters summary and help message.
+  - command:
+      type: string
+      description: An example command to run the pipeline, to show in the help message and the summary.
+  - cli_typecast:
+      type: boolean
+      description: |
+        Whether to apply typecasting to the parameters given via the CLI before validation.
+        Set this to `null` to use the default behavior.
 output:
   - dummy_emit:
       type: boolean
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index c977917..1fd1eac 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -31,6 +31,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -63,6 +64,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -95,6 +97,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -127,6 +130,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -160,6 +164,7 @@ nextflow_workflow {
                 input[6] = "Before"
                 input[7] = "After"
                 input[8] = "nextflow run test/test"
+                input[9] = null
                 """
             }
         }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index f6537cc..fd71cb8 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@2.6.1"
+    id "nf-schema@2.7.2"
 }
 
 validation {
diff --git a/tests/.nftignore b/tests/.nftignore
index 153205a..6441f81 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -14,6 +14,12 @@ domain_annotation/pfam/l_arginase.domtbl.gz
 domain_annotation/funfam/T1024.domtbl.gz
 domain_annotation/funfam/T1026.domtbl.gz
 domain_annotation/funfam/l_arginase.domtbl.gz
+domain_annotation/nmpfams/T1024.domtbl.gz
+domain_annotation/nmpfams/T1026.domtbl.gz
+domain_annotation/nmpfams/l_arginase.domtbl.gz
+domain_annotation/metagroot/T1024.domtbl.gz
+domain_annotation/metagroot/T1026.domtbl.gz
+domain_annotation/metagroot/l_arginase.domtbl.gz
 functional_annotation/interproscan/T1024/T1024.gff3
 functional_annotation/interproscan/T1024/T1024.tsv
 functional_annotation/interproscan/T1026/T1026.gff3
diff --git a/tests/default.nf.test b/tests/default.nf.test
index b0d55a4..6c508a0 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -16,21 +16,21 @@ 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 ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_proteinannotator_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/default.nf.test.snap b/tests/default.nf.test.snap
index ac75f97..f889235 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,20 +1,32 @@
 {
     "-profile test": {
         "content": [
-            32,
+            40,
             {
                 "ARIA2": {
-                    "aria2": "1.36.0"
+                    "aria2": "1.37.0"
                 },
                 "ARIA2_FUNFAM": {
-                    "aria2": "1.36.0"
+                    "aria2": "1.37.0"
+                },
+                "ARIA2_METAGROOT": {
+                    "aria2": "1.37.0"
+                },
+                "ARIA2_NMPFAMS": {
+                    "aria2": "1.37.0"
                 },
                 "ARIA2_PFAM": {
-                    "aria2": "1.36.0"
+                    "aria2": "1.37.0"
                 },
                 "HMMSEARCH_FUNFAM": {
                     "hmmer": 3.4
                 },
+                "HMMSEARCH_METAGROOT": {
+                    "hmmer": 3.4
+                },
+                "HMMSEARCH_NMPFAMS": {
+                    "hmmer": 3.4
+                },
                 "HMMSEARCH_PFAM": {
                     "hmmer": 3.4
                 },
@@ -34,16 +46,16 @@
                     "seqkit": "2.9.0"
                 },
                 "SEQKIT_RMDUP": {
-                    "seqkit": "v2.9.0"
+                    "seqkit": "2.9.0"
                 },
                 "SEQKIT_SEQ": {
-                    "seqkit": "v2.9.0"
+                    "seqkit": "2.9.0"
                 },
                 "UNTAR": {
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/proteinannotator": "v1.0.0"
+                    "nf-core/proteinannotator": "v1.1.0"
                 }
             },
             [
@@ -52,6 +64,14 @@
                 "domain_annotation/funfam/T1024.domtbl.gz",
                 "domain_annotation/funfam/T1026.domtbl.gz",
                 "domain_annotation/funfam/l_arginase.domtbl.gz",
+                "domain_annotation/metagroot",
+                "domain_annotation/metagroot/T1024.domtbl.gz",
+                "domain_annotation/metagroot/T1026.domtbl.gz",
+                "domain_annotation/metagroot/l_arginase.domtbl.gz",
+                "domain_annotation/nmpfams",
+                "domain_annotation/nmpfams/T1024.domtbl.gz",
+                "domain_annotation/nmpfams/T1026.domtbl.gz",
+                "domain_annotation/nmpfams/l_arginase.domtbl.gz",
                 "domain_annotation/pfam",
                 "domain_annotation/pfam/T1024.domtbl.gz",
                 "domain_annotation/pfam/T1026.domtbl.gz",
@@ -78,6 +98,8 @@
                 "downloaded_dbs/interproscan_db/tigrfam/15.0/TIGRFAMs_15.0_HMM.LIB",
                 "downloaded_dbs/interproscan_db/tigrfam/15.0/TIGRFAMs_HMM.LIB",
                 "downloaded_dbs/interproscan_test.tar.gz",
+                "downloaded_dbs/metagroot_test.hmm.gz",
+                "downloaded_dbs/nmpfamsdb_test.hmm.gz",
                 "functional_annotation",
                 "functional_annotation/interproscan",
                 "functional_annotation/interproscan/T1024",
@@ -182,6 +204,8 @@
                 "TIGRFAMs_15.0_HMM.LIB:md5,64f2b2c9e834b47b17d91bb9a6a0067e",
                 "TIGRFAMs_HMM.LIB:md5,543da3f4b65eed9ec393986c6c6ff0ba",
                 "interproscan_test.tar.gz:md5,cde88c0cd841c84dc1203e64854c762b",
+                "metagroot_test.hmm.gz:md5,d23de95bf39fb6e27ffb266ce61ac98e",
+                "nmpfamsdb_test.hmm.gz:md5,ad7a094618ccfdaeed1c03e93f6abf1e",
                 "T1024.json:md5,0288f7551a14faedc409dd374b3e073e",
                 "T1024.xml:md5,63a3db0eb0e1f76403411602c23b721e",
                 "T1026.json:md5,5c2a40474b1cfb50cd043fe0be5e5d52",
@@ -218,10 +242,10 @@
                 "GI|225038609|EFDID|719595|FULL.ss2:md5,e7d8eaa84d46a6a714ffe00d7f21cdfb"
             ]
         ],
+        "timestamp": "2026-05-05T11:10:57.929189129",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-04T12:43:32.273407057"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index db52597..519bc8e 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -7,7 +7,7 @@
 // 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/proteinannotator'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/proteinannotator/'
 }
 
 aws.client.anonymous = true
diff --git a/workflows/proteinannotator.nf b/workflows/proteinannotator.nf
index fae1d7a..2b7f0b3 100644
--- a/workflows/proteinannotator.nf
+++ b/workflows/proteinannotator.nf
@@ -21,26 +21,34 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_prot
 
 workflow PROTEINANNOTATOR {
     take:
-    ch_samplesheet      // channel: samplesheet read in from --input
-    skip_preprocessing  // boolean
-    skip_pfam           // boolean
-    pfam_db             // string, path to the pfam HMM database, if already exists
-    pfam_latest_link    // string, path to the latest pfam HMM database, to download
-    skip_funfam         // boolean
-    funfam_db           // string, path to the pfam HMM database, if already exists
-    funfam_latest_link  // string, path to the latest pfam HMM database, to download
-    skip_interproscan   // boolean
-    interproscan_db_url // string, url to download db
-    interproscan_db     // string, existing db
-    skip_s4pred         // boolean
+    ch_samplesheet // channel: samplesheet read in from --input
+    multiqc_config
+    multiqc_logo
+    multiqc_methods_description
+    outdir
+    skip_preprocessing      // boolean
+    skip_pfam               // boolean
+    pfam_db                 // string, path to the pfam HMM database, if already exists
+    pfam_latest_link        // string, path to the latest pfam HMM database, to download
+    skip_funfam             // boolean
+    funfam_db               // string, path to the pfam HMM database, if already exists
+    funfam_latest_link      // string, path to the latest pfam HMM database, to download
+    skip_nmpfams            // boolean
+    nmpfams_db              // string
+    nmpfams_latest_link     // string
+    skip_metagroot          // boolean
+    metagroot_db            // string, path to the metagroot HMM database, if already exists
+    metagroot_latest_link   // string, path to the latest metagroot HMM database, to download
+    skip_interproscan       // boolean
+    interproscan_db_url     // string, url to download db
+    interproscan_db         // string, existing db
+    skip_s4pred             // boolean
 
     main:
-
-    ch_versions      = channel.empty()
-    ch_multiqc_files = channel.empty()
+    def ch_versions = channel.empty()
+    def ch_multiqc_files = channel.empty()
 
     FAA_SEQFU_SEQKIT( ch_samplesheet, skip_preprocessing )
-    ch_versions = ch_versions.mix( FAA_SEQFU_SEQKIT.out.versions )
 
     DOMAIN_ANNOTATION (
         FAA_SEQFU_SEQKIT.out.fasta,
@@ -49,7 +57,13 @@ workflow PROTEINANNOTATOR {
         pfam_latest_link,
         skip_funfam,
         funfam_db,
-        funfam_latest_link
+        funfam_latest_link,
+        skip_nmpfams,
+        nmpfams_db,
+        nmpfams_latest_link,
+        skip_metagroot,
+        metagroot_db,
+        metagroot_latest_link
     )
     ch_versions = ch_versions.mix( DOMAIN_ANNOTATION.out.versions )
 
@@ -59,7 +73,6 @@ workflow PROTEINANNOTATOR {
         interproscan_db_url,
         interproscan_db
     )
-    ch_versions = ch_versions.mix( FUNCTIONAL_ANNOTATION.out.versions )
 
     if (!skip_s4pred) {
         S4PRED_RUNMODEL( FAA_SEQFU_SEQKIT.out.fasta )
@@ -86,59 +99,42 @@ workflow PROTEINANNOTATOR {
             "${process}:\n${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: "${params.outdir}/pipeline_info",
-            name: 'nf_core_' + 'proteinannotator_software_' + 'mqc_' + 'versions.yml',
+            storeDir: "${outdir}/pipeline_info",
+            name: 'nf_core_'  +  'proteinannotator_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
-            newLine: 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,
-        )
-    )
-
+    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("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
     ch_multiqc_files = ch_multiqc_files.mix(FAA_SEQFU_SEQKIT.out.multiqc_files.collect{ f -> f[1] }.ifEmpty([]))
-
     MULTIQC(
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList(),
-        [],
-        [],
+        ch_multiqc_files.flatten().collect().map { files ->
+            [
+                [id: 'proteinannotator'],
+                files,
+                multiqc_config
+                    ? file(multiqc_config, checkIfExists: true)
+                    : file("${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
-    versions = ch_versions // channel: [ path(versions.yml) ]
+    emit:multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html
+    versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }