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 3bca66c..0000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,125 +0,0 @@
-# `nf-core/funcprofiler`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving nf-core/funcprofiler.
-
-We try to manage the required tasks for nf-core/funcprofiler 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/funcprofiler then the best place to ask is on the nf-core Slack [#funcprofiler](https://nfcore.slack.com/channels/funcprofiler) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Contribution workflow
-
-If you'd like to write some code for nf-core/funcprofiler, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [nf-core/funcprofiler issues](https://github.com/nf-core/funcprofiler/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/funcprofiler repository](https://github.com/nf-core/funcprofiler) 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/funcprofiler documentation](https://nf-co.re/funcprofiler/usage) and don't hesitate to get in touch on the nf-core Slack [#funcprofiler](https://nfcore.slack.com/channels/funcprofiler) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Pipeline contribution conventions
-
-To make the `nf-core/funcprofiler` 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/funcprofiler/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 f7d3c8b..1b90bf3 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/funcprofiler/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/funcprofiler/tree/main/docs/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/funcprofiler/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/funcprofiler/tree/main/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/funcprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 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: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index bf44d96..ad686e8 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -20,24 +20,24 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,10 +48,12 @@ 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
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
     - name: Run nf-test
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 39b4062..91f761d 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -23,26 +23,45 @@ jobs:
           echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/funcprofiler/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/funcprofiler/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'funcprofiler'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *funcprofiler/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *funcprofiler/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/funcprofiler/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/funcprofiler/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 49116c5..1daec37 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -12,22 +12,22 @@ 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: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/funcprofiler/work-${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/funcprofiler/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/funcprofiler/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/funcprofiler/results-test-${{ github.sha }}"
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index a6d4926..7406ffa 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 ac030fd..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@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - 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 999bcc3..a7bf4fc 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -38,15 +38,18 @@ 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@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -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@dev
+          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@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        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 19f7b8d..aab307a 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -31,30 +31,26 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
-        with:
-          python-version: "3.13"
-
-      - 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'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        if: steps.prek.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
 
       - 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"
@@ -67,21 +63,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a3..7780b2d 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -13,16 +13,16 @@ jobs:
     steps:
       - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+
       - 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: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
@@ -31,13 +31,16 @@ jobs:
         uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # 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 +48,10 @@ 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 +59,7 @@ 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 }}
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc2..e73b0fc 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
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index e4c1a5d..4ae1315 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.4"
   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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -78,13 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.10.4"
+          - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -94,7 +95,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
-          NXF_VER: ${{ matrix.NXF_VER }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 0f73249..78d5dbe 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -14,7 +14,11 @@ jobs:
         run: |
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
-      - uses: rzr/fediverse-action@master
+      - name: get description
+        id: get_description
+        run: |
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
+      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)
@@ -22,7 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
@@ -30,7 +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 beb5c77..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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        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 a56ac51..976250d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,3 +14,4 @@ dontcommit
 tmp/
 .data/
 *.code-workspace
+.lineage/
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 83599f6..0000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
-  - name: Update Nextflow and setup pre-commit
-    command: |
-      pre-commit install --install-hooks
-      nextflow self-update
-
-vscode:
-  extensions:
-    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index 667bd08..24b1ed9 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,18 +1,22 @@
-repository_type: pipeline
-
-nf_core_version: 3.5.2
-
 lint:
   files_unchanged:
     - assets/nf-core-funcprofiler_logo_light.png
     - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/linting.yml
+    - .github/workflows/linting_comment.yml
+    - .gitignore
+  modules:
+    - main_nf_version_topic:
+        - multiqc
+nf_core_version: 4.0.2
+repository_type: pipeline
 
 template:
-  org: nf-core
-  name: funcprofiler
-  description: Read-based functional profiling of microbiome sequencing data
   author: Nick Waters
-  version: 1.0.0dev
-  force: true
-  outdir: .
+  description: Read-based functional profiling of microbiome sequencing data
+  force: false
   is_nfcore: true
+  name: funcprofiler
+  org: nf-core
+  outdir: .
+  version: 1.0.0dev
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bb41bee..f51e1a2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,24 +4,30 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.6.2
+          - prettier@3.8.3
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
         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 dd749d4..63cde50 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/
diff --git a/README.md b/README.md
index 48329e4..6e4b342 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,13 @@
   </picture>
 </h1>
 
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/funcprofiler)
 [![GitHub Actions CI Status](https://github.com/nf-core/funcprofiler/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/funcprofiler/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/funcprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcprofiler/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/funcprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![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/)
@@ -45,7 +46,7 @@ Supported profilers and current status:
 ## 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:
 
@@ -83,7 +84,7 @@ nextflow run nf-core/funcprofiler \
 ```
 
 > [!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/funcprofiler/usage) and the [parameter documentation](https://nf-co.re/funcprofiler/parameters).
 
@@ -103,7 +104,7 @@ 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 `#funcprofiler` channel](https://nfcore.slack.com/channels/funcprofiler) (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 4a0a4e4..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/funcprofiler 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/nf-core-funcprofiler_logo_light.png b/assets/nf-core-funcprofiler_logo_light.png
index e2abc52..fe1d759 100644
Binary files a/assets/nf-core-funcprofiler_logo_light.png and b/assets/nf-core-funcprofiler_logo_light.png differ
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index db3564c..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/funcprofiler ${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 05c9d05..a172f13 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/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
new file mode 100644
index 0000000..7eb6e8f
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,185 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `nf-core/funcprofiler`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving nf-core/funcprofiler.
+
+This page describes the recommended nf-core way to contribute to both nf-core/funcprofiler 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/funcprofiler.
+
+> [!NOTE]
+> If you need help using or modifying nf-core/funcprofiler, ask on the nf-core Slack [#funcprofiler](https://nfcore.slack.com/channels/funcprofiler) 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/funcprofiler/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/funcprofiler repository](https://github.com/nf-core/funcprofiler) 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/funcprofiler documentation](https://nf-co.re/funcprofiler/usage) or ask on the nf-core [#funcprofiler](https://nfcore.slack.com/channels/funcprofiler) Slack channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+### GitHub Codespaces
+
+You can contribute to nf-core/funcprofiler 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/funcprofiler/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/funcprofiler code and processing logic more understandable for new contributors and to ensure quality.
+
+#### Add a new pipeline step
+
+To contribute a new step to the pipeline, follow the general nf-core coding procedure.
+Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines):
+
+- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel.
+- [ ] Install a module with nf-core/tools, or write a local module (see [default processes resource requirements](#default-processes-resource-requirements)), and add it to the target `<workflow>.nf`.
+- [ ] Define the output channel if needed. Mix the version output channel into `ch_versions` and relevant files into `ch_multiqc`.
+- [ ] Add new or updated parameters to `nextflow.config` with a [default value](#default-parameter-values).
+- [ ] Add new or updated parameters and relevant help text to `nextflow_schema.json` with [nf-core/tools](#default-parameter-values).
+- [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow.
+- [ ] Perform local tests to validate that the new code works as expected.
+  - [ ] If applicable, add a new test in the `tests` directory.
+- [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate.
+- [ ] [Lint](lint) the code with nf-core/tools.
+- [ ] Update any diagrams or pipeline images as necessary.
+- [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order.
+- [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module.
+- [ ] Add a description of the output files and, if relevant, images from the MultiQC report to `docs/output.md`.
+
+To update the minimum required Nextflow version, see the [Nextflow version bumping](#nextflow-version-bumping) section below. For more information about pipeline contributions, see [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines).
+
+#### Channel naming schemes
+
+Use the following naming schemes for channels to make the channel flow easier to understand:
+
+- Initial process channel: `ch_output_from_<process>`
+- Intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+
+#### Default parameter values
+
+Parameters should be initialised and defined with default values within the `params` scope in `nextflow.config`.
+They should also be documented in the pipeline JSON schema.
+
+To update `nextflow_schema.json`, run:
+
+```bash
+nf-core pipelines schema build
+```
+
+The schema builder interface that loads in your browser should automatically update the defaults in the parameter documentation.
+
+#### Default processes resource requirements
+
+If you write a local module, specify a default set of resource requirements for the process.
+
+Sensible defaults for process resource requirements (CPUs, memory, time) should be defined in `conf/base.config`.
+Specify these with generic `withLabel:` selectors, so they can be shared across multiple processes and steps of the pipeline.
+
+nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
+These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements.
+
+Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+
+#### Nextflow version bumping
+
+If you use a new feature from core Nextflow, bump the minimum required Nextflow version in the pipeline with:
+
+```bash
+nf-core pipelines bump-version --nextflow . <min_nf_version>
+```
+
+#### Images and figures guidelines
+
+If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics).
+
+## Pipeline specific contribution guidelines
+
+<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->
diff --git a/docs/images/nf-core-funcprofiler_logo_dark.png b/docs/images/nf-core-funcprofiler_logo_dark.png
index 7e733e3..764bc28 100644
Binary files a/docs/images/nf-core-funcprofiler_logo_dark.png and b/docs/images/nf-core-funcprofiler_logo_dark.png differ
diff --git a/docs/images/nf-core-funcprofiler_logo_light.png b/docs/images/nf-core-funcprofiler_logo_light.png
index a67fe7a..80aea4f 100644
Binary files a/docs/images/nf-core-funcprofiler_logo_light.png and b/docs/images/nf-core-funcprofiler_logo_light.png differ
diff --git a/docs/usage.md b/docs/usage.md
index 857640a..e04fad3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -304,7 +304,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `shifter`
   - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
 - `charliecloud`
-  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+  - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
@@ -328,19 +328,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
-To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
+To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website.
 
 ### Custom Containers
 
 In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
-To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
+To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website.
 
 ### Custom Tool Arguments
 
 A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
 
-To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
+To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website.
 
 ### nf-core/configs
 
diff --git a/main.nf b/main.nf
index 148fb6c..2aa6239 100644
--- a/main.nf
+++ b/main.nf
@@ -38,9 +38,13 @@ workflow NFCORE_FUNCPROFILER {
     //
     // WORKFLOW: Run pipeline
     //
-    FUNCPROFILER(
+    FUNCPROFILER (
         samplesheet,
         databases,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
     )
 
     emit:
diff --git a/modules.json b/modules.json
index cca0816..42acdef 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "5d28ea7cfaebcfae6f74d1067ea766d8ff19dff3",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastx": {
                         "branch": "master",
-                        "git_sha": "8d52ac1b6f035f46c005a27b3510873c2a67ea41",
+                        "git_sha": "1b534ad2336876dbe82e9fea2773334cb624b426",
                         "installed_by": ["modules"]
                     },
                     "eggnogmapper": {
                         "branch": "master",
-                        "git_sha": "e11b95631ff49d1e2530b0e493289e7579ee259b",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "4f6c351f7bbc62173b30f5a430e21ec907720676",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
@@ -32,22 +32,22 @@
                     },
                     "metaphlan/metaphlan": {
                         "branch": "master",
-                        "git_sha": "fe0ec4b67b1abd71ff9b5ece41fd5a4d8abadad5",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cb9f4bec379866ca560f7f79d9a9a06bea8c9b51",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     },
                     "rgi/bwt": {
                         "branch": "master",
-                        "git_sha": "d6ba7c11771e7d7b65136b4ecd11fbea49261cbb",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "seqkit/fq2fa": {
                         "branch": "master",
-                        "git_sha": "bf70cbf44b42ff4a81afcb673fcef604f5ef3a85",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "untar": {
@@ -61,17 +61,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70",
+                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
+                        "git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/local/humann/humann/main.nf b/modules/local/humann/humann/main.nf
index 507c812..b4e374a 100644
--- a/modules/local/humann/humann/main.nf
+++ b/modules/local/humann/humann/main.nf
@@ -11,7 +11,7 @@ process HUMANN3 {
 
     input:
     tuple val(meta), path(input)
-    tuple val(meta), path(profile)
+    tuple val(_meta), path(profile)
     path nucleotide_db
     path protein_db
     path utility_db
diff --git a/modules/local/humann4/humann/main.nf b/modules/local/humann4/humann/main.nf
index 13cddd4..07dea89 100644
--- a/modules/local/humann4/humann/main.nf
+++ b/modules/local/humann4/humann/main.nf
@@ -8,7 +8,7 @@ process HUMANN4 {
 
     input:
     tuple val(meta), path(input)
-    tuple val(meta), path(profile)
+    tuple val(_meta), path(profile)
     path nucleotide_db
     path protein_db
     path utility_db
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 24c0e92..8d12a78 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -3,7 +3,7 @@ process CAT_FASTQ {
     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'}"
 
@@ -26,8 +26,7 @@ process CAT_FASTQ {
             """
             cat ${readList.join(' ')} ${compress} > ${prefix}.merged.fastq.gz
             """
-        }
-        else {
+        } else {
             error("Could not find any FASTQ files to concatenate in the process input")
         }
     }
@@ -40,8 +39,7 @@ process CAT_FASTQ {
             cat ${read1.join(' ')} ${compress} > ${prefix}_1.merged.fastq.gz
             cat ${read2.join(' ')} ${compress} > ${prefix}_2.merged.fastq.gz
             """
-        }
-        else {
+        } else {
             error("Could not find any FASTQ file pairs to concatenate in the process input")
         }
     }
@@ -54,8 +52,7 @@ process CAT_FASTQ {
             """
             echo '' | gzip > ${prefix}.merged.fastq.gz
             """
-        }
-        else {
+        } else {
             error("Could not find any FASTQ files to concatenate in the process input")
         }
     }
@@ -65,8 +62,7 @@ process CAT_FASTQ {
             echo '' | gzip > ${prefix}_1.merged.fastq.gz
             echo '' | gzip > ${prefix}_2.merged.fastq.gz
             """
-        }
-        else {
+        } else {
             error("Could not find any FASTQ file pairs to concatenate in the process input")
         }
     }
diff --git a/modules/nf-core/diamond/blastx/environment.yml b/modules/nf-core/diamond/blastx/environment.yml
index 0a8bf62..cca5cbb 100644
--- a/modules/nf-core/diamond/blastx/environment.yml
+++ b/modules/nf-core/diamond/blastx/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::diamond=2.1.16
+  - bioconda::diamond=2.1.24
diff --git a/modules/nf-core/diamond/blastx/main.nf b/modules/nf-core/diamond/blastx/main.nf
index 4ccae60..2b03de0 100644
--- a/modules/nf-core/diamond/blastx/main.nf
+++ b/modules/nf-core/diamond/blastx/main.nf
@@ -3,9 +3,9 @@ process DIAMOND_BLASTX {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/diamond:2.1.16--h13889ed_0'
-        : 'biocontainers/diamond:2.1.16--h13889ed_0'}"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/diamond:2.1.24--hf93d47f_0'
+        : 'quay.io/biocontainers/diamond:2.1.24--hf93d47f_0'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/diamond/blastx/tests/main.nf.test.snap b/modules/nf-core/diamond/blastx/tests/main.nf.test.snap
index 5544e39..80340d2 100644
--- a/modules/nf-core/diamond/blastx/tests/main.nf.test.snap
+++ b/modules/nf-core/diamond/blastx/tests/main.nf.test.snap
@@ -6,16 +6,16 @@
                     [
                         "DIAMOND_BLASTX",
                         "diamond",
-                        "2.1.16"
+                        "2.1.24"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-13T13:57:52.653837571",
         "meta": {
-            "nf-test": "0.9.4",
+            "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        }
+        },
+        "timestamp": "2026-04-22T15:47:51.928317786"
     },
     "Should search for transcriptome hits against a DIAMOND db and return the default tab separated output file of hits": {
         "content": [
@@ -32,15 +32,15 @@
                     [
                         "DIAMOND_BLASTX",
                         "diamond",
-                        "2.1.16"
+                        "2.1.24"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-13T13:57:44.281029658",
         "meta": {
-            "nf-test": "0.9.4",
+            "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        }
+        },
+        "timestamp": "2026-04-22T15:47:45.383426326"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/eggnogmapper/main.nf b/modules/nf-core/eggnogmapper/main.nf
index 9799f8f..cff118e 100644
--- a/modules/nf-core/eggnogmapper/main.nf
+++ b/modules/nf-core/eggnogmapper/main.nf
@@ -1,47 +1,47 @@
 process EGGNOGMAPPER {
-    tag "${meta.id}"
+    tag "$meta.id"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.13--pyhdfd78af_2'
-        : 'biocontainers/eggnog-mapper:2.1.13--pyhdfd78af_2'}"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.13--pyhdfd78af_2':
+        'quay.io/biocontainers/eggnog-mapper:2.1.13--pyhdfd78af_2' }"
 
     input:
     tuple val(meta), path(fasta)
     tuple val(search_mode), path(db)
-    path eggnog_data_dir
+    path(eggnog_data_dir)
 
     output:
-    tuple val(meta), path("*.emapper.annotations"), emit: annotations
+    tuple val(meta), path("*.emapper.annotations")   , emit: annotations
     tuple val(meta), path("*.emapper.seed_orthologs"), emit: orthologs, optional: true
-    tuple val(meta), path("*.emapper.hits"), emit: hits, optional: true
+    tuple val(meta), path("*.emapper.hits")          , emit: hits     , optional: true
     tuple val("${task.process}"), val('eggnog-mapper'), eval("emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\\+\\.[0-9]\\+\\.[0-9]\\+' | sed 's/emapper-//'"), topic: versions, emit: versions_eggnogmapper
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args          = task.ext.args   ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
     def is_compressed = fasta.extension == '.gz'
-    def fasta_name = is_compressed ? fasta.baseName : "${fasta}"
+    def fasta_name    = is_compressed ? fasta.baseName : "$fasta"
     def db_flags = ['diamond': '--dmnd_db', 'novel_fams': '--dmnd_db', 'mmseqs': '--mmseqs_db', 'hmmer': '--database', 'no_search': '--annotate_hits_table', 'cache': '--cache']
-    def db_path = db instanceof Path && db.isDirectory() ? "${db}/${db.name}" : "${db}"
-    def db_arg = db && db_flags[search_mode] ? "${db_flags[search_mode]} ${db_path}" : ''
-    def dbmem = task.memory.toMega() > 40000 ? '--dbmem' : ''
+    def db_path  = (db instanceof Path && db.isDirectory()) ? "${db}/${db.name}"                    : "$db"
+    def db_arg   = db && db_flags[search_mode]              ? "${db_flags[search_mode]} ${db_path}" : ''
+    def dbmem    = task.memory.toMega() > 40000             ? '--dbmem'                             : ''
     """
-    if [ "${is_compressed}" == "true" ]; then
-        gzip -c -d ${fasta} > ${fasta_name}
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
     fi
 
     emapper.py \\
-        ${args} \\
+        $args \\
         --cpu ${task.cpus} \\
         -i ${fasta_name} \\
         --data_dir ${eggnog_data_dir} \\
         -m ${search_mode} \\
-        ${db_arg} \\
+        $db_arg \\
         ${dbmem} \\
         --output ${prefix}
     """
@@ -49,7 +49,7 @@ process EGGNOGMAPPER {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    echo ${args}
+    echo $args
 
     touch ${prefix}.emapper.annotations
     touch ${prefix}.emapper.seed_orthologs
diff --git a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
new file mode 100644
index 0000000..7770ccd
--- /dev/null
+++ b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
@@ -0,0 +1,822 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/fastqc-0.12.1-hdfd78af_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+- 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-ecosystem-1-0.tar.bz2
+- conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-13.2.1-h6083320_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-ha1258a1_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.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/libcups-2.3.3-h7a8fb5f_6.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/libedit-3.1.20250104-pl5321h7949ede_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/libglib-2.86.4-h6548e54_1.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/libiconv-1.18-h3b78370_2.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/liblzma-5.8.2-hb03c661_0.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/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/libxcrypt-4.4.36-hd590300_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openjdk-25.0.2-ha668962_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/linux-64/pcre2-10.47-haa7fec5_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_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/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.13-he1eb515_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb03c661_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.7-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-6.0.2-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.8.2-hb9d3cd8_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrandr-1.5.5-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.12-hb9d3cd8_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.1-hb9d3cd8_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.5-hb9d3cd8_3.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+packages:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+build_number: 20
+sha256: 1dd3fffd892081df9726d7eb7e0dea6198962ba775bd88842135a4ddb4deb3c9
+md5: a9f577daf3de00bca7c3c76c0ecbd1de
+depends:
+- __glibc >=2.17,<3.0.a0
+- libgomp >=7.5.0
+constrains:
+- openmp_impl <0.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 28948
+timestamp: 1770939786096
+- conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
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+md5: dcdc58c15961dbf17a0621312b01f5cb
+depends:
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+- libgcc >=14
+license: LGPL-2.1-or-later
+license_family: GPL
+size: 584660
+timestamp: 1768327524772
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
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+md5: d2ffd7602c02f2b316fd921d39876885
+depends:
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+- libgcc >=14
+license: bzip2-1.0.6
+license_family: BSD
+size: 260182
+timestamp: 1771350215188
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+sha256: 67cc7101b36421c5913a1687ef1b99f85b5d6868da3abbf6ec1a4181e79782fc
+md5: 4492fd26db29495f0ba23f146cd5638d
+depends:
+- __unix
+license: ISC
+size: 147413
+timestamp: 1772006283803
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
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+md5: bb6c4808bfa69d6f7f6b07e5846ced37
+depends:
+- __glibc >=2.17,<3.0.a0
+- fontconfig >=2.15.0,<3.0a0
+- fonts-conda-ecosystem
+- icu >=78.1,<79.0a0
+- libexpat >=2.7.3,<3.0a0
+- libfreetype >=2.14.1
+- libfreetype6 >=2.14.1
+- libgcc >=14
+- libglib >=2.86.3,<3.0a0
+- libpng >=1.6.53,<1.7.0a0
+- libstdcxx >=14
+- libxcb >=1.17.0,<2.0a0
+- libzlib >=1.3.1,<2.0a0
+- pixman >=0.46.4,<1.0a0
+- xorg-libice >=1.1.2,<2.0a0
+- xorg-libsm >=1.2.6,<2.0a0
+- xorg-libx11 >=1.8.12,<2.0a0
+- xorg-libxext >=1.3.6,<2.0a0
+- xorg-libxrender >=0.9.12,<0.10.0a0
+license: LGPL-2.1-only or MPL-1.1
+size: 989514
+timestamp: 1766415934926
+- conda: https://conda.anaconda.org/bioconda/noarch/fastqc-0.12.1-hdfd78af_0.tar.bz2
+sha256: 7cc26225d590540ae95cd24940ff42f2da7479dd4cd22ae9ab9298665d06790c
+md5: c9f6a4b12229f7331f79c9a00dd6e240
+depends:
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+- fontconfig
+- openjdk >=8.0.144
+- perl
+license: GPL >=3
+size: 11664291
+timestamp: 1677946722445
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b
+md5: 0c96522c6bdaed4b1566d11387caaf45
+license: BSD-3-Clause
+license_family: BSD
+size: 397370
+timestamp: 1566932522327
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+sha256: c52a29fdac682c20d252facc50f01e7c2e7ceac52aa9817aaf0bb83f7559ec5c
+md5: 34893075a5c9e55cdafac56607368fc6
+license: OFL-1.1
+license_family: Other
+size: 96530
+timestamp: 1620479909603
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+sha256: 00925c8c055a2275614b4d983e1df637245e19058d79fc7dd1a93b8d9fb4b139
+md5: 4d59c254e01d9cde7957100457e2d5fb
+license: OFL-1.1
+license_family: Other
+size: 700814
+timestamp: 1620479612257
+- conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
+sha256: 2821ec1dc454bd8b9a31d0ed22a7ce22422c0aef163c59f49dfdf915d0f0ca14
+md5: 49023d73832ef61042f6a237cb2687e7
+license: LicenseRef-Ubuntu-Font-Licence-Version-1.0
+license_family: Other
+size: 1620504
+timestamp: 1727511233259
+- conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda
+sha256: aa4a44dba97151221100a637c7f4bde619567afade9c0265f8e1c8eed8d7bd8c
+md5: 867127763fbe935bab59815b6e0b7b5c
+depends:
+- __glibc >=2.17,<3.0.a0
+- libexpat >=2.7.4,<3.0a0
+- libfreetype >=2.14.1
+- libfreetype6 >=2.14.1
+- libgcc >=14
+- libuuid >=2.41.3,<3.0a0
+- libzlib >=1.3.1,<2.0a0
+license: MIT
+license_family: MIT
+size: 270705
+timestamp: 1771382710863
+- conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+sha256: a997f2f1921bb9c9d76e6fa2f6b408b7fa549edd349a77639c9fe7a23ea93e61
+md5: fee5683a3f04bd15cbd8318b096a27ab
+depends:
+- fonts-conda-forge
+license: BSD-3-Clause
+license_family: BSD
+size: 3667
+timestamp: 1566974674465
+- conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
+sha256: 54eea8469786bc2291cc40bca5f46438d3e062a399e8f53f013b6a9f50e98333
+md5: a7970cd949a077b7cb9696379d338681
+depends:
+- font-ttf-ubuntu
+- font-ttf-inconsolata
+- font-ttf-dejavu-sans-mono
+- font-ttf-source-code-pro
+license: BSD-3-Clause
+license_family: BSD
+size: 4059
+timestamp: 1762351264405
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda
+sha256: e9cbcbc94e151ada3d6dc365380aaaf591f65012c16d9a2abaea4b9b90adc402
+md5: ab7288cc39545556d1bc5e71ab2df9a9
+depends:
+- libgcc >=14
+- ncurses >=6.5,<7.0a0
+license: GPL-2.0-or-later AND LGPL-2.0-or-later
+license_family: GPL
+size: 636733
+timestamp: 1769712412683
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda
+sha256: 977dfb0cb3935d748521dd80262fe7169ab82920afd38ed14b7fee2ea5ec01ba
+md5: bb5a90c93e3bac3d5690acf76b4a6386
+depends:
+- libgcc >=13
+license: MIT
+license_family: MIT
+size: 8342
+timestamp: 1726803319942
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libice-1.1.2-h86ecc28_0.conda
+sha256: a2ba1864403c7eb4194dacbfe2777acf3d596feae43aada8d1b478617ce45031
+md5: c8d8ec3e00cd0fd8a231789b91a7c5b7
+depends:
+- libgcc >=13
+license: MIT
+license_family: MIT
+size: 60433
+timestamp: 1734229908988
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libsm-1.2.6-h0808dbd_0.conda
+sha256: b86a819cd16f90c01d9d81892155126d01555a20dabd5f3091da59d6309afd0a
+md5: 2d1409c50882819cb1af2de82e2b7208
+depends:
+- libgcc >=13
+- libuuid >=2.38.1,<3.0a0
+- xorg-libice >=1.1.2,<2.0a0
+license: MIT
+license_family: MIT
+size: 28701
+timestamp: 1741897678254
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libx11-1.8.13-h63a1b12_0.conda
+sha256: cf886160e2ff580d77f7eb8ec1a77c41c2c5b05343e329bc35f0ddf40b8d92ab
+md5: 22dd10425ef181e80e130db50675d615
+depends:
+- libgcc >=14
+- libxcb >=1.17.0,<2.0a0
+license: MIT
+license_family: MIT
+size: 869058
+timestamp: 1770819244991
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda
+sha256: e9f6e931feeb2f40e1fdbafe41d3b665f1ab6cb39c5880a1fcf9f79a3f3c84a5
+md5: 1c246e1105000c3660558459e2fd6d43
+depends:
+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 16317
+timestamp: 1762977521691
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda
+sha256: 128d72f36bcc8d2b4cdbec07507542e437c7d67f677b7d77b71ed9eeac7d6df1
+md5: bff06dcde4a707339d66d45d96ceb2e2
+depends:
+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 21039
+timestamp: 1762979038025
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxext-1.3.7-he30d5cf_0.conda
+sha256: db2188bc0d844d4e9747bac7f6c1d067e390bd769c5ad897c93f1df759dc5dba
+md5: fb42b683034619915863d68dd9df03a3
+depends:
+- libgcc >=14
+- xorg-libx11 >=1.8.12,<2.0a0
+license: MIT
+license_family: MIT
+size: 52409
+timestamp: 1769446753771
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxfixes-6.0.2-he30d5cf_0.conda
+sha256: 8cb9c88e25c57e47419e98f04f9ef3154ad96b9f858c88c570c7b91216a64d0e
+md5: e8b4056544341daf1d415eaeae7a040c
+depends:
+- libgcc >=14
+- xorg-libx11 >=1.8.12,<2.0a0
+license: MIT
+license_family: MIT
+size: 20704
+timestamp: 1759284028146
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxi-1.8.2-h57736b2_0.conda
+sha256: 7b587407ecb9ccd2bbaf0fb94c5dbdde4d015346df063e9502dc0ce2b682fb5e
+md5: eeee3bdb31c6acde2b81ad1b8c287087
+depends:
+- libgcc >=13
+- xorg-libx11 >=1.8.9,<2.0a0
+- xorg-libxext >=1.3.6,<2.0a0
+- xorg-libxfixes >=6.0.1,<7.0a0
+license: MIT
+license_family: MIT
+size: 48197
+timestamp: 1727801059062
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxrandr-1.5.5-he30d5cf_0.conda
+sha256: 9f5196665a8d72f4f119c40dcc4bafeb0b540b102cc7b8b299c2abf599e7919f
+md5: 1f64c613f0b8d67e9fb0e165d898fb6b
+depends:
+- libgcc >=14
+- xorg-libx11 >=1.8.12,<2.0a0
+- xorg-libxext >=1.3.6,<2.0a0
+- xorg-libxrender >=0.9.12,<0.10.0a0
+license: MIT
+license_family: MIT
+size: 31122
+timestamp: 1769445286951
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxrender-0.9.12-h86ecc28_0.conda
+sha256: ffd77ee860c9635a28cfda46163dcfe9224dc6248c62404c544ae6b564a0be1f
+md5: ae2c2dd0e2d38d249887727db2af960e
+depends:
+- libgcc >=13
+- xorg-libx11 >=1.8.10,<2.0a0
+license: MIT
+license_family: MIT
+size: 33649
+timestamp: 1734229123157
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxt-1.3.1-h57736b2_0.conda
+sha256: 7c109792b60720809a580612aba7f8eb2a0bd425b9fc078748a9d6ffc97cbfa8
+md5: a9e4852c8e0b68ee783e7240030b696f
+depends:
+- libgcc >=13
+- xorg-libice >=1.1.1,<2.0a0
+- xorg-libsm >=1.2.4,<2.0a0
+- xorg-libx11 >=1.8.9,<2.0a0
+license: MIT
+license_family: MIT
+size: 384752
+timestamp: 1731860572314
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxtst-1.2.5-h57736b2_3.conda
+sha256: 6eaffce5a34fc0a16a21ddeaefb597e792a263b1b0c387c1ce46b0a967d558e1
+md5: c05698071b5c8e0da82a282085845860
+depends:
+- libgcc >=13
+- xorg-libx11 >=1.8.9,<2.0a0
+- xorg-libxext >=1.3.6,<2.0a0
+- xorg-libxi >=1.7.10,<2.0a0
+license: MIT
+license_family: MIT
+size: 33786
+timestamp: 1727964907993
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9b4ae36..1085126 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -3,9 +3,9 @@ process FASTQC {
     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/fastqc:0.12.1--hdfd78af_0'
-        : 'biocontainers/fastqc:0.12.1--hdfd78af_0'}"
+        : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}"
 
     input:
     tuple val(meta), path(reads, stageAs: '?/*')
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 49164c8..2f6cfef 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -86,26 +86,26 @@ maintainers:
   - "@ewels"
   - "@FelixKrueger"
 containers:
-  conda:
-    linux_amd64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-af7a5314d5015c29_1/condalock
-    linux_arm64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-df99cb252670875a_2/condalock
   docker:
-    linux_amd64:
-      build_id: bd-af7a5314d5015c29_1
-      name: community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29
-      scanId: sc-a618548acbee5a8a_30
-    linux_arm64:
-      build_id: bd-df99cb252670875a_2
-      name: community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a
-      scanId: sc-b5913ed5d42b22d2_18
+    linux/arm64:
+      name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68
+      build_id: bd-e455e32f745abe68_1
+      scan_id: sc-f102f736465af88c_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2
+      build_id: bd-5cb1a2fa2f18c7c2_1
+      scan_id: sc-0c0466326b6b77d2_1
   singularity:
-    linux_amd64:
-      build_id: bd-104d26ddd9519960_1
-      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--104d26ddd9519960
-      https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:e0c976cb2eca5fee72618a581537a4f8ea42fcae24c9b201e2e0f764fd28648a
-    linux_arm64:
-      build_id: bd-d56b505a93aef38a_1
-      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--d56b505a93aef38a
-      https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd
+      build_id: bd-5c4bd442468d75dd_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035
+      build_id: bd-127a87fc06499035_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
diff --git a/modules/nf-core/metaphlan/metaphlan/main.nf b/modules/nf-core/metaphlan/metaphlan/main.nf
index 9865a9f..953abfc 100644
--- a/modules/nf-core/metaphlan/metaphlan/main.nf
+++ b/modules/nf-core/metaphlan/metaphlan/main.nf
@@ -3,9 +3,9 @@ process METAPHLAN_METAPHLAN {
     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/metaphlan:4.1.1--pyhdfd78af_0'
-        : 'biocontainers/metaphlan:4.1.1--pyhdfd78af_0'}"
+        : 'quay.io/biocontainers/metaphlan:4.1.1--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(input)
@@ -54,13 +54,10 @@ process METAPHLAN_METAPHLAN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def samfile_cmd = save_samfile ? "touch ${prefix}.sam" : ''
-    def input_type = "${input}" =~ /.*\.(fastq|fq)/
-        ? "fastq"
-        : "${input}" =~ /.*\.(fasta|fna|fa)/
-            ? "fasta"
-            : "${input}".endsWith(".bowtie2out.txt")
-                ? "bowtie2out"
-                : "sam"
+    def input_type = "${input}" =~ /.*\.(fastq|fq)/ ? "fastq" :
+        "${input}" =~ /.*\.(fasta|fna|fa)/? "fasta" :
+        "${input}".endsWith(".bowtie2out.txt") ? "bowtie2out" :
+        "sam"
     def bowtie2_cmd = "${input_type}" == "bowtie2out" || "${input_type}" == "sam" ? '' : "touch ${prefix}.bowtie2out.txt"
 
     """
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
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda#49f570f3bc4c874a06ea69b7225753af
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb
+https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda#2c21e66f50753a083cbe6b80f38268fa
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda#1b08cd684f34175e4514474793d44bcb
+https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda#c80d8a3b84358cb967fa81e7075fbc8a
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-hf4e2dac_0.conda#810d83373448da85c3f673fbcb7ad3a3
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda#0539938c55b6b1a59b560e843ad864a4
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610
+https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda#a443f87920815d41bfe611296e507995
+https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda#f111d4cfaf1fe9496f386bc98ae94452
+https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda#e4e60721757979d01d3964122f674959
+https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda#aaa2a381ccc56eac91d63b6c1240312f
+https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda#0caa1af407ecff61170c9437a808404d
+https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda#edd329d7d3a4ab45dcf905899a7a6115
+https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda#2934f256a8acfe48f6ebb4fce6cde29c
+https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda#c6b0543676ecb1fb2d7643941fe375f2
+https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda#a2ac7763a9ac75055b68f325d3255265
+https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda#8910d2c46f7e7b519129f486e0fe927a
+https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda#929471569c93acefb30282a22060dcd5
+https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda#a9167b9571f3baa9d448faa2139d1089
+https://conda.anaconda.org/conda-forge/noarch/click-8.3.2-pyhc90fa1f_0.conda#4d18bc3af7cfcea97bd817164672a08c
+https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda#7fe569c10905402ed47024fc481bb371
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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
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+https://conda.anaconda.org/conda-forge/linux-aarch64/numpy-2.4.3-py314haac167e_0.conda#25d896c331481145720a21e5145fad65
+https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda#071cf7b0ce333c81718b054066c15102
+https://conda.anaconda.org/conda-forge/linux-aarch64/expat-2.7.5-hfae3067_0.conda#d2bb0c889d94f2fdc5856392c3002976
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
+https://conda.anaconda.org/conda-forge/linux-aarch64/libpng-1.6.58-h1abf092_0.conda#f51503ac45a4888bce71af9027a2ecc9
+https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype6-2.14.3-hdae7a39_0.conda#b99ed99e42dafb27889483b3098cace7
+https://conda.anaconda.org/conda-forge/linux-aarch64/libfreetype-2.14.3-h8af1aa0_0.conda#a229e22d4d8814a07702b0919d8e6701
+https://conda.anaconda.org/conda-forge/linux-aarch64/fontconfig-2.17.1-hba86a56_0.conda#0fed1ff55f4938a65907f3ecf62609db
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681
+https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda#0a802cb9888dd14eeefc611f05c40b6e
+https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda#8e6923fc12f1fe8f8c4e5c9f343256ac
+https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda#164fc43f0b53b6e3a7bc7dce5e4f1dc9
+https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda#daddf757c3ecd6067b9af1df1f25d89e
+https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda#fb7130c190f9b4ec91219840a05ba3ac
+https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.1-pyhcf101f3_0.conda#e1c36c6121a7c9c76f2f148f1e83b983
+https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda#080594bf4493e6bae2607e65390c520a
+https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-3.0.3-py314hb76de3f_1.conda#e5de3c36dd548b35ff2a8aa49208dcb3
+https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda#04558c96691bed63104678757beb4f8d
+https://conda.anaconda.org/conda-forge/linux-aarch64/rpds-py-0.30.0-py314h02b7a91_0.conda#e7f6ed9e60043bb5cbcc527764897f0d
+https://conda.anaconda.org/conda-forge/noarch/referencing-0.37.0-pyhcf101f3_0.conda#870293df500ca7e18bedefa5838a22ab
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda#439cd0f567d697b20a8f45cb70a1005a
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda#ada41c863af263cc4c5fcbaff7c3e4dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda#4feebd0fbf61075a1a9c2e9b3936c257
+https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2#7b08314a6867a9d5648a1c3265e9eb8e
+https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda#6dd4f07147774bf720075a210f8026b9
+https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552
+https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.0-he8854b5_0.conda#ad8164bdeece883b825c50639c0c4725
+https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2#4f0d284f5d11e04277b552eb1c172c7f
+https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda#a85ba48648f6868016f2741fd9170250
+https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171
+https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda#a9138815598fe6b91a1d6782ca657b0c
+https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda#24e92d0942c799db387f5c9d7b81f1af
+https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda#8c6fd84f9c87ac00636007c6131e457d
+https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c
+https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2
+https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2
+https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3
+https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351
+https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964
+https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8
+https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c
+https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b
+https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684
+https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98
+https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910
+https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372
+https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7
+https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88
+https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58
+https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240
+https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6
+https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98
+https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c
+https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2
+https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac
+https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130
+https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59
+https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0
+https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66
+https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9
+https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a
+https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864
+https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6
+https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206
+https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b
+https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873
+https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f
+https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 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 5376aea..e80e8cd 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,9 +3,9 @@ process MULTIQC {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data'
-        : 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b'}"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
+        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ef434a9..2facc62 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -110,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
     linux/arm64:
-      lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
   docker:
     linux/amd64:
-      build_id: bd-ee7739d47738383b_1
-      name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b
-      scanId: sc-6ddec592dcadd583_4
+      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
+      build_id: bd-db7c73dae76bc9e6_1
+      scan_id: sc-66fc7138dbf1cf48_1
     linux/arm64:
-      build_id: bd-58d7dee710ab3aa8_1
-      name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8
-      scanId: sc-a04c42273e34c55c_2
+      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
+      build_id: bd-d167b8012595a136_1
+      scan_id: sc-ac701dfa631a2af9_1
   singularity:
     linux/amd64:
-      build_id: bd-e3576ddf588fa00d_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
+      build_id: bd-4fc8657c816047c0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
     linux/arm64:
-      build_id: bd-2537ca5f8445e3c2_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
+      build_id: bd-7fbd82d945c06726_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 3bfc524..7c2f370 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -81,7 +81,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
@@ -175,7 +175,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
@@ -221,7 +221,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
@@ -314,7 +314,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
@@ -408,7 +408,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.34"
                     ]
                 ]
             }
diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index b2fca0c..8fa5e2b 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -3,9 +3,9 @@ process RGI_BWT {
     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/rgi:6.0.5--pyh05cac1d_0'
-        : 'biocontainers/rgi:6.0.5--pyh05cac1d_0'}"
+        : 'quay.io/biocontainers/rgi:6.0.5--pyh05cac1d_0'}"
 
     input:
     tuple val(meta), path(reads, arity: '1..2')
@@ -16,8 +16,8 @@ process RGI_BWT {
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt"), emit: tsv
     tuple val(meta), path("temp/"), emit: tmp
-    tuple val("${task.process}"), val('rgi'), eval("rgi main --version"), emit: versions_rgi, topic: versions
-    tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION"), emit: versions_db, topic: versions
+    tuple val("${task.process}"), val('rgi'), eval("rgi main --version"),  emit: versions_rgi, topic: versions
+    tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION"),  emit: versions_db , topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/seqkit/fq2fa/main.nf b/modules/nf-core/seqkit/fq2fa/main.nf
index ccd2161..313af89 100644
--- a/modules/nf-core/seqkit/fq2fa/main.nf
+++ b/modules/nf-core/seqkit/fq2fa/main.nf
@@ -1,11 +1,11 @@
 process SEQKIT_FQ2FA {
-    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/seqkit:2.9.0--h9ee0642_0'
-        : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastq)
@@ -24,10 +24,10 @@ process SEQKIT_FQ2FA {
     """
     seqkit \\
         fq2fa \\
-        ${args} \\
-        -j ${task.cpus} \\
+        $args \\
+        -j $task.cpus \\
         -o ${prefix}.fa.gz \\
-        ${fastq}
+        $fastq
     """
 
     stub:
diff --git a/nextflow.config b/nextflow.config
index 4717299..8ef1874 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,4 +1,5 @@
 /*
+/*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     nf-core/funcprofiler Nextflow config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -31,7 +32,6 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = null
     help                         = false
     help_full                    = false
     show_hidden                  = false
@@ -74,6 +74,10 @@ params {
 
 }
 
+// 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'
 
@@ -117,7 +121,18 @@ profiles {
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g) --platform linux/x86_64'
     }
-    arm {
+    arm64 {
+        process.arch            = 'arm64'
+        // TODO https://github.com/nf-core/modules/issues/6694
+        // For now if you're using arm64 you have to use wave for the sake of the maintainers
+        // wave profile
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    emulate_amd64 {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
@@ -183,18 +198,6 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    gitpod {
-        executor.name           = 'local'
-        executor.cpus           = 4
-        executor.memory         = 8.GB
-        process {
-            resourceLimits = [
-                memory: 8.GB,
-                cpus  : 4,
-                time  : 1.h
-            ]
-        }
-    }
     gpu {
         docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
         apptainer.runOptions    = '--nv'
@@ -286,47 +289,19 @@ manifest {
     description     = """Read-based functional profiling of microbiome sequencing data"""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=24.10.5'
+    nextflowVersion = '!>=25.10.4'
     version         = '1.0.0dev'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
-    help {
-        enabled = true
-        command = "nextflow run nf-core/funcprofiler -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
-        showHiddenParameter = "show_hidden"
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  nf-core/funcprofiler ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/nf-core/funcprofiler/blob/main/CITATIONS.md
-"""
-    }
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }
 }
-
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a68335d..f63b96f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -243,13 +243,6 @@
                     "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",
@@ -287,6 +280,18 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
+                },
+                "help": {
+                    "type": ["boolean", "string"],
+                    "description": "Display the help message."
+                },
+                "help_full": {
+                    "type": "boolean",
+                    "description": "Display the full detailed help message."
+                },
+                "show_hidden": {
+                    "type": "boolean",
+                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                 }
             }
         }
diff --git a/nf-test.config b/nf-test.config
index b7936af..d712a84 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,18 +1,21 @@
 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'
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 0acf7d1..60f2645 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -1,6 +1,6 @@
 {
     "@context": [
-        "https://w3id.org/ro/crate/1.1/context",
+        "https://w3id.org/ro/crate/1.2/context",
         {
             "GithubService": "https://w3id.org/ro/terms/test#GithubService",
             "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-08-13T15:15:55+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-funcprofiler_logo_dark.png\">\n    <img alt=\"nf-core/funcprofiler\" src=\"docs/images/nf-core-funcprofiler_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/funcprofiler/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/funcprofiler/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcprofiler/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/funcprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcprofiler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcprofiler)[![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<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n\n**nf-core/funcprofiler** is a bioinformatics pipeline for read-based functional profiling of microbiome sequencing data. It accepts short-read (Illumina) and long-read (Oxford Nanopore) FASTQ files and runs one or more functional profilers against user-supplied databases, producing gene family abundances, pathway abundances, pathway coverages, and antimicrobial resistance profiles.\n\n### Pipeline Summary\n\n![](./assets/pipeline_light.svg)\n\nSupported profilers:\n\n1. [**HUMANn v3**](https://huttenhower.sph.harvard.edu/humann/) \u2014 functional profiling via MetaPhlAn + HUMANn 3 (`--run_humann_v3`)\n2. [**HUMANn v4**](https://huttenhower.sph.harvard.edu/humann/) \u2014 functional profiling via MetaPhlAn + HUMANn 4 (`--run_humann_v4`)\n3. [**FMH FunProfiler**](https://github.com/dib-lab/fmh_funprofiler) \u2014 sketch-based functional profiling (`--run_fmhfunprofiler`)\n4. [**RGI**](https://github.com/arpcard/rgi) \u2014 antimicrobial resistance gene identification (`--run_rgi`, available)\n5. [**mifaser**](https://bromberglab.org/project/mifaser/) \u2014 functional profiling via mifaser (`--run_mifaser`, available)\n6. [**DIAMOND**](https://github.com/bbuchfink/diamond) \u2014 alignment with DIAMOND blastx (`--run_diamond`, available)\n7. [**eggNOG-mapper**](https://academic.oup.com/mbe/article/38/12/5825/6379734) \u2014 functional annotation, orthology assignments and domain prediction (`--run_eggnogmapper`, available)\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:\n\n`samplesheet.csv`:\n\n```csv\nsample,run_accession,instrument_platform,fastq_1,fastq_2,fasta\nSAMPLE1,RUN1,ILLUMINA,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz,\nSAMPLE2,RUN1,OXFORD_NANOPORE,/path/to/sample2.fastq.gz,,\n```\n\nEach row represents a sequencing run. Multiple rows with the same `sample` and different `run_accession` values will be merged before profiling.\n\nThen prepare a databases sheet \u2014 see [docs/usage.md](docs/usage.md) for the full format. Here is an abbreviated example for running HUMANn (which requires 4 databases):\n\n`databases.csv`\n\n```csv\ntool,db_name,db_entity,db_params,db_type,db_path\nhumann_v3,uniref90_v3,humann_metaphlan,,,/data/databases/metaphlan_db\nhumann_v3,uniref90_v3,humann_nucleotide,,,/data/databases/chocophlan\nhumann_v3,uniref90_v3,humann_protein,,,/data/databases/uniref90_diamond\nhumann_v3,uniref90_v3,humann_utility,,,/data/databases/utility_mapping\n```\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/funcprofiler \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --databases databases.csv \\\n   --run_humann_v3\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/funcprofiler/usage) and the [parameter documentation](https://nf-co.re/funcprofiler/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/funcprofiler/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/funcprofiler/output).\n\n## Credits\n\nnf-core/funcprofiler was written by Nick Waters, Vini Salazar, Yixuan Yang, Mirae Baichoo.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcprofiler` channel](https://nfcore.slack.com/channels/funcprofiler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/funcprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-funcprofiler_logo_dark.png\">\n    <img alt=\"nf-core/funcprofiler\" src=\"docs/images/nf-core-funcprofiler_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/funcprofiler)\n[![GitHub Actions CI Status](https://github.com/nf-core/funcprofiler/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/funcprofiler/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcprofiler/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/funcprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcprofiler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcprofiler)[![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<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n\n**nf-core/funcprofiler** is a bioinformatics pipeline for read-based functional profiling of microbiome sequencing data. It accepts short-read (Illumina) and long-read (Oxford Nanopore) FASTQ files and runs one or more functional profilers against user-supplied databases, producing gene family abundances, pathway abundances, pathway coverages, and antimicrobial resistance profiles.\n\n### Pipeline Summary\n\n![](./assets/pipeline_light.svg)\n\nSupported profilers and current status:\n\n1. [**HUMANn v3**](https://huttenhower.sph.harvard.edu/humann/) \u2014 functional profiling via MetaPhlAn + HUMANn 3 (`--run_humann_v3`)\n2. [**HUMANn v4**](https://huttenhower.sph.harvard.edu/humann/) \u2014 functional profiling via MetaPhlAn + HUMANn 4 (`--run_humann_v4`)\n3. [**FMH FunProfiler**](https://github.com/dib-lab/fmh_funprofiler) \u2014 sketch-based functional profiling (`--run_fmhfunprofiler`)\n4. [**RGI**](https://github.com/arpcard/rgi) \u2014 antimicrobial resistance gene identification (`--run_rgi`, available)\n5. [**mifaser**](https://bromberglab.org/project/mifaser/) \u2014 functional profiling via mifaser (`--run_mifaser`, available)\n6. [**DIAMOND**](https://github.com/bbuchfink/diamond) \u2014 alignment with DIAMOND blastx (`--run_diamond`, work in progress / beta)\n7. [**eggNOG-mapper**](https://academic.oup.com/mbe/article/38/12/5825/6379734) \u2014 functional annotation, orthology assignments and domain prediction (`--run_eggnogmapper`, work in progress / beta)\n\n> [!WARNING]\n> DIAMOND and eggNOG-mapper support is currently in beta and should be treated as work in progress. These modules are still being validated in the full pipeline, including database handling, output behavior, and downstream reporting. Use them with caution, expect potential issues, and independently review results before using them for production analyses or interpretation.\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:\n\n`samplesheet.csv`:\n\n```csv\nsample,run_accession,instrument_platform,fastq_1,fastq_2,fasta\nSAMPLE1,RUN1,ILLUMINA,/path/to/sample1_R1.fastq.gz,/path/to/sample1_R2.fastq.gz,\nSAMPLE2,RUN1,OXFORD_NANOPORE,/path/to/sample2.fastq.gz,,\n```\n\nEach row represents a sequencing run. Multiple rows with the same `sample` and different `run_accession` values will be merged before profiling.\n\nThen prepare a databases sheet \u2014 see [docs/usage.md](docs/usage.md) for the full format. Here is an abbreviated example for running HUMANn (which requires 4 databases):\n\n`databases.csv`\n\n```csv\ntool,db_name,db_entity,db_params,db_type,db_path\nhumann_v3,uniref90_v3,humann_metaphlan,,,/data/databases/metaphlan_db\nhumann_v3,uniref90_v3,humann_nucleotide,,,/data/databases/chocophlan\nhumann_v3,uniref90_v3,humann_protein,,,/data/databases/uniref90_diamond\nhumann_v3,uniref90_v3,humann_utility,,,/data/databases/utility_mapping\n```\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/funcprofiler \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --databases databases.csv \\\n   --run_humann_v3\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/funcprofiler/usage) and the [parameter documentation](https://nf-co.re/funcprofiler/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/funcprofiler/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/funcprofiler/output).\n\n## Credits\n\nnf-core/funcprofiler was written by Nick Waters, Vini Salazar, Yixuan Yang, Mirae Baichoo.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcprofiler` channel](https://nfcore.slack.com/channels/funcprofiler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/funcprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#43d93482-10b4-4a4a-9aae-56cf094b0489"
+                    "@id": "#322dad57-f56e-4262-8284-302faf41fa1d"
                 }
             ],
             "name": "nf-core/funcprofiler"
@@ -112,7 +112,7 @@
             },
             "conformsTo": [
                 {
-                    "@id": "https://w3id.org/ro/crate/1.1"
+                    "@id": "https://w3id.org/ro/crate/1.2"
                 },
                 {
                     "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
@@ -126,13 +126,13 @@
                 "SoftwareSourceCode",
                 "ComputationalWorkflow"
             ],
-            "creator": [
+            "contributor": [
                 {
-                    "@id": "#nickp60@users.noreply.github.com"
+                    "@id": "#c6f629b9-26a9-487e-bd5f-f9ca5b819419"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-08-13T11:15:55Z",
+            "dateModified": "2026-04-30T13:32:35Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -141,11 +141,6 @@
             "license": [
                 "MIT"
             ],
-            "maintainer": [
-                {
-                    "@id": "#nickp60@users.noreply.github.com"
-                }
-            ],
             "name": [
                 "nf-core/funcprofiler"
             ],
@@ -173,14 +168,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.10.5"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "#43d93482-10b4-4a4a-9aae-56cf094b0489",
+            "@id": "#322dad57-f56e-4262-8284-302faf41fa1d",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#d1cf13a7-6e4d-4a5b-9196-57c7109be07f"
+                    "@id": "#42032b30-363e-40c3-9805-13ea4dc9ae5d"
                 }
             ],
             "mainEntity": {
@@ -189,7 +184,7 @@
             "name": "Test suite for nf-core/funcprofiler"
         },
         {
-            "@id": "#d1cf13a7-6e4d-4a5b-9196-57c7109be07f",
+            "@id": "#42032b30-363e-40c3-9805-13ea4dc9ae5d",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/funcprofiler",
             "resource": "repos/nf-core/funcprofiler/actions/workflows/nf-test.yml",
@@ -318,7 +313,7 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "#nickp60@users.noreply.github.com",
+            "@id": "#c6f629b9-26a9-487e-bd5f-f9ca5b819419",
             "@type": "Person",
             "email": "nickp60@users.noreply.github.com",
             "name": "Nick Waters"
diff --git a/subworkflows/local/profile/main.nf b/subworkflows/local/profile/main.nf
index 9e6c0d5..48cbb4e 100644
--- a/subworkflows/local/profile/main.nf
+++ b/subworkflows/local/profile/main.nf
@@ -167,7 +167,8 @@ workflow PROFILING {
     // channel element order in sync with each other
 
     // PAIRED-END READ TOOLS
-    rgi_inputs = prepareInputs(reads, databases, 'rgi', false)
+    ch_input_for_rgi = prepareInputs(reads, databases, 'rgi', false)
+    ch_input_for_eggnogmapper = prepareInputs(reads_concat, databases, 'eggnogmapper', true)
 
     // CONCAT READ TOOLS
     ch_input_for_fmhfunprofiler = prepareInputs(reads_concat, databases, 'fmhfunprofiler', true)
@@ -199,8 +200,8 @@ workflow PROFILING {
         ch_humann3_input = ch_input_for_humann_v3.reads
             .join(MPAHUMANN3.out.profile, by: 0)  // Join on meta map
         HUMANN3(
-            ch_humann3_input.map { meta, reads, profile -> [meta, reads] },  // Extract reads
-            ch_humann3_input.map { meta, reads, profile -> [meta, profile] }, // Extract profile
+            ch_humann3_input.map { it -> [it[0], it[1]] },  // Extract reads
+            ch_humann3_input.map { it -> [it[0], it[2]] }, // Extract profile
             getDbPath(ch_input_for_humann_v3.db, 'humann_nucleotide'),
             getDbPath(ch_input_for_humann_v3.db, 'humann_protein'),
             getDbPath(ch_input_for_humann_v3.db, 'humann_utility'),
@@ -220,8 +221,8 @@ workflow PROFILING {
             .join(MPAHUMANN4.out.profile, by: 0)  // Join on meta map
 
         HUMANN4(
-            ch_humann4_input.map { meta, reads, profile -> [meta, reads] },  // Extract reads
-            ch_humann4_input.map { meta, reads, profile -> [meta, profile] }, // Extract profile
+            ch_humann4_input.map { it -> [it[0], it[1]] },  // Extract reads
+            ch_humann4_input.map { it -> [it[0], it[2]] }, // Extract profile
             getDbPath(ch_input_for_humann_v4.db, 'humann_nucleotide'),
             getDbPath(ch_input_for_humann_v4.db, 'humann_protein'),
             getDbPath(ch_input_for_humann_v4.db, 'humann_utility'),
diff --git a/subworkflows/local/utils_nfcore_funcprofiler_pipeline/main.nf b/subworkflows/local/utils_nfcore_funcprofiler_pipeline/main.nf
index bef2036..9d65ed8 100644
--- a/subworkflows/local/utils_nfcore_funcprofiler_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_funcprofiler_pipeline/main.nf
@@ -39,7 +39,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -85,6 +85,7 @@ workflow PIPELINE_INITIALISATION {
         before_text,
         after_text,
         command,
+        null,
     )
 
     //
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index e2761d2..37939ac 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -10,9 +10,9 @@
 
 workflow UTILS_NEXTFLOW_PIPELINE {
     take:
-    print_version // boolean: print version
-    dump_parameters // boolean: dump parameters
-    outdir //    path: base directory used to publish pipeline results
+    print_version        // boolean: print version
+    dump_parameters      // boolean: dump parameters
+    outdir               //    path: base directory used to publish pipeline results
     check_conda_channels // boolean: check conda channels
 
     main:
@@ -72,12 +72,24 @@ 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)
-    temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr)
-
-    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    def filename  = "params_${timestamp}.json"
+    def temp_pf       = workflow.launchDir.resolve(".${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)
+    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()
 }
 
@@ -111,8 +123,7 @@ def checkCondaChannels() {
     def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn(
-            """\
+        log.warn """\
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
             There is a problem with your Conda configuration!
             You will need to set-up the conda-forge and bioconda channels correctly.
@@ -123,6 +134,5 @@ def checkCondaChannels() {
             ${required_channels_in_order}
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         """.stripIndent(true)
-        )
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index bf568a0..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
 }
 
 /*
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 17a8a01..0d9d4e0 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -2,25 +2,31 @@
 // Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
 //
 
-include { paramsSummaryLog } from 'plugin/nf-schema'
+include { paramsSummaryLog   } from 'plugin/nf-schema'
 include { validateParameters } from 'plugin/nf-schema'
-include { paramsHelp } from 'plugin/nf-schema'
+include { paramsHelp         } from 'plugin/nf-schema'
 
 workflow UTILS_NFSCHEMA_PLUGIN {
+
     take:
-    input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow
-    validate_params // boolean:  validate the parameters
-    parameters_schema // string:   path to the parameters JSON schema.
-    help // boolean:  show help message
-    help_full // boolean:  show full help message
-    show_hidden // boolean:  show hidden parameters in help message
-    before_text // string:   text to show before the help message and parameters summary
-    after_text // string:   text to show after the help message and parameters summary
-    command // string:   an example command of the pipeline
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+    help                // boolean:  show help message
+    help_full           // boolean:  show full help message
+    show_hidden         // boolean:  show hidden parameters in help message
+    before_text         // string:   text to show before the help message and parameters summary
+    after_text          // string:   text to show after the help message and parameters summary
+    command             // string:   an example command of the pipeline
+    cli_typecast        // boolean:  whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour
 
     main:
 
-    if (help || help_full) {
+    if(help || help_full) {
         help_options = [
             beforeText: before_text,
             afterText: after_text,
@@ -28,16 +34,14 @@ workflow UTILS_NFSCHEMA_PLUGIN {
             showHidden: show_hidden,
             fullHelp: help_full,
         ]
-        if (parameters_schema) {
+        if(parameters_schema) {
             help_options << [parametersSchema: parameters_schema]
         }
-        log.info(
-            paramsHelp(
-                help_options,
-                params.help instanceof String && params.help != "true" ? params.help : "",
-            )
+        log.info paramsHelp(
+            help_options,
+            (help instanceof String && help != "true") ? help : "",
         )
-        exit(0)
+        exit 0
     }
 
     //
@@ -46,22 +50,25 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     //
 
     summary_options = [:]
-    if (parameters_schema) {
+    if(parameters_schema) {
         summary_options << [parametersSchema: parameters_schema]
     }
-    log.info(before_text)
-    log.info(paramsSummaryLog(summary_options, input_workflow))
-    log.info(after_text)
+    log.info before_text
+    log.info paramsSummaryLog(summary_options, input_workflow)
+    log.info after_text
 
     //
     // Validate the parameters using nextflow_schema.json or the schema
     // given via the validation.parametersSchema configuration option
     //
-    if (validate_params) {
+    if(validate_params) {
         validateOptions = [:]
-        if (parameters_schema) {
+        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 8d5c319..890fac6 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,10 +1,11 @@
 .DS_Store
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/multiqc_data/BETA-multiqc.parquet
+multiqc/multiqc_data/multiqc.parquet
 multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 multiqc/multiqc_data/llms-full.txt
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 61d2235..e181c87 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -13,21 +13,19 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', '**/*.log', '**/*.biom'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore',  ignore: ['**/*.log', '**/*.biom'])
+            // 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_funcprofiler_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/workflows/funcprofiler.nf b/workflows/funcprofiler.nf
index 371c4af..d730b0f 100644
--- a/workflows/funcprofiler.nf
+++ b/workflows/funcprofiler.nf
@@ -9,28 +9,6 @@ include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pi
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_funcprofiler_pipeline'
 
-// Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.databases,
-//                            params.longread_hostremoval_index,
-//                            params.hostremoval_reference, params.shortread_hostremoval_index,
-//                            params.multiqc_config, params.shortread_qc_adapterlist,
-//                            params.krona_taxonomy_directory,
-//                            params.taxpasta_taxonomy_dir,
-//                            params.multiqc_logo, params.multiqc_methods_description
-                        ]
-checkPathParamList.each{param ->
-    if (param) { file(param, checkIfExists: true) }
-}
-
-// Check mandatory parameters (stolen from taxprofiler
-if ( params.input ) {
-    ch_input              = file(params.input, checkIfExists: true)
-} else {
-    error("Input samplesheet not specified")
-}
-
-if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { error('Input database sheet not specified!') }
-
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -69,14 +47,16 @@ workflow FUNCPROFILER {
     take:
     samplesheet // channel: samplesheet read in from --input
     databases // channel: databases from --databases
+    multiqc_config
+    multiqc_logo
+    multiqc_methods_description
+    outdir
 
     main:
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-
-
     DATAPREP (
 	samplesheet
     )
@@ -90,69 +70,35 @@ workflow FUNCPROFILER {
 	DBPREP.out.dbs
     )
 
-   softwareVersionsToYAML(ch_versions)
+    def ch_collated_versions = softwareVersionsToYAML(ch_versions)
         .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
+            storeDir: "${outdir}/pipeline_info",
             name: 'nf_core_'  +  'funcprofiler_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
-        ).set { ch_collated_versions }
-
+        )
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
-        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
-    ch_multiqc_logo          = params.multiqc_logo ?
-        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        Channel.empty()
-
-    def summary_params      = paramsSummaryMap(
-        workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
-        file(params.multiqc_methods_description, checkIfExists: true) :
-        file("$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
-        )
-    )
-
-
-
-    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
-
-    // 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("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
-    // def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    // ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
-
+    def ch_summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def ch_workflow_summary = channel.value(paramsSummaryMultiqc(ch_summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    def ch_multiqc_custom_methods_description = multiqc_methods_description
+        ? file(multiqc_methods_description, checkIfExists: true)
+        : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
     MULTIQC(
         ch_multiqc_files.flatten().collect().map { files ->
             [
                 [id: 'funcprofiler'],
                 files,
-                params.multiqc_config
-                    ? file(params.multiqc_config, checkIfExists: true)
+                multiqc_config
+                    ? file(multiqc_config, checkIfExists: true)
                     : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true),
-                params.multiqc_logo ? file(params.multiqc_logo, checkIfExists: true) : [],
+                multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [],
                 [],
                 [],
             ]
@@ -163,7 +109,6 @@ workflow FUNCPROFILER {
     multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html
 
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
-
 }
 
 /*