diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 97c8c97f..237c9ed0 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore",
     "image": "nfcore/devcontainer:latest",
 
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
deleted file mode 100644
index 358d2650..00000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,125 +0,0 @@
-# `nf-core/references`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving nf-core/references.
-
-We try to manage the required tasks for nf-core/references 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/references then the best place to ask is on the nf-core Slack [#references](https://nfcore.slack.com/channels/references) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Contribution workflow
-
-If you'd like to write some code for nf-core/references, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [nf-core/references issues](https://github.com/nf-core/references/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/references repository](https://github.com/nf-core/references) 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/references documentation](https://nf-co.re/references/usage) and don't hesitate to get in touch on the nf-core Slack [#references](https://nfcore.slack.com/channels/references) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Pipeline contribution conventions
-
-To make the `nf-core/references` 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/references/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 034a6fc9..ca8b406f 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/references/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/references/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/references/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/references/tree/main/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/references _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 34085279..e2833ee9 100644
--- a/.github/actions/get-shards/action.yml
+++ b/.github/actions/get-shards/action.yml
@@ -21,7 +21,7 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 3b9724c7..ad686e8e 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -20,24 +20,24 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
         python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,7 +48,7 @@ runs:
 
     - name: Conda setup
       if: contains(inputs.profile, 'conda')
-      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
         auto-update-conda: true
         conda-solver: libmamba
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index f6366711..5c83e2c1 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -23,7 +23,7 @@ jobs:
           echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
@@ -33,14 +33,33 @@ jobs:
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
           workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/references/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'references'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *references/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *references/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/references/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 18f73be8..fa15547e 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Seqera Platform CLI tool action
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 705a8ecb..9451d06f 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/build_reference.yml b/.github/workflows/build_reference.yml
deleted file mode 100644
index 01d6c9ca..00000000
--- a/.github/workflows/build_reference.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: Build reference genomes that changed
-on:
-  push:
-    branches:
-      - main
-    paths:
-      - "assets/genomes/*.yml"
-
-jobs:
-  run-tower:
-    name: Run AWS full tests
-    if: github.repository == 'nf-core/nascent'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Find changed genomes
-        id: changed-genome-files
-        uses: tj-actions/changed-files@v42
-        with:
-          files: |
-            assets/genomes/*.yml
-      - name: Concatinate all the yamls together
-        if: steps.changed-files-specific.outputs.any_changed == 'true'
-        env:
-          CHANGED_FILES: ${{ steps.changed-files-specific.outputs.all_changed_files }}
-        run: cat ${CHANGED_FILES} > samplesheet.yml
-      # - name: Upload samplesheet.yml to s3 or Tower Datasets
-      #   run: TODO
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
-        with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_SCRATCH_BUCKET }}/work
-          parameters: |
-            {
-              "input": "samplesheet.yml"
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nascent/results-${{ github.sha }}"
-            }
-          profiles: cloud
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: Tower debug log file
-          path: |
-            tower_action_*.log
-            tower_action_*.json
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 6adb0fff..172de6f3 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
+      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 45884ff9..5b6592c1 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -39,12 +39,12 @@ jobs:
     needs: configure
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
@@ -54,10 +54,16 @@ jobs:
         with:
           apptainer-version: 1.3.4
 
+      - name: Read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Make a cache directory for the container images
         run: |
@@ -127,7 +133,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 6c8fcc16..0ec6677b 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -31,22 +31,18 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
+      # Install and run prek
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -54,7 +50,7 @@ jobs:
 
       - name: Commit & push changes
         id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a34..8738ffc9 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,33 +11,31 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
@@ -45,12 +43,10 @@ jobs:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -58,7 +54,7 @@ jobs:
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc26..5b0c24f7 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
+        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index fd742d1b..13d9851d 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.5"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.10.0"
-          - "latest-everything"
+          - 26.04.0
+          - latest-everything
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 431d3d44..78d5dbe0 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@master
+      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)
@@ -34,7 +34,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
+      - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index e8560fc7..ea30827e 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
@@ -29,7 +29,7 @@ jobs:
         run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with:
@@ -42,5 +42,5 @@ jobs:
             > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
             > Please update your pipeline to the latest version.
             >
-            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
           #
diff --git a/.gitignore b/.gitignore
index 2adaff46..a35a3b66 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,8 +7,11 @@ testing/
 testing*
 *.pyc
 null/
+.lineage/
 .idea
 *.log
 tmp/
 .nf-test
 .vscode
+modules/nf-*/**/tests/
+subworkflows/nf-*/**/tests/
diff --git a/.nf-core.yml b/.nf-core.yml
index ed2fd060..2e7bf6bf 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -9,7 +9,7 @@ lint:
     - assets/nf-core-references_logo_light.png
     - docs/images/nf-core-references_logo_light.png
     - docs/images/nf-core-references_logo_dark.png
-nf_core_version: 3.5.1
+nf_core_version: 4.0.1
 repository_type: pipeline
 template:
   author: "@maxulysse"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d06777a8..f51e1a28 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.6.2
+          - prettier@3.8.3
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -13,15 +13,21 @@ repos:
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
       - id: end-of-file-fixer
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
+        args: ["-output", "json"]
diff --git a/.prettierignore b/.prettierignore
index dd749d43..63cde500 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/
diff --git a/README.md b/README.md
index 3c108428..e4d3aaa4 100644
--- a/README.md
+++ b/README.md
@@ -7,22 +7,17 @@
 
 [![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/references)
 [![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/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/references/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14576225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14576225)
+[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/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/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14576225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14576225)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![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/references)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)
-[![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)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![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)
 
 ## Introduction
 
@@ -79,7 +74,7 @@ Datasheets are stored in [references-datasheets](https://github.com/nf-core/refe
 ## Running
 
 > [!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.
 
 `asset.yml`:
 
@@ -107,7 +102,7 @@ nextflow run nf-core/references \
 ```
 
 > [!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/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).
 
@@ -132,7 +127,7 @@ 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 `#references` channel](https://nfcore.slack.com/channels/references) (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 3082847d..00000000
--- a/assets/adaptivecard.json
+++ /dev/null
@@ -1,67 +0,0 @@
-{
-    "type": "message",
-    "attachments": [
-        {
-            "contentType": "application/vnd.microsoft.card.adaptive",
-            "contentUrl": null,
-            "content": {
-                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
-                "msteams": {
-                    "width": "Full"
-                },
-                "type": "AdaptiveCard",
-                "version": "1.2",
-                "body": [
-                    {
-                        "type": "TextBlock",
-                        "size": "Large",
-                        "weight": "Bolder",
-                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "nf-core/references v${version} - ${runName}",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "spacing": "None",
-                        "text": "Completed at ${dateComplete} (duration: ${duration})",
-                        "isSubtle": true,
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "The command used to launch the workflow was as follows:",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "${commandLine}",
-                        "isSubtle": true,
-                        "wrap": true
-                    }
-                ],
-                "actions": [
-                    {
-                        "type": "Action.ShowCard",
-                        "title": "Pipeline Configuration",
-                        "card": {
-                            "type": "AdaptiveCard",
-                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
-                            "body": [
-                                {
-                                    "type": "FactSet",
-                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
-                                    ]
-                                }
-                            ]
-                        }
-                    }
-                ]
-            }
-        }
-    ]
-}
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index f7e97e9d..00000000
--- a/assets/slackreport.json
+++ /dev/null
@@ -1,34 +0,0 @@
-{
-    "attachments": [
-        {
-            "fallback": "Plain-text summary of the attachment.",
-            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/references ${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 ffd5ffa6..a34f0f1a 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/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
new file mode 100644
index 00000000..a9ecd5d6
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,185 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `nf-core/references`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving nf-core/references.
+
+This page describes the recommended nf-core way to contribute to both nf-core/references 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/references.
+
+> [!NOTE]
+> If you need help using or modifying nf-core/references, ask on the nf-core Slack [#references](https://nfcore.slack.com/channels/references) 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/references/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/references repository](https://github.com/nf-core/references) 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/references documentation](https://nf-co.re/references/usage) or ask on the nf-core [#references](https://nfcore.slack.com/channels/references) Slack channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+### GitHub Codespaces
+
+You can contribute to nf-core/references 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/references/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/references code and processing logic more understandable for new contributors and to ensure quality.
+
+#### Add a new pipeline step
+
+To contribute a new step to the pipeline, follow the general nf-core coding procedure.
+Please also refer to the [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines):
+
+- [ ] Define the corresponding [input channel](#channel-naming-schemes) into your new process from the expected previous process channel.
+- [ ] Install a module with nf-core/tools, or write a local module (see [default processes resource requirements](#default-processes-resource-requirements)), and add it to the target `<workflow>.nf`.
+- [ ] Define the output channel if needed. Mix the version output channel into `ch_versions` and relevant files into `ch_multiqc`.
+- [ ] Add new or updated parameters to `nextflow.config` with a [default value](#default-parameter-values).
+- [ ] Add new or updated parameters and relevant help text to `nextflow_schema.json` with [nf-core/tools](#default-parameter-values).
+- [ ] Add validation for relevant parameters to the pipeline utilisation section of `utils_nfcore_\_pipeline/main.nf` subworkflow.
+- [ ] Perform local tests to validate that the new code works as expected.
+  - [ ] If applicable, add a new test in the `tests` directory.
+- [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate.
+- [ ] [Lint](lint) the code with nf-core/tools.
+- [ ] Update any diagrams or pipeline images as necessary.
+- [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order.
+- [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module.
+- [ ] Add a description of the output files and, if relevant, images from the MultiQC report to `docs/output.md`.
+
+To update the minimum required Nextflow version, see the [Nextflow version bumping](#nextflow-version-bumping) section below. For more information about pipeline contributions, see [pipeline-specific contribution guidelines](#pipeline-specific-contribution-guidelines).
+
+#### Channel naming schemes
+
+Use the following naming schemes for channels to make the channel flow easier to understand:
+
+- Initial process channel: `ch_output_from_<process>`
+- Intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+
+#### Default parameter values
+
+Parameters should be initialised and defined with default values within the `params` scope in `nextflow.config`.
+They should also be documented in the pipeline JSON schema.
+
+To update `nextflow_schema.json`, run:
+
+```bash
+nf-core pipelines schema build
+```
+
+The schema builder interface that loads in your browser should automatically update the defaults in the parameter documentation.
+
+#### Default processes resource requirements
+
+If you write a local module, specify a default set of resource requirements for the process.
+
+Sensible defaults for process resource requirements (CPUs, memory, time) should be defined in `conf/base.config`.
+Specify these with generic `withLabel:` selectors, so they can be shared across multiple processes and steps of the pipeline.
+
+nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
+These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements.
+
+Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+
+#### Nextflow version bumping
+
+If you use a new feature from core Nextflow, bump the minimum required Nextflow version in the pipeline with:
+
+```bash
+nf-core pipelines bump-version --nextflow . <min_nf_version>
+```
+
+#### Images and figures guidelines
+
+If you update images or graphics, follow the nf-core [style guidelines](https://nf-co.re/docs/community/brand/workflow-schematics).
+
+## Pipeline specific contribution guidelines
+
+<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->
diff --git a/docs/usage.md b/docs/usage.md
index 6ed95620..a0c8d49a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -52,7 +52,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
 > [!WARNING]
-> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -148,19 +148,19 @@ 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 63352508..ab9440c1 100644
--- a/main.nf
+++ b/main.nf
@@ -15,17 +15,20 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { ARCHIVE_EXTRACT         } from './subworkflows/nf-core/archive_extract'
-include { DATASHEET_TO_CHANNEL    } from './subworkflows/local/datasheet_to_channel'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_references_pipeline'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_references_pipeline'
-include { REFERENCES              } from "./workflows/references"
+include { ARCHIVE_EXTRACT                                } from './subworkflows/nf-core/archive_extract'
+include { NCBIDATASETSCLI_DATASETS as NCBIDOWNLOAD_FASTA } from './modules/local/ncbidatasetscli/datasets'
+include { NCBIDATASETSCLI_DATASETS as NCBIDOWNLOAD_GFF   } from './modules/local/ncbidatasetscli/datasets'
+include { NCBIDATASETSCLI_DATASETS as NCBIDOWNLOAD_GTF   } from './modules/local/ncbidatasetscli/datasets'
+include { DATASHEET_TO_CHANNEL                           } from './subworkflows/local/datasheet_to_channel'
+include { PIPELINE_COMPLETION                            } from './subworkflows/local/utils_nfcore_references_pipeline'
+include { PIPELINE_INITIALISATION                        } from './subworkflows/local/utils_nfcore_references_pipeline'
+include { REFERENCES                                     } from "./workflows/references"
 
 // MULTIQC & versions
-include { MULTIQC                 } from './modules/nf-core/multiqc'
-include { softwareVersionsToYAML  } from 'plugin/nf-core-utils'
-include { methodsDescriptionText  } from './subworkflows/local/utils_nfcore_references_pipeline'
-include { paramsSummaryMap        } from 'plugin/nf-schema'
+include { MULTIQC                                        } from './modules/nf-core/multiqc'
+include { softwareVersionsToYAML                         } from 'plugin/nf-core-utils'
+include { methodsDescriptionText                         } from './subworkflows/local/utils_nfcore_references_pipeline'
+include { paramsSummaryMap                               } from 'plugin/nf-schema'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -50,9 +53,18 @@ workflow NFCORE_REFERENCES {
     ascat_loci_gc_input = need_extract(DATASHEET_TO_CHANNEL.out.ascat_loci_gc, 'ascat_loci_gc')
     ascat_loci_rt_input = need_extract(DATASHEET_TO_CHANNEL.out.ascat_loci_rt, 'ascat_loci_rt')
     chr_dir_input = need_extract(DATASHEET_TO_CHANNEL.out.chr_dir, 'chr_dir')
-    fasta_input = need_extract(DATASHEET_TO_CHANNEL.out.fasta, 'fasta')
-    gff_input = need_extract(DATASHEET_TO_CHANNEL.out.gff, 'gff')
-    gtf_input = need_extract(DATASHEET_TO_CHANNEL.out.gtf, 'gtf')
+
+    fasta_download_input = need_ncbi_download(DATASHEET_TO_CHANNEL.out.fasta, 'fasta')
+    gff_download_input = need_ncbi_download(DATASHEET_TO_CHANNEL.out.gff, 'gff')
+    gtf_download_input = need_ncbi_download(DATASHEET_TO_CHANNEL.out.gtf, 'gtf')
+
+    NCBIDOWNLOAD_FASTA(fasta_download_input.to_download.map { meta, _file -> [meta + [accession: meta.source_version], 'genome'] })
+    NCBIDOWNLOAD_GFF(gff_download_input.to_download.map { meta, _file -> [meta + [accession: meta.source_version], 'gff3'] })
+    NCBIDOWNLOAD_GTF(gtf_download_input.to_download.map { meta, _file -> [meta + [accession: meta.source_version], 'gtf'] })
+
+    fasta_input = need_extract(fasta_download_input.not_downloaded, 'fasta')
+    gff_input = need_extract(gff_download_input.not_downloaded, 'gff')
+    gtf_input = need_extract(gtf_download_input.not_downloaded, 'gtf')
 
     // gather all archived references
     archive_to_extract = channel.empty()
@@ -101,12 +113,12 @@ workflow NFCORE_REFERENCES {
         ascat_loci_gc_input.not_extracted.mix(extracted_reference.ascat_loci_gc),
         ascat_loci_rt_input.not_extracted.mix(extracted_reference.ascat_loci_rt),
         chr_dir_input.not_extracted.mix(extracted_reference.chr_dir),
-        fasta_input.not_extracted.mix(extracted_reference.fasta),
+        fasta_input.not_extracted.mix(extracted_reference.fasta, NCBIDOWNLOAD_FASTA.out.fna),
         DATASHEET_TO_CHANNEL.out.fasta_dict,
         DATASHEET_TO_CHANNEL.out.fasta_fai,
         DATASHEET_TO_CHANNEL.out.fasta_sizes,
-        gff_input.not_extracted.mix(extracted_reference.gff),
-        gtf_input.not_extracted.mix(extracted_reference.gtf),
+        gff_input.not_extracted.mix(extracted_reference.gff, NCBIDOWNLOAD_GFF.out.gff),
+        gtf_input.not_extracted.mix(extracted_reference.gtf, NCBIDOWNLOAD_GTF.out.gtf),
         DATASHEET_TO_CHANNEL.out.intervals_bed,
         DATASHEET_TO_CHANNEL.out.splice_sites,
         DATASHEET_TO_CHANNEL.out.transcript_fasta,
@@ -132,6 +144,7 @@ workflow {
     PIPELINE_INITIALISATION(
         params.version,
         params.validate_params,
+        params.monochrome_logs,
         args,
         params.outdir,
         params.input,
@@ -161,30 +174,37 @@ workflow {
         newLine: true,
     )
 
-    // methods description
-    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)).collectFile(name: 'methods_description_mqc.yaml', sort: true)
+    // MODULE: MultiQC
+    def multiqc_report = channel.empty()
 
-    // workflow summary
-    ch_workflow_summary = channel.value(paramsSummaryMultiqc(paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json"))).collectFile(name: 'workflow_summary_mqc.yaml')
+    // MULTIQC
+    def multiqc_files = channel.empty()
 
-    ch_multiqc_files = channel.empty()
+    multiqc_files = multiqc_files.mix(collated_versions)
 
-    ch_multiqc_config = channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config = params.multiqc_config ? channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty()
-    ch_multiqc_logo = params.multiqc_logo ? channel.fromPath(params.multiqc_logo, checkIfExists: true) : channel.empty()
-    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary)
-    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description)
-    ch_multiqc_files = ch_multiqc_files.mix(collated_versions)
+    def summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
+    def multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    def methods_description = channel.value(methodsDescriptionText(multiqc_custom_methods_description))
+
+    multiqc_files = multiqc_files.mix(workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    multiqc_files = multiqc_files.mix(methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
 
     MULTIQC(
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList(),
-        [],
-        [],
+        multiqc_files.flatten().collect().map { files ->
+            [
+                [id: 'references'],
+                files,
+                params.multiqc_config
+                    ? file(params.multiqc_config, checkIfExists: true)
+                    : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true),
+                params.multiqc_logo ? file(params.multiqc_logo, checkIfExists: true) : [],
+                [],
+                [],
+            ]
+        }
     )
+    multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList()
 
     // SUBWORKFLOW: Run completion tasks
     PIPELINE_COMPLETION(
@@ -193,13 +213,12 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         MULTIQC.out.report.toList(),
     )
 
     publish:
     multiqc    = MULTIQC.out.data.mix(MULTIQC.out.plots, MULTIQC.out.report)
-    references = NFCORE_REFERENCES.out.references.filter { _meta, file -> !(file instanceof String) }.map { meta, file ->
+    references = NFCORE_REFERENCES.out.references.filter { _meta, file -> !(file instanceof String) }.filter { _meta, file -> !(file.toString().startsWith('/nf-core')) }.map { meta, file ->
         // Filter out the run_ keys from the meta for a clearer index file
         def invalid_keys = meta.keySet().findAll { key -> key.startsWith('run_') }
 
@@ -267,7 +286,7 @@ workflow {
             path = "Annotation/${meta.source_vcf}/${file.fileName}"
         }
 
-        [meta + [path: "${meta.species}/${meta.source}/${meta.genome}/${path}"] - meta.subMap(invalid_keys), file]
+        [meta + [path: path] - meta.subMap(invalid_keys), file]
     }
 }
 
@@ -276,12 +295,13 @@ output {
         path "multiqc"
     }
     references {
-        path { meta, path -> path >> meta.path }
-
         index {
             path "index.json"
             sep ":"
         }
+        path { meta, path ->
+            path >> "${meta.species}/${meta.source}/${meta.genome}/${meta.path}"
+        }
     }
 }
 
@@ -336,3 +356,15 @@ def need_extract(channel, type) {
             not_extracted: true
         }
 }
+
+// Helper function to check if a reference needs to be downloaded from ncbi
+// Add the reference type to the meta
+// Depending on the extension, return the appropriate channel
+def need_ncbi_download(channel, type) {
+    return channel
+        .map { meta, reference_ -> [meta + [reference: type], reference_] }
+        .branch { _meta, reference_ ->
+            to_download: reference_.toString().contains('ncbi.nlm.nih.gov')
+            not_downloaded: true
+        }
+}
diff --git a/modules.json b/modules.json
index 86077cfa..195c1371 100644
--- a/modules.json
+++ b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "0902eac3012baaf4f9ab6513c8c55acc9353c96c",
                         "installed_by": ["archive_extract"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["archive_extract"]
                     },
                     "unzip": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["archive_extract"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "archive_extract": {
                         "branch": "master",
-                        "git_sha": "875cffac4d196e4811d8a8d6b6fa55da513b885e",
+                        "git_sha": "1298fbd2004c2913d6682ce4a419647d97a8fc3f",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/local/ncbidatasetscli/datasets/environment.yml b/modules/local/ncbidatasetscli/datasets/environment.yml
new file mode 100644
index 00000000..18474328
--- /dev/null
+++ b/modules/local/ncbidatasetscli/datasets/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+dependencies:
+  - conda-forge::ncbi-datasets-cli=18.25.0
+  - conda-forge::p7zip=16.02
diff --git a/modules/local/ncbidatasetscli/datasets/main.nf b/modules/local/ncbidatasetscli/datasets/main.nf
new file mode 100644
index 00000000..9fdbf7fd
--- /dev/null
+++ b/modules/local/ncbidatasetscli/datasets/main.nf
@@ -0,0 +1,33 @@
+process NCBIDATASETSCLI_DATASETS {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1a/1aa4bda9c572b2003c96a5710c07d6d793f96fdea0336fa5c750be2da2e8aed6/data'
+        : 'community.wave.seqera.io/library/ncbi-datasets-cli_p7zip:f0c05932b8712591'}"
+
+    input:
+    tuple val(meta), val(reference)
+
+    output:
+    tuple val(meta), path("*enomic.fna"), emit: fna, optional: true
+    tuple val(meta), path("*enomic.gff"), emit: gff, optional: true
+    tuple val(meta), path("*enomic.gtf"), emit: gtf, optional: true
+    tuple val("${task.process}"), val('ncbidatasetscli'), eval('datasets --version'), topic: versions, emit: versions_ncbidatasetscli
+    tuple val("${task.process}"), val('gunzip'), eval('gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//"'), topic: versions, emit: versions_gunzip
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    datasets download genome accession ${meta.accession} --reference --include ${reference}
+    7za \\
+        x \\
+        -o"data"/ \\
+        ncbi_dataset.zip
+
+    mv data/ncbi_dataset/data/${meta.accession}/* .
+    """
+}
diff --git a/modules/local/ncbidatasetscli/datasets/meta.yml b/modules/local/ncbidatasetscli/datasets/meta.yml
new file mode 100644
index 00000000..500d6adc
--- /dev/null
+++ b/modules/local/ncbidatasetscli/datasets/meta.yml
@@ -0,0 +1,66 @@
+name: ncbi-datasets-cli
+description: Compresses and decompresses files.
+keywords:
+  - ncbi-datasets-cli
+tools:
+  - ncbi-datasets-cli:
+      description: |
+        gzip is a file format and a software application used for file compression and decompression.
+      documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+      licence: ["GPL-3.0-or-later"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Optional groovy Map containing meta information
+          e.g. [ id:'test', single_end:false ]
+    - reference:
+        type: string
+        description: reference to download
+        pattern: "*.*"
+        ontologies: []
+output:
+  gunzip:
+    - - meta:
+          type: file
+          description: Compressed/uncompressed file
+          pattern: "*.*"
+          ontologies: []
+      - ${gunzip}:
+          type: file
+          description: Compressed/uncompressed file
+          pattern: "*.*"
+          ontologies: []
+  versions_gunzip:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - gunzip:
+          type: string
+          description: The tool name
+      - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - gunzip:
+          type: string
+          description: The tool name
+      - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+  - "@gallvp"
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 3ffc8e92..6edffc59 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -3,7 +3,7 @@ process GUNZIP {
     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'}"
 
@@ -12,15 +12,16 @@ process GUNZIP {
 
     output:
     tuple val(meta), path("${gunzip}"), emit: gunzip
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('gunzip'), eval('gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//"'), topic: versions, emit: versions_gunzip
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def extension = (archive.toString() - '.gz').tokenize('.')[-1]
-    def name = archive.toString() - '.gz' - ".${extension}"
+    def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name
+	def extension = file(nameWithoutGz).extension
+	def name = file(nameWithoutGz).baseName
     def prefix = task.ext.prefix ?: name
     gunzip = prefix + ".${extension}"
     """
@@ -32,24 +33,15 @@ process GUNZIP {
         ${args} \\
         ${archive} \\
         > ${gunzip}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def extension = (archive.toString() - '.gz').tokenize('.')[-1]
-    def name = archive.toString() - '.gz' - ".${extension}"
+    def nameWithoutGz = archive.extension == 'gz' ? archive.baseName : archive.name
+	def extension = file(nameWithoutGz).extension
+	def name = file(nameWithoutGz).baseName
     def prefix = task.ext.prefix ?: name
     gunzip = prefix + ".${extension}"
     """
     touch ${gunzip}
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
index 926bb22a..bba6b3ba 100644
--- a/modules/nf-core/gunzip/meta.yml
+++ b/modules/nf-core/gunzip/meta.yml
@@ -34,13 +34,29 @@ output:
           description: Compressed/uncompressed file
           pattern: "*.*"
           ontologies: []
+  versions_gunzip:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - gunzip:
+          type: string
+          description: The tool name
+      - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - gunzip:
+          type: string
+          description: The tool name
+      - gunzip --version 2>&1 | head -1 | sed "s/^.*(gzip) //; s/ Copyright.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
new file mode 100644
index 00000000..a55a4d49
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
@@ -0,0 +1,126 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
new file mode 100644
index 00000000..f787dbe1
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
@@ -0,0 +1,125 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-aarch64
+@EXPLICIT
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+https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2
+https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2
+https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3
+https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351
+https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964
+https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8
+https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c
+https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b
+https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684
+https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98
+https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910
+https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372
+https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7
+https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88
+https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58
+https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240
+https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6
+https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98
+https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c
+https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2
+https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac
+https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130
+https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59
+https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0
+https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66
+https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9
+https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a
+https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864
+https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6
+https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206
+https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b
+https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873
+https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f
+https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index d02016a0..37e7612d 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.32
+  - bioconda::multiqc=1.34
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 5d0780af..e80e8cd8 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,24 +1,21 @@
 process MULTIQC {
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
-        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
+        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
 
     input:
-    path  multiqc_files, stageAs: "?/*"
-    path(multiqc_config)
-    path(extra_multiqc_config)
-    path(multiqc_logo)
-    path(replace_names)
-    path(sample_names)
+    tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
 
     output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
+    tuple val(meta), path("*.html"), emit: report
+    tuple val(meta), path("*_data"), emit: data
+    tuple val(meta), path("*_plots"), emit: plots, optional: true
+    // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,27 +23,20 @@ process MULTIQC {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
-    def config = multiqc_config ? "--config $multiqc_config" : ''
-    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : ""
     def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
     def replace = replace_names ? "--replace-names ${replace_names}" : ''
     def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
-        $args \\
-        $config \\
-        $prefix \\
-        $extra_config \\
-        $logo \\
-        $replace \\
-        $samples \\
+        ${args} \\
+        ${config} \\
+        ${prefix} \\
+        ${logo} \\
+        ${replace} \\
+        ${samples} \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
@@ -54,11 +44,7 @@ process MULTIQC {
     mkdir multiqc_data
     touch multiqc_data/.stub
     mkdir multiqc_plots
+    touch multiqc_plots/.stub
     touch multiqc_report.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ce30eb73..2facc627 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,6 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into
-  a single report
+description: Aggregate results from bioinformatics analyses across many samples
+  into a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,74 +12,91 @@ tools:
         It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
-      licence: ["GPL-3.0-or-later"]
+      licence:
+        - "GPL-3.0-or-later"
       identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-      ontologies: []
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-      ontologies:
-        - edam: http://edamontology.org/format_3750 # YAML
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections
-        in multiqc_config.
-      pattern: "*.{yml,yaml}"
-      ontologies:
-        - edam: http://edamontology.org/format_3750 # YAML
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-      ontologies: []
-  - replace_names:
-      type: file
-      description: |
-        Optional two-column sample renaming file. First column a set of
-        patterns, second column a set of corresponding replacements. Passed via
-        MultiQC's `--replace-names` option.
-      pattern: "*.{tsv}"
-      ontologies:
-        - edam: http://edamontology.org/format_3475 # TSV
-  - sample_names:
-      type: file
-      description: |
-        Optional TSV file with headers, passed to the MultiQC --sample_names
-        argument.
-      pattern: "*.{tsv}"
-      ontologies:
-        - edam: http://edamontology.org/format_3475 # TSV
-output:
-  report:
-    - "*multiqc_report.html":
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'sample1', single_end:false ]
+    - multiqc_files:
         type: file
-        description: MultiQC report file
-        pattern: "multiqc_report.html"
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
         ontologies: []
-  data:
-    - "*_data":
-        type: directory
-        description: MultiQC data dir
-        pattern: "multiqc_data"
-  plots:
-    - "*_plots":
+    - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+    - multiqc_logo:
         type: file
-        description: Plots created by MultiQC
-        pattern: "*_data"
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
         ontologies: []
-  versions:
-    - versions.yml:
+    - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+    - sample_names:
         type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3475
+output:
+  report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.html":
+          type: file
+          description: MultiQC report file
+          pattern: ".html"
+          ontologies: []
+  data:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
+  plots:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_plots"
+          ontologies: []
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - multiqc:
+          type: string
+          description: The tool name
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@abhi18av"
   - "@bunop"
@@ -90,3 +107,27 @@ maintainers:
   - "@bunop"
   - "@drpatelh"
   - "@jfy133"
+containers:
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
+      build_id: bd-db7c73dae76bc9e6_1
+      scan_id: sc-66fc7138dbf1cf48_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
+      build_id: bd-d167b8012595a136_1
+      scan_id: sc-ac701dfa631a2af9_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
+      build_id: bd-4fc8657c816047c0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
+      build_id: bd-7fbd82d945c06726_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index e712ebe6..bf2c056c 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -3,7 +3,7 @@ process UNTAR {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
         ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
         : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
@@ -12,7 +12,7 @@ process UNTAR {
 
     output:
     tuple val(meta), path("${prefix}"), emit: untar
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('untar'), eval('tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//"'), emit: versions_untar, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -43,10 +43,6 @@ process UNTAR {
             ${args2}
     fi
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -75,10 +71,5 @@ process UNTAR {
             fi
         done
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
index 1b6bf491..571d8078 100644
--- a/modules/nf-core/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -1,5 +1,5 @@
 name: untar
-description: Extract files.
+description: Extract files from tar, tar.gz, tar.bz2, tar.xz archives
 keywords:
   - untar
   - uncompress
@@ -7,7 +7,7 @@ keywords:
 tools:
   - untar:
       description: |
-        Extract tar.gz files.
+        Extract tar, tar.gz, tar.bz2, tar.xz files.
       documentation: https://www.gnu.org/software/tar/manual/
       licence: ["GPL-3.0-or-later"]
       identifier: ""
@@ -19,8 +19,8 @@ input:
           e.g. [ id:'test', single_end:false ]
     - archive:
         type: file
-        description: File to be untar
-        pattern: "*.{tar}.{gz}"
+        description: File to be untarred
+        pattern: "*.{tar,tar.gz,tar.bz2,tar.xz}"
         ontologies:
           - edam: http://edamontology.org/format_3981 # TAR format
           - edam: http://edamontology.org/format_3989 # GZIP format
@@ -38,13 +38,29 @@ output:
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
           pattern: "*/"
+  versions_untar:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - untar:
+          type: string
+          description: The name of the tool
+      - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - untar:
+          type: string
+          description: The name of the tool
+      - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf
index a0c02109..45c1910a 100644
--- a/modules/nf-core/unzip/main.nf
+++ b/modules/nf-core/unzip/main.nf
@@ -3,9 +3,9 @@ process UNZIP {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/p7zip:16.02' :
-        'biocontainers/p7zip:16.02' }"
+        'quay.io/biocontainers/p7zip:16.02' }"
 
     input:
     tuple val(meta), path(archive)
@@ -35,7 +35,6 @@ process UNZIP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
     prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName)
     """
diff --git a/nextflow.config b/nextflow.config
index 14ddfe72..01b7afe1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -29,12 +29,12 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
     version                      = false
     references_base_path         = null
+    modules_testdata_base_path   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
     trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
@@ -51,7 +51,7 @@ params {
     validate_params            = true
 }
 
-// workflow output
+// Backwards compatibility for publishDir syntax
 outputDir = params.outdir
 workflow.output.mode = params.publish_dir_mode
 
@@ -275,21 +275,21 @@ manifest {
     description     = """help community build references"""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=25.10.0'
+    nextflowVersion = '!>=26.04.0'
     version         = '0.2'
     doi             = '10.5281/zenodo.14576225'
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.6.1'     // Validation of pipeline parameters and creation of an input channel from a sample sheet
     id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
+    id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
+    defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
 }
-
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 includeConfig 'conf/prepare_genome.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a2eaaad5..83a606b4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -168,13 +168,6 @@
                     "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",
@@ -200,6 +193,13 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
+                "modules_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/",
+                    "hidden": true
+                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
diff --git a/nf-test.config b/nf-test.config
index 0950166e..3cc52321 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,25 +1,39 @@
 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/*', 'modules/nf-side/**/tests/*', 'subworkflows/nf-side/**/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 'conf/test.config', 'nextflow.config', 'nextflow_schema.json', 'nf-test.config', 'tests/.nftignore', 'tests/nextflow.config', '**/schema_references.json'
+    triggers = [
+        '.github/actions/nf-test/action.yml',
+        '.github/workflows/nf-test.yml',
+        'assets/schema_input.json',
+        'bin/*',
+        'conf/test.config',
+        'nextflow.config',
+        'nextflow_schema.json',
+        'nf-test.config',
+        'tests/.nftignore',
+        'tests/nextflow.config',
+    ]
 
     // load the necessary plugins
     plugins {
-        load "nft-utils@0.0.7"
+        load "nft-utils@0.0.9"
         load "nft-vcf@1.0.7"
     }
 }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 04d27e2c..f353f84e 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -1,6 +1,6 @@
 {
     "@context": [
-        "https://w3id.org/ro/crate/1.1/context",
+        "https://w3id.org/ro/crate/1.2/context",
         {
             "GithubService": "https://w3id.org/ro/terms/test#GithubService",
             "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
@@ -22,15 +22,12 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-11-20T13:44:12+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-references_logo_dark.png\">\n    <img alt=\"nf-core/references\" src=\"docs/images/nf-core-references_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/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/linting.yml)\n[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/references/results)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14576225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14576225)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)\n[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)\n[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)\n[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that build references.\n\nFor most common organisms references will be stored them in the cloud, similar to [AWS iGenomes](https://github.com/ewels/AWS-iGenomes/), to allow for fast and simple access and better reproducibility.\nReferences can also be built locally for any organisms.\n\n![nf-core/references metro map](docs/images/nf-core-references_metro_map_color.png)\n\n## DNASEQ\n\nFor DNASEQ pipelines (ie [nf-core/sarek](https://nf-co.re/sarek)), needing only a fasta file, it will be able to build the following references:\n\n- [BWA-MEM](https://arxiv.org/abs/1303.3997v2) index\n- [BWA-MEM2](https://ieeexplore.ieee.org/document/8820962) index\n- [DragMap](https://github.com/Illumina/DRAGMAP) hashtable\n- Fasta dictionary (with [GATK4](https://pubmed.ncbi.nlm.nih.gov/20644199/))\n- Fasta fai (with [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/))\n- Fasta intervals bed (with [GATK4](https://pubmed.ncbi.nlm.nih.gov/20644199/))\n- [MSISensorPro](https://www.sciencedirect.com/science/article/pii/S1672022920300218) list\n- [SNAP](https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1/) index\n\nIt will compress VCF files, if it was not already compressed, and tabix index it.\n\n- [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)\n\nAnd with metadata, it will be able to download annotation caches from:\n\n- [EnsemblVEP](https://pubmed.ncbi.nlm.nih.gov/27268795/)\n- [snpEff](https://pcingola.github.io/SnpEff/)\n\n## RNASEQ\n\nFor RNASEQ pipelines (ie [nf-core/rnaseq](https://nf-co.re/rnaseq) or [nf-core/rnavar](https://nf-co.re/rnavar)), providing additional files describing genes' structures (either GFF3 or GTF), it will be able to build the following references:\n\n- [Bowtie1](http://genomebiology.com/2009/10/3/R25) index\n- [Bowtie2](https://www.nature.com/articles/nmeth.1923) index\n- Fasta dictionary (with [GATK4](https://pubmed.ncbi.nlm.nih.gov/20644199/))\n- Fasta sizes (with [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/))\n- GTF (from GFF3 with [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/))\n- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/) index\n- [Kallisto](https://pachterlab.github.io/kallisto/) index\n- [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/) index\n- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) index\n- [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/) index\n- Splice sites (with [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/))\n- Transcript fasta (with [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/))\n\n## Datasheets\n\nDatasheets are stored in [references-datasheets](https://github.com/nf-core/references-datasheets).\n\n## Running\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n`asset.yml`:\n\n```yml\n- genome: GRCh38_chr21\n  fasta: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa\"\n  gtf: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf\"\n  source_version: \"CUSTOM\"\n  readme: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md\"\n  source: \"nf-core/references\"\n  source_vcf: \"GATK_BUNDLE\"\n  species: \"Homo_sapiens\"\n  vcf: \"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz\"\n```\n\nEach line represents a source for building a reference, a reference already built, or metadata.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/references \\\n   -profile <docker/singularity/.../institute> \\\n   --input datasheet.yml \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/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/references/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/references/output).\n\n## Credits\n\nnf-core/references was originally written by [Maxime U Garcia](https://github.com/maxulysse) | [Edmund Miller](https://github.com/edmundmiller) | [Phil Ewels](https://github.com/ewels).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Adam Talbot](https://github.com/adamrtalbot)\n- [Friederike Hanssen](https://github.com/FriederikeHanssen)\n- [Harshil Patel](https://github.com/drpatelh)\n- [James Fellows Yates](https://github.com/jfy133)\n- [Jonathan Manning](https://github.com/pinin4fjords)\n- [Nicolas Vannieuwkerke](https://github.com/nvnieuwk)\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 `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/references for your analysis, please cite it using the following doi: [10.5281/zenodo.14576225](https://doi.org/10.5281/zenodo.14576225)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-04-30T07:36:54+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-references_logo_dark.png\">\n    <img alt=\"nf-core/references\" src=\"docs/images/nf-core-references_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/references)\n[![GitHub Actions CI Status](https://github.com/nf-core/references/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/references/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/references/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/references/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/references/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14576225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14576225)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23references-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/references)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that build references.\n\nFor most common organisms references will be stored them in the cloud, similar to [AWS iGenomes](https://github.com/ewels/AWS-iGenomes/), to allow for fast and simple access and better reproducibility.\nReferences can also be built locally for any organisms.\n\n![nf-core/references metro map](docs/images/nf-core-references_metro_map_color.png)\n\n## DNASEQ\n\nFor DNASEQ pipelines (ie [nf-core/sarek](https://nf-co.re/sarek)), needing only a fasta file, it will be able to build the following references:\n\n- [BWA-MEM](https://arxiv.org/abs/1303.3997v2) index\n- [BWA-MEM2](https://ieeexplore.ieee.org/document/8820962) index\n- [DragMap](https://github.com/Illumina/DRAGMAP) hashtable\n- Fasta dictionary (with [GATK4](https://pubmed.ncbi.nlm.nih.gov/20644199/))\n- Fasta fai (with [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/))\n- Fasta intervals bed (with [GATK4](https://pubmed.ncbi.nlm.nih.gov/20644199/))\n- [MSISensorPro](https://www.sciencedirect.com/science/article/pii/S1672022920300218) list\n- [SNAP](https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1/) index\n\nIt will compress VCF files, if it was not already compressed, and tabix index it.\n\n- [Tabix](https://academic.oup.com/bioinformatics/article/27/5/718/262743)\n\nAnd with metadata, it will be able to download annotation caches from:\n\n- [EnsemblVEP](https://pubmed.ncbi.nlm.nih.gov/27268795/)\n- [snpEff](https://pcingola.github.io/SnpEff/)\n\n## RNASEQ\n\nFor RNASEQ pipelines (ie [nf-core/rnaseq](https://nf-co.re/rnaseq) or [nf-core/rnavar](https://nf-co.re/rnavar)), providing additional files describing genes' structures (either GFF3 or GTF), it will be able to build the following references:\n\n- [Bowtie1](http://genomebiology.com/2009/10/3/R25) index\n- [Bowtie2](https://www.nature.com/articles/nmeth.1923) index\n- Fasta dictionary (with [GATK4](https://pubmed.ncbi.nlm.nih.gov/20644199/))\n- Fasta sizes (with [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/))\n- GTF (from GFF3 with [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/))\n- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/) index\n- [Kallisto](https://pachterlab.github.io/kallisto/) index\n- [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/) index\n- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) index\n- [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/) index\n- Splice sites (with [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/))\n- Transcript fasta (with [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/))\n\n## Datasheets\n\nDatasheets are stored in [references-datasheets](https://github.com/nf-core/references-datasheets).\n\n## Running\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n`asset.yml`:\n\n```yml\n- genome: GRCh38_chr21\n  fasta: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa\"\n  gtf: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf\"\n  source_version: \"CUSTOM\"\n  readme: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md\"\n  source: \"nf-core/references\"\n  source_vcf: \"GATK_BUNDLE\"\n  species: \"Homo_sapiens\"\n  vcf: \"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz\"\n```\n\nEach line represents a source for building a reference, a reference already built, or metadata.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/references \\\n   -profile <docker/singularity/.../institute> \\\n   --input datasheet.yml \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/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/references/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/references/output).\n\n## Credits\n\nnf-core/references was originally written by [Maxime U Garcia](https://github.com/maxulysse) | [Edmund Miller](https://github.com/edmundmiller) | [Phil Ewels](https://github.com/ewels).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Adam Talbot](https://github.com/adamrtalbot)\n- [Friederike Hanssen](https://github.com/FriederikeHanssen)\n- [Harshil Patel](https://github.com/drpatelh)\n- [James Fellows Yates](https://github.com/jfy133)\n- [Jonathan Manning](https://github.com/pinin4fjords)\n- [Nicolas Vannieuwkerke](https://github.com/nvnieuwk)\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 `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/references for your analysis, please cite it using the following doi: [10.5281/zenodo.14576225](https://doi.org/10.5281/zenodo.14576225)\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"
                 },
-                {
-                    "@id": "docs/images/nf-core-references_metro_map_color.png"
-                },
                 {
                     "@id": "assets/"
                 },
@@ -102,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#5a35cf14-07e7-4cf2-9670-a8b7e98a4ffc"
+                    "@id": "#35c27ac5-ba08-4fc5-8c56-0fc212432378"
                 }
             ],
             "name": "nf-core/references"
@@ -115,7 +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"
@@ -129,12 +126,14 @@
                 "SoftwareSourceCode",
                 "ComputationalWorkflow"
             ],
+            "contributor": [
+                {
+                    "@id": "#acf498d1-a568-46fd-a16a-d61b2c70186b"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-11-20T14:44:12Z",
+            "dateModified": "2026-04-30T07:36:54Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "image": {
-                "@id": "docs/images/nf-core-references_metro_map_color.png"
-            },
             "keywords": [
                 "nf-core",
                 "nextflow",
@@ -172,22 +171,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.10.0"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "docs/images/nf-core-references_metro_map_color.png",
-            "@type": [
-                "File",
-                "ImageObject"
-            ],
-            "name": "Workflow diagram"
-        },
-        {
-            "@id": "#5a35cf14-07e7-4cf2-9670-a8b7e98a4ffc",
+            "@id": "#35c27ac5-ba08-4fc5-8c56-0fc212432378",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#c3164952-a469-484e-bb65-0395159cc065"
+                    "@id": "#dab1c7d4-bc70-4d03-b9f9-3547c29de632"
                 }
             ],
             "mainEntity": {
@@ -196,7 +187,7 @@
             "name": "Test suite for nf-core/references"
         },
         {
-            "@id": "#c3164952-a469-484e-bb65-0395159cc065",
+            "@id": "#dab1c7d4-bc70-4d03-b9f9-3547c29de632",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/references",
             "resource": "repos/nf-core/references/actions/workflows/nf-test.yml",
@@ -323,6 +314,11 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#acf498d1-a568-46fd-a16a-d61b2c70186b",
+            "@type": "Person",
+            "name": "@maxulysse"
         }
     ]
 }
\ No newline at end of file
diff --git a/subworkflows/local/datasheet_to_channel/main.nf b/subworkflows/local/datasheet_to_channel/main.nf
index 89b12735..d5239f04 100644
--- a/subworkflows/local/datasheet_to_channel/main.nf
+++ b/subworkflows/local/datasheet_to_channel/main.nf
@@ -12,7 +12,7 @@ workflow DATASHEET_TO_CHANNEL {
 
     ascat_alleles_branch = datasheet.branch { meta, _readme ->
         file: meta.ascat_alleles
-        return [reduceMeta(meta), meta.ascat_alleles]
+        return [reduceMeta(meta), file(meta.ascat_alleles, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -21,7 +21,7 @@ workflow DATASHEET_TO_CHANNEL {
 
     ascat_loci_branch = datasheet.branch { meta, _readme ->
         file: meta.ascat_loci
-        return [reduceMeta(meta), meta.ascat_loci]
+        return [reduceMeta(meta), file(meta.ascat_loci, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -30,7 +30,7 @@ workflow DATASHEET_TO_CHANNEL {
 
     ascat_loci_gc_branch = datasheet.branch { meta, _readme ->
         file: meta.ascat_loci_gc
-        return [reduceMeta(meta), meta.ascat_loci_gc]
+        return [reduceMeta(meta), file(meta.ascat_loci_gc, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -39,7 +39,7 @@ workflow DATASHEET_TO_CHANNEL {
 
     ascat_loci_rt_branch = datasheet.branch { meta, _readme ->
         file: meta.ascat_loci_rt
-        return [reduceMeta(meta), meta.ascat_loci_rt]
+        return [reduceMeta(meta), file(meta.ascat_loci_rt, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -48,7 +48,7 @@ workflow DATASHEET_TO_CHANNEL {
 
     chr_dir_branch = datasheet.branch { meta, _readme ->
         file: meta.chr_dir
-        return [reduceMeta(meta), meta.chr_dir]
+        return [reduceMeta(meta), file(meta.chr_dir, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -57,7 +57,7 @@ workflow DATASHEET_TO_CHANNEL {
 
     intervals_bed_branch = datasheet.branch { meta, _readme ->
         file: meta.intervals_bed
-        return [reduceMeta(meta), meta.intervals_bed]
+        return [reduceMeta(meta), file(meta.intervals_bed, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -82,7 +82,7 @@ workflow DATASHEET_TO_CHANNEL {
         meta_extra += [run_rsem_make_transcript_fasta: meta.transcript_fasta ? false : true]
         meta_extra += [run_salmon: meta.salmon_index ? false : true]
         meta_extra += [run_star: meta.star_index ? false : true]
-        return [reduceMeta(meta) + meta_extra, meta.fasta]
+        return [reduceMeta(meta) + meta_extra, meta.fasta.contains('ncbi.nlm.nih.gov') ? meta.fasta : file(meta.fasta, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -103,7 +103,7 @@ workflow DATASHEET_TO_CHANNEL {
         file: meta.fasta_fai
         // If we have intervals_bed, then we don't need to run faidx
         def meta_extra = [run_intervals: meta.intervals_bed ? false : true]
-        return [reduceMeta(meta) + meta_extra, meta.fasta_fai]
+        return [reduceMeta(meta) + meta_extra, file(meta.fasta_fai, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -125,7 +125,7 @@ workflow DATASHEET_TO_CHANNEL {
         // (gff, gtf or transcript_fasta)
         def meta_extra = [run_gffread: meta.fasta && !meta.gtf ?: false]
         meta_extra += [run_hisat2: meta.splice_sites ? false : true]
-        return [reduceMeta(meta) + meta_extra, meta.gff]
+        return [reduceMeta(meta) + meta_extra, meta.gtf.contains('ncbi.nlm.nih.gov') ? meta.gff : file(meta.gff, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -137,7 +137,7 @@ workflow DATASHEET_TO_CHANNEL {
         // If any of the reference exists, then adding run_tools to false and skip the reference creation from the annotation derived file
         // (gff, gtf or transcript_fasta)
         def meta_extra = [run_hisat2: meta.splice_sites ? false : true]
-        return [reduceMeta(meta) + meta_extra, meta.gtf]
+        return [reduceMeta(meta) + meta_extra, meta.gtf.contains('ncbi.nlm.nih.gov') ? meta.gtf : file(meta.gtf, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -162,7 +162,7 @@ workflow DATASHEET_TO_CHANNEL {
         meta_extra += [run_rsem: meta.rsem_index ? false : true]
         meta_extra += [run_salmon: meta.salmon_index ? false : true]
         meta_extra += [run_star: meta.star_index ? false : true]
-        return [reduceMeta(meta) + meta_extra, meta.transcript_fasta]
+        return [reduceMeta(meta) + meta_extra, file(meta.transcript_fasta, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -178,7 +178,7 @@ workflow DATASHEET_TO_CHANNEL {
         def meta_extra = [run_tabix: meta.vcf_dbsnp_vcf_tbi || meta.vcf_dbsnp_vcf.endsWith('.vcf') ? false : true]
         meta_extra += [run_bgziptabix: meta.vcf_dbsnp_vcf.endsWith('.vcf') ?: false]
         meta_extra += [type: 'dbsnp', source_vcf: meta.vcf_dbsnp_vcf_source]
-        return [reduceMeta(meta) + meta_extra, meta.vcf_dbsnp_vcf.contains('{') ? file(meta.vcf_dbsnp_vcf) : meta.vcf_dbsnp_vcf]
+        return [reduceMeta(meta) + meta_extra, files(meta.vcf_dbsnp_vcf, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -190,7 +190,7 @@ workflow DATASHEET_TO_CHANNEL {
         def meta_extra = [run_tabix: meta.vcf_germline_resource_vcf_tbi || meta.vcf_germline_resource_vcf.endsWith('.vcf') ? false : true]
         meta_extra += [run_bgziptabix: meta.vcf_germline_resource_vcf.endsWith('.vcf') ?: false]
         meta_extra += [type: 'germline_resource', source_vcf: meta.vcf_germline_resource_vcf_source]
-        return [reduceMeta(meta) + meta_extra, meta.vcf_germline_resource_vcf]
+        return [reduceMeta(meta) + meta_extra, file(meta.vcf_germline_resource_vcf, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -202,7 +202,7 @@ workflow DATASHEET_TO_CHANNEL {
         def meta_extra = [run_tabix: meta.vcf_known_indels_vcf_tbi || meta.vcf_known_indels_vcf.endsWith('.vcf') ? false : true]
         meta_extra += [run_bgziptabix: meta.vcf_known_indels_vcf.endsWith('.vcf') ?: false]
         meta_extra += [type: 'known_indels', source_vcf: meta.vcf_known_indels_vcf_source]
-        return [reduceMeta(meta) + meta_extra, meta.vcf_known_indels_vcf]
+        return [reduceMeta(meta) + meta_extra, file(meta.vcf_known_indels_vcf, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -214,7 +214,7 @@ workflow DATASHEET_TO_CHANNEL {
         def meta_extra = [run_tabix: meta.vcf_known_snps_vcf_tbi || meta.vcf_known_snps_vcf.endsWith('.vcf') ? false : true]
         meta_extra += [run_bgziptabix: meta.vcf_known_snps_vcf.endsWith('.vcf') ?: false]
         meta_extra += [type: 'known_snps', source_vcf: meta.vcf_known_snps_vcf_source]
-        return [reduceMeta(meta) + meta_extra, meta.vcf_known_snps_vcf]
+        return [reduceMeta(meta) + meta_extra, file(meta.vcf_known_snps_vcf, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
@@ -226,7 +226,7 @@ workflow DATASHEET_TO_CHANNEL {
         def meta_extra = [run_tabix: meta.vcf_pon_vcf_tbi || meta.vcf_pon_vcf.endsWith('.vcf') ? false : true]
         meta_extra += [run_bgziptabix: meta.vcf_pon_vcf.endsWith('.vcf') ?: false]
         meta_extra += [type: 'pon', source_vcf: meta.vcf_pon_vcf_source]
-        return [reduceMeta(meta) + meta_extra, meta.vcf_pon_vcf]
+        return [reduceMeta(meta) + meta_extra, file(meta.vcf_pon_vcf, checkIfExists: true)]
         other: true
         // If the reference doesn't exist, then we return nothing
         return null
diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf
index fda7095e..f0ce15c4 100644
--- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_references_pipeline/main.nf
@@ -17,7 +17,6 @@ include { completionEmail        } from 'plugin/nf-core-utils'
 include { completionSummary      } from 'plugin/nf-core-utils'
 include { dumpParametersToJSON   } from 'plugin/nf-core-utils'
 include { getWorkflowVersion     } from 'plugin/nf-core-utils'
-include { imNotification         } from 'plugin/nf-core-utils'
 
 include { paramsHelp             } from 'plugin/nf-schema'
 include { paramsSummaryLog       } from 'plugin/nf-schema'
@@ -35,6 +34,7 @@ workflow PIPELINE_INITIALISATION {
     take:
     version // boolean: Display version and exit
     validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
+    monochrome_logs // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir //  string: The output directory where the results will be saved
     asset //  string: Path to asset yaml file
@@ -64,6 +64,9 @@ workflow PIPELINE_INITIALISATION {
 
     // Validate parameters and generate parameter summary to stdout
     //
+
+    def before_text = ""
+    def after_text = ""
     before_text = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -81,6 +84,10 @@ workflow PIPELINE_INITIALISATION {
 * Software dependencies
     https://github.com/nf-core/references/blob/main/CITATIONS.md
 """
+    if (monochrome_logs) {
+        before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '')
+    }
+
     command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
     if (help || help_full) {
@@ -157,7 +164,6 @@ workflow PIPELINE_COMPLETION {
     plaintext_email // boolean: Send plain-text email instead of HTML
     outdir //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url //  string: hook URL for notifications
     multiqc_report //  string: Path to MultiQC report
 
     main:
@@ -181,13 +187,10 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
     }
 
     workflow.onError {
-        log.error("Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting")
+        log.error("Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting")
     }
 }
 
diff --git a/subworkflows/nf-core/archive_extract/main.nf b/subworkflows/nf-core/archive_extract/main.nf
index 13cd9e44..356750e9 100644
--- a/subworkflows/nf-core/archive_extract/main.nf
+++ b/subworkflows/nf-core/archive_extract/main.nf
@@ -7,7 +7,7 @@ workflow ARCHIVE_EXTRACT {
     archive // Channel: [[meta], archive]
 
     main:
-    versions = Channel.empty()
+    versions = channel.empty()
 
     archive_to_extract = archive.branch { _meta, archive_ ->
         tar: archive_.toString().endsWith('.tar.gz')
@@ -25,7 +25,7 @@ workflow ARCHIVE_EXTRACT {
     UNTAR(archive_to_extract.tar)
     UNZIP(archive_to_extract.zip)
 
-    extracted = Channel
+    extracted = channel
         .empty()
         .mix(
             GUNZIP.out.gunzip,
@@ -33,12 +33,10 @@ workflow ARCHIVE_EXTRACT {
             UNZIP.out.unzipped_archive,
         )
 
-    versions = versions.mix(GUNZIP.out.versions)
-    versions = versions.mix(UNTAR.out.versions)
     versions = versions.mix(UNZIP.out.versions)
 
     emit:
-    extracted     // channel: [ meta, extracted_archive ]
-    not_extracted // channel: [ meta, not_extracted_archive ]
+    extracted = extracted     // channel: [ meta, extracted_archive ]
+    not_extracted = not_extracted // channel: [ meta, not_extracted_archive ]
     versions      // channel: [ versions.yml ]
 }
diff --git a/tests/createsequencedictionary.nf.test b/tests/createsequencedictionary.nf.test
index 3e0a1ef3..c109da99 100644
--- a/tests/createsequencedictionary.nf.test
+++ b/tests/createsequencedictionary.nf.test
@@ -6,29 +6,31 @@ nextflow_pipeline {
 
     test("-profile test --tools createsequencedictionary") {
 
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
                 tools  = 'createsequencedictionary'
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/createsequencedictionary.nf.test.snap b/tests/createsequencedictionary.nf.test.snap
index 7338aca4..d58c75ee 100644
--- a/tests/createsequencedictionary.nf.test.snap
+++ b/tests/createsequencedictionary.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools createsequencedictionary": {
         "content": [
+            2,
             {
                 "GATK4_CREATESEQUENCEDICTIONARY": {
                     "gatk": "4.6.1.0"
@@ -32,10 +33,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:25:57.485529971",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:44:32.157311293"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 22a0d21c..baf8d395 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -5,28 +5,30 @@ nextflow_pipeline {
     tag "pipeline"
 
     test("-profile test") {
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 4669744b..5d61f771 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test": {
         "content": [
+            6,
             {
                 "BOWTIE1_BUILD": {
                     "bowtie": "1.3.1"
@@ -112,10 +113,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:27:00.400984209",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:26:42.652887516"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test
index 62e3d657..eb492a58 100644
--- a/tests/hisat2.nf.test
+++ b/tests/hisat2.nf.test
@@ -20,19 +20,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -40,11 +42,11 @@ nextflow_pipeline {
 
     test("-profile test --tools hisat2,hisat2_extractsplicesites") {
 
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
                 tools  = 'hisat2,hisat2_extractsplicesites'
                 // TODO REMOVE ME when the module is fixed
                 // cf https://github.com/nf-core/modules/issues/7045
@@ -53,19 +55,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
index 4bc73609..0cd40402 100644
--- a/tests/hisat2.nf.test.snap
+++ b/tests/hisat2.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools hisat2,hisat2_extractsplicesites --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": {
         "content": [
+            2,
             {
                 "HISAT2_BUILD": {
                     "hisat2": "2.2.1"
@@ -48,14 +49,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:03:12.129814483",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:47:21.954921108"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools hisat2,hisat2_extractsplicesites": {
         "content": [
+            4,
             {
                 "GFFREAD": {
                     "gffread": "0.12.7"
@@ -115,10 +117,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:30:01.145090085",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:48:24.752339407"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test
index f49f1ae3..9ede214c 100644
--- a/tests/kallisto.nf.test
+++ b/tests/kallisto.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -37,29 +39,31 @@ nextflow_pipeline {
 
     test("-profile test --tools kallisto,rsem_make_transcript_fasta") {
 
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
                 tools  = 'kallisto,rsem_make_transcript_fasta'
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
index 0204bf54..86d0b5e1 100644
--- a/tests/kallisto.nf.test.snap
+++ b/tests/kallisto.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools kallisto,rsem_make_transcript_fasta": {
         "content": [
+            4,
             {
                 "GFFREAD": {
                     "gffread": "0.12.7"
@@ -46,14 +47,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T15:57:10.384204424",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:50:13.684163497"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools kallisto,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": {
         "content": [
+            2,
             {
                 "KALLISTO_INDEX": {
                     "kallisto": "0.51.1"
@@ -86,10 +88,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T15:56:50.407246621",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:48:54.722152131"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/multiple.nf.test b/tests/multiple.nf.test
index 15ef88c5..e9a94b7f 100644
--- a/tests/multiple.nf.test
+++ b/tests/multiple.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -55,8 +57,10 @@ nextflow_pipeline {
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
diff --git a/tests/multiple.nf.test.snap b/tests/multiple.nf.test.snap
index 37a55aa5..cddc2121 100644
--- a/tests/multiple.nf.test.snap
+++ b/tests/multiple.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools bwamem1,createsequencedictionary,faidx,intervals --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_chr22.yml": {
         "content": [
+            9,
             {
                 "BUILD_INTERVALS": {
                     "gawk": "5.3.0"
@@ -82,14 +83,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:34:18.615057144",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:32:53.633810585"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     },
     "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/GATK/GRCh37_GRCh38_multiple_dbsnps_globs.yml": {
         "content": [
+            5,
             {
                 "TABIX_TABIX": {
                     "tabix": "1.21"
@@ -130,10 +132,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:34:53.027597524",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:33:25.90199516"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/rsem.nf.test b/tests/rsem.nf.test
index d877a445..295cc8ad 100644
--- a/tests/rsem.nf.test
+++ b/tests/rsem.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -37,29 +39,31 @@ nextflow_pipeline {
 
     test("-profile test --tools rsem,rsem_make_transcript_fasta") {
 
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
                 tools  = 'rsem,rsem_make_transcript_fasta'
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/rsem.nf.test.snap b/tests/rsem.nf.test.snap
index fd6abe83..ede21148 100644
--- a/tests/rsem.nf.test.snap
+++ b/tests/rsem.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools rsem,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": {
         "content": [
+            2,
             {
                 "RSEM_PREPAREREFERENCE_GENOME": {
                     "rsem": "1.3.1",
@@ -79,14 +80,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:06:44.791909632",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:52:54.851545772"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools rsem,rsem_make_transcript_fasta": {
         "content": [
+            4,
             {
                 "GFFREAD": {
                     "gffread": "0.12.7"
@@ -178,10 +180,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:37:36.256698472",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:54:31.207444454"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test
index d9e974ff..51536db1 100644
--- a/tests/salmon.nf.test
+++ b/tests/salmon.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -37,29 +39,31 @@ nextflow_pipeline {
 
     test("-profile test --tools salmon,rsem_make_transcript_fasta") {
 
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
                 tools  = 'salmon,rsem_make_transcript_fasta'
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
index b80a902c..4780df6e 100644
--- a/tests/salmon.nf.test.snap
+++ b/tests/salmon.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools salmon,rsem_make_transcript_fasta --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": {
         "content": [
+            2,
             {
                 "SALMON_INDEX": {
                     "salmon": "1.10.3"
@@ -57,14 +58,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:09:11.675553276",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:55:46.182193326"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools salmon,rsem_make_transcript_fasta": {
         "content": [
+            4,
             {
                 "GFFREAD": {
                     "gffread": "0.12.7"
@@ -134,10 +136,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:40:03.501871668",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:56:31.902100907"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/samtools.nf.test b/tests/samtools.nf.test
index 38e97634..fd47cbfd 100644
--- a/tests/samtools.nf.test
+++ b/tests/samtools.nf.test
@@ -6,29 +6,31 @@ nextflow_pipeline {
 
     test("-profile test --tools faidx,intervals,sizes") {
 
-        options "-output-dir $outputDir"
+        options "-output-dir ${outputDir}"
 
         when {
             params {
-                outdir = "$outputDir"
+                outdir = "${outputDir}"
                 tools  = 'faidx,intervals,sizes'
             }
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -47,19 +49,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -78,19 +82,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/samtools.nf.test.snap b/tests/samtools.nf.test.snap
index 5f904c0f..e6a4af75 100644
--- a/tests/samtools.nf.test.snap
+++ b/tests/samtools.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools faidx,intervals,sizes --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": {
         "content": [
+            2,
             {
                 "BUILD_INTERVALS": {
                     "gawk": "5.3.0"
@@ -32,14 +33,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:10:30.34680381",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:57:10.974116767"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools faidx,intervals,sizes --input references-datasheets/latest/genomes/Homo_sapiens/nf-core/GRCh38_chr21.yml": {
         "content": [
+            1,
             {
                 
             },
@@ -62,14 +64,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:10:43.92484123",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:57:29.976409216"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools faidx,intervals,sizes": {
         "content": [
+            3,
             {
                 "BUILD_INTERVALS": {
                     "gawk": "5.3.0"
@@ -110,10 +113,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:40:27.407837236",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:39:15.908885182"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/sarek.nf.test b/tests/sarek.nf.test
index d4d21075..cfd5e059 100644
--- a/tests/sarek.nf.test
+++ b/tests/sarek.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -48,19 +50,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/sarek.nf.test.snap b/tests/sarek.nf.test.snap
index 95f1a0be..abce54df 100644
--- a/tests/sarek.nf.test.snap
+++ b/tests/sarek.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools bwamem1,bwamem2,createsequencedictionary,dragmap,faidx,intervals,msisensorpro,tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/GATK/GRCh38_chr22.yml": {
         "content": [
+            11,
             {
                 "BUILD_INTERVALS": {
                     "gawk": "5.3.0"
@@ -108,14 +109,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T15:57:51.433637102",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:40:39.747672409"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "-profile test --tools bwamem1,bwamem2,createsequencedictionary,dragmap,faidx,intervals,msisensorpro,tabix --input references-datasheets/latest/genomes/Homo_sapiens/GATK/GRCh38_chr22.yml": {
         "content": [
+            2,
             {
                 "MSISENSORPRO_SCAN": {
                     "msisensor-pro": "1.3.0"
@@ -147,10 +149,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:00:36.157261789",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:58:49.531702963"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/tabix.nf.test b/tests/tabix.nf.test
index e08e29f7..d78376d4 100644
--- a/tests/tabix.nf.test
+++ b/tests/tabix.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -48,19 +50,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/tabix.nf.test.snap b/tests/tabix.nf.test.snap
index e0a56db4..3f62ee6f 100644
--- a/tests/tabix.nf.test.snap
+++ b/tests/tabix.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_chr22.yml": {
         "content": [
+            1,
             {
                 
             },
@@ -23,14 +24,15 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T13:49:48.65709389",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2025-10-22T13:59:06.940925897"
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.4"
+        }
     },
     "-profile test --tools tabix --input references-datasheets/latest/genomes_source/Homo_sapiens/nf-core/GRCh38_chr21_MT.yml": {
         "content": [
+            5,
             {
                 "TABIX_BGZIPTABIX": {
                     "tabix": "1.21"
@@ -74,10 +76,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:11:10.049971239",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:41:42.457020033"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/tests/wbcel235.nf.test b/tests/wbcel235.nf.test
index 37464f65..e0e51563 100644
--- a/tests/wbcel235.nf.test
+++ b/tests/wbcel235.nf.test
@@ -17,19 +17,21 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assert workflow.success
             assertAll(
                 { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
-                    removeFromYamlMap("${params.outdir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
+                    removeFromYamlMap("${outputDir}/pipeline_info/nf_core_references_software_mqc_versions.yml", 'Workflow'),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/wbcel235.nf.test.snap b/tests/wbcel235.nf.test.snap
index fae729ef..f84da148 100644
--- a/tests/wbcel235.nf.test.snap
+++ b/tests/wbcel235.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "-profile test --tools bwamem1,createsequencedictionary,faidx,intervals,rsem,star --input Caenorhabditis_elegans/NCBI/WBcel235.yml": {
         "content": [
+            10,
             {
                 "BUILD_INTERVALS": {
                     "gawk": "5.3.0"
@@ -11,8 +12,17 @@
                 "GATK4_CREATESEQUENCEDICTIONARY": {
                     "gatk": "4.6.1.0"
                 },
-                "GUNZIP": {
-                    "gunzip": 1.13
+                "NCBIDOWNLOAD_FASTA": {
+                    "gunzip": "1.12",
+                    "ncbidatasetscli": "datasets version: 18.25.0"
+                },
+                "NCBIDOWNLOAD_GFF": {
+                    "gunzip": "1.12",
+                    "ncbidatasetscli": "datasets version: 18.25.0"
+                },
+                "NCBIDOWNLOAD_GTF": {
+                    "gunzip": "1.12",
+                    "ncbidatasetscli": "datasets version: 18.25.0"
                 },
                 "RSEM_PREPAREREFERENCE_GENOME": {
                     "rsem": "1.3.1",
@@ -33,8 +43,8 @@
                 "Caenorhabditis_elegans/NCBI/WBcel235",
                 "Caenorhabditis_elegans/NCBI/WBcel235/Annotation",
                 "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes",
-                "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/GCF_000002985.6_WBcel235_genomic.gff",
-                "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/GCF_000002985.6_WBcel235_genomic.gtf",
+                "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/genomic.gff",
+                "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/Genes/genomic.gtf",
                 "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/intervals",
                 "Caenorhabditis_elegans/NCBI/WBcel235/Annotation/intervals/WBcel235.bed",
                 "Caenorhabditis_elegans/NCBI/WBcel235/Sequence",
@@ -110,8 +120,8 @@
                 "pipeline_info/nf_core_references_software_mqc_versions.yml"
             ],
             [
-                "GCF_000002985.6_WBcel235_genomic.gff:md5,cdfa038e7ba342b73dab1e85ffdf0a4a",
-                "GCF_000002985.6_WBcel235_genomic.gtf:md5,efc0320858e37f3e818a392df1e07a85",
+                "genomic.gff:md5,cdfa038e7ba342b73dab1e85ffdf0a4a",
+                "genomic.gtf:md5,efc0320858e37f3e818a392df1e07a85",
                 "WBcel235.bed:md5,84cb3d6e8ed7c8475fc9735b19b66908",
                 "GCF_000002985.6_WBcel235_genomic.amb:md5,a0741fa25fb4e5a52ac61ecc5b679ac2",
                 "GCF_000002985.6_WBcel235_genomic.ann:md5,7e46a49f983e0ca1fb6ee14be12251d3",
@@ -160,10 +170,10 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ]
         ],
+        "timestamp": "2026-05-04T16:26:31.767288789",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-15T13:47:02.887729686"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/workflows/references/main.nf b/workflows/references.nf
similarity index 85%
rename from workflows/references/main.nf
rename to workflows/references.nf
index 12eb35ff..bd8a5e8d 100644
--- a/workflows/references/main.nf
+++ b/workflows/references.nf
@@ -1,5 +1,5 @@
-include { PREPARE_GENOME_DNASEQ } from '../../subworkflows/nf-side/prepare_genome_dnaseq'
-include { PREPARE_GENOME_RNASEQ } from '../../subworkflows/nf-side/prepare_genome_rnaseq'
+include { PREPARE_GENOME_DNASEQ } from '../subworkflows/nf-side/prepare_genome_dnaseq'
+include { PREPARE_GENOME_RNASEQ } from '../subworkflows/nf-side/prepare_genome_rnaseq'
 
 workflow REFERENCES {
     take:
@@ -60,30 +60,27 @@ workflow REFERENCES {
         tools.split(',').contains('snapaligner'),
     )
 
-    // This works with a mixture of input and computed references
-    fasta_dict = fasta_dict.mix(PREPARE_GENOME_DNASEQ.out.fasta_dict)
-    fasta_fai = fasta_fai.mix(PREPARE_GENOME_DNASEQ.out.fasta_fai, PREPARE_GENOME_RNASEQ.out.fasta_fai)
-    fasta_sizes = fasta_sizes.mix(PREPARE_GENOME_RNASEQ.out.fasta_sizes)
-    gtf = gtf.mix(PREPARE_GENOME_RNASEQ.out.gtf)
-    intervals_bed = intervals_bed.mix(PREPARE_GENOME_DNASEQ.out.intervals_bed)
-    splice_sites = splice_sites.mix(PREPARE_GENOME_RNASEQ.out.splice_sites)
-    transcript_fasta = transcript_fasta.mix(PREPARE_GENOME_RNASEQ.out.transcript_fasta)
-
-    // TODO: This does not work YET with a mixture of input and computed references
     bowtie1_index = PREPARE_GENOME_RNASEQ.out.bowtie1_index
     bowtie2_index = PREPARE_GENOME_RNASEQ.out.bowtie2_index
     bwamem1_index = PREPARE_GENOME_DNASEQ.out.bwamem1_index
     bwamem2_index = PREPARE_GENOME_DNASEQ.out.bwamem2_index
     dragmap_hashmap = PREPARE_GENOME_DNASEQ.out.dragmap_hashmap
+    fasta_dict = PREPARE_GENOME_DNASEQ.out.fasta_dict
+    fasta_fai = PREPARE_GENOME_DNASEQ.out.fasta_fai
+    fasta_sizes = PREPARE_GENOME_RNASEQ.out.fasta_sizes
+    gtf = PREPARE_GENOME_RNASEQ.out.gtf
     hisat2_index = PREPARE_GENOME_RNASEQ.out.hisat2_index
+    intervals_bed = PREPARE_GENOME_DNASEQ.out.intervals_bed
     kallisto_index = PREPARE_GENOME_RNASEQ.out.kallisto_index
     msisensorpro_list = PREPARE_GENOME_DNASEQ.out.msisensorpro_list
     rsem_index = PREPARE_GENOME_RNASEQ.out.rsem_index
     salmon_index = PREPARE_GENOME_RNASEQ.out.salmon_index
+    splice_sites = PREPARE_GENOME_RNASEQ.out.splice_sites
     star_index = PREPARE_GENOME_RNASEQ.out.star_index
+    transcript_fasta = PREPARE_GENOME_RNASEQ.out.transcript_fasta
     vcf_tbi = PREPARE_GENOME_DNASEQ.out.vcf_tbi
 
-    // TODO: need to rescue the vcf files
+    // TODO: need to rescue these files
     // vcf.map { meta, reference_ -> [meta + [file: "${meta.type}_vcf"], reference_] },
 
     references = channel.empty()