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 bdd34869..00000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,125 +0,0 @@
-# `nf-core/stableexpression`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving nf-core/stableexpression.
-
-We try to manage the required tasks for nf-core/stableexpression 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/stableexpression then the best place to ask is on the nf-core Slack [#stableexpression](https://nfcore.slack.com/channels/stableexpression) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Contribution workflow
-
-If you'd like to write some code for nf-core/stableexpression, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [nf-core/stableexpression issues](https://github.com/nf-core/stableexpression/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/stableexpression repository](https://github.com/nf-core/stableexpression) 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/stableexpression documentation](https://nf-co.re/stableexpression/usage) and don't hesitate to get in touch on the nf-core Slack [#stableexpression](https://nfcore.slack.com/channels/stableexpression) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Pipeline contribution conventions
-
-To make the `nf-core/stableexpression` 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/stableexpression/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 2c2997d7..c50916ca 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/stableexpression/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/stableexpression/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/stableexpression/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/stableexpression/tree/main/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/stableexpression _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: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 41ec7fc3..52e502ae 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -20,24 +20,24 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ 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 a5f81c34..ec5e6879 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/stableexpression/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'stableexpression'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *stableexpression/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *stableexpression/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/stableexpression/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 429570cd..0891da1d 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 db9f5352..7f6ade3f 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 6adb0fff..172de6f3 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
+      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 45884ff9..a7bf4fc2 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -38,13 +38,16 @@ jobs:
     runs-on: ubuntu-latest
     needs: configure
     steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
@@ -54,10 +57,15 @@ jobs:
         with:
           apptainer-version: 1.3.4
 
+      - name: Read .nf-core.yml
+        id: read_yml
+        run: |
+          echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Make a cache directory for the container images
         run: |
@@ -127,7 +135,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 6df255c4..785e698d 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 1668cf73..3f04ed2a 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.4"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.4"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 431d3d44..78d5dbe0 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@master
+      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)
@@ -34,7 +34,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
+      - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index e8560fc7..ea30827e 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
@@ -29,7 +29,7 @@ jobs:
         run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with:
@@ -42,5 +42,5 @@ jobs:
             > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
             > Please update your pipeline to the latest version.
             >
-            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
           #
diff --git a/.gitignore b/.gitignore
index b91d76b2..1086ed6d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@ testing/
 testing*
 *.pyc
 null/
+.lineage/
 .nf-test*
 .idea/
 .vscode/
diff --git a/.nf-core.yml b/.nf-core.yml
index 9d83d644..9ea0fa32 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -16,12 +16,17 @@ lint:
     - tests/test_data/genorm/compute_m_measure/input/std.1.2.parquet
     - tests/test_data/genorm/compute_m_measure/input/std.1.2.parquet
   schema_lint: false
-
-nf_core_version: 3.5.2
+  template_strings:
+    - tests/test_data/genorm/compute_m_measure/input/std.0.0.parquet
+    - tests/test_data/genorm/compute_m_measure/input/std.1.2.parquet
+    - tests/test_data/genorm/compute_m_measure/input/std.1.2.parquet
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: Olivier Coen
-  description: This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.
+  description: This pipeline is dedicated to identifying the most stable genes within
+    a single or multiple expression dataset(s). This is particularly useful for identifying
+    the most suitable RT-qPCR reference genes for a specific species.
   force: false
   is_nfcore: true
   name: stableexpression
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c7942f15..41edd594 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,9 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.6.2
-        exclude: galaxy/
-
+          - prettier@3.8.3
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -15,27 +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/astral-sh/ruff-pre-commit
-    rev: v0.14.1
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.3.0
     hooks:
-      # Run the linter.
-      - id: ruff
-        files: \.py$
-        args: [--fix]
-        exclude: bin/old/
-      # Run the formatter.
-      - id: ruff-format
-        files: \.py$
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
+        args: ["-output", "json"]
diff --git a/.prettierignore b/.prettierignore
index 7cc55006..0973951c 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 798c10f1..a5f02f32 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0.0 - 18/03/2026
+## v1.0.0 - 11/06/2026
 
 First complete, official release of nf-core/stableexpression.
 
diff --git a/README.md b/README.md
index bea23099..c2a7522d 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,8 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/stableexpression/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/stableexpression/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/stableexpression/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with apptainer](https://custom-icon-badges.demolab.com/badge/run%20with-apptainer-4545?logo=apptainer&color=teal&labelColor=000000)](https://apptainer.org/)
 [![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/)
@@ -110,7 +110,7 @@ nextflow run nf-core/stableexpression -profile test,<docker/apptainer/conda/micr
 ## Basic usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.
 
 To search the most stable genes in a species considering all public datasets, simply run:
 
@@ -121,6 +121,8 @@ nextflow run nf-core/stableexpression \
    --outdir <OUTDIR (example: ./results)> \
    -resume
 ```
+> [!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/running/run-pipelines#using-parameter-files).
 
 ## More advanced usage
 
@@ -163,7 +165,7 @@ We thank the following people for their assistance in the development of this pi
 
 ## 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 `#stableexpression` channel](https://nfcore.slack.com/channels/stableexpression) (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 c7518adb..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/stableexpression 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/email_template.html b/assets/email_template.html
index 711c3b4b..42e5f6b5 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/stableexpression: This pipeline is dedicated to finding the most stable genes across count datasets">
+  <meta name="description" content="nf-core/stableexpression: This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.">
   <title>nf-core/stableexpression Pipeline Report</title>
 </head>
 <body>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 565c88e2..e28b158d 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,6 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/stableexpression/releases/tag/1.0.0" target="_blank">nf-core/stableexpression</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/stableexpression/1.0.0/docs/output" target="_blank">documentation</a>.
-
+  This report has been generated by the <a href="https://github.com/nf-core/stableexpression/releases/tag/1.0.0" target="_blank">nf-core/stableexpression</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/stableexpression/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-stableexpression-methods-description":
     order: -1000
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index 3de29ab4..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/stableexpression ${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 12e88c25..9f927238 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -30,7 +30,7 @@ process {
             'ignore'
         } else if (task.exitStatus == 101) { // connection errors that should be retried
             'retry'
-        } else if (task.exitStatus in ((130..145) + 104 + 175)) { // OOM & related errors; should be retried as long as memory does not fit
+        } else if (task.exitStatus in ((130..145) + 104 + (175..177))) { // OOM & related errors; should be retried as long as memory does not fit
             sleep(Math.pow(2, task.attempt) * 200 as long)
             'retry'
         } else if (task.attempt <= 3) { // all other errors should be retried with exponential backoff with max retry = 3
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
new file mode 100644
index 00000000..f487ba40
--- /dev/null
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
new file mode 100644
index 00000000..e9a3fedc
--- /dev/null
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
new file mode 100644
index 00000000..01b59df5
--- /dev/null
+++ b/conf/containers_docker_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
new file mode 100644
index 00000000..7785cb13
--- /dev/null
+++ b/conf/containers_docker_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
new file mode 100644
index 00000000..754821b3
--- /dev/null
+++ b/conf/containers_singularity_https_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
new file mode 100644
index 00000000..93071de8
--- /dev/null
+++ b/conf/containers_singularity_https_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
new file mode 100644
index 00000000..952881d8
--- /dev/null
+++ b/conf/containers_singularity_oras_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
new file mode 100644
index 00000000..498ec506
--- /dev/null
+++ b/conf/containers_singularity_oras_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
new file mode 100644
index 00000000..4687cd98
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,185 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `nf-core/stableexpression`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving nf-core/stableexpression.
+
+This page describes the recommended nf-core way to contribute to both nf-core/stableexpression 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/stableexpression.
+
+> [!NOTE]
+> If you need help using or modifying nf-core/stableexpression, ask on the nf-core Slack [#stableexpression](https://nfcore.slack.com/channels/stableexpression) 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/stableexpression/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/stableexpression repository](https://github.com/nf-core/stableexpression) 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/stableexpression documentation](https://nf-co.re/stableexpression/usage) or ask on the nf-core [#stableexpression](https://nfcore.slack.com/channels/stableexpression) Slack channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+### GitHub Codespaces
+
+You can contribute to nf-core/stableexpression 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/stableexpression/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/stableexpression 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 2bc85a3c..2d2c0238 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -264,7 +264,7 @@ 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:
 
@@ -384,19 +384,19 @@ 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 be4d42ea..cd789bcd 100644
--- a/main.nf
+++ b/main.nf
@@ -82,7 +82,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         NFCORE_STABLEEXPRESSION.out.multiqc_report
     )
 }
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
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+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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diff --git a/nextflow.config b/nextflow.config
index 910a3ec7..562cc714 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -76,7 +76,6 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
@@ -97,6 +96,10 @@ params {
     validate_params            = true
 }
 
+// Backwards compatibility for publishDir syntax
+outputDir = params.outdir
+workflow.output.mode = params.publish_dir_mode
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -303,10 +306,10 @@ manifest {
         ],
     ]
     homePage        = 'https://github.com/nf-core/stableexpression'
-    description     = """This pipeline is dedicated to finding the most stable genes across count datasets"""
+    description     = """This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species."""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=25.04.0'
+    nextflowVersion = '!>=25.10.4'
     version         = '1.0.0'
     doi             = ''
 }
@@ -320,6 +323,5 @@ validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
 }
-
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8109b426..c524d78a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -451,13 +451,6 @@
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
-                "hook_url": {
-                    "type": "string",
-                    "description": "Incoming hook URL for messaging service",
-                    "fa_icon": "fas fa-people-group",
-                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
-                    "hidden": true
-                },
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
diff --git a/nf-test.config b/nf-test.config
index a0a009fd..0ad2211d 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,23 +1,35 @@
 config {
     // location for all nf-test tests
-    testsDir "."
+    testsDir = "."
 
     // nf-test directory including temporary files for each test
-    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    testsDir "tests"
-    workDir ".nf-test"
-    configFile "tests/nextflow.config"
+    configFile = "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
+    ignore = [
+        'modules/nf-core/**/tests/*',
+        'subworkflows/nf-core/**/tests/*',
+    ]
 
     // run all test with defined profile(s) from the main nextflow.config
     //profile "apptainer"
 
     // list of filenames or patterns that should be trigger a full test run
-    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+    triggers = [
+        '.github/actions/nf-test/action.yml',
+        '.github/workflows/nf-test.yml',
+        'assets/schema_input.json',
+        'bin/*',
+        'conf/test.config',
+        'nextflow.config',
+        'nextflow_schema.json',
+        'nf-test.config',
+        'tests/.nftignore',
+        'tests/nextflow.config',
+    ]
 
     // load the necessary plugins
     requires (
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index e99a20e2..a4826b2b 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -1,6 +1,6 @@
 {
     "@context": [
-        "https://w3id.org/ro/crate/1.1/context",
+        "https://w3id.org/ro/crate/1.2/context",
         {
             "GithubService": "https://w3id.org/ro/terms/test#GithubService",
             "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2026-03-14T09:55:43+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-stableexpression_logo_dark.png\">\n    <img alt=\"nf-core/stableexpression\" src=\"docs/images/nf-core-stableexpression_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/stableexpression)\n[![GitHub Actions CI Status](https://github.com/nf-core/stableexpression/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/stableexpression/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/stableexpression/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/stableexpression/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/stableexpression/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with apptainer](https://custom-icon-badges.demolab.com/badge/run%20with-apptainer-4545?logo=apptainer&color=teal&labelColor=000000)](https://apptainer.org/)\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/stableexpression)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23stableexpression-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/stableexpression)[![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/stableexpression** is a bioinformatics pipeline aiming to aggregate multiple count datasets for a specific species and find the most stable genes. The datasets can be either downloaded from public databases (EBI, NCBI) or provided directly by the user. Both RNA-seq and Microarray count datasets can be utilised.\n\n<p align=\"center\">\n    <img title=\"Stableexpression Workflow\" src=\"docs/images/nf_core_stableexpression.metromap.png\" width=100%>\n</p>\n\nIt takes as main inputs :\n\n- a species name (mandatory)\n- keywords for Expression Atlas / GEO search (optional)\n- a CSV input file listing your own raw / normalised count datasets (optional).\n\n**Use cases**:\n\n- **find the most suitable genes as RT-qPCR reference genes for a specific species (and optionally specific conditions)**\n- download all Expression Atlas and / or NCBI GEO datasets for a species (and optionally keywords)\n\n## Pipeline overview\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:\n\n#### 1. Get accessions from public databases\n\n- Get [Expression Atlas](https://www.ebi.ac.uk/gxa/home) dataset accessions corresponding to the provided species (and optionally keywords)\n  This step is run by default but is optional. Set `--skip_fetch_eatlas_accessions` to skip it.\n- Get NBCI [GEO](https://www.ncbi.nlm.nih.gov/gds) **microarray** dataset accessions corresponding to the provided species (and optionally keywords)\n  This is optional and **NOT** run by default. Set `--fetch_geo_accessions` to run it.\n\n#### 2. Download data (see [usage](./conf/usage.md#3-provide-your-own-accessions))\n\n- Download [Expression Atlas](https://www.ebi.ac.uk/gxa/home) data if any\n- Download NBCI [GEO](https://www.ncbi.nlm.nih.gov/gds) data if any\n\n> [!NOTE]\n> At this point, datasets downloaded from public databases are merged with datasets provided by the user using the `--datasets` parameter. See [usage](./conf/usage.md#4-use-your-own-expression-datasets) for more information about local datasets.\n\n#### 3. ID Mapping (see [usage](./conf/usage.md#5-custom-gene-id-mapping--metadata))\n\n- Gene IDs are cleaned\n- Map gene IDS to NCBI Entrez Gene IDS (or Ensembl IDs) for standardisation among datasets using [g:Profiler](https://biit.cs.ut.ee/gprofiler/gost) (run by default; optional)\n- Rare genes are filtered out\n\n#### 4. Sample filtering\n\nSamples that show too high ratios of zeros or missing values are removed from the analysis.\n\n#### 5. Normalisation of expression\n\n- Normalize RNAseq raw data using TPM (necessitates downloading the corresponding genome and computing transcript lengths) or CPM.\n- Perform quantile normalisation on each dataset separately using [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.quantile_transform.html)\n\n#### 6. Merge all data\n\nAll datasets are merged into one single dataframe.\n\n#### 7. Imputation of missing values\n\nMissing values are replaced by imputed values using a specific algorithm provided by [scikit-learn](https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.quantile_transform.html). The user can choose the method of imputation with the `--missing_value_imputer` parameter.\n\n#### 8. General statistics for each gene\n\nBase statistics are computed for each gene, platform-wide and for each platform (RNAseq and microarray).\n\n#### 9. Scoring\n\n- The whole list of genes is divided in multiple sections, based on their expression level.\n- Based on the coefficient of variation, a shortlist of candidates genes is extracted for each section.\n- Run optimised, scalable version of [Normfinder](https://www.moma.dk/software/normfinder)\n- Run optimised, scalable version of [Genorm](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2002-3-7-research0034) (run by default; optional)\n- Compute stability scores for each candidate gene\n\n#### 10. Reporting\n\n- Result aggregation\n- Make [`MultiQC`](http://multiqc.info/) report\n- Prepare [Dash Plotly](https://dash.plotly.com/) app for further investigation of gene / sample counts\n\n## Test pipeline\n\nYou can test the execution of the pipeline locally with:\n\n```bash\nnextflow run nf-core/stableexpression -profile test,<docker/apptainer/conda/micromamba/...>\n```\n\n## Basic usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nTo search the most stable genes in a species considering all public datasets, simply run:\n\n```bash\nnextflow run nf-core/stableexpression \\\n   -profile <PROFILE (examples: docker / apptainer / conda / micromamba)> \\\n   --species <SPECIES (examples: arabidopsis_thaliana / \"drosophila melanogaster\")> \\\n   --outdir <OUTDIR (example: ./results)> \\\n   -resume\n```\n\n## More advanced usage\n\nFor more specific scenarios, like:\n\n- **fetching only specific conditions**\n- **using your own expression dataset(s)**\n\nplease refer to the [usage documentation](https://nf-co.re/stableexpression/usage).\n\n## Resource allocation\n\nFor setting pipeline CPU / memory usage, see [here](./docs/configuration.md).\n\n## Profiles\n\nSee [here](https://nf-co.re/stableexpression/usage#profiles) for more information about profiles.\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/stableexpression/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/stableexpression/output).\n\n## Support us\n\nIf you like nf-core/stableexpression, please make sure you give it a star on GitHub!\n\n[![stars - stableexpression](https://img.shields.io/github/stars/nf-core/stableexpression?style=social)](https://github.com/nf-core/stableexpression)\n\n## Credits\n\nnf-core/stableexpression was originally written by Olivier Coen.\n\nWe thank the following people for their assistance in the development of this pipeline:\n\n- R\u00e9my Costa\n- Shaheen Acheche\n- Janine Soares\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 `#stableexpression` channel](https://nfcore.slack.com/channels/stableexpression) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/stableexpression for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-04-30T13:33:11+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-stableexpression_logo_dark.png\">\n    <img alt=\"nf-core/stableexpression\" src=\"docs/images/nf-core-stableexpression_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/stableexpression)\n[![GitHub Actions CI Status](https://github.com/nf-core/stableexpression/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/stableexpression/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/stableexpression/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/stableexpression/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/stableexpression/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/stableexpression)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23stableexpression-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/stableexpression)[![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/stableexpression** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/stableexpression \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/stableexpression/usage) and the [parameter documentation](https://nf-co.re/stableexpression/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/stableexpression/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/stableexpression/output).\n\n## Credits\n\nnf-core/stableexpression was originally written by Olivier Coen.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#stableexpression` channel](https://nfcore.slack.com/channels/stableexpression) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/stableexpression for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -105,7 +105,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#6aa6a373-9bb0-4502-a8f4-2fce1f6296ee"
+                    "@id": "#a2b5baf2-98f5-4401-9942-3b4d4023b1cb"
                 }
             ],
             "name": "nf-core/stableexpression"
@@ -118,7 +118,7 @@
             },
             "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"
@@ -127,50 +127,26 @@
         },
         {
             "@id": "main.nf",
-            "@type": [
-                "File",
-                "SoftwareSourceCode",
-                "ComputationalWorkflow"
-            ],
-            "creator": [
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "contributor": [
                 {
                     "@id": "https://orcid.org/0000-0003-3387-1040"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-03-14T10:55:43Z",
+            "dateModified": "2026-04-30T13:33:11Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "keywords": [
-                "nf-core",
-                "nextflow",
-                "expression",
-                "housekeeping-genes",
-                "qpcr-analysis"
-            ],
-            "license": [
-                "MIT"
-            ],
-            "maintainer": [
-                {
-                    "@id": "https://orcid.org/0000-0003-3387-1040"
-                }
-            ],
-            "name": [
-                "nf-core/stableexpression"
-            ],
+            "keywords": ["nf-core", "nextflow", "expression", "housekeeping-genes", "qpcr-analysis"],
+            "license": ["MIT"],
+            "name": ["nf-core/stableexpression"],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": [
-                "https://github.com/nf-core/stableexpression",
-                "https://nf-co.re/stableexpression/1.0.0/"
-            ],
-            "version": [
-                "1.0.0"
-            ]
+            "url": ["https://github.com/nf-core/stableexpression", "https://nf-co.re/stableexpression/1.0.0/"],
+            "version": ["1.0.0"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -182,14 +158,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.04.0"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "#6aa6a373-9bb0-4502-a8f4-2fce1f6296ee",
+            "@id": "#a2b5baf2-98f5-4401-9942-3b4d4023b1cb",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#2fa3572f-894b-4153-a0a8-dca4386f0cea"
+                    "@id": "#d117b875-0f4d-4a4b-b9c8-e651afc9282b"
                 }
             ],
             "mainEntity": {
@@ -198,7 +174,7 @@
             "name": "Test suite for nf-core/stableexpression"
         },
         {
-            "@id": "#2fa3572f-894b-4153-a0a8-dca4386f0cea",
+            "@id": "#d117b875-0f4d-4a4b-b9c8-e651afc9282b",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/stableexpression",
             "resource": "repos/nf-core/stableexpression/actions/workflows/nf-test.yml",
diff --git a/subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf b/subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf
index ed736dd6..ddae19ce 100644
--- a/subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf
@@ -13,7 +13,6 @@ include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -51,6 +50,9 @@ 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
@@ -68,7 +70,11 @@ workflow PIPELINE_INITIALISATION {
 * Software dependencies
     https://github.com/nf-core/stableexpression/blob/main/CITATIONS.md
 """
-    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --species <species> --outdir <OUTDIR>"
+    if (monochrome_logs) {
+        before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '')
+    }
+
+    command = "nextflow run ${workflow.manifest.name} -profile <docker/apptainer/singularity/.../institute> --species <species> --outdir <OUTDIR>"
 
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
@@ -123,7 +129,6 @@ 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:
@@ -147,13 +152,11 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
+
     }
 
     workflow.onError {
-        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+        log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting"
     }
 }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index bfd25876..4229d45f 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE {
     checkProfileProvided(nextflow_cli_args)
 
     emit:
-    valid_config
+    valid_config = valid_config
 }
 
 /*
@@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) {
         log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
-
-//
-// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
-//
-def imNotification(summary_params, hook_url) {
-    def summary = [:]
-    summary_params
-        .keySet()
-        .sort()
-        .each { group ->
-            summary << summary_params[group]
-        }
-
-    def misc_fields = [:]
-    misc_fields['start']          = workflow.start
-    misc_fields['complete']       = workflow.complete
-    misc_fields['scriptfile']     = workflow.scriptFile
-    misc_fields['scriptid']       = workflow.scriptId
-    if (workflow.repository) {
-        misc_fields['repository'] = workflow.repository
-    }
-    if (workflow.commitId) {
-        misc_fields['commitid']   = workflow.commitId
-    }
-    if (workflow.revision) {
-        misc_fields['revision']   = workflow.revision
-    }
-    misc_fields['nxf_version']    = workflow.nextflow.version
-    misc_fields['nxf_build']      = workflow.nextflow.build
-    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
-
-    def msg_fields = [:]
-    msg_fields['version']      = getWorkflowVersion()
-    msg_fields['runName']      = workflow.runName
-    msg_fields['success']      = workflow.success
-    msg_fields['dateComplete'] = workflow.complete
-    msg_fields['duration']     = workflow.duration
-    msg_fields['exitStatus']   = workflow.exitStatus
-    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-    msg_fields['projectDir']   = workflow.projectDir
-    msg_fields['summary']      = summary << misc_fields
-
-    // Render the JSON template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    // Different JSON depending on the service provider
-    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
-    def json_template = engine.createTemplate(hf).make(msg_fields)
-    def json_message  = json_template.toString()
-
-    // POST
-    def post = new URL(hook_url).openConnection()
-    post.setRequestMethod("POST")
-    post.setDoOutput(true)
-    post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"))
-    def postRC = post.getResponseCode()
-    if (!postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText())
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
new file mode 100644
index 00000000..8940d32d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap
new file mode 100644
index 00000000..859d1030
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index acb39724..1df8b76f 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
         }
         log.info paramsHelp(
             help_options,
-            params.help instanceof String ? params.help : "",
+            (params.help instanceof String && params.help != "true") ? params.help : "",
         )
         exit 0
     }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 8d8c7371..f6537cc3 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.5.1"
+    id "nf-schema@2.6.1"
 }
 
 validation {
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 58102a53..bd37dddd 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -117,19 +117,19 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_stableexpression_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 70fa952f..3fefb69c 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -8,7 +8,7 @@
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/stableexpression'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/stableexpression/'
 }
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners