From 89c9f31a5b7abfd76e94bfa23f7344d0d8f41cd6 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 28 Apr 2026 11:21:04 +0000
Subject: [PATCH 1/6] Template update for nf-core/tools version 4.0.0

---
 .devcontainer/devcontainer.json               |    1 +
 .github/CONTRIBUTING.md                       |  125 --
 .github/PULL_REQUEST_TEMPLATE.md              |    4 +-
 .github/actions/get-shards/action.yml         |    2 +-
 .github/actions/nf-test/action.yml            |   10 +-
 .github/workflows/awsfulltest.yml             |   25 +-
 .github/workflows/awstest.yml                 |    4 +-
 .github/workflows/branch.yml                  |    2 +-
 .github/workflows/clean-up.yml                |    2 +-
 .github/workflows/download_pipeline.yml       |   14 +-
 .github/workflows/fix_linting.yml             |   22 +-
 .github/workflows/linting.yml                 |   34 +-
 .github/workflows/linting_comment.yml         |    4 +-
 .github/workflows/nf-test.yml                 |    8 +-
 .github/workflows/release-announcements.yml   |    4 +-
 .../workflows/template-version-comment.yml    |    6 +-
 .gitignore                                    |    1 +
 .nf-core.yml                                  |    8 +-
 .pre-commit-config.yaml                       |   16 +-
 .prettierignore                               |    2 -
 CHANGELOG.md                                  |    2 +-
 README.md                                     |   12 +-
 assets/adaptivecard.json                      |   67 -
 assets/multiqc_config.yml                     |    4 +-
 assets/schema_input.json                      |    2 +-
 assets/slackreport.json                       |   34 -
 conf/base.config                              |    2 +-
 conf/containers_conda_lock_files_amd64.config |    2 +
 conf/containers_conda_lock_files_arm64.config |    2 +
 conf/containers_docker_amd64.config           |    2 +
 conf/containers_docker_arm64.config           |    2 +
 .../containers_singularity_https_amd64.config |    2 +
 .../containers_singularity_https_arm64.config |    2 +
 conf/containers_singularity_oras_amd64.config |    2 +
 conf/containers_singularity_oras_arm64.config |    2 +
 docs/CONTRIBUTING.md                          |  185 ++
 docs/usage.md                                 |    8 +-
 main.nf                                       |    7 +-
 modules.json                                  |    8 +-
 .../linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt     |  822 +++++++++
 .../linux_arm64-bd-e455e32f745abe68_1.txt     |  769 ++++++++
 modules/nf-core/fastqc/main.nf                |   43 +-
 modules/nf-core/fastqc/meta.yml               |   51 +-
 modules/nf-core/fastqc/tests/main.nf.test     |   12 +-
 .../nf-core/fastqc/tests/main.nf.test.snap    |  228 ++-
 .../linux_amd64-bd-c1f4a7982b743963_1.txt     | 1552 +++++++++++++++++
 .../linux_amd64-bd-db7c73dae76bc9e6_1.txt     |  126 ++
 .../linux_arm64-bd-40bf3b435e89dc22_1.txt     | 1502 ++++++++++++++++
 .../linux_arm64-bd-d167b8012595a136_1.txt     |  125 ++
 modules/nf-core/multiqc/environment.yml       |    2 +-
 modules/nf-core/multiqc/main.nf               |   51 +-
 modules/nf-core/multiqc/meta.yml              |  165 +-
 .../multiqc/tests/custom_prefix.config        |    5 +
 modules/nf-core/multiqc/tests/main.nf.test    |  191 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |  435 ++++-
 modules/nf-core/multiqc/tests/nextflow.config |    1 +
 nextflow.config                               |   12 +-
 nextflow_schema.json                          |    9 +-
 nf-test.config                                |   26 +-
 ro-crate-metadata.json                        |   44 +-
 .../utils_nfcore_phaseimpute_pipeline/main.nf |   19 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |   66 +-
 .../utils_nfcore_pipeline/tests/main.nf.test  |   29 +
 .../tests/main.nf.test.snap                   |   19 +
 .../nf-core/utils_nfschema_plugin/main.nf     |    3 +-
 .../tests/nextflow.config                     |    2 +-
 tests/default.nf.test                         |   14 +-
 tests/nextflow.config                         |    2 +-
 workflows/phaseimpute.nf                      |   84 +-
 69 files changed, 6300 insertions(+), 750 deletions(-)
 delete mode 100644 .github/CONTRIBUTING.md
 delete mode 100644 assets/adaptivecard.json
 delete mode 100644 assets/slackreport.json
 create mode 100644 conf/containers_conda_lock_files_amd64.config
 create mode 100644 conf/containers_conda_lock_files_arm64.config
 create mode 100644 conf/containers_docker_amd64.config
 create mode 100644 conf/containers_docker_arm64.config
 create mode 100644 conf/containers_singularity_https_amd64.config
 create mode 100644 conf/containers_singularity_https_arm64.config
 create mode 100644 conf/containers_singularity_oras_amd64.config
 create mode 100644 conf/containers_singularity_oras_arm64.config
 create mode 100644 docs/CONTRIBUTING.md
 create mode 100644 modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
 create mode 100644 modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
 create mode 100644 modules/nf-core/multiqc/tests/custom_prefix.config
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 97c8c97f..237c9ed0 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,4 +1,5 @@
 {
+    "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json",
     "name": "nfcore",
     "image": "nfcore/devcontainer:latest",
 
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
deleted file mode 100644
index e357adf5..00000000
--- a/.github/CONTRIBUTING.md
+++ /dev/null
@@ -1,125 +0,0 @@
-# `nf-core/phaseimpute`: Contributing Guidelines
-
-Hi there!
-Many thanks for taking an interest in improving nf-core/phaseimpute.
-
-We try to manage the required tasks for nf-core/phaseimpute 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/phaseimpute then the best place to ask is on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Contribution workflow
-
-If you'd like to write some code for nf-core/phaseimpute, the standard workflow is as follows:
-
-1. Check that there isn't already an issue about your idea in the [nf-core/phaseimpute issues](https://github.com/nf-core/phaseimpute/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/phaseimpute repository](https://github.com/nf-core/phaseimpute) 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/phaseimpute documentation](https://nf-co.re/phaseimpute/usage) and don't hesitate to get in touch on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) channel ([join our Slack here](https://nf-co.re/join/slack)).
-
-## Pipeline contribution conventions
-
-To make the `nf-core/phaseimpute` 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/phaseimpute/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 c34e0b42..7f4d9e6f 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/phaseimpute/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/phaseimpute/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/phaseimpute/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/phaseimpute/tree/main/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/phaseimpute _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 34085279..e2833ee9 100644
--- a/.github/actions/get-shards/action.yml
+++ b/.github/actions/get-shards/action.yml
@@ -21,7 +21,7 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 3b9724c7..ad686e8e 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -20,24 +20,24 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
+      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
       with:
         python-version: "3.14"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,7 +48,7 @@ runs:
 
     - name: Conda setup
       if: contains(inputs.profile, 'conda')
-      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
         auto-update-conda: true
         conda-solver: libmamba
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 8091a48c..5a20217d 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/phaseimpute/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'phaseimpute'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *phaseimpute/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *phaseimpute/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/phaseimpute/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 27284429..b3900639 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 30076fc1..10d5448f 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 6adb0fff..172de6f3 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
+      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 45884ff9..5b6592c1 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -39,12 +39,12 @@ jobs:
     needs: configure
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
@@ -54,10 +54,16 @@ jobs:
         with:
           apptainer-version: 1.3.4
 
+      - name: Read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Make a cache directory for the container images
         run: |
@@ -127,7 +133,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 395b65dc..e5e049df 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -31,22 +31,18 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
+      # Install and run prek
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -54,7 +50,7 @@ jobs:
 
       - name: Commit & push changes
         id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 7a527a34..bfe46c98 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,33 +11,31 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
@@ -45,12 +43,10 @@ jobs:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -58,7 +54,7 @@ jobs:
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index e6e9bc26..2bc3c07f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
+        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index c98d76ec..efd72d65 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.4"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.4"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 431d3d44..78d5dbe0 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@master
+      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)
@@ -34,7 +34,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
+      - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index e8560fc7..ea30827e 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
@@ -29,7 +29,7 @@ jobs:
         run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with:
@@ -42,5 +42,5 @@ jobs:
             > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
             > Please update your pipeline to the latest version.
             >
-            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
           #
diff --git a/.gitignore b/.gitignore
index a42ce016..cc2b1a77 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.lineage/
diff --git a/.nf-core.yml b/.nf-core.yml
index caf15409..04e47cf2 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,4 +1,8 @@
-nf_core_version: 3.5.1
+lint:
+  files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
+  nf_test_content: false
+nf_core_version: 4.0.0
 repository_type: pipeline
 template:
   author: Louis Le Nezet, Anabella Trigila
@@ -8,4 +12,4 @@ template:
   name: phaseimpute
   org: nf-core
   outdir: .
-  version: 1.0.0
+  version: 1.2.0dev
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d06777a8..f51e1a28 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.6.2
+          - prettier@3.8.3
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -13,15 +13,21 @@ repos:
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
       - id: end-of-file-fixer
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
-              modules/nf-core/.*|
-              subworkflows/nf-core/.*|
+              modules/(?!local/).*|
+              subworkflows/(?!local/).*|
               .*\.snap$
           )$
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
+        args: ["-output", "json"]
diff --git a/.prettierignore b/.prettierignore
index dd749d43..63cde500 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ded7b9a6..12e3313a 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 - [date]
+## v1.2.0dev - [date]
 
 Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/README.md b/README.md
index 85461d02..e696bc5a 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,8 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -30,13 +30,13 @@
 -->
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -66,7 +66,7 @@ nextflow run nf-core/phaseimpute \
 ```
 
 > [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/parameters).
 
@@ -86,7 +86,7 @@ We thank the following people for their extensive assistance in the development
 
 ## Contributions and Support
 
-If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).
 
 For further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (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 e7079ad6..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/phaseimpute v${version} - ${runName}",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "spacing": "None",
-                        "text": "Completed at ${dateComplete} (duration: ${duration})",
-                        "isSubtle": true,
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "The command used to launch the workflow was as follows:",
-                        "wrap": true
-                    },
-                    {
-                        "type": "TextBlock",
-                        "text": "${commandLine}",
-                        "isSubtle": true,
-                        "wrap": true
-                    }
-                ],
-                "actions": [
-                    {
-                        "type": "Action.ShowCard",
-                        "title": "Pipeline Configuration",
-                        "card": {
-                            "type": "AdaptiveCard",
-                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
-                            "body": [
-                                {
-                                    "type": "FactSet",
-                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
-                                    ]
-                                }
-                            ]
-                        }
-                    }
-                ]
-            }
-        }
-    ]
-}
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 9fb2992a..4770e881 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/phaseimpute/releases/tag/1.0.0" target="_blank">nf-core/phaseimpute</a>
+  This report has been generated by the <a href="https://github.com/nf-core/phaseimpute/tree/dev" target="_blank">nf-core/phaseimpute</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/phaseimpute/1.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/phaseimpute/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-phaseimpute-methods-description":
     order: -1000
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 1293a50c..16d974a7 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/main/assets/schema_input.json",
     "title": "nf-core/phaseimpute pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
diff --git a/assets/slackreport.json b/assets/slackreport.json
deleted file mode 100644
index 264f3bed..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/phaseimpute ${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 af284ec0..46f04c25 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + (175..177)) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
new file mode 100644
index 00000000..d3ee1b4e
--- /dev/null
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
new file mode 100644
index 00000000..2b90ac4f
--- /dev/null
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
new file mode 100644
index 00000000..65f1814a
--- /dev/null
+++ b/conf/containers_docker_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
new file mode 100644
index 00000000..6c845ba4
--- /dev/null
+++ b/conf/containers_docker_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
new file mode 100644
index 00000000..838f2484
--- /dev/null
+++ b/conf/containers_singularity_https_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
new file mode 100644
index 00000000..090173be
--- /dev/null
+++ b/conf/containers_singularity_https_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
new file mode 100644
index 00000000..773f3698
--- /dev/null
+++ b/conf/containers_singularity_oras_amd64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
new file mode 100644
index 00000000..798cc638
--- /dev/null
+++ b/conf/containers_singularity_oras_arm64.config
@@ -0,0 +1,2 @@
+process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
new file mode 100644
index 00000000..b82e4bb6
--- /dev/null
+++ b/docs/CONTRIBUTING.md
@@ -0,0 +1,185 @@
+---
+title: Contributing
+markdownPlugin: checklist
+---
+
+# `nf-core/phaseimpute`: Contributing guidelines
+
+Hi there!
+Thanks for taking an interest in improving nf-core/phaseimpute.
+
+This page describes the recommended nf-core way to contribute to both nf-core/phaseimpute 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/phaseimpute.
+
+> [!NOTE]
+> If you need help using or modifying nf-core/phaseimpute, ask on the nf-core Slack [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) 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/phaseimpute/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/phaseimpute repository](https://github.com/nf-core/phaseimpute) 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/phaseimpute documentation](https://nf-co.re/phaseimpute/usage) or ask on the nf-core [#phaseimpute](https://nfcore.slack.com/channels/phaseimpute) Slack channel ([join our Slack here](https://nf-co.re/join/slack)).
+
+### GitHub Codespaces
+
+You can contribute to nf-core/phaseimpute 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/phaseimpute/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/phaseimpute 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 ec0f8106..75615e46 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -76,7 +76,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
 > [!WARNING]
-> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -173,19 +173,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
-To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
+To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website.
 
 ### Custom Containers
 
 In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
-To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
+To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website.
 
 ### Custom Tool Arguments
 
 A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
 
-To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
+To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website.
 
 ### nf-core/configs
 
diff --git a/main.nf b/main.nf
index 6feac1c1..fb465e07 100644
--- a/main.nf
+++ b/main.nf
@@ -51,7 +51,11 @@ workflow NFCORE_PHASEIMPUTE {
     // WORKFLOW: Run pipeline
     //
     PHASEIMPUTE (
-        samplesheet
+        samplesheet,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
     )
     emit:
     multiqc_report = PHASEIMPUTE.out.multiqc_report // channel: /path/to/multiqc_report.html
@@ -95,7 +99,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         NFCORE_PHASEIMPUTE.out.multiqc_report
     )
 }
diff --git a/modules.json b/modules.json
index 4f205e44..5111f87f 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                         "installed_by": ["modules"]
                     }
                 }
@@ -26,12 +26,12 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
+                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
new file mode 100644
index 00000000..7770ccd5
--- /dev/null
+++ b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
@@ -0,0 +1,822 @@
+
+version: 6
+environments:
+default:
+channels:
+- url: https://conda.anaconda.org/conda-forge/
+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
+linux-64:
+- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
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diff --git a/modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
new file mode 100644
index 00000000..cdc434ca
--- /dev/null
+++ b/modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
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+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxtst-1.2.5-h57736b2_3.conda
+sha256: 6eaffce5a34fc0a16a21ddeaefb597e792a263b1b0c387c1ce46b0a967d558e1
+md5: c05698071b5c8e0da82a282085845860
+depends:
+- libgcc >=13
+- xorg-libx11 >=1.8.9,<2.0a0
+- xorg-libxext >=1.3.6,<2.0a0
+- xorg-libxi >=1.7.10,<2.0a0
+license: MIT
+license_family: MIT
+size: 33786
+timestamp: 1727964907993
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
+- libzlib >=1.3.1,<2.0a0
+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 23e16634..10851264 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,37 +1,40 @@
 process FASTQC {
     tag "${meta.id}"
-    label 'process_medium'
+    label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
-        'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0'
+        : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads, stageAs: '?/*')
 
     output:
     tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
+    tuple val(meta), path("*.zip"), emit: zip
+    tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args          = task.ext.args ?: ''
-    def prefix        = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to     = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
-    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
+    // Dividing the task.memory by task.cpus allows to stick to requested amount of RAM in the label
+    def memory_in_mb = task.memory
+        ? (task.memory.toUnit('MB') / task.cpus).intValue()
+        : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+    def fastqc_memory_arg = fastqc_memory ? "--memory ${fastqc_memory}" : ''
 
     """
     printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
@@ -41,13 +44,8 @@ process FASTQC {
     fastqc \\
         ${args} \\
         --threads ${task.cpus} \\
-        --memory ${fastqc_memory} \\
+        ${fastqc_memory_arg} \\
         ${renamed_files}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 
     stub:
@@ -55,10 +53,5 @@ process FASTQC {
     """
     touch ${prefix}.html
     touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index c8d9d025..2f6cfef6 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -53,13 +53,28 @@ output:
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
           ontologies: []
+  versions_fastqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - fastqc:
+          type: string
+          description: The tool name
+      - fastqc --version | sed "/FastQC v/!d; s/.*v//":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@drpatelh"
   - "@grst"
@@ -70,3 +85,27 @@ maintainers:
   - "@grst"
   - "@ewels"
   - "@FelixKrueger"
+containers:
+  docker:
+    linux/arm64:
+      name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68
+      build_id: bd-e455e32f745abe68_1
+      scan_id: sc-f102f736465af88c_1
+    linux/amd64:
+      name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2
+      build_id: bd-5cb1a2fa2f18c7c2_1
+      scan_id: sc-0c0466326b6b77d2_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd
+      build_id: bd-5c4bd442468d75dd_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035
+      build_id: bd-127a87fc06499035_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index e9d79a07..66c44da9 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -58,7 +58,7 @@ nextflow_process {
                 { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
                 { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
                 { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -82,7 +82,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -106,7 +106,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -142,7 +142,7 @@ nextflow_process {
                 { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
                 { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
                 { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
@@ -166,7 +166,7 @@ nextflow_process {
                 { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
                 { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
                 { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() }
             )
         }
     }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index d5db3092..c8ee120f 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,15 +1,21 @@
 {
     "sarscov2 custom_prefix": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:16.374038"
+        "timestamp": "2025-10-28T16:39:14.518503"
     },
     "sarscov2 single-end [fastq] - stub": {
         "content": [
@@ -33,7 +39,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -44,8 +54,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -59,10 +73,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:24.993809"
+        "timestamp": "2025-10-28T16:39:19.309008"
     },
     "sarscov2 custom_prefix - stub": {
         "content": [
@@ -86,7 +100,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -97,8 +115,12 @@
                         "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -112,58 +134,82 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:03:10.93942"
+        "timestamp": "2025-10-28T16:39:44.94888"
     },
     "sarscov2 interleaved [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:42.355718"
+        "timestamp": "2025-10-28T16:38:45.168496"
     },
     "sarscov2 paired-end [bam]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:53.276274"
+        "timestamp": "2025-10-28T16:38:53.268919"
     },
     "sarscov2 multiple [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:05.527626"
+        "timestamp": "2025-10-28T16:39:05.050305"
     },
     "sarscov2 paired-end [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:31.188871"
+        "timestamp": "2025-10-28T16:38:37.2373"
     },
     "sarscov2 paired-end [fastq] - stub": {
         "content": [
@@ -187,7 +233,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -198,8 +248,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -213,10 +267,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:34.273566"
+        "timestamp": "2025-10-28T16:39:24.450398"
     },
     "sarscov2 multiple [fastq] - stub": {
         "content": [
@@ -240,7 +294,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -251,8 +309,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -266,22 +328,28 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:03:02.304411"
+        "timestamp": "2025-10-28T16:39:39.758762"
     },
     "sarscov2 single-end [fastq]": {
         "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:01:19.095607"
+        "timestamp": "2025-10-28T16:38:29.555068"
     },
     "sarscov2 interleaved [fastq] - stub": {
         "content": [
@@ -305,7 +373,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -316,8 +388,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -331,10 +407,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:44.640184"
+        "timestamp": "2025-10-28T16:39:29.193136"
     },
     "sarscov2 paired-end [bam] - stub": {
         "content": [
@@ -358,7 +434,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "html": [
                     [
@@ -369,8 +449,12 @@
                         "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                "versions_fastqc": [
+                    [
+                        "FASTQC",
+                        "fastqc",
+                        "0.12.1"
+                    ]
                 ],
                 "zip": [
                     [
@@ -384,9 +468,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-07-22T11:02:53.550742"
+        "timestamp": "2025-10-28T16:39:34.144919"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
new file mode 100644
index 00000000..76190304
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
new file mode 100644
index 00000000..a55a4d49
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
@@ -0,0 +1,126 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6
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+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb
+https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda#2c21e66f50753a083cbe6b80f38268fa
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda#1b08cd684f34175e4514474793d44bcb
+https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda#c80d8a3b84358cb967fa81e7075fbc8a
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-hf4e2dac_0.conda#810d83373448da85c3f673fbcb7ad3a3
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
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+https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec
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index 00000000..a58231a0
--- /dev/null
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+- libzlib >=1.3.1,<2.0a0
+- ncurses >=6.5,<7.0a0
+- readline >=8.3,<9.0a0
+license: blessing
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
new file mode 100644
index 00000000..f787dbe1
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
@@ -0,0 +1,125 @@
+
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-aarch64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958
+https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6
+https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1
+https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc
+https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f
+https://conda.anaconda.org/conda-forge/linux-aarch64/libexpat-2.7.5-hfae3067_0.conda#05d1e0b30acd816a192c03dc6e164f4d
+https://conda.anaconda.org/conda-forge/linux-aarch64/libffi-3.5.2-h376a255_0.conda#2f364feefb6a7c00423e80dcb12db62a
+https://conda.anaconda.org/conda-forge/linux-aarch64/liblzma-5.8.3-he30d5cf_0.conda#76298a9e6d71ee6e832a8d0d7373b261
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+https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda#439cd0f567d697b20a8f45cb70a1005a
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda#ada41c863af263cc4c5fcbaff7c3e4dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-15.2.0-he9431aa_18.conda#4feebd0fbf61075a1a9c2e9b3936c257
+https://conda.anaconda.org/conda-forge/linux-aarch64/mathjax-2.7.7-h8af1aa0_3.tar.bz2#7b08314a6867a9d5648a1c3265e9eb8e
+https://conda.anaconda.org/conda-forge/linux-aarch64/nspr-4.38-h3ad9384_0.conda#6dd4f07147774bf720075a210f8026b9
+https://conda.anaconda.org/conda-forge/linux-aarch64/nss-3.118-h544fa81_0.conda#4540f9570d12db2150f42ba036154552
+https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.0-he8854b5_0.conda#ad8164bdeece883b825c50639c0c4725
+https://conda.anaconda.org/conda-forge/linux-aarch64/kaleido-core-0.2.1-he5a581e_0.tar.bz2#4f0d284f5d11e04277b552eb1c172c7f
+https://conda.anaconda.org/conda-forge/linux-aarch64/libjpeg-turbo-3.1.4.1-he30d5cf_0.conda#a85ba48648f6868016f2741fd9170250
+https://conda.anaconda.org/conda-forge/linux-aarch64/lerc-4.1.0-h52b7260_0.conda#d13423b06447113a90b5b1366d4da171
+https://conda.anaconda.org/conda-forge/linux-aarch64/libdeflate-1.25-h1af38f5_0.conda#a9138815598fe6b91a1d6782ca657b0c
+https://conda.anaconda.org/conda-forge/linux-aarch64/libwebp-base-1.6.0-ha2e29f5_0.conda#24e92d0942c799db387f5c9d7b81f1af
+https://conda.anaconda.org/conda-forge/linux-aarch64/libtiff-4.7.1-hdb009f0_1.conda#8c6fd84f9c87ac00636007c6131e457d
+https://conda.anaconda.org/conda-forge/linux-aarch64/lcms2-2.18-h9d5b58d_0.conda#bb960f01525b5e001608afef9d47b79c
+https://conda.anaconda.org/conda-forge/linux-aarch64/pthread-stubs-0.4-h86ecc28_1002.conda#bb5a90c93e3bac3d5690acf76b4a6386
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda#1c246e1105000c3660558459e2fd6d43
+https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda#bff06dcde4a707339d66d45d96ceb2e2
+https://conda.anaconda.org/conda-forge/linux-aarch64/libxcb-1.17.0-h262b8f6_0.conda#cd14ee5cca2464a425b1dbfc24d90db2
+https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda#ba0a9221ce1063f31692c07370d062f3
+https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda#592132998493b3ff25fd7479396e8351
+https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda#5b5203189eb668f042ac2b0826244964
+https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda#e941e85e273121222580723010bd4fa2
+https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8
+https://conda.anaconda.org/conda-forge/linux-aarch64/openjpeg-2.5.4-h5da879a_0.conda#cea962410e327262346d48d01f05936c
+https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda#f731af71c723065d91b4c01bb822641b
+https://conda.anaconda.org/conda-forge/linux-aarch64/pillow-12.2.0-py314hac3e5ec_0.conda#87d58d103b47c4a8567b3d7666647684
+https://conda.anaconda.org/conda-forge/noarch/narwhals-2.20.0-pyhcf101f3_0.conda#6cac1a50359219d786453c6fef819f98
+https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda#3e9427ee186846052e81fadde8ebe96a
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-32-1.40.0-py310hff09b76_0.conda#d5628a33ce7652511e38fc98643dc910
+https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34
+https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372
+https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7
+https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88
+https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58
+https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc
+https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240
+https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6
+https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98
+https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c
+https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2
+https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac
+https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130
+https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59
+https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0
+https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66
+https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9
+https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a
+https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864
+https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6
+https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206
+https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b
+https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873
+https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f
+https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index d02016a0..37e7612d 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.32
+  - bioconda::multiqc=1.34
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index c1158fb0..e80e8cd8 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,24 +1,21 @@
 process MULTIQC {
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
-        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
+        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
 
     input:
-    path  multiqc_files, stageAs: "?/*"
-    path(multiqc_config)
-    path(extra_multiqc_config)
-    path(multiqc_logo)
-    path(replace_names)
-    path(sample_names)
+    tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
 
     output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
+    tuple val(meta), path("*.html"), emit: report
+    tuple val(meta), path("*_data"), emit: data
+    tuple val(meta), path("*_plots"), emit: plots, optional: true
+    // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever
+    tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,38 +23,28 @@ process MULTIQC {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
-    def config = multiqc_config ? "--config $multiqc_config" : ''
-    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : ""
     def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
     def replace = replace_names ? "--replace-names ${replace_names}" : ''
     def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
-        $args \\
-        $config \\
-        $prefix \\
-        $extra_config \\
-        $logo \\
-        $replace \\
-        $samples \\
+        ${args} \\
+        ${config} \\
+        ${prefix} \\
+        ${logo} \\
+        ${replace} \\
+        ${samples} \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 
     stub:
     """
     mkdir multiqc_data
+    touch multiqc_data/.stub
     mkdir multiqc_plots
+    touch multiqc_plots/.stub
     touch multiqc_report.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ce30eb73..2facc627 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,6 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into
-  a single report
+description: Aggregate results from bioinformatics analyses across many samples
+  into a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,74 +12,91 @@ tools:
         It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
-      licence: ["GPL-3.0-or-later"]
+      licence:
+        - "GPL-3.0-or-later"
       identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-      ontologies: []
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-      ontologies:
-        - edam: http://edamontology.org/format_3750 # YAML
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections
-        in multiqc_config.
-      pattern: "*.{yml,yaml}"
-      ontologies:
-        - edam: http://edamontology.org/format_3750 # YAML
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-      ontologies: []
-  - replace_names:
-      type: file
-      description: |
-        Optional two-column sample renaming file. First column a set of
-        patterns, second column a set of corresponding replacements. Passed via
-        MultiQC's `--replace-names` option.
-      pattern: "*.{tsv}"
-      ontologies:
-        - edam: http://edamontology.org/format_3475 # TSV
-  - sample_names:
-      type: file
-      description: |
-        Optional TSV file with headers, passed to the MultiQC --sample_names
-        argument.
-      pattern: "*.{tsv}"
-      ontologies:
-        - edam: http://edamontology.org/format_3475 # TSV
-output:
-  report:
-    - "*multiqc_report.html":
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'sample1', single_end:false ]
+    - multiqc_files:
         type: file
-        description: MultiQC report file
-        pattern: "multiqc_report.html"
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
         ontologies: []
-  data:
-    - "*_data":
-        type: directory
-        description: MultiQC data dir
-        pattern: "multiqc_data"
-  plots:
-    - "*_plots":
+    - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+    - multiqc_logo:
         type: file
-        description: Plots created by MultiQC
-        pattern: "*_data"
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
         ontologies: []
-  versions:
-    - versions.yml:
+    - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+    - sample_names:
         type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3475
+output:
+  report:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.html":
+          type: file
+          description: MultiQC report file
+          pattern: ".html"
+          ontologies: []
+  data:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
+  plots:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_plots"
+          ontologies: []
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - multiqc:
+          type: string
+          description: The tool name
+      - multiqc --version | sed "s/.* //g":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@abhi18av"
   - "@bunop"
@@ -90,3 +107,27 @@ maintainers:
   - "@bunop"
   - "@drpatelh"
   - "@jfy133"
+containers:
+  conda:
+    linux/amd64:
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+    linux/arm64:
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+  docker:
+    linux/amd64:
+      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
+      build_id: bd-db7c73dae76bc9e6_1
+      scan_id: sc-66fc7138dbf1cf48_1
+    linux/arm64:
+      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
+      build_id: bd-d167b8012595a136_1
+      scan_id: sc-ac701dfa631a2af9_1
+  singularity:
+    linux/amd64:
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
+      build_id: bd-4fc8657c816047c0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+    linux/arm64:
+      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
+      build_id: bd-7fbd82d945c06726_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config
new file mode 100644
index 00000000..b30b1358
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/custom_prefix.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = "custom_prefix"
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index 33316a7d..4cbdb95d 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -15,25 +15,84 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    []
+                ])
                 """
             }
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
-                { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
-            )
+            assert process.success
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - custom prefix") {
+        config "./custom_prefix.config"
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    []
+                ])
+                """
+            }
         }
 
+        then {
+            assert process.success
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
+        }
     }
 
     test("sarscov2 single-end [fastqc] [config]") {
@@ -41,23 +100,85 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true),
+                    [],
+                    [],
+                    []
+                ])
                 """
             }
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
-                { assert process.out.data[0] ==~ ".*/multiqc_data" },
-                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
-            )
+            assert process.success
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] [multiple configs]") {
+
+        when {
+            process {
+                """
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [
+                        file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true),
+                        file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true)
+                    ],
+                    [],
+                    [],
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(
+                sanitizeOutput(process.out).collectEntries { key, val ->
+                        if (key == "data") {
+                            return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "plots") {
+                            return [key, val.collect { [
+                                "pdf",
+                                path("${it[1]}/pdf").list().collect { file(it.toString()).name },
+                                "png",
+                                path("${it[1]}/png").list().collect { file(it.toString()).name },
+                                "svg",
+                                path("${it[1]}/svg").list().collect { file(it.toString()).name }] }]
+                        }
+                        else if (key == "report") {
+                            return [key, file(val[0][1].toString()).name]
+                        }
+                        return [key, val]
+                    }
+            ).match()
         }
     }
 
@@ -68,25 +189,23 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                input[5] = []
+                input[0] = channel.of([
+                    [ id: 'FASTQC' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    []
+                ])
                 """
             }
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.report.collect { file(it).getName() } +
-                                process.out.data.collect { file(it).getName() } +
-                                process.out.plots.collect { file(it).getName() } +
-                                process.out.versions ).match("multiqc_stub") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
-
     }
 }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index a88bafd6..7c2f370f 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -1,41 +1,422 @@
 {
-    "multiqc_versions_single": {
+    "sarscov2 single-end [fastqc] [multiple configs]": {
         "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "multiqc_report.html",
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.34"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-17T16:15:42.577775492",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:33:24.356715"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
-    "multiqc_stub": {
+    "sarscov2 single-end [fastqc]": {
         "content": [
-            [
-                "multiqc_report.html",
-                "multiqc_data",
-                "multiqc_plots",
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_software_versions.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "multiqc_report.html",
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.34"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-17T16:21:17.072841555",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:34:11.103619"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
-    "multiqc_versions_config": {
+    "sarscov2 single-end [fastqc] - stub": {
         "content": [
-            [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
-            ]
+            {
+                "data": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        [
+                            ".stub:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        [
+                            ".stub:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "report": [
+                    [
+                        {
+                            "id": "FASTQC"
+                        },
+                        "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.34"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-02-26T15:14:39.789193051",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-10-27T13:34:04.615233"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 single-end [fastqc] [config]": {
+        "content": [
+            {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "multiqc_report.html",
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.34"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-17T16:15:30.372239611",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 single-end [fastqc] - custom prefix": {
+        "content": [
+            {
+                "data": [
+                    [
+                        [
+                            "fastqc-status-check-heatmap.txt",
+                            "fastqc_overrepresented_sequences_plot.txt",
+                            "fastqc_per_base_n_content_plot.txt",
+                            "fastqc_per_base_sequence_quality_plot.txt",
+                            "fastqc_per_sequence_gc_content_plot_Counts.txt",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.txt",
+                            "fastqc_per_sequence_quality_scores_plot.txt",
+                            "fastqc_sequence_counts_plot.txt",
+                            "fastqc_sequence_duplication_levels_plot.txt",
+                            "fastqc_sequence_length_distribution_plot.txt",
+                            "fastqc_top_overrepresented_sequences_table.txt",
+                            "llms-full.txt",
+                            "multiqc.log",
+                            "multiqc.parquet",
+                            "multiqc_citations.txt",
+                            "multiqc_data.json",
+                            "multiqc_fastqc.txt",
+                            "multiqc_general_stats.txt",
+                            "multiqc_software_versions.txt",
+                            "multiqc_sources.txt"
+                        ]
+                    ]
+                ],
+                "plots": [
+                    [
+                        "pdf",
+                        [
+                            "fastqc-status-check-heatmap.pdf",
+                            "fastqc_overrepresented_sequences_plot.pdf",
+                            "fastqc_per_base_n_content_plot.pdf",
+                            "fastqc_per_base_sequence_quality_plot.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Counts.pdf",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.pdf",
+                            "fastqc_per_sequence_quality_scores_plot.pdf",
+                            "fastqc_sequence_counts_plot-cnt.pdf",
+                            "fastqc_sequence_counts_plot-pct.pdf",
+                            "fastqc_sequence_duplication_levels_plot.pdf",
+                            "fastqc_sequence_length_distribution_plot.pdf",
+                            "fastqc_top_overrepresented_sequences_table.pdf"
+                        ],
+                        "png",
+                        [
+                            "fastqc-status-check-heatmap.png",
+                            "fastqc_overrepresented_sequences_plot.png",
+                            "fastqc_per_base_n_content_plot.png",
+                            "fastqc_per_base_sequence_quality_plot.png",
+                            "fastqc_per_sequence_gc_content_plot_Counts.png",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.png",
+                            "fastqc_per_sequence_quality_scores_plot.png",
+                            "fastqc_sequence_counts_plot-cnt.png",
+                            "fastqc_sequence_counts_plot-pct.png",
+                            "fastqc_sequence_duplication_levels_plot.png",
+                            "fastqc_sequence_length_distribution_plot.png",
+                            "fastqc_top_overrepresented_sequences_table.png"
+                        ],
+                        "svg",
+                        [
+                            "fastqc-status-check-heatmap.svg",
+                            "fastqc_overrepresented_sequences_plot.svg",
+                            "fastqc_per_base_n_content_plot.svg",
+                            "fastqc_per_base_sequence_quality_plot.svg",
+                            "fastqc_per_sequence_gc_content_plot_Counts.svg",
+                            "fastqc_per_sequence_gc_content_plot_Percentages.svg",
+                            "fastqc_per_sequence_quality_scores_plot.svg",
+                            "fastqc_sequence_counts_plot-cnt.svg",
+                            "fastqc_sequence_counts_plot-pct.svg",
+                            "fastqc_sequence_duplication_levels_plot.svg",
+                            "fastqc_sequence_length_distribution_plot.svg",
+                            "fastqc_top_overrepresented_sequences_table.svg"
+                        ]
+                    ]
+                ],
+                "report": "custom_prefix.html",
+                "versions": [
+                    [
+                        "MULTIQC",
+                        "multiqc",
+                        "1.34"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-17T16:15:18.189023981",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
index c537a6a3..374dfef2 100644
--- a/modules/nf-core/multiqc/tests/nextflow.config
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -1,5 +1,6 @@
 process {
     withName: 'MULTIQC' {
         ext.prefix = null
+        ext.args = '-p'
     }
 }
diff --git a/nextflow.config b/nextflow.config
index 532d0b1d..e000f4fe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,7 +32,6 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
@@ -53,6 +52,10 @@ params {
     validate_params            = true
 }
 
+// Backwards compatibility for publishDir syntax
+outputDir = params.outdir
+workflow.output.mode = params.publish_dir_mode
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -258,9 +261,9 @@ manifest {
     homePage        = 'https://github.com/nf-core/phaseimpute'
     description     = """Phasing and imputation pipeline"""
     mainScript      = 'main.nf'
-    defaultBranch   = 'master'
-    nextflowVersion = '!>=25.04.0'
-    version         = '1.0.0'
+    defaultBranch   = 'main'
+    nextflowVersion = '!>=25.10.4'
+    version         = '1.2.0dev'
     doi             = ''
 }
 
@@ -273,6 +276,5 @@ 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 3950236e..cf2882de 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/main/nextflow_schema.json",
     "title": "nf-core/phaseimpute pipeline parameters",
     "description": "Phasing and imputation pipeline",
     "type": "object",
@@ -180,13 +180,6 @@
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
-                "hook_url": {
-                    "type": "string",
-                    "description": "Incoming hook URL for messaging service",
-                    "fa_icon": "fas fa-people-group",
-                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
-                    "hidden": true
-                },
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
diff --git a/nf-test.config b/nf-test.config
index 3a1fff59..f7aaeb4a 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,21 +1,35 @@
 config {
     // location for all nf-test tests
-    testsDir "."
+    testsDir = "."
 
     // nf-test directory including temporary files for each test
-    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+    workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "tests/nextflow.config"
+    configFile = "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
+    ignore = [
+        'modules/nf-core/**/tests/*',
+        'subworkflows/nf-core/**/tests/*',
+    ]
 
     // run all test with defined profile(s) from the main nextflow.config
-    profile "test"
+    profile = "test"
 
     // list of filenames or patterns that should be trigger a full test run
-    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+    triggers = [
+        '.github/actions/nf-test/action.yml',
+        '.github/workflows/nf-test.yml',
+        'assets/schema_input.json',
+        'bin/*',
+        'conf/test.config',
+        'nextflow.config',
+        'nextflow_schema.json',
+        'nf-test.config',
+        'tests/.nftignore',
+        'tests/nextflow.config',
+    ]
 
     // load the necessary plugins
     plugins {
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 85401412..f6555235 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -1,6 +1,6 @@
 {
     "@context": [
-        "https://w3id.org/ro/crate/1.1/context",
+        "https://w3id.org/ro/crate/1.2/context",
         {
             "GithubService": "https://w3id.org/ro/terms/test#GithubService",
             "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
@@ -21,9 +21,9 @@
         {
             "@id": "./",
             "@type": "Dataset",
-            "creativeWorkStatus": "Stable",
-            "datePublished": "2025-11-20T09:32:44+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/nf-core-phaseimpute_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/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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/phaseimpute** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/phaseimpute \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/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/phaseimpute/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/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le Nezet, Anabella Trigila.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (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/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2026-04-28T11:20:55+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/nf-core-phaseimpute_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/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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/phaseimpute** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/phaseimpute \\\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/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/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/phaseimpute/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/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le Nezet, Anabella Trigila.\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 `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (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/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#6f3eda99-ba4d-4a37-a520-1f85deaf2a59"
+                    "@id": "#6d4899af-4cbc-4fed-b749-049c648f1851"
                 }
             ],
             "name": "nf-core/phaseimpute"
@@ -112,7 +112,7 @@
             },
             "conformsTo": [
                 {
-                    "@id": "https://w3id.org/ro/crate/1.1"
+                    "@id": "https://w3id.org/ro/crate/1.2"
                 },
                 {
                     "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
@@ -122,8 +122,16 @@
         {
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "contributor": [
+                {
+                    "@id": "#b4249e73-838c-4c50-9a17-c955ad06b959"
+                },
+                {
+                    "@id": "#95e1840c-22d1-4a05-90b7-7aaed626c201"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-11-20T09:32:44Z",
+            "dateModified": "2026-04-28T11:20:55Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "genotype", "imputation", "low-pass-sequencing", "phasing"],
             "license": ["MIT"],
@@ -134,8 +142,8 @@
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/phaseimpute", "https://nf-co.re/phaseimpute/1.0.0/"],
-            "version": ["1.0.0"]
+            "url": ["https://github.com/nf-core/phaseimpute", "https://nf-co.re/phaseimpute/dev/"],
+            "version": ["1.2.0dev"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -147,14 +155,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.04.0"
+            "version": "!>=25.10.4"
         },
         {
-            "@id": "#6f3eda99-ba4d-4a37-a520-1f85deaf2a59",
+            "@id": "#6d4899af-4cbc-4fed-b749-049c648f1851",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#86e85e64-9604-4edc-b9c8-3f4d5d8f4611"
+                    "@id": "#e7682c09-4df7-45ef-9e9d-123b43d80ccc"
                 }
             ],
             "mainEntity": {
@@ -163,7 +171,7 @@
             "name": "Test suite for nf-core/phaseimpute"
         },
         {
-            "@id": "#86e85e64-9604-4edc-b9c8-3f4d5d8f4611",
+            "@id": "#e7682c09-4df7-45ef-9e9d-123b43d80ccc",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/phaseimpute",
             "resource": "repos/nf-core/phaseimpute/actions/workflows/nf-test.yml",
@@ -290,6 +298,16 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#b4249e73-838c-4c50-9a17-c955ad06b959",
+            "@type": "Person",
+            "name": "Louis Le Nezet"
+        },
+        {
+            "@id": "#95e1840c-22d1-4a05-90b7-7aaed626c201",
+            "@type": "Person",
+            "name": "Anabella Trigila"
         }
     ]
 }
diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
index 953700c5..04f0cdf7 100644
--- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
@@ -14,7 +14,6 @@ include { samplesheetToList         } from 'plugin/nf-schema'
 include { paramsHelp                } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
@@ -54,6 +53,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+
+    def before_text = ""
+    def after_text = ""
     before_text = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -69,8 +71,12 @@ workflow PIPELINE_INITIALISATION {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/phaseimpute/blob/master/CITATIONS.md
+    https://github.com/nf-core/phaseimpute/blob/main/CITATIONS.md
 """
+    if (monochrome_logs) {
+        before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '')
+    }
+
     command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
     UTILS_NFSCHEMA_PLUGIN (
@@ -102,7 +108,7 @@ workflow PIPELINE_INITIALISATION {
     //
 
     channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -140,7 +146,6 @@ workflow PIPELINE_COMPLETION {
     plaintext_email // boolean: Send plain-text email instead of HTML
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url        //  string: hook URL for notifications
     multiqc_report  //  string: Path to MultiQC report
 
     main:
@@ -164,13 +169,11 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
+
     }
 
     workflow.onError {
-        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+        log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting"
     }
 }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 2f30e9a4..afca5439 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE {
     checkProfileProvided(nextflow_cli_args)
 
     emit:
-    valid_config
+    valid_config = valid_config
 }
 
 /*
@@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) {
         log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
-
-//
-// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
-//
-def imNotification(summary_params, hook_url) {
-    def summary = [:]
-    summary_params
-        .keySet()
-        .sort()
-        .each { group ->
-            summary << summary_params[group]
-        }
-
-    def misc_fields = [:]
-    misc_fields['start']          = workflow.start
-    misc_fields['complete']       = workflow.complete
-    misc_fields['scriptfile']     = workflow.scriptFile
-    misc_fields['scriptid']       = workflow.scriptId
-    if (workflow.repository) {
-        misc_fields['repository'] = workflow.repository
-    }
-    if (workflow.commitId) {
-        misc_fields['commitid']   = workflow.commitId
-    }
-    if (workflow.revision) {
-        misc_fields['revision']   = workflow.revision
-    }
-    misc_fields['nxf_version']    = workflow.nextflow.version
-    misc_fields['nxf_build']      = workflow.nextflow.build
-    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
-
-    def msg_fields = [:]
-    msg_fields['version']      = getWorkflowVersion()
-    msg_fields['runName']      = workflow.runName
-    msg_fields['success']      = workflow.success
-    msg_fields['dateComplete'] = workflow.complete
-    msg_fields['duration']     = workflow.duration
-    msg_fields['exitStatus']   = workflow.exitStatus
-    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
-    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
-    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
-    msg_fields['projectDir']   = workflow.projectDir
-    msg_fields['summary']      = summary << misc_fields
-
-    // Render the JSON template
-    def engine       = new groovy.text.GStringTemplateEngine()
-    // Different JSON depending on the service provider
-    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
-    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
-    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
-    def json_template = engine.createTemplate(hf).make(msg_fields)
-    def json_message  = json_template.toString()
-
-    // POST
-    def post = new URL(hook_url).openConnection()
-    post.setRequestMethod("POST")
-    post.setDoOutput(true)
-    post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"))
-    def postRC = post.getResponseCode()
-    if (!postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText())
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
new file mode 100644
index 00000000..8940d32d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap
new file mode 100644
index 00000000..859d1030
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index ee4738c8..1df8b76f 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
         }
         log.info paramsHelp(
             help_options,
-            params.help instanceof String ? params.help : "",
+            (params.help instanceof String && params.help != "true") ? params.help : "",
         )
         exit 0
     }
@@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     emit:
     dummy_emit = true
 }
-
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 8d8c7371..f6537cc3 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.5.1"
+    id "nf-schema@2.6.1"
 }
 
 validation {
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 53f9cdbb..b09bc800 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -13,19 +13,19 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
-            // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name)
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assert workflow.success
             assertAll(
-                { assert workflow.success},
                 { assert snapshot(
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_phaseimpute_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 555fee96..8c46ee59 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/phaseimpute'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/'
 }
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
diff --git a/workflows/phaseimpute.nf b/workflows/phaseimpute.nf
index e86cdb34..3fa5aed3 100644
--- a/workflows/phaseimpute.nf
+++ b/workflows/phaseimpute.nf
@@ -20,23 +20,25 @@ workflow PHASEIMPUTE {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
+    multiqc_config
+    multiqc_logo
+    multiqc_methods_description
+    outdir
+
     main:
 
-    ch_versions = channel.empty()
-    ch_multiqc_files = channel.empty()
+    def ch_versions = channel.empty()
+    def ch_multiqc_files = channel.empty()
     //
     // MODULE: Run FastQC
     //
-    FASTQC (
-        ch_samplesheet
-    )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    FASTQC(ch_samplesheet)
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.map{ _meta, file -> file })
 
     //
     // Collate and save software versions
     //
-    def topic_versions = Channel.topic("versions")
+    def topic_versions = channel.topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path
@@ -53,59 +55,43 @@ workflow PHASEIMPUTE {
             "${process}:\n${tool_versions.join('\n')}"
         }
 
-    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+    def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
         .mix(topic_versions_string)
         .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
+            storeDir: "${outdir}/pipeline_info",
             name: 'nf_core_'  +  'phaseimpute_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
-        ).set { ch_collated_versions }
-
+        )
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = channel.fromPath(
-        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config = params.multiqc_config ?
-        channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        channel.empty()
-    ch_multiqc_logo          = params.multiqc_logo ?
-        channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        channel.empty()
-
-    summary_params      = paramsSummaryMap(
-        workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
-        file(params.multiqc_methods_description, checkIfExists: true) :
-        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = channel.value(
-        methodsDescriptionText(ch_multiqc_custom_methods_description))
-
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_methods_description.collectFile(
-            name: 'methods_description_mqc.yaml',
-            sort: true
-        )
-    )
-
-    MULTIQC (
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList(),
-        [],
-        []
+    def ch_summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def ch_workflow_summary = channel.value(paramsSummaryMultiqc(ch_summary_params))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    def ch_multiqc_custom_methods_description = multiqc_methods_description
+        ? file(multiqc_methods_description, checkIfExists: true)
+        : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
+    MULTIQC(
+        ch_multiqc_files.flatten().collect().map { files ->
+            [
+                [id: 'phaseimpute'],
+                files,
+                multiqc_config
+                    ? file(multiqc_config, checkIfExists: true)
+                    : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true),
+                multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [],
+                [],
+                [],
+            ]
+        }
     )
-
-    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
-
 }
 
 /*

From 12fcc98ff9c58f2f909505a4705946379c5b5ec4 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 30 Apr 2026 13:33:19 +0000
Subject: [PATCH 2/6] Template update for nf-core/tools version 4.0.2

---
 .github/workflows/download_pipeline.yml |  8 +++++---
 .github/workflows/fix_linting.yml       |  2 +-
 .github/workflows/linting.yml           |  2 +-
 .github/workflows/linting_comment.yml   |  2 +-
 .nf-core.yml                            |  2 +-
 README.md                               |  2 +-
 nextflow_schema.json                    |  1 -
 ro-crate-metadata.json                  | 22 +++++++++++-----------
 8 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 5b6592c1..a7bf4fc2 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -38,6 +38,9 @@ jobs:
     runs-on: ubuntu-latest
     needs: configure
     steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
@@ -55,10 +58,9 @@ jobs:
           apptainer-version: 1.3.4
 
       - name: Read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
-        with:
-          config: ${{ github.workspace }}/.nf-core.yml
+        run: |
+          echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT"
 
       - name: Install dependencies
         run: |
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index e5e049df..56e3cda1 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -37,7 +37,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index bfe46c98..8738ffc9 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -17,7 +17,7 @@ jobs:
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Run prek
-        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 2bc3c07f..5b0c24f7 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.nf-core.yml b/.nf-core.yml
index 04e47cf2..a326ebb3 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,7 +2,7 @@ lint:
   files_unchanged:
     - .github/PULL_REQUEST_TEMPLATE.md
   nf_test_content: false
-nf_core_version: 4.0.0
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: Louis Le Nezet, Anabella Trigila
diff --git a/README.md b/README.md
index e696bc5a..c8dcdab2 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index cf2882de..2f53ce28 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -74,7 +74,6 @@
                 },
                 "igenomes_base": {
                     "type": "string",
-                    "format": "directory-path",
                     "description": "The base path to the igenomes reference files",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index f6555235..795eb595 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2026-04-28T11:20:55+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/nf-core-phaseimpute_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/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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/phaseimpute** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/phaseimpute \\\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/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/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/phaseimpute/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/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le Nezet, Anabella Trigila.\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 `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (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/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2026-04-30T13:33:11+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/nf-core-phaseimpute_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/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/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/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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/phaseimpute** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/phaseimpute \\\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/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/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/phaseimpute/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/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le Nezet, Anabella Trigila.\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 `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (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/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#6d4899af-4cbc-4fed-b749-049c648f1851"
+                    "@id": "#4523c1cb-b6ae-4871-9a4c-c970c6c684a6"
                 }
             ],
             "name": "nf-core/phaseimpute"
@@ -124,14 +124,14 @@
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "contributor": [
                 {
-                    "@id": "#b4249e73-838c-4c50-9a17-c955ad06b959"
+                    "@id": "#32c13a3a-bd4f-4eed-9cb9-3cf957c074fe"
                 },
                 {
-                    "@id": "#95e1840c-22d1-4a05-90b7-7aaed626c201"
+                    "@id": "#5ec5ec66-4931-45a0-9654-094fab4fb10a"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-04-28T11:20:55Z",
+            "dateModified": "2026-04-30T13:33:11Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "genomics", "genotype", "imputation", "low-pass-sequencing", "phasing"],
             "license": ["MIT"],
@@ -158,11 +158,11 @@
             "version": "!>=25.10.4"
         },
         {
-            "@id": "#6d4899af-4cbc-4fed-b749-049c648f1851",
+            "@id": "#4523c1cb-b6ae-4871-9a4c-c970c6c684a6",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#e7682c09-4df7-45ef-9e9d-123b43d80ccc"
+                    "@id": "#1818bbea-c49a-4561-95c2-e596c87e16cb"
                 }
             ],
             "mainEntity": {
@@ -171,7 +171,7 @@
             "name": "Test suite for nf-core/phaseimpute"
         },
         {
-            "@id": "#e7682c09-4df7-45ef-9e9d-123b43d80ccc",
+            "@id": "#1818bbea-c49a-4561-95c2-e596c87e16cb",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/phaseimpute",
             "resource": "repos/nf-core/phaseimpute/actions/workflows/nf-test.yml",
@@ -300,12 +300,12 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "#b4249e73-838c-4c50-9a17-c955ad06b959",
+            "@id": "#32c13a3a-bd4f-4eed-9cb9-3cf957c074fe",
             "@type": "Person",
             "name": "Louis Le Nezet"
         },
         {
-            "@id": "#95e1840c-22d1-4a05-90b7-7aaed626c201",
+            "@id": "#5ec5ec66-4931-45a0-9654-094fab4fb10a",
             "@type": "Person",
             "name": "Anabella Trigila"
         }

From 84dd2c78b644881446469dccdad0634e2c44d767 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmail.com>
Date: Wed, 20 May 2026 15:27:27 +0200
Subject: [PATCH 3/6] Update modules and changelog

---
 .gitignore                                    |   3 -
 CHANGELOG.md                                  |   3 +-
 conf/containers_conda_lock_files_amd64.config |   2 +-
 conf/containers_conda_lock_files_arm64.config |   2 +-
 conf/containers_docker_amd64.config           |   2 +-
 conf/containers_docker_arm64.config           |   2 +-
 .../containers_singularity_https_amd64.config |   2 +-
 .../containers_singularity_https_arm64.config |   2 +-
 conf/containers_singularity_oras_amd64.config |   2 +-
 conf/containers_singularity_oras_arm64.config |   2 +-
 modules.json                                  |   4 +-
 ... => linux_amd64-bd-839587b417d23042_1.txt} | 767 +++++++++---------
 ... => linux_arm64-bd-3e45d17b40a576b4_1.txt} | 766 +++++++++--------
 modules/nf-core/multiqc/environment.yml       |   2 +-
 modules/nf-core/multiqc/main.nf               |   6 +-
 modules/nf-core/multiqc/meta.yml              |  28 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |  10 +-
 ro-crate-metadata.json                        |  17 +-
 18 files changed, 772 insertions(+), 850 deletions(-)
 rename modules/nf-core/multiqc/.conda-lock/{linux_amd64-bd-c1f4a7982b743963_1.txt => linux_amd64-bd-839587b417d23042_1.txt} (75%)
 rename modules/nf-core/multiqc/.conda-lock/{linux_arm64-bd-40bf3b435e89dc22_1.txt => linux_arm64-bd-3e45d17b40a576b4_1.txt} (75%)

diff --git a/.gitignore b/.gitignore
index 3acfe1dc..cc2b1a77 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,7 +7,4 @@ testing/
 testing*
 *.pyc
 null/
-*.code-workspace
-.nf-test*
-*.xml.bkp
 .lineage/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0604e875..ffe80a04 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#273](https://github.com/nf-core/phaseimpute/pull/273) - Update nf-core modules, fix syntax. Remove `SAMTOOLS_REHEADER` patch and pass command through meta map. Update nf-test in Github Action to 0.9.4.
 - [#276](https://github.com/nf-core/phaseimpute/pull/276) - Migrate all `params.value` usage to entry workflow. Use groovy map to store parameters for each step. Use nextflow 25.10 for `getGenomeAttribute()`.
 - [#286](https://github.com/nf-core/phaseimpute/pull/286) - Remove unecessary `saveAs` from config thanks to topic migration.
+- [#](https://github.com/nf-core/phaseimpute/pull/209) - Update TEMPLATE to nf-core tools version 4.0.2.
 
 ### `Fixed`
 
@@ -54,7 +55,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `bedtools` | 2.31.1      | No longer used |
 | `samtools` | 1.22.1      | 1.23           |
 | `gawk`     | 5.3.0       | 5.3.1          |
-| `multiqc`  | 1.32        | 1.33           |
+| `multiqc`  | 1.32        | 1.35           |
 
 ### New contributors
 
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index f6b0997e..a05393e6 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index 0cd12a28..7b7f2b66 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock' } }
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
index dd93726b..66a4c027 100644
--- a/conf/containers_docker_amd64.config
+++ b/conf/containers_docker_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
index 23418fef..209188f0 100644
--- a/conf/containers_docker_arm64.config
+++ b/conf/containers_docker_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
index d04c5be3..2465ec54 100644
--- a/conf/containers_singularity_https_amd64.config
+++ b/conf/containers_singularity_https_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
index 4a031237..80ca27ed 100644
--- a/conf/containers_singularity_https_arm64.config
+++ b/conf/containers_singularity_https_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
index 2d8d51fc..19753cfe 100644
--- a/conf/containers_singularity_oras_amd64.config
+++ b/conf/containers_singularity_oras_amd64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
index c3210dd0..e5439f67 100644
--- a/conf/containers_singularity_oras_arm64.config
+++ b/conf/containers_singularity_oras_arm64.config
@@ -1 +1 @@
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0' } }
diff --git a/modules.json b/modules.json
index bd712cb4..06b37534 100644
--- a/modules.json
+++ b/modules.json
@@ -153,7 +153,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "79b36b51048048374b642289bfe9e591ef56fe05",
+                        "git_sha": "cd0ad387832473916b1f1c80c2ca673a7883bf94",
                         "installed_by": ["modules"]
                     },
                     "quilt/quilt": {
@@ -272,7 +272,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "f0b535b3ae20080f8db03dd5388876ad1ec29d70",
+                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
similarity index 75%
rename from modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
rename to modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
index 76190304..33a1c692 100644
--- a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
@@ -14,17 +14,17 @@ linux-64:
 - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.5.0-py314h680f03e_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.6-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.4.22-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.4.0-pyhc90fa1f_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_4.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/colormath-3.0.0-pyhd8ed1ab_4.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.4-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.8.0-hecca717_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
@@ -36,98 +36,95 @@ linux-64:
 - conda: https://conda.anaconda.org/conda-forge/noarch/humanfriendly-10.0-pyh707e725_8.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/humanize-4.15.0-pyhd8ed1ab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.13-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/kaleido-core-0.2.1-h3644ca4_0.tar.bz2
-- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.19.1-h0c24ade_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.1.0-hdb68285_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-5_h4a7cf45_openblas.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-5_h0358290_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-7_h4a7cf45_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-7_h0358290_openblas.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.4-hecca717_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.0-hecca717_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.3-ha770c72_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.3-h73754d4_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.2-hb03c661_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-5_h47877c9_openblas.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-h68bc16d_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_19.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.4.1-hb03c661_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.11.0-7_h47877c9_openblas.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_4.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.55-h421ea60_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-hf4e2dac_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.33-pthreads_h94d23a6_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.58-h421ea60_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.1-h0c1763c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_19.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42.1-h5347b49_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/markdown-3.10.2-pyhcf101f3_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.0.0-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/markdown-it-py-4.2.0-pyhd8ed1ab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py314h67df5f8_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/mathjax-2.7.7-ha770c72_3.tar.bz2
 - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
-- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.33-pyhdfd78af_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.18.1-pyhcf101f3_1.conda
+- conda: https://conda.anaconda.org/bioconda/noarch/multiqc-1.35-pyhdfd78af_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/narwhals-2.21.2-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/natsort-8.4.0-pyhcf101f3_2.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/networkx-3.6.1-pyhcf101f3_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/nspr-4.38-h29cc59b_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/nss-3.118-h445c969_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.3-py314h2b28147_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/numpy-2.4.5-py314h2b28147_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.1.1-py314h8ec4b1a_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.2-pyhc364b38_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pillow-12.2.0-py314h8ec4b1a_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/plotly-6.6.0-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.39.3-pyh58ad624_1.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.39.3-py310hffdcd12_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-compat-1.39.3-py310hbcd5346_1.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/polars-1.40.1-pyh58ad624_1.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-32-1.40.1-py310h49dadd8_1.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/procps-ng-4.0.6-h18c060e_0.conda
 - conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.12.5-pyhcf101f3_1.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py314h2e6c369_1.conda
-- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.4-pyhcf101f3_0.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.46.4-py314h2e6c369_0.conda
+- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
+- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
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 license_family: MIT
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 timestamp: 1773935801332
-- conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
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 noarch: generic
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 license_family: MIT
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 license: MIT
 license_family: MIT
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 license_family: Apache
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-- libcblas   3.11.0   5*_openblas
-- blas 2.305   openblas
-- liblapacke 3.11.0   5*_openblas
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 license_family: BSD
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-- blas 2.305   openblas
-- liblapack  3.11.0   5*_openblas
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 constrains:
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 license_family: MIT
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-- libgomp 15.2.0 he0feb66_18
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 constrains:
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 license: GPL-3.0-only WITH GCC-exception-3.1
 license_family: GPL
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 license_family: GPL
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 depends:
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 constrains:
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 license: 0BSD
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 constrains:
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 license: BSD-3-Clause
 license_family: BSD
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 constrains:
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+- libstdcxx-ng ==15.2.0=*_19
 license: GPL-3.0-only WITH GCC-exception-3.1
 license_family: GPL
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 md5: cd5a90476766d53e901500df9215e927
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 md5: aea31d2e5b1091feca96fcfe945c3cf9
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 license_family: BSD
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 timestamp: 1770694658918
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 license: MIT
 license_family: MIT
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 md5: 9a17c4307d23318476d7fbf0fedc0cde
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 timestamp: 1733255681319
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 depends:
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@@ -870,10 +854,10 @@ depends:
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-- python >=3.8,!=3.14.1
+- python >=3.9,!=3.14.1
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 license_family: GPL3
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 license_family: MIT
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 md5: a2c1eeadae7a309daed9d62c96012a2b
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 license_family: MOZILLA
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+- python_abi 3.14.* *_cp314
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 constrains:
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 license: BSD-3-Clause
 license_family: BSD
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 md5: 11b3379b191f63139e29c0d19dee24cd
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 license_family: BSD
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 license: Apache-2.0
 license_family: Apache
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 depends:
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 license_family: APACHE
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+- libxcb >=1.17.0,<2.0a0
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-- python_abi 3.14.* *_cp314
-- tk >=8.6.13,<8.7.0a0
 - libjpeg-turbo >=3.1.2,<4.0a0
-- libxcb >=1.17.0,<2.0a0
-- openjpeg >=2.5.4,<3.0a0
+- python_abi 3.14.* *_cp314
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+- libfreetype6 >=2.14.3
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-- libtiff >=4.7.1,<4.8.0a0
-- libfreetype >=2.14.1
-- libfreetype6 >=2.14.1
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 license: HPND
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 license_family: MIT
 size: 5251872
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 depends:
-- polars-runtime-32 ==1.39.3
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 constrains:
@@ -1061,44 +1046,17 @@ constrains:
 - pyiceberg >=0.7.1
 - altair >=5.4.0
 - great_tables >=0.8.0
-- polars-runtime-32 ==1.39.3
-- polars-runtime-64 ==1.39.3
-- polars-runtime-compat ==1.39.3
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-- __glibc >=2.17,<3.0.a0
-- _python_abi3_support 1.*
-- cpython >=3.10
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-- __glibc >=2.17
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 license: MIT
 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/polars-runtime-compat-1.39.3-py310hbcd5346_1.conda
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 noarch: python
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 depends:
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 license: MIT
 license_family: MIT
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 md5: f2c23a77b25efcad57d377b34bd84941
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 license_family: MIT
 size: 14645
 timestamp: 1736766960536
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 depends:
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-- typing-extensions >=4.6.1
 - annotated-types >=0.6.0
-- pydantic-core ==2.41.5
+- pydantic-core ==2.46.4
 - python
 license: MIT
 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.41.5-py314h2e6c369_1.conda
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 depends:
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 license: MIT
 license_family: MIT
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-- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.2-pyhd8ed1ab_0.conda
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 depends:
-- python >=3.9
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 license: BSD-2-Clause
 license_family: BSD
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 sha256: ba3b032fa52709ce0d9fd388f63d330a026754587a2f461117cac9ab73d8d0d8
 md5: 461219d1a5bd61342293efa2c0c90eac
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 license_family: BSD
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 timestamp: 1733217331982
-- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
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 depends:
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-- libexpat >=2.7.3,<3.0a0
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 - libgcc >=14
 - liblzma >=5.8.2,<6.0a0
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-- libsqlite >=3.51.2,<4.0a0
-- libuuid >=2.41.3,<3.0a0
-- libzlib >=1.3.1,<2.0a0
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+- libzlib >=1.3.2,<2.0a0
 - ncurses >=6.5,<7.0a0
-- openssl >=3.5.5,<4.0a0
+- openssl >=3.5.6,<4.0a0
 - python_abi 3.14.* *_cp314
 - readline >=8.3,<9.0a0
 - tk >=8.6.13,<8.7.0a0
 - tzdata
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 license: Python-2.0
-size: 36702440
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 python_site_packages_path: lib/python3.14/site-packages
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
 sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5
@@ -1228,15 +1185,15 @@ license: BSD-3-Clause
 license_family: BSD
 size: 27848
 timestamp: 1772388605021
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
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-md5: 235765e4ea0d0301c75965985163b5a1
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+md5: e4e60721757979d01d3964122f674959
 depends:
-- cpython 3.14.3.*
+- cpython 3.14.4.*
 - python_abi * *_cp314
 license: Python-2.0
-size: 50062
-timestamp: 1770674497152
+size: 49806
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 - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2
 sha256: e17bf63a30aec33432f1ead86e15e9febde9fc40a7f869c0e766be8d2db44170
 md5: 310259a5b03ff02289d7705f39e2b1d2
@@ -1294,9 +1251,9 @@ license: MIT
 license_family: MIT
 size: 51788
 timestamp: 1760379115194
-- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.2.28-py314h5bd0f2a_0.conda
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-md5: 3c8b6a8c4d0ff5a264e9831eac4941f4
+- conda: https://conda.anaconda.org/conda-forge/linux-64/regex-2026.5.9-py314h5bd0f2a_0.conda
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 depends:
 - __glibc >=2.17,<3.0.a0
 - libgcc >=14
@@ -1304,27 +1261,27 @@ depends:
 - python_abi 3.14.* *_cp314
 license: Apache-2.0 AND CNRI-Python
 license_family: PSF
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-- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda
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 depends:
 - python >=3.10
-- certifi >=2017.4.17
+- certifi >=2023.5.7
 - charset-normalizer >=2,<4
 - idna >=2.5,<4
-- urllib3 >=1.21.1,<3
+- urllib3 >=1.26,<3
 - python
 constrains:
-- chardet >=3.0.2,<6
+- chardet >=3.0.2,<8
 license: Apache-2.0
 license_family: APACHE
-size: 63602
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-- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
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 depends:
 - markdown-it-py >=2.2.0
 - pygments >=2.13.0,<3.0.0
@@ -1333,8 +1290,8 @@ depends:
 - python
 license: MIT
 license_family: MIT
-size: 208472
-timestamp: 1771572730357
+size: 208577
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 md5: 0c20a8ebcddb24a45da89d5e917e6cb9
@@ -1373,20 +1330,19 @@ license: MIT
 license_family: MIT
 size: 22284
 timestamp: 1735770589188
-- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.52.0-h04a0ce9_0.conda
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-md5: 7d9d7efe9541d4bb71b5934e8ee348ea
+- conda: https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.53.1-hbc0de68_0.conda
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 depends:
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-- icu >=78.2,<79.0a0
 - libgcc >=14
-- libsqlite 3.52.0 hf4e2dac_0
-- libzlib >=1.3.1,<2.0a0
-- ncurses >=6.5,<7.0a0
+- libsqlite 3.53.1 h0c1763c_0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
 - readline >=8.3,<9.0a0
 license: blessing
-size: 203641
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 md5: d705f9d8a1185a2b01cced191177a028
@@ -1427,20 +1383,20 @@ depends:
 license: MPL-2.0 and MIT
 size: 94132
 timestamp: 1770153424136
-- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda
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-md5: 260af1b0a94f719de76b4e14094e9a3b
+- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda
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 depends:
-- importlib-metadata >=3.6
-- python >=3.10
-- typing-extensions >=4.10.0
 - typing_extensions >=4.14.0
+- python >=3.10
+- importlib-metadata >=3.6
+- python
 constrains:
 - pytest >=7
 license: MIT
 license_family: MIT
-size: 36838
-timestamp: 1771532971545
+size: 38297
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
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 md5: edd329d7d3a4ab45dcf905899a7a6115
@@ -1450,16 +1406,17 @@ license: PSF-2.0
 license_family: PSF
 size: 91383
 timestamp: 1756220668932
-- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda
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-md5: a0a4a3035667fc34f29bfbd5c190baa6
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda
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 depends:
 - python >=3.10
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+- python
 license: MIT
 license_family: MIT
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda
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 md5: 0caa1af407ecff61170c9437a808404d
@@ -1476,9 +1433,9 @@ md5: ad659d0a2b3e47e38d829aa8cad2d610
 license: LicenseRef-Public-Domain
 size: 119135
 timestamp: 1767016325805
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
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-md5: 9272daa869e03efe68833e3dc7a02130
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
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 depends:
 - backports.zstd >=1.0.0
 - brotli-python >=1.2.0
@@ -1487,8 +1444,8 @@ depends:
 - python >=3.10
 license: MIT
 license_family: MIT
-size: 103172
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda
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 md5: b2895afaf55bf96a8c8282a2e47a5de0
@@ -1519,16 +1476,16 @@ license: MIT
 license_family: MIT
 size: 85189
 timestamp: 1753484064210
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
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-md5: 30cd29cb87d819caead4d55184c1d115
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
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 depends:
 - python >=3.10
 - python
 license: MIT
 license_family: MIT
-size: 24194
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+size: 24190
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.3-hceb46e0_1.conda
 sha256: ea4e50c465d70236408cb0bfe0115609fd14db1adcd8bd30d8918e0291f8a75f
 md5: 2aadb0d17215603a82a2a6b0afd9a4cb
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
similarity index 75%
rename from modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
rename to modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
index a58231a0..492ce480 100644
--- a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
+++ b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
@@ -14,17 +14,17 @@ linux-aarch64:
 - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
 - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
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@@ -173,15 +170,15 @@ license: MIT
 license_family: MIT
 size: 64927
 timestamp: 1773935801332
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 license: BSD-3-Clause AND MIT AND EPL-2.0
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@@ -206,42 +203,41 @@ license: bzip2-1.0.6
 license_family: BSD
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 noarch: generic
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 license_family: MIT
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 license_family: Apache
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 license_family: BSD
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 constrains:
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-- liblapacke 3.11.0   5*_openblas
-- blas 2.305   openblas
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 constrains:
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 depends:
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 constrains:
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 md5: 7b9813e885482e3ccb1fa212b86d7fd0
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 license_family: BSD
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 constrains:
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 license_family: GPL
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-- python >=3.8,!=3.14.1
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 license_family: MIT
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 timestamp: 1770905275632
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 license: X11 AND BSD-3-Clause
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 md5: a2c1eeadae7a309daed9d62c96012a2b
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 license_family: MOZILLA
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 timestamp: 1763490303490
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-- libblas >=3.9.0,<4.0a0
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 constrains:
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 license: BSD-3-Clause
 license_family: BSD
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 md5: cea962410e327262346d48d01f05936c
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 license_family: BSD
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 license: Apache-2.0
 license_family: Apache
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-- libfreetype >=2.14.1
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 license: HPND
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 md5: 3e9427ee186846052e81fadde8ebe96a
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 license_family: MIT
 size: 5251872
 timestamp: 1772628857717
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 depends:
-- polars-runtime-32 ==1.39.3
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 constrains:
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-- polars-runtime-64 ==1.39.3
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 license: MIT
 license_family: MIT
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 noarch: python
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 constrains:
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 license: MIT
 license_family: MIT
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 md5: ab7288cc39545556d1bc5e71ab2df9a9
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 license_family: MIT
 size: 14645
 timestamp: 1736766960536
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-md5: c3946ed24acdb28db1b5d63321dbca7d
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-- pydantic-core ==2.41.5
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 license: MIT
 license_family: MIT
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 depends:
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 license: MIT
 license_family: MIT
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 depends:
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 license: BSD-2-Clause
 license_family: BSD
-size: 889287
-timestamp: 1750615908735
+size: 893031
+timestamp: 1774796815820
 - conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
 sha256: ba3b032fa52709ce0d9fd388f63d330a026754587a2f461117cac9ab73d8d0d8
 md5: 461219d1a5bd61342293efa2c0c90eac
@@ -1153,31 +1111,31 @@ license: BSD-3-Clause
 license_family: BSD
 size: 21085
 timestamp: 1733217331982
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.3-hb06a95a_101_cp314.conda
-build_number: 101
-sha256: 87e9dff5646aba87cecfbc08789634c855871a7325169299d749040b0923a356
-md5: 205011b36899ff0edf41b3db0eda5a44
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.14.4-hfd9ac0a_100_cp314.conda
+build_number: 100
+sha256: d29da77f75e8f9184cc9502d5c44be87397291a9e88819d5418322a173f76303
+md5: 3cfbe780f0f51cc8cba41db9f8a28bfe
 depends:
 - bzip2 >=1.0.8,<2.0a0
 - ld_impl_linux-aarch64 >=2.36.1
-- libexpat >=2.7.3,<3.0a0
+- libexpat >=2.7.5,<3.0a0
 - libffi >=3.5.2,<3.6.0a0
 - libgcc >=14
 - liblzma >=5.8.2,<6.0a0
 - libmpdec >=4.0.0,<5.0a0
-- libsqlite >=3.51.2,<4.0a0
-- libuuid >=2.41.3,<3.0a0
-- libzlib >=1.3.1,<2.0a0
+- libsqlite >=3.52.0,<4.0a0
+- libuuid >=2.42,<3.0a0
+- libzlib >=1.3.2,<2.0a0
 - ncurses >=6.5,<7.0a0
-- openssl >=3.5.5,<4.0a0
+- openssl >=3.5.6,<4.0a0
 - python_abi 3.14.* *_cp314
 - readline >=8.3,<9.0a0
 - tk >=8.6.13,<8.7.0a0
 - tzdata
 - zstd >=1.5.7,<1.6.0a0
 license: Python-2.0
-size: 37305578
-timestamp: 1770674395875
+size: 37409899
+timestamp: 1775613674766
 python_site_packages_path: lib/python3.14/site-packages
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda
 sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5
@@ -1188,15 +1146,15 @@ license: BSD-3-Clause
 license_family: BSD
 size: 27848
 timestamp: 1772388605021
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
-sha256: 233aebd94c704ac112afefbb29cf4170b7bc606e22958906f2672081bc50638a
-md5: 235765e4ea0d0301c75965985163b5a1
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda
+sha256: 36ff7984e4565c85149e64f8206303d412a0652e55cf806dcb856903fa056314
+md5: e4e60721757979d01d3964122f674959
 depends:
-- cpython 3.14.3.*
+- cpython 3.14.4.*
 - python_abi * *_cp314
 license: Python-2.0
-size: 50062
-timestamp: 1770674497152
+size: 49806
+timestamp: 1775614307464
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2
 sha256: e17bf63a30aec33432f1ead86e15e9febde9fc40a7f869c0e766be8d2db44170
 md5: 310259a5b03ff02289d7705f39e2b1d2
@@ -1253,9 +1211,9 @@ license: MIT
 license_family: MIT
 size: 51788
 timestamp: 1760379115194
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.2.28-py314h51f160d_0.conda
-sha256: 2080ecea825e1ef91a2422cc0bc63e85db9e38908ed17657fb8f41de7a6eee71
-md5: 818aa2c9f6b3c808da5e7be22a9a424c
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.5.9-py314h51f160d_0.conda
+sha256: 05ef55f09f31eabd0a205f6b065e13fc746675f41924620977692ef0ffe5aad8
+md5: 34ed7bc9febeca70f55b757ca09c354d
 depends:
 - libgcc >=14
 - python >=3.14,<3.15.0a0
@@ -1263,27 +1221,27 @@ depends:
 - python_abi 3.14.* *_cp314
 license: Apache-2.0 AND CNRI-Python
 license_family: PSF
-size: 408097
-timestamp: 1772255205521
-- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.32.5-pyhcf101f3_1.conda
-sha256: 7813c38b79ae549504b2c57b3f33394cea4f2ad083f0994d2045c2e24cb538c5
-md5: c65df89a0b2e321045a9e01d1337b182
+size: 409780
+timestamp: 1778374195988
+- conda: https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda
+sha256: 1715246b19c9f85ee022933b4845f2fc14ac9184981b7b7d9b728bec8e9588da
+md5: 4a85203c1d80c1059086ae860836ffb9
 depends:
 - python >=3.10
-- certifi >=2017.4.17
+- certifi >=2023.5.7
 - charset-normalizer >=2,<4
 - idna >=2.5,<4
-- urllib3 >=1.21.1,<3
+- urllib3 >=1.26,<3
 - python
 constrains:
-- chardet >=3.0.2,<6
+- chardet >=3.0.2,<8
 license: Apache-2.0
 license_family: APACHE
-size: 63602
-timestamp: 1766926974520
-- conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
-sha256: b06ce84d6a10c266811a7d3adbfa1c11f13393b91cc6f8a5b468277d90be9590
-md5: 7a6289c50631d620652f5045a63eb573
+size: 68709
+timestamp: 1778851103479
+- conda: https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda
+sha256: 3d6ba2c0fcdac3196ba2f0615b4104e532525ffa1335b50a2878be5ff488814a
+md5: 0242025a3c804966bf71aa04eee82f66
 depends:
 - markdown-it-py >=2.2.0
 - pygments >=2.13.0,<3.0.0
@@ -1292,8 +1250,8 @@ depends:
 - python
 license: MIT
 license_family: MIT
-size: 208472
-timestamp: 1771572730357
+size: 208577
+timestamp: 1775991661559
 - conda: https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda
 sha256: aa3fcb167321bae51998de2e94d199109c9024f25a5a063cb1c28d8f1af33436
 md5: 0c20a8ebcddb24a45da89d5e917e6cb9
@@ -1331,19 +1289,18 @@ license: MIT
 license_family: MIT
 size: 22284
 timestamp: 1735770589188
-- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.52.0-hf1c7be2_0.conda
-sha256: 4f8523f5341f0d9e1547085206c6c1f71f9fc7c277443ca363a8cf98add8fc01
-md5: d9634079df93a65ee045b3c75f35cae1
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.53.1-he8854b5_0.conda
+sha256: 27467e4bfb0681546f149718c33b806fec078185fbaa6a4d17d440bc8f56185c
+md5: 46009bdca2315a99e0a3a7d0ba1af3b9
 depends:
-- icu >=78.2,<79.0a0
 - libgcc >=14
-- libsqlite 3.52.0 h10b116e_0
-- libzlib >=1.3.1,<2.0a0
-- ncurses >=6.5,<7.0a0
+- libsqlite 3.53.1 h022381a_0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
 - readline >=8.3,<9.0a0
 license: blessing
-size: 209416
-timestamp: 1772818891689
+size: 209964
+timestamp: 1777986493350
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda
 sha256: c1da41c79262b27efa168407cfecc47b20270e5fc071a8307f95a2c85fb94170
 md5: 55bf7b559202236157b14323b40f19e6
@@ -1382,20 +1339,20 @@ depends:
 license: MPL-2.0 and MIT
 size: 94132
 timestamp: 1770153424136
-- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda
-sha256: 39d8ae33c43cdb8f771373e149b0b4fae5a08960ac58dcca95b2f1642bb17448
-md5: 260af1b0a94f719de76b4e14094e9a3b
+- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda
+sha256: 59d7851d32fddb5b510272e6557aa982edeb927d349648dac27f5bf01d18bb26
+md5: 4460f039b7dedf15f7df086446ca75ae
 depends:
-- importlib-metadata >=3.6
-- python >=3.10
-- typing-extensions >=4.10.0
 - typing_extensions >=4.14.0
+- python >=3.10
+- importlib-metadata >=3.6
+- python
 constrains:
 - pytest >=7
 license: MIT
 license_family: MIT
-size: 36838
-timestamp: 1771532971545
+size: 38297
+timestamp: 1778779291237
 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
 sha256: 7c2df5721c742c2a47b2c8f960e718c930031663ac1174da67c1ed5999f7938c
 md5: edd329d7d3a4ab45dcf905899a7a6115
@@ -1405,16 +1362,17 @@ license: PSF-2.0
 license_family: PSF
 size: 91383
 timestamp: 1756220668932
-- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda
-sha256: 70db27de58a97aeb7ba7448366c9853f91b21137492e0b4430251a1870aa8ff4
-md5: a0a4a3035667fc34f29bfbd5c190baa6
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda
+sha256: 8b90d2f19f9458b8c58a55e1fcdc1d90c1603a847a47654d8a454549413ba60a
+md5: 53f5409c5cfd6c5a66417d68e3f0a864
 depends:
 - python >=3.10
 - typing_extensions >=4.12.0
+- python
 license: MIT
 license_family: MIT
-size: 18923
-timestamp: 1764158430324
+size: 20935
+timestamp: 1777105465795
 - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda
 sha256: 032271135bca55aeb156cee361c81350c6f3fb203f57d024d7e5a1fc9ef18731
 md5: 0caa1af407ecff61170c9437a808404d
@@ -1431,9 +1389,9 @@ md5: ad659d0a2b3e47e38d829aa8cad2d610
 license: LicenseRef-Public-Domain
 size: 119135
 timestamp: 1767016325805
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
-sha256: af641ca7ab0c64525a96fd9ad3081b0f5bcf5d1cbb091afb3f6ed5a9eee6111a
-md5: 9272daa869e03efe68833e3dc7a02130
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
+sha256: feff959a816f7988a0893201aa9727bbb7ee1e9cec2c4f0428269b489eb93fb4
+md5: cbb88288f74dbe6ada1c6c7d0a97223e
 depends:
 - backports.zstd >=1.0.0
 - brotli-python >=1.2.0
@@ -1442,8 +1400,8 @@ depends:
 - python >=3.10
 license: MIT
 license_family: MIT
-size: 103172
-timestamp: 1767817860341
+size: 103560
+timestamp: 1778188657149
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda
 sha256: e9f6e931feeb2f40e1fdbafe41d3b665f1ab6cb39c5880a1fcf9f79a3f3c84a5
 md5: 1c246e1105000c3660558459e2fd6d43
@@ -1471,16 +1429,16 @@ license: MIT
 license_family: MIT
 size: 88088
 timestamp: 1753484092643
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
-sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae
-md5: 30cd29cb87d819caead4d55184c1d115
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+md5: ba3dcdc8584155c97c648ae9c044b7a3
 depends:
 - python >=3.10
 - python
 license: MIT
 license_family: MIT
-size: 24194
-timestamp: 1764460141901
+size: 24190
+timestamp: 1779159948016
 - conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
 sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
 md5: f731af71c723065d91b4c01bb822641b
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 009874d4..7a970e2b 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.33
+  - bioconda::multiqc=1.35
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 5376aea1..4c593a97 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,9 +3,9 @@ process MULTIQC {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data'
-        : 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b'}"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data'
+        : 'community.wave.seqera.io/library/multiqc:1.35--839587b417d23042'}"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 57cf43ca..b85d0e35 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -110,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-839587b417d23042_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-3e45d17b40a576b4_1.txt
   docker:
     linux/amd64:
-      name: community.wave.seqera.io/library/multiqc:1.33--c1f4a7982b743963
-      build_id: bd-c1f4a7982b743963_1
-      scan_id: sc-b7b7f470b2a16699_1
+      name: community.wave.seqera.io/library/multiqc:1.35--839587b417d23042
+      build_id: bd-839587b417d23042_1
+      scan_id: sc-f87d7a31551c029f_1
     linux/arm64:
-      name: community.wave.seqera.io/library/multiqc:1.33--40bf3b435e89dc22
-      build_id: bd-40bf3b435e89dc22_1
-      scan_id: sc-0e2108a0e7368d2f_1
+      name: community.wave.seqera.io/library/multiqc:1.35--3e45d17b40a576b4
+      build_id: bd-3e45d17b40a576b4_1
+      scan_id: sc-1d0cf4ed1a4b61e0_1
   singularity:
     linux/amd64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--9b3473b1c4bb0493
-      build_id: bd-9b3473b1c4bb0493_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c4/c4e6d9f669e1a99b53c7dc5cdd6b8e7fd6654032c755bb783cc9849e8203f4d1/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--cb7458fda84d6393
+      build_id: bd-cb7458fda84d6393_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/12/1297c0f5075c19486da167ebf1b6136907d6b5339697b87b29fda335221785b3/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.33--e1ef2065eb21b530
-      build_id: bd-e1ef2065eb21b530_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2acce766e3efb280fa43acdbe85305ea6496ddadbcaa2d806ac4985dfe4686ce/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--f79e87603d312ac0
+      build_id: bd-f79e87603d312ac0_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c007304153702edc622f1a76b41505e7fca65c7145e5b8b2ddce62a5c59af207/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 3bfc524f..44899216 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -81,7 +81,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.35"
                     ]
                 ]
             }
@@ -175,7 +175,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.35"
                     ]
                 ]
             }
@@ -221,7 +221,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.35"
                     ]
                 ]
             }
@@ -314,7 +314,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.35"
                     ]
                 ]
             }
@@ -408,7 +408,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.33"
+                        "1.35"
                     ]
                 ]
             }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 3bd2b4dc..dd5c8ded 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2026-04-30T13:33:11+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/nf-core-phaseimpute_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/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/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/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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/phaseimpute** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/phaseimpute \\\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/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/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/phaseimpute/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/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le Nezet, Anabella Trigila.\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 `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (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/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/logo/nf-core-phaseimpute_logo_dark.png\">\n    <img alt=\"nf-core/phaseimpute\" src=\"docs/images/logo/nf-core-phaseimpute_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/phaseimpute)\n[![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/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/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14329225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14329225)\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/phaseimpute)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23phaseimpute-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/phaseimpute)[![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/phaseimpute** is a bioinformatics pipeline to phase and impute genetic data.\n\n<picture>\n  <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/metro/MetroMap_animated_dark.svg\">\n  <img src=\"docs/images/metro/MetroMap_animated.svg\" alt=\"metromap\"/>\n</picture>\n\nThe whole pipeline consists of five main steps, each of which can be run separately and independently. Users are not required to run all steps sequentially and can select specific steps based on their needs:\n\n1. **QC: Chromosome Name Check**: Ensures compatibility by validating that all expected contigs are present in the variant and alignment files.\n\n2. **Simulation (`--simulate`)**: Generates artificial datasets by downsampling high-density data to simulate low-pass genetic information. This enables the comparison of imputation results against a high-quality dataset (truth set). Simulations may include:\n   - **Low-pass data generation** by downsampling BAM or CRAM files with [`samtools view -s`](https://www.htslib.org/doc/samtools-view.html) at different depths.\n\n3. **Panel Preparation (`--panelprep`)**: Prepares the reference panel through phasing, quality control, variant filtering, and annotation. Key processes include:\n   - **Normalization** of the reference panel to retain essential variants.\n   - **Phasing** of haplotypes in the reference panel using [Shapeit5](https://odelaneau.github.io/shapeit5/).\n   - **Chunking** of the reference panel into specific regions across chromosomes.\n   - **Position Extraction** for targeted imputation sites.\n\n4. **Imputation (`--impute`)**: This is the primary step, where genotypes in the target dataset are imputed using the prepared reference panel. The main steps are:\n   - **Imputation** of the target dataset using tools like [Glimpse1](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html), [Glimpse2](https://odelaneau.github.io/GLIMPSE/), [Stitch](https://github.com/rwdavies/stitch), [Quilt/Quilt2](https://github.com/rwdavies/QUILT), [Beagle5](https://faculty.washington.edu/browning/beagle/beagle.html) or [Minimac4](https://github.com/statgen/Minimac4).\n   - **Ligation** of imputed chunks to produce a final VCF file per sample, with all chromosomes unified.\n\n5. **Validation (`--validate`)**: Assesses imputation accuracy by comparing the imputed dataset to a truth dataset. This step leverages the [Glimpse2](https://odelaneau.github.io/GLIMPSE/) concordance process to summarize differences between two VCF files.\n\nFor more detailed instructions, please refer to the [usage documentation](https://nf-co.re/phaseimpute/usage).\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\nThe primary function of this pipeline is to impute a target dataset based on a phased panel. Begin by preparing a samplesheet with your input data, formatted as follows:\n\n```csv title=\"samplesheet.csv\"\nsample,file,index\nSAMPLE_1X,/path/to/.<bam/cram>,/path/to/.<bai,crai>\n```\n\nEach row represents either a bam or a cram file along with its corresponding index file. Ensure that all input files have consistent file extensions.\n\nFor certain tools and steps within the pipeline, you will also need to provide a samplesheet for the reference panel. Here's an example of what a final samplesheet for a reference panel might look like, covering three chromosomes:\n\n```csv title=\"panel.csv\"\npanel,chr,vcf,index\nPhase3,1,ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\nPhase3,2,ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\nPhase3,3,ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz,ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.csi\n```\n\n## Running the pipeline\n\nRun one of the steps of the pipeline (imputation with glimpse1) using the following command and test profile:\n\n```bash\nnextflow run nf-core/phaseimpute \\\n   -profile test, <docker/singularity/.../institute> \\\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/phaseimpute/usage) and the [parameter documentation](https://nf-co.re/phaseimpute/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/phaseimpute/results) tab on the nf-core website pipeline page.\nFor more details on the output files and reports, please refer to the [output documentation](https://nf-co.re/phaseimpute/output).\n\n## Credits\n\nnf-core/phaseimpute was originally written by Louis Le N\u00e9zet & Anabella Trigila.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Saul Pierotti\n- Eugenia Fontecha\n- Matias Romero Victorica\n- Hemanoel Passarelli\n- Gaspard Ichas\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md). Further development tips can be found in the [development documentation](docs/development.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#phaseimpute` channel](https://nfcore.slack.com/channels/phaseimpute) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.14329225](https://doi.org/10.5281/zenodo.14329225)\n\nAn extensive list of references for the tools used by the pipeline, including QUILT, GLIMPSE, and STITCH, 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"
@@ -124,7 +124,11 @@
         },
         {
             "@id": "main.nf",
-            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
             "contributor": [
                 {
                     "@id": "#32c13a3a-bd4f-4eed-9cb9-3cf957c074fe"
@@ -157,8 +161,13 @@
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/phaseimpute", "https://nf-co.re/phaseimpute/dev/"],
-            "version": ["1.2.0dev"]
+            "url": [
+                "https://github.com/nf-core/phaseimpute",
+                "https://nf-co.re/phaseimpute/dev/"
+            ],
+            "version": [
+                "1.2.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",

From a956db9c37d4b379d134c2b5ce7f7220212fa4cb Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmail.com>
Date: Wed, 20 May 2026 15:29:43 +0200
Subject: [PATCH 4/6] Update changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ffe80a04..279c9b75 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,7 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#273](https://github.com/nf-core/phaseimpute/pull/273) - Update nf-core modules, fix syntax. Remove `SAMTOOLS_REHEADER` patch and pass command through meta map. Update nf-test in Github Action to 0.9.4.
 - [#276](https://github.com/nf-core/phaseimpute/pull/276) - Migrate all `params.value` usage to entry workflow. Use groovy map to store parameters for each step. Use nextflow 25.10 for `getGenomeAttribute()`.
 - [#286](https://github.com/nf-core/phaseimpute/pull/286) - Remove unecessary `saveAs` from config thanks to topic migration.
-- [#](https://github.com/nf-core/phaseimpute/pull/209) - Update TEMPLATE to nf-core tools version 4.0.2.
+- [#291](https://github.com/nf-core/phaseimpute/pull/291) - Update TEMPLATE to nf-core tools version 4.0.2.
 
 ### `Fixed`
 

From 35d50d496fae08b24d619a385d95a67d43d5b9b0 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmail.com>
Date: Wed, 20 May 2026 15:54:49 +0200
Subject: [PATCH 5/6] Remove repeat

---
 subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
index dc34219d..ce8fc58c 100644
--- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
@@ -60,9 +60,8 @@ workflow PIPELINE_INITIALISATION {
     // Validate parameters and generate parameter summary to stdout
     //
 
-    def before_text = ""
     def after_text = ""
-    before_text = """
+    def before_text = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
 \033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m

From e13e49816be50fabc65118f6432a9dacc3012767 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmail.com>
Date: Wed, 20 May 2026 16:02:06 +0200
Subject: [PATCH 6/6] Update .gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index cc2b1a77..b53389df 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,6 @@ testing*
 *.pyc
 null/
 .lineage/
+*.code-workspace
+.nf-test*
+*.xml.bkp