From 5cd9b23a3bf4ca1bfe20babdf89e093ecb298553 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 8 Jul 2025 11:39:08 +0000
Subject: [PATCH 1/2] Template update for nf-core/tools version 3.3.2

---
 .github/actions/nf-test/action.yml            |   4 -
 .github/workflows/linting.yml                 |   2 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/nf-test.yml                 |  45 +++----
 .github/workflows/release-announcements.yml   |   2 +-
 .nf-core.yml                                  |   4 +-
 .pre-commit-config.yaml                       |   2 +-
 CHANGELOG.md                                  |   2 +-
 README.md                                     |   6 +-
 assets/multiqc_config.yml                     |   4 +-
 assets/schema_input.json                      |   4 +-
 conf/base.config                              |   1 +
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/environment.yml        |   2 +
 modules/nf-core/fastqc/main.nf                |   2 +-
 modules/nf-core/fastqc/meta.yml               |  23 ++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |   4 +-
 modules/nf-core/multiqc/meta.yml              | 110 ++++++++++--------
 .../nf-core/multiqc/tests/main.nf.test.snap   |  18 +--
 nextflow.config                               |   7 +-
 nf-test.config                                |   2 +-
 ro-crate-metadata.json                        |  20 ++--
 .../tests/nextflow.config                     |   2 +-
 tests/.nftignore                              |   1 +
 tests/nextflow.config                         |   6 +-
 26 files changed, 153 insertions(+), 130 deletions(-)

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 243e782..bf44d96 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -54,13 +54,9 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index f2d7d1d..8b0f88c 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 7e8050f..d43797d 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@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index f03aea0..e7b5844 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,12 +1,5 @@
 name: Run nf-test
 on:
-  push:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   pull_request:
     paths-ignore:
       - "docs/**"
@@ -35,7 +28,7 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test-changes
+      - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -69,7 +62,7 @@ jobs:
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test
+      - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
     strategy:
       fail-fast: false
@@ -85,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -97,23 +90,39 @@ jobs:
           fetch-depth: 0
 
       - name: Run nf-test
+        id: run_nf_test
         uses: ./.github/actions/nf-test
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+
+      - name: Report test status
+        if: ${{ always() }}
+        run: |
+          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
+            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
+            # Add to workflow summary
+            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
+            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
+              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
+            fi
+            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+              exit 1
+            fi
+          fi
+
   confirm-pass:
     needs: [nf-test]
     if: always()
     runs-on: # use self-hosted runners
-      - runs-on=$-confirm-pass
+      - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -132,11 +141,3 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
-
-      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        if: always()
-        run: |
-          ls -la ./
-          rm -rf ./* || true
-          rm -rf ./.??* || true
-          ls -la ./
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 4abaf48..0f73249 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.nf-core.yml b/.nf-core.yml
index 95bac5c..cc42028 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,4 +1,4 @@
-nf_core_version: 3.3.1
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Christopher Hakkaart
@@ -8,4 +8,4 @@ template:
   name: demo
   org: nf-core
   outdir: .
-  version: 1.0.0
+  version: 1.0.2
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9d0b248..bb41bee 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.5.0
+          - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 55f7175..b8027cb 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]
+## v1.0.2 - [date]
 
 Initial release of nf-core/demo, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/README.md b/README.md
index b207f50..5415bc1 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,12 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)
+[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![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/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 1a9c348..dd180e7 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/demo/releases/tag/1.0.0" target="_blank">nf-core/demo</a>
+  This report has been generated by the <a href="https://github.com/nf-core/demo/releases/tag/1.0.2" target="_blank">nf-core/demo</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/demo/1.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/demo/1.0.2/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-demo-methods-description":
     order: -1000
diff --git a/assets/schema_input.json b/assets/schema_input.json
index af0934a..58bebb9 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -17,14 +17,14 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
diff --git a/conf/base.config b/conf/base.config
index f76c4d3..938165b 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -61,5 +61,6 @@ process {
     }
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
     }
 }
diff --git a/modules.json b/modules.json
index 1974b10..1061a1a 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 691d4c7..f9f54ee 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f415..23e1663 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,7 @@ process FASTQC {
     // 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').toFloat() / task.cpus : null
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b..c8d9d02 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -29,9 +29,10 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
+        ontologies: []
 output:
-  - html:
-      - meta:
+  html:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -40,8 +41,9 @@ output:
           type: file
           description: FastQC report
           pattern: "*_{fastqc.html}"
-  - zip:
-      - meta:
+          ontologies: []
+  zip:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -50,11 +52,14 @@ output:
           type: file
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a27122c..812fc4c 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.27
+  - bioconda::multiqc=1.29
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313..0ac3c36 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c187..ce30eb7 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -15,57 +15,71 @@ tools:
       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
-  - - multiqc_config:
-        type: file
-        description: Optional config yml for MultiQC
-        pattern: "*.{yml,yaml}"
-  - - extra_multiqc_config:
-        type: file
-        description: Second optional config yml for MultiQC. Will override common sections
-          in multiqc_config.
-        pattern: "*.{yml,yaml}"
-  - - multiqc_logo:
+  - 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":
         type: file
-        description: Optional logo file for MultiQC
-        pattern: "*.{png}"
-  - - replace_names:
+        description: MultiQC report file
+        pattern: "multiqc_report.html"
+        ontologies: []
+  data:
+    - "*_data":
+        type: directory
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+  plots:
+    - "*_plots":
         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}"
-  - - sample_names:
+        description: Plots created by MultiQC
+        pattern: "*_data"
+        ontologies: []
+  versions:
+    - versions.yml:
         type: file
-        description: |
-          Optional TSV file with headers, passed to the MultiQC --sample_names
-          argument.
-        pattern: "*.{tsv}"
-output:
-  - report:
-      - "*multiqc_report.html":
-          type: file
-          description: MultiQC report file
-          pattern: "multiqc_report.html"
-  - data:
-      - "*_data":
-          type: directory
-          description: MultiQC data dir
-          pattern: "multiqc_data"
-  - plots:
-      - "*_plots":
-          type: file
-          description: Plots created by MultiQC
-          pattern: "*_data"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c132..88e9057 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:29:57.631982377"
+        "timestamp": "2025-05-22T11:50:41.182332996"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:34.743726958"
+        "timestamp": "2025-05-22T11:51:22.448739369"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:21.44383553"
+        "timestamp": "2025-05-22T11:51:06.198928424"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 952e5f9..9d6c221 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -235,7 +235,6 @@ dag {
 
 manifest {
     name            = 'nf-core/demo'
-    author          = """Christopher Hakkaart""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
         // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
@@ -251,14 +250,14 @@ manifest {
     description     = """An nf-core demo pipeline"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=24.04.2'
-    version         = '1.0.0'
+    nextflowVersion = '!>=24.10.5'
+    version         = '1.0.2'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
index 889df76..3a1fff5 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,7 +9,7 @@ config {
     configFile "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
 
     // run all test with defined profile(s) from the main nextflow.config
     profile "test"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index f0bd6b8..9aba009 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-06-03T11:01:08+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n    <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** 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/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Christopher Hakkaart.\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (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/demo 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": "2025-07-08T11:39:03+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n    <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** 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/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Christopher Hakkaart.\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (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/demo 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": "#45209ed9-bae4-4876-89b4-505c8ca5d932"
+                    "@id": "#246b126d-c3e5-4139-91d8-0c1a4138213f"
                 }
             ],
             "name": "nf-core/demo"
@@ -123,7 +123,7 @@
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "dateCreated": "",
-            "dateModified": "2025-06-03T11:01:08Z",
+            "dateModified": "2025-07-08T11:39:03Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "demo", "minimal-example", "training", "tutorial"],
             "license": ["MIT"],
@@ -134,8 +134,8 @@
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/1.0.0/"],
-            "version": ["1.0.0"]
+            "url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/1.0.2/"],
+            "version": ["1.0.2"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -147,14 +147,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.04.2"
+            "version": "!>=24.10.5"
         },
         {
-            "@id": "#45209ed9-bae4-4876-89b4-505c8ca5d932",
+            "@id": "#246b126d-c3e5-4139-91d8-0c1a4138213f",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#bc540ef0-e713-48bd-8bd6-960f63f3edda"
+                    "@id": "#ffafd653-8724-44e6-becc-7ba2b8d6d6ae"
                 }
             ],
             "mainEntity": {
@@ -163,7 +163,7 @@
             "name": "Test suite for nf-core/demo"
         },
         {
-            "@id": "#bc540ef0-e713-48bd-8bd6-960f63f3edda",
+            "@id": "#ffafd653-8724-44e6-becc-7ba2b8d6d6ae",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/demo",
             "resource": "repos/nf-core/demo/actions/workflows/nf-test.yml",
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 0907ac5..09ef842 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@2.1.0"
+    id "nf-schema@2.4.2"
 }
 
 validation {
diff --git a/tests/.nftignore b/tests/.nftignore
index c10bc1f..158c83c 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,5 +1,6 @@
 .DS_Store
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/BETA-multiqc.parquet
 multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 783f100..db709dd 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -6,7 +6,9 @@
 
 // TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
-params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/demo'
+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/demo'
+}
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From 35ef9b0362bc26347f5f76241f6a73f2139a3bd0 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 16 Oct 2025 13:37:53 +0000
Subject: [PATCH 2/2] Template update for nf-core/tools version 3.4.1

---
 .devcontainer/devcontainer.json               | 28 ++++----
 .devcontainer/setup.sh                        | 13 ++++
 .github/actions/nf-test/action.yml            |  6 +-
 .github/workflows/awsfulltest.yml             | 12 ++--
 .github/workflows/awstest.yml                 | 12 ++--
 .github/workflows/clean-up.yml                |  2 +-
 .github/workflows/download_pipeline.yml       |  6 +-
 .github/workflows/fix_linting.yml             | 16 ++---
 .github/workflows/linting.yml                 | 14 ++--
 .github/workflows/linting_comment.yml         |  2 +-
 .github/workflows/nf-test.yml                 |  9 +--
 .github/workflows/release-announcements.yml   |  7 ++
 .../workflows/template-version-comment.yml    |  2 +-
 .gitpod.yml                                   | 10 ---
 .nf-core.yml                                  |  2 +-
 .pre-commit-config.yaml                       |  2 +-
 .prettierignore                               |  1 +
 README.md                                     |  5 +-
 docs/usage.md                                 |  2 +-
 main.nf                                       |  5 +-
 modules.json                                  |  8 +--
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   | 18 +++---
 modules/nf-core/multiqc/tests/tags.yml        |  2 -
 nextflow.config                               | 64 ++++++-------------
 nextflow_schema.json                          | 12 ++++
 ro-crate-metadata.json                        | 16 ++---
 .../local/utils_nfcore_demo_pipeline/main.nf  | 31 ++++++++-
 .../utils_nextflow_pipeline/tests/tags.yml    |  2 -
 .../utils_nfcore_pipeline/tests/tags.yml      |  2 -
 .../nf-core/utils_nfschema_plugin/main.nf     | 40 ++++++++++--
 .../utils_nfschema_plugin/tests/main.nf.test  | 56 ++++++++++++++++
 .../tests/nextflow.config                     |  4 +-
 tests/.nftignore                              |  3 +-
 tests/default.nf.test                         |  2 -
 36 files changed, 267 insertions(+), 155 deletions(-)
 create mode 100755 .devcontainer/setup.sh
 delete mode 100644 .gitpod.yml
 delete mode 100644 modules/nf-core/multiqc/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index b290e09..97c8c97 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,20 +1,20 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
-    "remoteUser": "gitpod",
-    "runArgs": ["--privileged"],
+    "image": "nfcore/devcontainer:latest",
 
-    // Configure tool-specific properties.
-    "customizations": {
-        // Configure properties specific to VS Code.
-        "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
-            },
+    "remoteUser": "root",
+    "privileged": true,
 
-            // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
+    "remoteEnv": {
+        // Workspace path on the host for mounting with docker-outside-of-docker
+        "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+    },
+
+    "onCreateCommand": "./.devcontainer/setup.sh",
+
+    "hostRequirements": {
+        "cpus": 4,
+        "memory": "16gb",
+        "storage": "32gb"
     }
 }
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 0000000..09d0cdf
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Customise the terminal command prompt
+echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
+echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
+export PROMPT_DIRTRIM=2
+export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
+
+# Update Nextflow
+nextflow self-update
+
+# Update welcome message
+echo "Welcome to the nf-core/demo devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index bf44d96..3b9724c 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -25,9 +25,9 @@ runs:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
       with:
-        python-version: "3.13"
+        python-version: "3.14"
 
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
@@ -52,6 +52,8 @@ runs:
       with:
         auto-update-conda: true
         conda-solver: libmamba
+        channels: conda-forge
+        channel-priority: strict
         conda-remove-defaults: true
 
     - name: Run nf-test
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 290ad83..f7a1050 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -28,15 +28,15 @@ jobs:
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/demo/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/demo/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/demo/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/demo/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
@@ -44,5 +44,5 @@ jobs:
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 0317918..5b04033 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -14,14 +14,14 @@ jobs:
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/demo/work-${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/demo/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/demo/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/demo/results-test-${{ github.sha }}"
             }
           profiles: test
 
@@ -29,5 +29,5 @@ jobs:
         with:
           name: Seqera Platform debug log file
           path: |
-            seqera_platform_action_*.log
-            seqera_platform_action_*.json
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index ac030fd..6adb0ff 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
+      - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 999bcc3..6d94bcb 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -44,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -57,7 +57,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@dev
+          pip install git+https://github.com/nf-core/tools.git
 
       - name: Make a cache directory for the container images
         run: |
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index d7c131c..6f02703 100644
--- a/.github/workflows/fix_linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
       # indication that the linting is being fixed
       - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: eyes
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,7 +47,7 @@ jobs:
       # indication that the linting has finished
       - name: react if linting finished succesfully
         if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: "+1"
@@ -67,21 +67,21 @@ jobs:
       - name: react if linting errors were fixed
         id: react-if-fixed
         if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: hooray
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           comment-id: ${{ github.event.comment.id }}
           reactions: confused
 
       - name: react if linting errors were not fixed
         if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
         with:
           issue-number: ${{ github.event.issue.number }}
           body: |
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8b0f88c..30e6602 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,12 +11,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - name: Set up Python 3.14
+        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -28,14 +28,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
       - name: read .nf-core.yml
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index d43797d..e6e9bc2 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -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@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2
         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 e7b5844..e20bf6d 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.2"
+  NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.04.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           fetch-depth: 0
 
@@ -95,6 +95,7 @@ jobs:
         continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          NXF_VERSION: ${{ matrix.NXF_VER }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 0f73249..e64cebd 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -14,6 +14,11 @@ jobs:
         run: |
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
+      - name: get description
+        id: get_topics
+        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
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -23,6 +28,8 @@ jobs:
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
 
+            ${{ steps.get_topics.outputs.description }}
+
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index beb5c77..c5988af 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 83599f6..0000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
-  - name: Update Nextflow and setup pre-commit
-    command: |
-      pre-commit install --install-hooks
-      nextflow self-update
-
-vscode:
-  extensions:
-    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index cc42028..0bd76ea 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,4 +1,4 @@
-nf_core_version: 3.3.2
+nf_core_version: 3.4.1
 repository_type: pipeline
 template:
   author: Christopher Hakkaart
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bb41bee..d06777a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
diff --git a/.prettierignore b/.prettierignore
index edd29f0..2255e3e 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,4 +10,5 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
diff --git a/README.md b/README.md
index 5415bc1..e4dc9d5 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,13 @@
   </picture>
 </h1>
 
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/demo)
 [![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-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-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/docs/usage.md b/docs/usage.md
index c80968d..30ce1a4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -149,7 +149,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `shifter`
   - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
 - `charliecloud`
-  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+  - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
diff --git a/main.nf b/main.nf
index bded524..5bb01f6 100644
--- a/main.nf
+++ b/main.nf
@@ -74,7 +74,10 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden
     )
 
     //
diff --git a/modules.json b/modules.json
index 1061a1a..73c637f 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 812fc4c..dd513cb 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=1.29
+  - bioconda::multiqc=1.31
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 0ac3c36..5288f5c 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' :
+        'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 88e9057..17881d1 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-22T11:50:41.182332996"
+        "timestamp": "2025-09-08T20:57:36.139055243"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-22T11:51:22.448739369"
+        "timestamp": "2025-09-08T20:59:15.142230631"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-22T11:51:06.198928424"
+        "timestamp": "2025-09-08T20:58:29.629087066"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
deleted file mode 100644
index bea6c0d..0000000
--- a/modules/nf-core/multiqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-multiqc:
-  - modules/nf-core/multiqc/**
diff --git a/nextflow.config b/nextflow.config
index 9d6c221..0e534b8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,13 +32,15 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     monochrome_logs              = false
-    hook_url                     = null
+    hook_url                     = System.getenv('HOOK_URL')
     help                         = false
     help_full                    = false
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+
+    // Config options
     config_profile_name        = null
     config_profile_description = null
 
@@ -91,7 +93,18 @@ profiles {
         apptainer.enabled       = false
         docker.runOptions       = '-u $(id -u):$(id -g)'
     }
-    arm {
+    arm64 {
+        process.arch            = 'arm64'
+        // TODO https://github.com/nf-core/modules/issues/6694
+        // For now if you're using arm64 you have to use wave for the sake of the maintainers
+        // wave profile
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
+    emulate_amd64 {
         docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
@@ -148,18 +161,6 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-    gitpod {
-        executor.name           = 'local'
-        executor.cpus           = 4
-        executor.memory         = 8.GB
-        process {
-            resourceLimits = [
-                memory: 8.GB,
-                cpus  : 4,
-                time  : 1.h
-            ]
-        }
-    }
     gpu {
         docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
         apptainer.runOptions    = '--nv'
@@ -169,6 +170,8 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
+// Set AWS client to anonymous when using the default igenomes_base
+aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false
 // Load nf-core custom profiles from different institutions
 
 // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
@@ -250,46 +253,19 @@ manifest {
     description     = """An nf-core demo pipeline"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=24.10.5'
+    nextflowVersion = '!>=25.04.0'
     version         = '1.0.2'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
-    help {
-        enabled = true
-        command = "nextflow run nf-core/demo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
-        showHiddenParameter = "show_hidden"
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  nf-core/demo ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/nf-core/demo/blob/master/CITATIONS.md
-"""
-    }
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 619342b..3566057 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -224,6 +224,18 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
+                },
+                "help": {
+                    "type": ["boolean", "string"],
+                    "description": "Display the help message."
+                },
+                "help_full": {
+                    "type": "boolean",
+                    "description": "Display the full detailed help message."
+                },
+                "show_hidden": {
+                    "type": "boolean",
+                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                 }
             }
         }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 9aba009..20fc0b9 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-07-08T11:39:03+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n    <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** 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/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Christopher Hakkaart.\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (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/demo 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": "2025-10-16T13:37:48+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-demo_logo_dark.png\">\n    <img alt=\"nf-core/demo\" src=\"docs/images/nf-core-demo_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/demo)\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/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-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** 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/demo \\\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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Christopher Hakkaart.\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (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/demo 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": "#246b126d-c3e5-4139-91d8-0c1a4138213f"
+                    "@id": "#14615137-63c4-4f42-8173-494b53cd500d"
                 }
             ],
             "name": "nf-core/demo"
@@ -123,7 +123,7 @@
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "dateCreated": "",
-            "dateModified": "2025-07-08T11:39:03Z",
+            "dateModified": "2025-10-16T13:37:48Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "demo", "minimal-example", "training", "tutorial"],
             "license": ["MIT"],
@@ -147,14 +147,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.10.5"
+            "version": "!>=25.04.0"
         },
         {
-            "@id": "#246b126d-c3e5-4139-91d8-0c1a4138213f",
+            "@id": "#14615137-63c4-4f42-8173-494b53cd500d",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#ffafd653-8724-44e6-becc-7ba2b8d6d6ae"
+                    "@id": "#35c3f719-1c32-45f1-a4cc-1b1420d57bed"
                 }
             ],
             "mainEntity": {
@@ -163,7 +163,7 @@
             "name": "Test suite for nf-core/demo"
         },
         {
-            "@id": "#ffafd653-8724-44e6-becc-7ba2b8d6d6ae",
+            "@id": "#35c3f719-1c32-45f1-a4cc-1b1420d57bed",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/demo",
             "resource": "repos/nf-core/demo/actions/workflows/nf-test.yml",
diff --git a/subworkflows/local/utils_nfcore_demo_pipeline/main.nf b/subworkflows/local/utils_nfcore_demo_pipeline/main.nf
index 637a7c0..7cfb6a4 100644
--- a/subworkflows/local/utils_nfcore_demo_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_demo_pipeline/main.nf
@@ -11,6 +11,7 @@
 include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 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'
@@ -32,6 +33,9 @@ workflow PIPELINE_INITIALISATION {
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
     input             //  string: Path to input samplesheet
+    help              // boolean: Display help message and exit
+    help_full         // boolean: Show the full help message
+    show_hidden       // boolean: Show hidden parameters in the help message
 
     main:
 
@@ -50,10 +54,35 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+    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
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  nf-core/demo ${workflow.manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/nf-core/demo/blob/master/CITATIONS.md
+"""
+    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
         validate_params,
-        null
+        null,
+        help,
+        help_full,
+        show_hidden,
+        before_text,
+        after_text,
+        command
     )
 
     //
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f847611..0000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
-  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
deleted file mode 100644
index ac8523c..0000000
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfcore_pipeline:
-  - subworkflows/nf-core/utils_nfcore_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 4994303..ee4738c 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -4,6 +4,7 @@
 
 include { paramsSummaryLog   } from 'plugin/nf-schema'
 include { validateParameters } from 'plugin/nf-schema'
+include { paramsHelp         } from 'plugin/nf-schema'
 
 workflow UTILS_NFSCHEMA_PLUGIN {
 
@@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN {
                         //           when this input is empty it will automatically use the configured schema or
                         //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
                         //           for meta pipelines
+    help                // boolean:  show help message
+    help_full           // boolean:  show full help message
+    show_hidden         // boolean:  show hidden parameters in help message
+    before_text         // string:   text to show before the help message and parameters summary
+    after_text          // string:   text to show after the help message and parameters summary
+    command             // string:   an example command of the pipeline
 
     main:
 
+    if(help || help_full) {
+        help_options = [
+            beforeText: before_text,
+            afterText: after_text,
+            command: command,
+            showHidden: show_hidden,
+            fullHelp: help_full,
+        ]
+        if(parameters_schema) {
+            help_options << [parametersSchema: parameters_schema]
+        }
+        log.info paramsHelp(
+            help_options,
+            params.help instanceof String ? params.help : "",
+        )
+        exit 0
+    }
+
     //
     // Print parameter summary to stdout. This will display the parameters
     // that differ from the default given in the JSON schema
     //
+
+    summary_options = [:]
     if(parameters_schema) {
-        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
-    } else {
-        log.info paramsSummaryLog(input_workflow)
+        summary_options << [parametersSchema: parameters_schema]
     }
+    log.info before_text
+    log.info paramsSummaryLog(summary_options, input_workflow)
+    log.info after_text
 
     //
     // Validate the parameters using nextflow_schema.json or the schema
     // given via the validation.parametersSchema configuration option
     //
     if(validate_params) {
+        validateOptions = [:]
         if(parameters_schema) {
-            validateParameters(parameters_schema:parameters_schema)
-        } else {
-            validateParameters()
+            validateOptions << [parametersSchema: parameters_schema]
         }
+        validateParameters(validateOptions)
     }
 
     emit:
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 8fb3016..c977917 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -25,6 +25,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = ""
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -51,6 +57,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = ""
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -77,6 +89,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -103,6 +121,12 @@ nextflow_workflow {
                 input[0] = workflow
                 input[1] = validate_params
                 input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                input[3] = false
+                input[4] = false
+                input[5] = false
+                input[6] = ""
+                input[7] = ""
+                input[8] = ""
                 """
             }
         }
@@ -114,4 +138,36 @@ nextflow_workflow {
             )
         }
     }
+
+    test("Should create a help message") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                input[3] = true
+                input[4] = false
+                input[5] = false
+                input[6] = "Before"
+                input[7] = "After"
+                input[8] = "nextflow run test/test"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
 }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 09ef842..8d8c737 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,8 +1,8 @@
 plugins {
-    id "nf-schema@2.4.2"
+    id "nf-schema@2.5.1"
 }
 
 validation {
     parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
     monochromeLogs = true
-}
\ No newline at end of file
+}
diff --git a/tests/.nftignore b/tests/.nftignore
index 158c83c..e128a12 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,10 +1,11 @@
 .DS_Store
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
-multiqc/multiqc_data/BETA-multiqc.parquet
+multiqc/multiqc_data/multiqc.parquet
 multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 fastqc/*_fastqc.{html,zip}
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 0c7ad6a..77adde5 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -20,8 +20,6 @@ nextflow_pipeline {
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
-                    // Number of successful tasks
-                    workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_demo_software_mqc_versions.yml"),
                     // All stable path name, with a relative path