From a425f93c49dd2f50f18b45a135e7968bbe6c3a03 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 16:26:48 +0100
Subject: [PATCH 01/20] Template update for nf-core/tools version 3.3.0.dev0

---
 .editorconfig                                 |  33 --
 .github/CONTRIBUTING.md                       |  36 +-
 .github/ISSUE_TEMPLATE/bug_report.yml         |  88 ++---
 .github/ISSUE_TEMPLATE/feature_request.yml    |   2 +-
 .github/PULL_REQUEST_TEMPLATE.md              |  10 +-
 .gitignore                                    |   1 +
 .gitpod.yml                                   |  14 +-
 .nf-core.yml                                  |  87 ++--
 .pre-commit-config.yaml                       |  26 +-
 .prettierignore                               |   1 +
 .prettierrc.yml                               |   5 +
 .vscode/settings.json                         |   3 +
 CHANGELOG.md                                  |   6 +-
 CITATIONS.md                                  |   6 +-
 LICENSE                                       |   2 +-
 README.md                                     |  29 +-
 assets/adaptivecard.json                      |   2 +-
 assets/email_template.html                    |  14 +-
 assets/email_template.txt                     |   8 +-
 assets/methods_description_template.yml       |   8 +-
 assets/multiqc_config.yml                     |   6 +-
 assets/schema_input.json                      |   6 +-
 assets/sendmail_template.txt                  |   6 +-
 assets/slackreport.json                       |   2 +-
 conf/base.config                              |  38 +-
 conf/test.config                              |  17 +-
 conf/test_full.config                         |   2 +-
 docs/README.md                                |   4 +-
 docs/images/mqc_fastqc_adapter.png            | Bin 23458 -> 0 bytes
 docs/images/mqc_fastqc_counts.png             | Bin 33918 -> 0 bytes
 docs/images/mqc_fastqc_quality.png            | Bin 55769 -> 0 bytes
 docs/output.md                                |  12 +-
 docs/usage.md                                 |  45 +--
 main.nf                                       |  28 +-
 modules.json                                  |  16 +-
 modules/nf-core/fastqc/environment.yml        |   2 -
 modules/nf-core/fastqc/main.nf                |  25 +-
 modules/nf-core/fastqc/meta.yml               |  58 +--
 modules/nf-core/fastqc/tests/main.nf.test     | 225 ++++++++---
 .../nf-core/fastqc/tests/main.nf.test.snap    | 370 ++++++++++++++++--
 modules/nf-core/fastqc/tests/tags.yml         |   2 -
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |  16 +-
 modules/nf-core/multiqc/meta.yml              |  78 ++--
 modules/nf-core/multiqc/tests/main.nf.test    |   8 +
 .../nf-core/multiqc/tests/main.nf.test.snap   |  24 +-
 modules/nf-core/multiqc/tests/nextflow.config |   5 +
 nextflow.config                               | 150 +++----
 nextflow_schema.json                          | 125 +-----
 ro-crate-metadata.json                        | 242 ++++++++++++
 .../main.nf                                   |  69 ++--
 .../nf-core/utils_nextflow_pipeline/main.nf   |  72 ++--
 .../tests/main.workflow.nf.test               |  10 +-
 .../tests/nextflow.config                     |   2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     | 367 ++++++++---------
 .../tests/main.function.nf.test               |  46 +--
 .../tests/main.function.nf.test.snap          |  30 --
 .../nf-core/utils_nfschema_plugin/main.nf     |  46 +++
 .../nf-core/utils_nfschema_plugin/meta.yml    |  35 ++
 .../utils_nfschema_plugin/tests/main.nf.test  | 117 ++++++
 .../tests/nextflow.config                     |   8 +
 .../tests/nextflow_schema.json                |   8 +-
 .../nf-core/utils_nfvalidation_plugin/main.nf |  62 ---
 .../utils_nfvalidation_plugin/meta.yml        |  44 ---
 .../tests/main.nf.test                        | 200 ----------
 .../utils_nfvalidation_plugin/tests/tags.yml  |   2 -
 workflows/{aggregate.nf => nf-aggregate.nf}   |  25 +-
 67 files changed, 1722 insertions(+), 1318 deletions(-)
 delete mode 100644 .editorconfig
 create mode 100644 .vscode/settings.json
 delete mode 100755 docs/images/mqc_fastqc_adapter.png
 delete mode 100755 docs/images/mqc_fastqc_counts.png
 delete mode 100755 docs/images/mqc_fastqc_quality.png
 delete mode 100644 modules/nf-core/fastqc/tests/tags.yml
 create mode 100644 modules/nf-core/multiqc/tests/nextflow.config
 create mode 100644 ro-crate-metadata.json
 rename subworkflows/local/{utils_nfcore_aggregate_pipeline => utils_nfcore_nf-aggregate_pipeline}/main.nf (78%)
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
 rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%)
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
 delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
 rename workflows/{aggregate.nf => nf-aggregate.nf} (90%)

diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 72dda28..0000000
--- a/.editorconfig
+++ /dev/null
@@ -1,33 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-indent_size = unset
-
-# ignore python and markdown
-[*.{py,md}]
-indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 79732e0..74bd21c 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,9 +1,9 @@
-# nf/aggregate: Contributing Guidelines
+# `seqeralabs/nf-aggregate`: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf/aggregate.
+Many thanks for taking an interest in improving seqeralabs/nf-aggregate.
 
-We try to manage the required tasks for nf/aggregate using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for seqeralabs/nf-aggregate using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
@@ -11,12 +11,12 @@ Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for nf/aggregate, the standard workflow is as follows:
+If you'd like to write some code for seqeralabs/nf-aggregate, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf/aggregate issues](https://github.com/nf/aggregate/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf/aggregate repository](https://github.com/nf/aggregate) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [seqeralabs/nf-aggregate issues](https://github.com/seqeralabs/nf-aggregate/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [seqeralabs/nf-aggregate repository](https://github.com/seqeralabs/nf-aggregate) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -37,7 +37,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -52,23 +52,23 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Pipeline contribution conventions
 
-To make the nf/aggregate code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `seqeralabs/nf-aggregate` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -77,13 +77,13 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -96,7 +96,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 
@@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf/aggregate/codespaces)
+- Open the repo in [Codespaces](https://github.com/seqeralabs/nf-aggregate/codespaces)
 - Tools installed
   - nf-core
   - Nextflow
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index d463e94..9d8b9f2 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,53 +2,41 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- type: textarea
-  id: description
-  attributes:
-    label: Description of the bug
-    description: A clear and concise description of what the bug is.
-  validations:
-    required: true
-- type: textarea
-  id: command_used
-  attributes:
-    label: Command used and terminal output
-    description: Steps to reproduce the behaviour. Please paste the command you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* Nextflow version _(eg. 23.04.0)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-      or Apptainer)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of nf/aggregate _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 23.04.0)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of seqeralabs/nf-aggregate _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 58c01f0..a68093b 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf/aggregate pipeline
+description: Suggest an idea for the seqeralabs/nf-aggregate pipeline
 labels: enhancement
 body:
   - type: textarea
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index beb0ea6..cd80aa3 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,22 +1,22 @@
 <!--
-# nf/aggregate pull request
+# seqeralabs/nf-aggregate pull request
 
-Many thanks for contributing to nf/aggregate!
+Many thanks for contributing to seqeralabs/nf-aggregate!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf/aggregate/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/seqeralabs/nf-aggregate/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf/aggregate/tree/master/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/seqeralabs/nf-aggregate/tree/master/.github/CONTRIBUTING.md)
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.gitignore b/.gitignore
index 5124c9a..a42ce01 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/
diff --git a/.gitpod.yml b/.gitpod.yml
index 105a182..83599f6 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,7 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+  extensions:
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index 20c0947..a84c570 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,38 +1,61 @@
 lint:
+  actions_ci: false
+  base_config: false
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-aggregate_logo_light.png
-  - docs/images/nf-core-aggregate_logo_light.png
-  - docs/images/nf-core-aggregate_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
-  - .github/workflows/branch.yml
-  - .github/workflows/ci.yml
-  - .github/workflows/linting_comment.yml
-  - .github/workflows/linting.yml
-  - conf/igenomes.config
-  - conf/igenomes.config
+    - .github/.dockstore.yml
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - CODE_OF_CONDUCT.md
+    - LICENSE
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/multiqc_config.yml
+    - assets/nf-core-nf-aggregate_logo_light.png
+    - assets/sendmail_template.txt
+    - conf/base.config
+    - conf/igenomes.config
+    - conf/modules.config
+    - conf/test.config
+    - conf/test_full.config
+    - docs/README.md
+    - docs/images/nf-core-nf-aggregate_logo_dark.png
+    - docs/images/nf-core-nf-aggregate_logo_light.png
+    - docs/output.md
+    - docs/usage.md
   files_unchanged:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-aggregate_logo_light.png
-  - docs/images/nf-core-aggregate_logo_light.png
-  - docs/images/nf-core-aggregate_logo_dark.png
-  - .github/ISSUE_TEMPLATE/bug_report.yml
-  multiqc_config:
-  - report_comment
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/linting.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-aggregate_logo_light.png
+    - docs/images/nf-aggregate_logo_dark.png
+    - docs/images/nf-aggregate_logo_light.png
+  modules_config: false
+  multiqc_config: false
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
-  - process.cpus
-  - process.memory
-  - process.time
-  - custom_config
-nf_core_version: 2.14.1
+    - custom_config
+    - manifest.homePage
+    - manifest.name
+    - process.cpus
+    - process.memory
+    - process.time
+  pipeline_name_conventions: false
+  schema_lint: false
+nf_core_version: 3.3.0.dev0
 repository_type: pipeline
 template:
-  prefix: nf
-  skip:
-  - ci
-  - igenomes
-  - nf_core_configs
+  author: SciDev Team, Seqera
+  description: Pipeline to aggregate pertinent metrics across pipeline runs on the
+    Seqera Platform.
+  force: false
+  is_nfcore: false
+  name: nf-aggregate
+  org: seqeralabs
+  outdir: .
+  skip_features:
+    - ci
+    - igenomes
+    - nf_core_configs
+  version: 0.5.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1d..9d0b248 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+          - prettier@3.5.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
diff --git a/.prettierignore b/.prettierignore
index 437d763..edd29f0 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a7..07dbd8b 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..a33b527
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 04678e1..1e26a54 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,11 @@
-# nf/aggregate: Changelog
+# seqeralabs/nf-aggregate: Changelog
 
 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).
 
-## v1.0dev - [date]
+## v0.5.0 - [date]
 
-Initial release of nf/aggregate, created with the [nf-core](https://nf-co.re/) template.
+Initial release of seqeralabs/nf-aggregate, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
diff --git a/CITATIONS.md b/CITATIONS.md
index 5b0c153..9465300 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -1,4 +1,4 @@
-# nf/aggregate: Citations
+# seqeralabs/nf-aggregate: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
@@ -12,11 +12,11 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
 
diff --git a/LICENSE b/LICENSE
index 8c23d97..a6e9acd 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) @drpatelh
+Copyright (c) The seqeralabs/nf-aggregate team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 8426481..62e9e87 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,19 @@
-[![GitHub Actions CI Status](https://github.com/nf/aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/nf/aggregate/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf/aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/nf/aggregate/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+# seqeralabs/nf-aggregate
+
+[![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)[![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/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![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-3.3.0.dev0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.0.dev0)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf/aggregate)
+[![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/seqeralabs/nf-aggregate)
 
 ## Introduction
 
-**nf/aggregate** is a bioinformatics pipeline that ...
+**seqeralabs/nf-aggregate** is a bioinformatics pipeline that ...
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
@@ -20,10 +23,7 @@
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
@@ -51,19 +51,18 @@ Now, you can run the pipeline using:
 <!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
 
 ```bash
-nextflow run nf/aggregate \
+nextflow run seqeralabs/nf-aggregate \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
 ```
 
 > [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
 ## Credits
 
-nf/aggregate was originally written by @drpatelh.
+seqeralabs/nf-aggregate was originally written by SciDev Team, Seqera.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -76,13 +75,13 @@ If you would like to contribute to this pipeline, please see the [contributing g
 ## Citations
 
 <!-- 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. -->
-<!-- If you use nf/aggregate for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use seqeralabs/nf-aggregate for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >
diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
index 291e629..4c28a60 100644
--- a/assets/adaptivecard.json
+++ b/assets/adaptivecard.json
@@ -17,7 +17,7 @@
                         "size": "Large",
                         "weight": "Bolder",
                         "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "nf/aggregate v${version} - ${runName}",
+                        "text": "seqeralabs/nf-aggregate v${version} - ${runName}",
                         "wrap": true
                     },
                     {
diff --git a/assets/email_template.html b/assets/email_template.html
index 44e697d..a01d25f 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -4,21 +4,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf/aggregate: Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform (beta)">
-  <title>nf/aggregate Pipeline Report</title>
+  <meta name="description" content="seqeralabs/nf-aggregate: Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform.">
+  <title>seqeralabs/nf-aggregate Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>nf/aggregate ${version}</h1>
+<h1>seqeralabs/nf-aggregate ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf/aggregate execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">seqeralabs/nf-aggregate execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -27,7 +27,7 @@ <h4 style="margin-top:0; color: inherit;">nf/aggregate execution completed unsuc
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf/aggregate execution completed successfully!
+        seqeralabs/nf-aggregate execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nf/aggregate</p>
-<p><a href="https://github.com/nf/aggregate">https://github.com/nf/aggregate</a></p>
+<p>seqeralabs/nf-aggregate</p>
+<p><a href="https://github.com/seqeralabs/nf-aggregate">https://github.com/seqeralabs/nf-aggregate</a></p>
 
 </div>
 
diff --git a/assets/email_template.txt b/assets/email_template.txt
index fcc81ab..b1d406e 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -1,10 +1,10 @@
 Run Name: $runName
 
 <% if (success){
-    out << "## nf/aggregate execution completed successfully! ##"
+    out << "## seqeralabs/nf-aggregate execution completed successfully! ##"
 } else {
     out << """####################################################
-## nf/aggregate execution completed unsuccessfully! ##
+## seqeralabs/nf-aggregate execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -27,5 +27,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf/aggregate
-https://github.com/nf/aggregate
+seqeralabs/nf-aggregate
+https://github.com/seqeralabs/nf-aggregate
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 4f80b9b..d584162 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -1,13 +1,13 @@
-id: "nf-aggregate-methods-description"
+id: "seqeralabs-nf-aggregate-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "nf/aggregate Methods Description"
-section_href: "https://github.com/nf/aggregate"
+section_name: "seqeralabs/nf-aggregate Methods Description"
+section_href: "https://github.com/seqeralabs/nf-aggregate"
 plot_type: "html"
 ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf/aggregate v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using seqeralabs/nf-aggregate v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 7684fa2..88e8175 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,12 +1,12 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf/aggregate/tree/dev" target="_blank">nf/aggregate</a>
+  This report has been generated by the <a href="https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0" target="_blank">seqeralabs/nf-aggregate</a>
   analysis pipeline.
 report_section_order:
-  "nf-aggregate-methods-description":
+  "seqeralabs-nf-aggregate-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "nf-aggregate-summary":
+  "seqeralabs-nf-aggregate-summary":
     order: -1002
 
 export_plots: true
diff --git a/assets/schema_input.json b/assets/schema_input.json
index aa4fbc0..89df827 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,7 +1,7 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf/aggregate/master/assets/schema_input.json",
-    "title": "nf/aggregate pipeline - params.input schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/seqeralabs/nf-aggregate/master/assets/schema_input.json",
+    "title": "seqeralabs/nf-aggregate pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
index b65216a..baa4f94 100644
--- a/assets/sendmail_template.txt
+++ b/assets/sendmail_template.txt
@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="nf-aggregate_logo.png"
+Content-Type: image/png;name="seqeralabs-nf-aggregate_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="nf-aggregate_logo_light.png"
+Content-Disposition: inline; filename="seqeralabs-nf-aggregate_logo_light.png"
 
-<% out << new File("$projectDir/assets/nf-aggregate_logo_light.png").
+<% out << new File("$projectDir/assets/seqeralabs-nf-aggregate_logo_light.png").
     bytes.
     encodeBase64().
     toString().
diff --git a/assets/slackreport.json b/assets/slackreport.json
index 3a342dc..c010b7a 100644
--- a/assets/slackreport.json
+++ b/assets/slackreport.json
@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf/aggregate ${version} - ${runName}",
+            "author_name": "seqeralabs/nf-aggregate ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [
diff --git a/conf/base.config b/conf/base.config
index 48af02e..9575ede 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    nf/aggregate Nextflow base config file
+    seqeralabs/nf-aggregate Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on
@@ -11,46 +11,46 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
+    // NOTE - Please try and reuse the labels below as much as possible.
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/conf/test.config b/conf/test.config
index 5d5ef25..ce603fb 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -5,24 +5,25 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf/aggregate -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run seqeralabs/nf-aggregate -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
-
-    
 }
diff --git a/conf/test_full.config b/conf/test_full.config
index ba3dcb6..9507659 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf/aggregate -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run seqeralabs/nf-aggregate -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
diff --git a/docs/README.md b/docs/README.md
index 02ede6e..44307ce 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,6 +1,6 @@
-# nf/aggregate: Documentation
+# seqeralabs/nf-aggregate: Documentation
 
-The nf/aggregate documentation is split into the following pages:
+The seqeralabs/nf-aggregate documentation is split into the following pages:
 
 - [Usage](usage.md)
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
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diff --git a/docs/output.md b/docs/output.md
index dd5273f..c68c346 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,4 +1,4 @@
-# nf/aggregate: Output
+# seqeralabs/nf-aggregate: Output
 
 ## Introduction
 
@@ -29,16 +29,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
-
 ### MultiQC
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index 4ef17ec..65ca4e1 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,4 +1,4 @@
-# nf/aggregate: Usage
+# seqeralabs/nf-aggregate: Usage
 
 > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
 
@@ -55,7 +55,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf/aggregate --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+nextflow run seqeralabs/nf-aggregate --input ./samplesheet.csv --outdir ./results  -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -73,22 +73,20 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
 ```bash
-nextflow run nf/aggregate -profile docker -params-file params.yaml
+nextflow run seqeralabs/nf-aggregate -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
-genome: 'GRCh37'
 <...>
 ```
 
@@ -99,28 +97,26 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
 
 ```bash
-nextflow pull nf/aggregate
+nextflow pull seqeralabs/nf-aggregate
 ```
 
 ### Reproducibility
 
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [nf/aggregate releases page](https://github.com/nf/aggregate/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
+First, go to the [seqeralabs/nf-aggregate releases page](https://github.com/seqeralabs/nf-aggregate/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen)
 
 ### `-profile`
 
@@ -128,14 +124,13 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!IMPORTANT]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment.
 
 - `test`
   - A profile with a complete configuration for automated testing
@@ -171,13 +166,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 ### Resource requests
 
-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
 ### Custom Containers
 
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
 To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
diff --git a/main.nf b/main.nf
index c7e90af..c703de1 100644
--- a/main.nf
+++ b/main.nf
@@ -1,24 +1,21 @@
 #!/usr/bin/env nextflow
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    nf/aggregate
+    seqeralabs/nf-aggregate
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Github : https://github.com/nf/aggregate
+    Github : https://github.com/seqeralabs/nf-aggregate
 ----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { AGGREGATE  } from './workflows/aggregate'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_aggregate_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_aggregate_pipeline'
-
+include { NF-AGGREGATE  } from './workflows/nf-aggregate'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_nf-aggregate_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_nf-aggregate_pipeline'
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -28,7 +25,7 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_aggr
 //
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
-workflow NF_AGGREGATE {
+workflow SEQERALABS_NF-AGGREGATE {
 
     take:
     samplesheet // channel: samplesheet read in from --input
@@ -38,13 +35,11 @@ workflow NF_AGGREGATE {
     //
     // WORKFLOW: Run pipeline
     //
-    AGGREGATE (
+    NF-AGGREGATE (
         samplesheet
     )
-
     emit:
-    multiqc_report = AGGREGATE.out.multiqc_report // channel: /path/to/multiqc_report.html
-
+    multiqc_report = NF-AGGREGATE.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -55,13 +50,11 @@ workflow NF_AGGREGATE {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
@@ -72,10 +65,9 @@ workflow {
     //
     // WORKFLOW: Run main workflow
     //
-    NF_AGGREGATE (
+    SEQERALABS_NF-AGGREGATE (
         PIPELINE_INITIALISATION.out.samplesheet
     )
-
     //
     // SUBWORKFLOW: Run completion tasks
     //
@@ -86,7 +78,7 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        NF_AGGREGATE.out.multiqc_report
+        SEQERALABS_NF-AGGREGATE.out.multiqc_report
     )
 }
 
diff --git a/modules.json b/modules.json
index afe6ee9..8d0f45d 100644
--- a/modules.json
+++ b/modules.json
@@ -1,18 +1,18 @@
 {
-    "name": "nf/aggregate",
-    "homePage": "https://github.com/nf/aggregate",
+    "name": "seqeralabs/nf-aggregate",
+    "homePage": "https://github.com/seqeralabs/nf-aggregate",
     "repos": {
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38..691d4c7 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c8..033f415 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,5 +1,5 @@
 process FASTQC {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -19,27 +19,30 @@ process FASTQC {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args          = task.ext.args ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    def rename_to     = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // 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
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
     """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        --memory $fastqc_memory \\
-        $renamed_files
+        ${args} \\
+        --threads ${task.cpus} \\
+        --memory ${fastqc_memory} \\
+        ${renamed_files}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e..2b2e62b 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,40 +11,50 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
+
         You get information about adapter contamination and other
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4..e9d79a0 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
-                                process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c31..d5db309 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
deleted file mode 100644
index 7834294..0000000
--- a/modules/nf-core/fastqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-fastqc:
-  - modules/nf-core/fastqc/**
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb6..a27122c 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.27
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352..58d9313 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
@@ -44,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc3..b16c187 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,40 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       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:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
+  - - 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:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - 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}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242..33316a7 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd80..7b7c132 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:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2025-01-27T09:29:57.631982377"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2025-01-27T09:30:34.743726958"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2025-01-27T09:30:21.44383553"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 0000000..c537a6a
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index 41949b2..e568cd1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    nf/aggregate Nextflow config file
+    seqeralabs/nf-aggregate Nextflow config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Default config options for all compute environments
 ----------------------------------------------------------------------------------------
@@ -29,26 +29,14 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    help_full                    = false
+    show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
-    // Config options
-    config_profile_name        = null
-    config_profile_description = null
-
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
+    validate_params            = true
 }
 
 // Load base.config by default for all pipelines
@@ -68,7 +56,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -152,23 +140,30 @@ profiles {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
+        process {
+            resourceLimits = [
+                memory: 8.GB,
+                cpus  : 4,
+                time  : 1.h
+            ]
+        }
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+
+
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
+
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
@@ -181,73 +176,82 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set bash options
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
 
 manifest {
-    name            = 'nf/aggregate'
-    author          = """@drpatelh"""
-    homePage        = 'https://github.com/nf/aggregate'
-    description     = """Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform (beta)"""
+    name            = 'seqeralabs/nf-aggregate'
+    author          = """SciDev Team, Seqera""" // 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
+        [
+            name: 'SciDev Team',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+        [
+            name: ' Seqera',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+    ]
+    homePage        = 'https://github.com/seqeralabs/nf-aggregate'
+    description     = """Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform."""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
+    defaultBranch   = 'master'
+    nextflowVersion = '!>=24.04.2'
+    version         = '0.5.0'
     doi             = ''
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
 
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
+validation {
+    defaultIgnoreParams = ["genomes"]
+    monochromeLogs = params.monochrome_logs
+    help {
+        enabled = true
+        command = "nextflow run seqeralabs/nf-aggregate -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 9a1880d..d8dd329 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,19 +1,16 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf/aggregate/master/nextflow_schema.json",
-    "title": "nf/aggregate pipeline parameters",
-    "description": "Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform (beta)",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/seqeralabs/nf-aggregate/master/nextflow_schema.json",
+    "title": "seqeralabs/nf-aggregate pipeline parameters",
+    "description": "Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform.",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -46,62 +43,6 @@
                 }
             }
         },
-        "institutional_config_options": {
-            "title": "Institutional config options",
-            "type": "object",
-            "fa_icon": "fas fa-university",
-            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
-            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
-            "properties": {
-                "config_profile_name": {
-                    "type": "string",
-                    "description": "Institutional config name.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
-                },
-                "config_profile_description": {
-                    "type": "string",
-                    "description": "Institutional config description.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-users-cog"
-                }
-            }
-        },
-        "max_job_request_options": {
-            "title": "Max job request options",
-            "type": "object",
-            "fa_icon": "fab fa-acquisitions-incorporated",
-            "description": "Set the top limit for requested resources for any single job.",
-            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
-            "properties": {
-                "max_cpus": {
-                    "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
-                    "fa_icon": "fas fa-microchip",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
-                },
-                "max_memory": {
-                    "type": "string",
-                    "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
-                    "fa_icon": "fas fa-memory",
-                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
-                },
-                "max_time": {
-                    "type": "string",
-                    "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
-                    "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
-                }
-            }
-        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -109,12 +50,6 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
@@ -127,14 +62,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -197,49 +125,28 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
+                },
+                "trace_report_suffix": {
+                    "type": "string",
+                    "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
                 }
             }
         }
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/institutional_config_options"
-        },
-        {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
-}
\ No newline at end of file
+}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
new file mode 100644
index 0000000..7a2c701
--- /dev/null
+++ b/ro-crate-metadata.json
@@ -0,0 +1,242 @@
+{
+    "@context": "https://w3id.org/ro/crate/1.1/context",
+    "@graph": [
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "creativeWorkStatus": "Stable",
+            "datePublished": "2025-02-26T15:26:45+00:00",
+            "description": "# seqeralabs/nf-aggregate\n\n[![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)[![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-3.3.0.dev0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.0.dev0)\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/seqeralabs/nf-aggregate)\n\n## Introduction\n\n**seqeralabs/nf-aggregate** 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/contributing/design_guidelines#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 seqeralabs/nf-aggregate \\\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\n## Credits\n\nseqeralabs/nf-aggregate was originally written by SciDev Team, Seqera.\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\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 seqeralabs/nf-aggregate 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\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "hasPart": [
+                {
+                    "@id": "main.nf"
+                },
+                {
+                    "@id": "assets/"
+                },
+                {
+                    "@id": "conf/"
+                },
+                {
+                    "@id": "docs/"
+                },
+                {
+                    "@id": "modules/"
+                },
+                {
+                    "@id": "modules/nf-core/"
+                },
+                {
+                    "@id": "workflows/"
+                },
+                {
+                    "@id": "subworkflows/"
+                },
+                {
+                    "@id": "nextflow.config"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "nextflow_schema.json"
+                },
+                {
+                    "@id": "CHANGELOG.md"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "CITATIONS.md"
+                },
+                {
+                    "@id": "modules.json"
+                },
+                {
+                    "@id": "docs/usage.md"
+                },
+                {
+                    "@id": "docs/output.md"
+                },
+                {
+                    "@id": ".nf-core.yml"
+                },
+                {
+                    "@id": ".pre-commit-config.yaml"
+                },
+                {
+                    "@id": ".prettierignore"
+                }
+            ],
+            "isBasedOn": "https://github.com/seqeralabs/nf-aggregate",
+            "license": "MIT",
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "name": "seqeralabs/nf-aggregate"
+        },
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": [
+                {
+                    "@id": "https://w3id.org/ro/crate/1.1"
+                },
+                {
+                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+                }
+            ]
+        },
+        {
+            "@id": "main.nf",
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
+            "dateCreated": "",
+            "dateModified": "2025-02-26T16:26:45Z",
+            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
+            "keywords": [
+                "nf-core",
+                "nextflow"
+            ],
+            "license": [
+                "MIT"
+            ],
+            "name": [
+                "seqeralabs/nf-aggregate"
+            ],
+            "programmingLanguage": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+            },
+            "sdPublisher": {
+                "@id": "https://nf-co.re/"
+            },
+            "url": [
+                "https://github.com/seqeralabs/nf-aggregate",
+                "https://nf-co.re/seqeralabs/nf-aggregate/0.5.0/"
+            ],
+            "version": [
+                "0.5.0"
+            ]
+        },
+        {
+            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
+            "@type": "ComputerLanguage",
+            "identifier": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "name": "Nextflow",
+            "url": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "version": "!>=24.04.2"
+        },
+        {
+            "@id": "assets/",
+            "@type": "Dataset",
+            "description": "Additional files"
+        },
+        {
+            "@id": "conf/",
+            "@type": "Dataset",
+            "description": "Configuration files"
+        },
+        {
+            "@id": "docs/",
+            "@type": "Dataset",
+            "description": "Markdown files for documenting the pipeline"
+        },
+        {
+            "@id": "modules/",
+            "@type": "Dataset",
+            "description": "Modules used by the pipeline"
+        },
+        {
+            "@id": "modules/nf-core/",
+            "@type": "Dataset",
+            "description": "nf-core modules"
+        },
+        {
+            "@id": "workflows/",
+            "@type": "Dataset",
+            "description": "Main pipeline workflows to be executed in main.nf"
+        },
+        {
+            "@id": "subworkflows/",
+            "@type": "Dataset",
+            "description": "Smaller subworkflows"
+        },
+        {
+            "@id": "nextflow.config",
+            "@type": "File",
+            "description": "Main Nextflow configuration file"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File",
+            "description": "Basic pipeline usage information"
+        },
+        {
+            "@id": "nextflow_schema.json",
+            "@type": "File",
+            "description": "JSON schema for pipeline parameter specification"
+        },
+        {
+            "@id": "CHANGELOG.md",
+            "@type": "File",
+            "description": "Information on changes made to the pipeline"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File",
+            "description": "The license - should be MIT"
+        },
+        {
+            "@id": "CITATIONS.md",
+            "@type": "File",
+            "description": "Citations needed when using the pipeline"
+        },
+        {
+            "@id": "modules.json",
+            "@type": "File",
+            "description": "Version information for modules from nf-core/modules"
+        },
+        {
+            "@id": "docs/usage.md",
+            "@type": "File",
+            "description": "Usage documentation"
+        },
+        {
+            "@id": "docs/output.md",
+            "@type": "File",
+            "description": "Output documentation"
+        },
+        {
+            "@id": ".nf-core.yml",
+            "@type": "File",
+            "description": "nf-core configuration file, configuring template features and linting rules"
+        },
+        {
+            "@id": ".pre-commit-config.yaml",
+            "@type": "File",
+            "description": "Configuration file for pre-commit hooks"
+        },
+        {
+            "@id": ".prettierignore",
+            "@type": "File",
+            "description": "Ignore file for prettier"
+        },
+        {
+            "@id": "https://nf-co.re/",
+            "@type": "Organization",
+            "name": "nf-core",
+            "url": "https://nf-co.re/"
+        }
+    ]
+}
\ No newline at end of file
diff --git a/subworkflows/local/utils_nfcore_aggregate_pipeline/main.nf b/subworkflows/local/utils_nfcore_nf-aggregate_pipeline/main.nf
similarity index 78%
rename from subworkflows/local/utils_nfcore_aggregate_pipeline/main.nf
rename to subworkflows/local/utils_nfcore_nf-aggregate_pipeline/main.nf
index 5edaa3f..04215ab 100644
--- a/subworkflows/local/utils_nfcore_aggregate_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_nf-aggregate_pipeline/main.nf
@@ -1,5 +1,5 @@
 //
-// Subworkflow with functionality specific to the nf/aggregate pipeline
+// Subworkflow with functionality specific to the seqeralabs/nf-aggregate pipeline
 //
 
 /*
@@ -8,29 +8,25 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -54,16 +50,10 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
 
     //
@@ -76,8 +66,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
+
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {
@@ -87,8 +78,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map {
-            validateInputSamplesheet(it)
+        .map { samplesheet ->
+            validateInputSamplesheet(samplesheet)
         }
         .map {
             meta, fastqs ->
@@ -102,9 +93,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -119,19 +110,26 @@ workflow PIPELINE_COMPLETION {
     multiqc_report  //  string: Path to MultiQC report
 
     main:
-
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def multiqc_reports = multiqc_report.toList()
 
     //
     // Completion email and summary
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                multiqc_reports.getVal(),
+            )
         }
 
         completionSummary(monochrome_logs)
-
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
@@ -143,9 +141,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -155,14 +153,13 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
 
     return [ metas[0], fastqs ]
 }
-
 //
 // Generate methods description for MultiQC
 //
@@ -193,7 +190,7 @@ def toolBibliographyText() {
 }
 
 def methodsDescriptionText(mqc_methods_yaml) {
-    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    // Convert  to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
     meta.workflow = workflow.toMap()
     meta["manifest_map"] = workflow.manifest.toMap()
@@ -204,8 +201,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28..d6e593e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,18 +2,13 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -76,13 +71,13 @@ def getWorkflowVersion() {
 // Dump pipeline parameters to a JSON file
 //
 def dumpParametersToJSON(outdir) {
-    def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    def filename   = "params_${timestamp}.json"
-    def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+    def filename  = "params_${timestamp}.json"
+    def temp_pf   = new File(workflow.launchDir.toString(), ".${filename}")
+    def jsonStr   = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text  = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,37 +85,42 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
         channels = config.channels
-    } catch(NullPointerException | IOException e) {
-        log.warn "Could not verify conda channel configuration."
-        return
+    }
+    catch (NullPointerException e) {
+        log.debug(e)
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.debug(e)
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
-    def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
-    }
+    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        log.warn """\
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            There is a problem with your Conda configuration!
+            You will need to set-up the conda-forge and bioconda channels correctly.
+            Please refer to https://bioconda.github.io/
+            The observed channel order is
+            ${channels}
+            but the following channel order is required:
+            ${required_channels_in_order}
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        """.stripIndent(true)
     }
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce..02dbf09 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926b..a09572e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3..bfd2587 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,17 +2,13 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
-        log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
+        )
         valid_config = false
     }
     return valid_config
@@ -52,39 +45,22 @@ def checkConfigProvided() {
 //
 def checkProfileProvided(nextflow_cli_args) {
     if (workflow.profile.endsWith(',')) {
-        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
     if (nextflow_cli_args[0]) {
-        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +78,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -113,8 +89,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -122,11 +98,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { processVersionsFromYAML(it) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -134,61 +106,40 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
-        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
-        if (group_params) {
-            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
-            summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
-                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
             }
-            summary_section += "    </dl>\n"
         }
-    }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text        += "plot_type: 'html'\n"
-    yaml_file_text        += "data: |\n"
-    yaml_file_text        += "${summary_section}"
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
 
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -200,79 +151,76 @@ def logColours(monochrome_logs=true) {
     colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
 
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                }
-                mqc_report = mqc_report[0]
-            }
-        }
-    } catch (all) {
-        if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
         }
+    } else {
+        return null
     }
-    return mqc_report
 }
 
 //
@@ -281,26 +229,35 @@ def attachMultiqcReport(multiqc_report) {
 def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
     misc_fields['Date Started']              = workflow.start
     misc_fields['Date Completed']            = workflow.complete
     misc_fields['Pipeline script file path'] = workflow.scriptFile
     misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    if (workflow.repository) {
+        misc_fields['Pipeline repository Git URL']    = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    }
+    misc_fields['Nextflow Version']          = workflow.nextflow.version
+    misc_fields['Nextflow Build']            = workflow.nextflow.build
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
@@ -317,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -337,40 +294,45 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html")
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
     output_tf.delete()
 }
 
@@ -378,15 +340,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
         }
-    } else {
-        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+        else {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
+        }
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -395,21 +359,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+    misc_fields['start']          = workflow.start
+    misc_fields['complete']       = workflow.complete
+    misc_fields['scriptfile']     = workflow.scriptFile
+    misc_fields['scriptid']       = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['repository'] = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['commitid']   = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['revision']   = workflow.revision
+    }
+    misc_fields['nxf_version']    = workflow.nextflow.version
+    misc_fields['nxf_build']      = workflow.nextflow.build
+    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
 
     def msg_fields = [:]
     msg_fields['version']      = getWorkflowVersion()
@@ -434,13 +407,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    def post = new URL(hook_url).openConnection()
     post.setRequestMethod("POST")
     post.setDoOutput(true)
     post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f..f117040 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
         }
     }
 
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function nfCoreLogo") {
+    test("Test Function without logColours") {
 
-        function "nfCoreLogo"
+        function "logColours"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = true
                 """
             }
         }
@@ -73,9 +61,8 @@ nextflow_function {
         }
     }
 
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
+    test("Test Function with logColours") {
+        function "logColours"
 
         when {
             function {
@@ -93,14 +80,13 @@ nextflow_function {
         }
     }
 
-    test("Test Function without logColours") {
-
-        function "logColours"
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = true
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
                 """
             }
         }
@@ -108,18 +94,22 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") }
             )
         }
     }
 
-    test("Test Function with logColours") {
-        function "logColours"
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -127,7 +117,9 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
             )
         }
     }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232..02c6701 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
         },
         "timestamp": "2024-02-28T12:02:59.729647"
     },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:10.562934"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:07.019761"
-    },
     "Test Function without logColours": {
         "content": [
             {
@@ -95,16 +75,6 @@
         },
         "timestamp": "2024-02-28T12:03:17.969323"
     },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:14.366181"
-    },
     "Test Function with logColours": {
         "content": [
             {
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 0000000..4994303
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 0000000..f7d9f02
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 0000000..8fb3016
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 0000000..0907ac5
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c..331e0d2 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
-    validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b0..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
deleted file mode 100644
index 5784a33..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,200 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-                outdir          = 1
-            }
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cff..0000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/workflows/aggregate.nf b/workflows/nf-aggregate.nf
similarity index 90%
rename from workflows/aggregate.nf
rename to workflows/nf-aggregate.nf
index bfc5f2a..2972aec 100644
--- a/workflows/aggregate.nf
+++ b/workflows/nf-aggregate.nf
@@ -3,13 +3,12 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_aggregate_pipeline'
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nf-aggregate_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -17,16 +16,14 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_aggr
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-workflow AGGREGATE {
+workflow NF-AGGREGATE {
 
     take:
     ch_samplesheet // channel: samplesheet read in from --input
-
     main:
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
-
     //
     // MODULE: Run FastQC
     //
@@ -42,11 +39,12 @@ workflow AGGREGATE {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name:  'nf-aggregate_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
 
+
     //
     // MODULE: MultiQC
     //
@@ -62,15 +60,14 @@ workflow AGGREGATE {
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     ch_methods_description                = Channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
@@ -83,12 +80,14 @@ workflow AGGREGATE {
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        [],
+        []
     )
 
-    emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
+
 }
 
 /*

From 832a12c5847a21ddd71efffe9cba0e9ab76eec0a Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Wed, 26 Feb 2025 17:26:36 +0100
Subject: [PATCH 02/20] Apply suggestions from code review

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

diff --git a/README.md b/README.md
index ad6726d..dde0843 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # seqeralabs/nf-aggregate
 
 [![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)
 [![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/)

From e8cc1fe9f71dfdb68ffc8915a3ca79d36bd61bf5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:31:18 +0100
Subject: [PATCH 03/20] fix rocrate

---
 nextflow.config        |   4 +-
 nextflow_schema.json   |  65 +++++++++++++++++---
 ro-crate-metadata.json | 134 +++++++++++++++++++++++++++++------------
 3 files changed, 154 insertions(+), 49 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 0d85f07..151493b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -41,7 +41,6 @@ params {
     show_hidden                  = false
     version                      = false
     modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
-    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')
 
     // Schema validation default options
@@ -313,7 +312,7 @@ manifest {
     homePage        = 'https://github.com/seqeralabs/nf-aggregate'
     description     = """Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform."""
     mainScript      = 'main.nf'
-    defaultBranch   = 'master'
+    defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
     version         = '0.5.0'
     doi             = ''
@@ -325,7 +324,6 @@ plugins {
 }
 
 validation {
-    defaultIgnoreParams = ["genomes"]
     monochromeLogs = params.monochrome_logs
     help {
         enabled = true
diff --git a/nextflow_schema.json b/nextflow_schema.json
index fff787b..3806fdb 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -31,6 +31,64 @@
                 }
             }
         },
+        "pipeline_options": {
+            "title": "Pipeline-specific options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Generic options for the pipeline.",
+            "help_text": "Generic options for the pipeline.",
+            "properties": {
+                "seqera_api_endpoint": {
+                    "type": "string",
+                    "default": "https://api.cloud.seqera.io",
+                    "description": "Seqera Platform API endpoint URL.",
+                    "fa_icon": "fas fa-question-circle"
+                },
+                "seqera_cli_extra_args": {
+                    "type": "string",
+                    "description": "Extra arguments to pass to the Seqera Platform CLI command in addition to defaults defined by the pipeline.",
+                    "fa_icon": "fas fa-plus"
+                },
+                "java_truststore_path": {
+                    "type": "string",
+                    "description": "Path to custom cacerts Java truststore used by Seqera Platform.",
+                    "fa_icon": "fas fa-key"
+                },
+                "java_truststore_password": {
+                    "type": "string",
+                    "description": "Password for custom cacerts Java truststore used by Seqera Platform.",
+                    "fa_icon": "fas fa-key"
+                },
+                "skip_run_gantt": {
+                    "type": "boolean",
+                    "description": "Skip GANTT chart creation for each run.",
+                    "fa_icon": "fas fa-fast-forward"
+                },
+                "skip_multiqc": {
+                    "type": "boolean",
+                    "description": "Skip MultiQC.",
+                    "fa_icon": "fas fa-fast-forward"
+                },
+                "generate_benchmark_report": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-tachometer-alt",
+                    "description": "Compile a benchmarking report for Seqera Platform runs."
+                },
+                "benchmark_aws_cur_report": {
+                    "type": "string",
+                    "fa_icon": "fas fa-dollar-sign",
+                    "description": "AWS CUR report from data exports.",
+                    "pattern": "^\\S+\\.parquet",
+                    "format": "file-path"
+                },
+                "remove_failed_tasks": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-times-circle",
+                    "description": "Remove failed tasks from the benchmark report."
+                }
+            },
+            "required": ["seqera_api_endpoint"]
+        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -119,13 +177,6 @@
                     "hidden": true,
                     "fa_icon": "fas fa-clone"
                 },
-                "pipelines_testdata_base_path": {
-                    "type": "string",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Base URL or local path to location of pipeline test dataset files",
-                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
-                    "hidden": true
-                },
                 "trace_report_suffix": {
                     "type": "string",
                     "fa_icon": "far calendar",
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 7a2c701..5153453 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -1,12 +1,29 @@
 {
-    "@context": "https://w3id.org/ro/crate/1.1/context",
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn"
+        }
+    ],
     "@graph": [
         {
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-02-26T15:26:45+00:00",
-            "description": "# seqeralabs/nf-aggregate\n\n[![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)[![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-3.3.0.dev0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.0.dev0)\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/seqeralabs/nf-aggregate)\n\n## Introduction\n\n**seqeralabs/nf-aggregate** 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/contributing/design_guidelines#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 seqeralabs/nf-aggregate \\\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\n## Credits\n\nseqeralabs/nf-aggregate was originally written by SciDev Team, Seqera.\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\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 seqeralabs/nf-aggregate 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\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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": "2025-02-26T16:30:32+00:00",
+            "description": "# seqeralabs/nf-aggregate\n\n[![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)\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-3.3.0.dev0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.0.dev0)\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/seqeralabs/nf-aggregate)\n\n## Introduction\n\n**seqeralabs/nf-aggregate** is a Nextflow pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform.\n\n<p align=\"center\">\n  <img src=\"assets/multiqc_screenshot.png\" alt=\"MultiQC screenshot\" width=\"75%\"/>\n</p>\n\nThe pipeline performs the following steps:\n\n1. Downloads run information via the Seqera CLI in parallel\n2. Runs MultiQC to aggregate all of the run metrics into a single report\n\nYou can download an example MultiQC report [here](assets/multiqc_report.html).\n\n## Prerequisites\n\n- [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) >=23.10.0\n- Account in [Seqera Platform](https://seqera.io/platform/)\n- [Access token](https://docs.seqera.io/platform/23.3.0/api/overview#authentication) which is your personal authorization token for the Seqera Platform CLI. This can be created in the user menu under **Your tokens**. Export the token as a shell variable directly into your terminal if running the pipelie locally. You will not need to set this if running the pipeline within the Seqera Platform as it will automatically be inherited from the executing environment.\n\n  ```bash\n  export TOWER_ACCESS_TOKEN=<your access token>\n  ```\n\n## Usage\n\nThe primary input to the pipeline is a file containing a list of run identifiers from the Seqera Platform. These can be obtained from details in the runs page for any pipeline execution. For example, we can create a file called `run_ids.csv` with the following contents:\n\n```\nid,workspace\n4Bi5xBK6E2Nbhj,community/showcase\n4LWT4uaXDaGcDY,community/showcase\n38QXz4OfQDpwOV,community/showcase\n2lXd1j7OwZVfxh,community/showcase\n```\n\nThis pipeline can then be executed with the following command:\n\n```\nnextflow run seqeralabs/nf-aggregate \\\n    --input run_ids.csv \\\n    --outdir ./results \\\n    -profile docker\n```\n\nIf you are using a Seqera Platform Enterprise instance that is secured with a private CA SSL certificate not recognized by default Java certificate authorities, you can specify a custom `cacerts` store path through the `--java_truststore_path` parameter and optionally, a password with the `--java_truststore_password`. This certificate will be used to achieve connectivity with your Seqera Platform instance through API and CLI.\n\n### Benchmark reports\n\nIf you want to generate a benchmark report comparing multiple runs, you can include a `group` column in your `run_ids.csv` file. This allows you to organize and analyze runs based on custom groupings in the final report.\n\n```\nid,workspace,group\n3VcLMAI8wyy0Ld,community/showcase,group1\n4VLRs7nuqbAhDy,community/showcase,group2\n```\n\nTo incorporate AWS cost data into the benchmark report, use the benchmark_aws_cur_report parameter. This should point to a valid AWS Cost and Usage Report (CUR) file in Parquet format, supporting both CUR 1.0 and CUR 2.0 schemas. The file can be stored locally or in a cloud bucket. To run nf-aggregate and generate benchmark reports, you can use the following command:\n\n```\nnextflow run seqeralabs/nf-aggregate \\\n    --input run_ids.csv \\\n    --outdir ./results \\\n    --run_benchmark \\\n    --benchmark_aws_cur_report ./aws_cost_report.parquet\n```\n\n## Output\n\nThe results from the pipeline will be published in the path specified by the `--outdir` and will consist of the following contents:\n\n```\n./results\n\u251c\u2500\u2500 multiqc/\n\u2502   \u251c\u2500\u2500 multiqc_data/\n\u2502   \u251c\u2500\u2500 multiqc_plots/\n\u2502   \u2514\u2500\u2500 multiqc_report.html                 ## MultiQC report\n\u251c\u2500\u2500 nf-core_rnaseq/\n\u2502   \u251c\u2500\u2500 gantt/\n\u2502   \u2502   \u2514\u2500\u2500 4Bi5xBK6E2Nbhj_gantt.html       ## Gantt plot for run\n\u2502   \u2514\u2500\u2500 runs_dump/\n\u2502       \u2514\u2500\u2500 4Bi5xBK6E2Nbhj/                 ## Output of 'tw runs dump'\n\u2502           \u251c\u2500\u2500 service-info.json\n\u2502           \u251c\u2500\u2500 workflow-launch.json\n\u2502           \u251c\u2500\u2500 workflow-load.json\n\u2502           \u251c\u2500\u2500 workflow-metrics.json\n\u2502           \u251c\u2500\u2500 workflow-tasks.json\n\u2502           \u2514\u2500\u2500 workflow.json\n\u2514\u2500\u2500 pipeline_info/\n```\n\n> [!NOTE]\n> Gantt plots depend on information derived from the Fusion logs. For that reason, Gantt plots will be ommitted from the pipeline outputs for non-Fusion runs, irrespective of whether the `--skip_run_gantt` parameter has been set.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Credits\n\nnf-aggregate was written by the Scientific Development and MultiQC teams at [Seqera Labs](https://seqera.io/).\n\n## Citations\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\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"
@@ -15,13 +32,13 @@
                     "@id": "assets/"
                 },
                 {
-                    "@id": "conf/"
+                    "@id": "bin/"
                 },
                 {
-                    "@id": "docs/"
+                    "@id": "modules/"
                 },
                 {
-                    "@id": "modules/"
+                    "@id": "modules/local/"
                 },
                 {
                     "@id": "modules/nf-core/"
@@ -44,21 +61,12 @@
                 {
                     "@id": "CHANGELOG.md"
                 },
-                {
-                    "@id": "LICENSE"
-                },
                 {
                     "@id": "CITATIONS.md"
                 },
                 {
                     "@id": "modules.json"
                 },
-                {
-                    "@id": "docs/usage.md"
-                },
-                {
-                    "@id": "docs/output.md"
-                },
                 {
                     "@id": ".nf-core.yml"
                 },
@@ -70,10 +78,14 @@
                 }
             ],
             "isBasedOn": "https://github.com/seqeralabs/nf-aggregate",
-            "license": "MIT",
             "mainEntity": {
                 "@id": "main.nf"
             },
+            "mentions": [
+                {
+                    "@id": "#d57e5f05-159d-42cc-ac7d-5688e10bf944"
+                }
+            ],
             "name": "seqeralabs/nf-aggregate"
         },
         {
@@ -98,15 +110,31 @@
                 "SoftwareSourceCode",
                 "ComputationalWorkflow"
             ],
+            "creator": [
+                {
+                    "@id": "#rob.syme@gmail.com"
+                },
+                {
+                    "@id": "#drpatelh@users.noreply.github.com"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-02-26T16:26:45Z",
+            "dateModified": "2025-02-26T17:30:32Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
                 "nextflow"
             ],
             "license": [
-                "MIT"
+                null
+            ],
+            "maintainer": [
+                {
+                    "@id": "#rob.syme@gmail.com"
+                },
+                {
+                    "@id": "#drpatelh@users.noreply.github.com"
+                }
             ],
             "name": [
                 "seqeralabs/nf-aggregate"
@@ -137,25 +165,56 @@
             },
             "version": "!>=24.04.2"
         },
+        {
+            "@id": "#d57e5f05-159d-42cc-ac7d-5688e10bf944",
+            "@type": "TestSuite",
+            "instance": [
+                {
+                    "@id": "#949b33a0-6b05-4775-9db5-620911520c56"
+                }
+            ],
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "name": "Test suite for seqeralabs/nf-aggregate"
+        },
+        {
+            "@id": "#949b33a0-6b05-4775-9db5-620911520c56",
+            "@type": "TestInstance",
+            "name": "GitHub Actions workflow for testing seqeralabs/nf-aggregate",
+            "resource": "repos/seqeralabs/nf-aggregate/actions/workflows/ci.yml",
+            "runsOn": {
+                "@id": "https://w3id.org/ro/terms/test#GithubService"
+            },
+            "url": "https://api.github.com"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#GithubService",
+            "@type": "TestService",
+            "name": "Github Actions",
+            "url": {
+                "@id": "https://github.com"
+            }
+        },
         {
             "@id": "assets/",
             "@type": "Dataset",
             "description": "Additional files"
         },
         {
-            "@id": "conf/",
+            "@id": "bin/",
             "@type": "Dataset",
-            "description": "Configuration files"
+            "description": "Scripts that must be callable from a pipeline process"
         },
         {
-            "@id": "docs/",
+            "@id": "modules/",
             "@type": "Dataset",
-            "description": "Markdown files for documenting the pipeline"
+            "description": "Modules used by the pipeline"
         },
         {
-            "@id": "modules/",
+            "@id": "modules/local/",
             "@type": "Dataset",
-            "description": "Modules used by the pipeline"
+            "description": "Pipeline-specific modules"
         },
         {
             "@id": "modules/nf-core/",
@@ -192,11 +251,6 @@
             "@type": "File",
             "description": "Information on changes made to the pipeline"
         },
-        {
-            "@id": "LICENSE",
-            "@type": "File",
-            "description": "The license - should be MIT"
-        },
         {
             "@id": "CITATIONS.md",
             "@type": "File",
@@ -207,16 +261,6 @@
             "@type": "File",
             "description": "Version information for modules from nf-core/modules"
         },
-        {
-            "@id": "docs/usage.md",
-            "@type": "File",
-            "description": "Usage documentation"
-        },
-        {
-            "@id": "docs/output.md",
-            "@type": "File",
-            "description": "Output documentation"
-        },
         {
             "@id": ".nf-core.yml",
             "@type": "File",
@@ -237,6 +281,18 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#rob.syme@gmail.com",
+            "@type": "Person",
+            "email": "rob.syme@gmail.com",
+            "name": "Rob Syme"
+        },
+        {
+            "@id": "#drpatelh@users.noreply.github.com",
+            "@type": "Person",
+            "email": "drpatelh@users.noreply.github.com",
+            "name": "Harshil Patel"
         }
     ]
 }
\ No newline at end of file

From baa709dfd18617ab0020810747af605b3da2fe01 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:34:12 +0100
Subject: [PATCH 04/20] fix lint

---
 .gitignore      | 2 +-
 .prettierignore | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 13a4265..0eeea49 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,7 +6,7 @@ results/
 testing/
 testing*
 *.pyc
+null/
 .nf-test*
 test.tap
 test.xml
-null/
diff --git a/.prettierignore b/.prettierignore
index 4705fd1..120a706 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,5 +10,5 @@ testing/
 testing*
 *.pyc
 bin/
-*.html
 ro-crate-metadata.json
+*.html

From 733d4163dc0593ea310c24797b09d0da7d2e2b60 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:39:11 +0100
Subject: [PATCH 05/20] fix failing test in nf-core lint

---
 .nf-core.yml           |  2 +-
 CHANGELOG.md           |  2 +-
 nextflow.config        |  2 +-
 nextflow_schema.json   | 28 ----------------------------
 ro-crate-metadata.json | 36 ++++++++++++++++++------------------
 5 files changed, 21 insertions(+), 49 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index a84c570..e341730 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -58,4 +58,4 @@ template:
     - ci
     - igenomes
     - nf_core_configs
-  version: 0.5.0
+  version: 0.6.0
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 86eef05..0193d3e 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).
 
-## dev
+## 0.6.0
 
 ### Credits
 
diff --git a/nextflow.config b/nextflow.config
index 151493b..d6086e9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -314,7 +314,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
-    version         = '0.5.0'
+    version         = '0.6.0'
     doi             = ''
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3806fdb..aecb6a3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -149,34 +149,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
-                "validationSkipDuplicateCheck": {
-                    "type": "boolean",
-                    "description": "Do not check samples are not duplicates of each other.",
-                    "help_text": "Allows samples in the samplesheet to be duplicates of each other.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-clone"
-                },
                 "trace_report_suffix": {
                     "type": "string",
                     "fa_icon": "far calendar",
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 5153453..9abb940 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "Stable",
-            "datePublished": "2025-02-26T16:30:32+00:00",
+            "datePublished": "2025-02-26T16:38:08+00:00",
             "description": "# seqeralabs/nf-aggregate\n\n[![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)\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-3.3.0.dev0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.0.dev0)\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/seqeralabs/nf-aggregate)\n\n## Introduction\n\n**seqeralabs/nf-aggregate** is a Nextflow pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform.\n\n<p align=\"center\">\n  <img src=\"assets/multiqc_screenshot.png\" alt=\"MultiQC screenshot\" width=\"75%\"/>\n</p>\n\nThe pipeline performs the following steps:\n\n1. Downloads run information via the Seqera CLI in parallel\n2. Runs MultiQC to aggregate all of the run metrics into a single report\n\nYou can download an example MultiQC report [here](assets/multiqc_report.html).\n\n## Prerequisites\n\n- [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) >=23.10.0\n- Account in [Seqera Platform](https://seqera.io/platform/)\n- [Access token](https://docs.seqera.io/platform/23.3.0/api/overview#authentication) which is your personal authorization token for the Seqera Platform CLI. This can be created in the user menu under **Your tokens**. Export the token as a shell variable directly into your terminal if running the pipelie locally. You will not need to set this if running the pipeline within the Seqera Platform as it will automatically be inherited from the executing environment.\n\n  ```bash\n  export TOWER_ACCESS_TOKEN=<your access token>\n  ```\n\n## Usage\n\nThe primary input to the pipeline is a file containing a list of run identifiers from the Seqera Platform. These can be obtained from details in the runs page for any pipeline execution. For example, we can create a file called `run_ids.csv` with the following contents:\n\n```\nid,workspace\n4Bi5xBK6E2Nbhj,community/showcase\n4LWT4uaXDaGcDY,community/showcase\n38QXz4OfQDpwOV,community/showcase\n2lXd1j7OwZVfxh,community/showcase\n```\n\nThis pipeline can then be executed with the following command:\n\n```\nnextflow run seqeralabs/nf-aggregate \\\n    --input run_ids.csv \\\n    --outdir ./results \\\n    -profile docker\n```\n\nIf you are using a Seqera Platform Enterprise instance that is secured with a private CA SSL certificate not recognized by default Java certificate authorities, you can specify a custom `cacerts` store path through the `--java_truststore_path` parameter and optionally, a password with the `--java_truststore_password`. This certificate will be used to achieve connectivity with your Seqera Platform instance through API and CLI.\n\n### Benchmark reports\n\nIf you want to generate a benchmark report comparing multiple runs, you can include a `group` column in your `run_ids.csv` file. This allows you to organize and analyze runs based on custom groupings in the final report.\n\n```\nid,workspace,group\n3VcLMAI8wyy0Ld,community/showcase,group1\n4VLRs7nuqbAhDy,community/showcase,group2\n```\n\nTo incorporate AWS cost data into the benchmark report, use the benchmark_aws_cur_report parameter. This should point to a valid AWS Cost and Usage Report (CUR) file in Parquet format, supporting both CUR 1.0 and CUR 2.0 schemas. The file can be stored locally or in a cloud bucket. To run nf-aggregate and generate benchmark reports, you can use the following command:\n\n```\nnextflow run seqeralabs/nf-aggregate \\\n    --input run_ids.csv \\\n    --outdir ./results \\\n    --run_benchmark \\\n    --benchmark_aws_cur_report ./aws_cost_report.parquet\n```\n\n## Output\n\nThe results from the pipeline will be published in the path specified by the `--outdir` and will consist of the following contents:\n\n```\n./results\n\u251c\u2500\u2500 multiqc/\n\u2502   \u251c\u2500\u2500 multiqc_data/\n\u2502   \u251c\u2500\u2500 multiqc_plots/\n\u2502   \u2514\u2500\u2500 multiqc_report.html                 ## MultiQC report\n\u251c\u2500\u2500 nf-core_rnaseq/\n\u2502   \u251c\u2500\u2500 gantt/\n\u2502   \u2502   \u2514\u2500\u2500 4Bi5xBK6E2Nbhj_gantt.html       ## Gantt plot for run\n\u2502   \u2514\u2500\u2500 runs_dump/\n\u2502       \u2514\u2500\u2500 4Bi5xBK6E2Nbhj/                 ## Output of 'tw runs dump'\n\u2502           \u251c\u2500\u2500 service-info.json\n\u2502           \u251c\u2500\u2500 workflow-launch.json\n\u2502           \u251c\u2500\u2500 workflow-load.json\n\u2502           \u251c\u2500\u2500 workflow-metrics.json\n\u2502           \u251c\u2500\u2500 workflow-tasks.json\n\u2502           \u2514\u2500\u2500 workflow.json\n\u2514\u2500\u2500 pipeline_info/\n```\n\n> [!NOTE]\n> Gantt plots depend on information derived from the Fusion logs. For that reason, Gantt plots will be ommitted from the pipeline outputs for non-Fusion runs, irrespective of whether the `--skip_run_gantt` parameter has been set.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Credits\n\nnf-aggregate was written by the Scientific Development and MultiQC teams at [Seqera Labs](https://seqera.io/).\n\n## Citations\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\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": [
                 {
@@ -83,7 +83,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#d57e5f05-159d-42cc-ac7d-5688e10bf944"
+                    "@id": "#64e2b660-1df5-45d8-a40a-7f30aaabe575"
                 }
             ],
             "name": "seqeralabs/nf-aggregate"
@@ -112,14 +112,14 @@
             ],
             "creator": [
                 {
-                    "@id": "#rob.syme@gmail.com"
+                    "@id": "#drpatelh@users.noreply.github.com"
                 },
                 {
-                    "@id": "#drpatelh@users.noreply.github.com"
+                    "@id": "#rob.syme@gmail.com"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-02-26T17:30:32Z",
+            "dateModified": "2025-02-26T17:38:08Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -130,10 +130,10 @@
             ],
             "maintainer": [
                 {
-                    "@id": "#rob.syme@gmail.com"
+                    "@id": "#drpatelh@users.noreply.github.com"
                 },
                 {
-                    "@id": "#drpatelh@users.noreply.github.com"
+                    "@id": "#rob.syme@gmail.com"
                 }
             ],
             "name": [
@@ -147,10 +147,10 @@
             },
             "url": [
                 "https://github.com/seqeralabs/nf-aggregate",
-                "https://nf-co.re/seqeralabs/nf-aggregate/0.5.0/"
+                "https://nf-co.re/seqeralabs/nf-aggregate/0.6.0/"
             ],
             "version": [
-                "0.5.0"
+                "0.6.0"
             ]
         },
         {
@@ -166,11 +166,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#d57e5f05-159d-42cc-ac7d-5688e10bf944",
+            "@id": "#64e2b660-1df5-45d8-a40a-7f30aaabe575",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#949b33a0-6b05-4775-9db5-620911520c56"
+                    "@id": "#d46b8e15-0f57-492e-a074-d3dfd14e3ba1"
                 }
             ],
             "mainEntity": {
@@ -179,7 +179,7 @@
             "name": "Test suite for seqeralabs/nf-aggregate"
         },
         {
-            "@id": "#949b33a0-6b05-4775-9db5-620911520c56",
+            "@id": "#d46b8e15-0f57-492e-a074-d3dfd14e3ba1",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing seqeralabs/nf-aggregate",
             "resource": "repos/seqeralabs/nf-aggregate/actions/workflows/ci.yml",
@@ -282,17 +282,17 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
-        {
-            "@id": "#rob.syme@gmail.com",
-            "@type": "Person",
-            "email": "rob.syme@gmail.com",
-            "name": "Rob Syme"
-        },
         {
             "@id": "#drpatelh@users.noreply.github.com",
             "@type": "Person",
             "email": "drpatelh@users.noreply.github.com",
             "name": "Harshil Patel"
+        },
+        {
+            "@id": "#rob.syme@gmail.com",
+            "@type": "Person",
+            "email": "rob.syme@gmail.com",
+            "name": "Rob Syme"
         }
     ]
 }
\ No newline at end of file

From 97b06bdadfdc34486ff2a11fb92cff31b931f98d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:44:08 +0100
Subject: [PATCH 06/20] update GHA

---
 .github/workflows/ci.yml      |  2 +-
 .github/workflows/linting.yml | 35 +++++++++++++++++++++++++----------
 2 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 78f57e6..842a9a8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,7 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFT_VER: "0.8.4"
+  NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index cec9ccb..a502573 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
-name: nf-aggregate linting
+name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -31,27 +31,42 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@2.14.1
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
@@ -59,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

From 9f9ce7f5f4e1230eacf0be6e70010ce1b738aea1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:45:27 +0100
Subject: [PATCH 07/20] fix nf-core tools version

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index e341730..ddca0fc 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -43,7 +43,7 @@ lint:
     - process.time
   pipeline_name_conventions: false
   schema_lint: false
-nf_core_version: 3.3.0.dev0
+nf_core_version: 3.3.0
 repository_type: pipeline
 template:
   author: SciDev Team, Seqera

From fbe0067b4a2b69f11660135252510eab86e449c5 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:46:58 +0100
Subject: [PATCH 08/20] REALLY fix nf-core tools version

---
 .nf-core.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index ddca0fc..d618ac6 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -43,7 +43,7 @@ lint:
     - process.time
   pipeline_name_conventions: false
   schema_lint: false
-nf_core_version: 3.3.0
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: SciDev Team, Seqera

From 334dfe41d5be6221f08a6dd40d3833a3377640b0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:49:50 +0100
Subject: [PATCH 09/20] use file from 3.2.0

---
 .prettierrc.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.prettierrc.yml b/.prettierrc.yml
index 07dbd8b..c81f9a7 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1,6 +1 @@
 printWidth: 120
-tabWidth: 4
-overrides:
-  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
-    options:
-      tabWidth: 2

From 693d2837e8e7f2795ef8dc884d3e7835f95eac1d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 17:52:12 +0100
Subject: [PATCH 10/20] fix author

---
 .nf-core.yml    | 2 +-
 nextflow.config | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index d618ac6..e19fb5b 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -46,7 +46,7 @@ lint:
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:
-  author: SciDev Team, Seqera
+  author: SciDev Team
   description: Pipeline to aggregate pertinent metrics across pipeline runs on the
     Seqera Platform.
   force: false
diff --git a/nextflow.config b/nextflow.config
index d6086e9..23bfe35 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -226,6 +226,7 @@ dag {
 
 manifest {
     name            = 'seqeralabs/nf-aggregate'
+    author          = 'SciDev Team'
     contributors    = [
         // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [

From 08d643a55f12016519576ab34325aa58ceaa05bc Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 18:02:03 +0100
Subject: [PATCH 11/20] langage server + @maxulysse code polish

---
 subworkflows/local/utils_nf_aggregate/main.nf | 13 ++--
 workflows/nf_aggregate/main.nf                | 64 +++++++++----------
 2 files changed, 39 insertions(+), 38 deletions(-)

diff --git a/subworkflows/local/utils_nf_aggregate/main.nf b/subworkflows/local/utils_nf_aggregate/main.nf
index c04e321..92cf80d 100644
--- a/subworkflows/local/utils_nf_aggregate/main.nf
+++ b/subworkflows/local/utils_nf_aggregate/main.nf
@@ -12,10 +12,10 @@ import java.nio.file.Paths
 ========================================================================================
 */
 
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline/main'
-include { getWorkflowVersion        } from '../../nf-core/utils_nextflow_pipeline/main'
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin/main.nf'
-include { samplesheetToList }         from 'plugin/nf-schema'
+include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
+include { getWorkflowVersion      } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
+include { samplesheetToList       } from 'plugin/nf-schema'
 
 /*
 ========================================================================================
@@ -43,7 +43,8 @@ workflow PIPELINE_INITIALISATION {
     def pre_help_text = ''
     def post_help_text = ''
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.txt --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
+
+    UTILS_NFSCHEMA_PLUGIN (
         params.help,
         workflow_command,
         pre_help_text,
@@ -59,7 +60,7 @@ workflow PIPELINE_INITIALISATION {
         .set { ch_ids }
 
     emit:
-    ids            = ch_ids
+    ids = ch_ids
 }
 
 /*
diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
index 5c955f4..9d662dc 100644
--- a/workflows/nf_aggregate/main.nf
+++ b/workflows/nf_aggregate/main.nf
@@ -2,26 +2,25 @@
 // WORKFLOW: Run main seqeralabs/nf-aggregate workflow
 //
 
-include { SEQERA_RUNS_DUMP     } from '../../modules/local/seqera_runs_dump'
+include { BENCHMARK_REPORT     } from '../../modules/local/benchmark_report'
 include { PLOT_RUN_GANTT       } from '../../modules/local/plot_run_gantt'
+include { SEQERA_RUNS_DUMP     } from '../../modules/local/seqera_runs_dump'
 include { MULTIQC              } from '../../modules/nf-core/multiqc'
-include { BENCHMARK_REPORT     } from '../../modules/local/benchmark_report'
-include { paramsSummaryMultiqc } from '../../subworkflows/local/utils_nf_aggregate'
 include { getProcessVersions   } from '../../subworkflows/local/utils_nf_aggregate'
 include { getWorkflowVersions  } from '../../subworkflows/local/utils_nf_aggregate'
+include { paramsSummaryMultiqc } from '../../subworkflows/local/utils_nf_aggregate'
 include { paramsSummaryMap     } from 'plugin/nf-schema'
 
 workflow NF_AGGREGATE {
-
     take:
-    ids                       // channel: run ids read in from --input
-    multiqc_custom_config     // channel: user specified custom config file used by MultiQC
-    multiqc_logo              // channel: logo rendered in MultiQC report
-    seqera_api_endpoint       //     val: Seqera Platform API endpoint URL
-    skip_run_gantt            //     val: Skip GANTT chart creation for each run
-    skip_multiqc              //     val: Skip MultiQC
-    java_truststore_path      //     val: Path to java truststore if using private certs
-    java_truststore_password  //     val: Password for java truststore if using private certs
+    ids                      // channel: run ids read in from --input
+    multiqc_custom_config    // channel: user specified custom config file used by MultiQC
+    multiqc_logo             // channel: logo rendered in MultiQC report
+    seqera_api_endpoint      //     val: Seqera Platform API endpoint URL
+    skip_run_gantt           //     val: Skip GANTT chart creation for each run
+    skip_multiqc             //     val: Skip MultiQC
+    java_truststore_path     //     val: Path to java truststore if using private certs
+    java_truststore_password //     val: Password for java truststore if using private certs
 
     main:
 
@@ -32,27 +31,24 @@ workflow NF_AGGREGATE {
     // MODULE: Fetch run information via the Seqera CLI
     //
 
-    SEQERA_RUNS_DUMP (
+    SEQERA_RUNS_DUMP(
         ids,
         seqera_api_endpoint,
         java_truststore_path ?: '',
-        java_truststore_password ?: ''
+        java_truststore_password ?: '',
     )
     ch_versions = ch_versions.mix(SEQERA_RUNS_DUMP.out.versions.first())
 
     //
     // MODULE: Generate Gantt chart for workflow execution
     //
-    SEQERA_RUNS_DUMP
-        .out
-        .run_dump
-        .filter {
-            meta, run_dir ->
-                meta.fusion && !params.skip_run_gantt
+    SEQERA_RUNS_DUMP.out.run_dump
+        .filter { meta, run_dir ->
+            meta.fusion && !skip_run_gantt
         }
-        .set { ch_runs_for_gantt }
+        .set {  -> ch_runs_for_gantt }
 
-    PLOT_RUN_GANTT (
+    PLOT_RUN_GANTT(
         ch_runs_for_gantt
     )
     ch_versions = ch_versions.mix(PLOT_RUN_GANTT.out.versions.first())
@@ -63,11 +59,11 @@ workflow NF_AGGREGATE {
     if (params.generate_benchmark_report) {
         aws_cur_report = params.benchmark_aws_cur_report ? Channel.fromPath(params.benchmark_aws_cur_report) : []
 
-        BENCHMARK_REPORT (
-            SEQERA_RUNS_DUMP.out.run_dump.collect{it[1]},
-            SEQERA_RUNS_DUMP.out.run_dump.collect{it[0].group},
+        BENCHMARK_REPORT(
+            SEQERA_RUNS_DUMP.out.run_dump.collect {  -> it[1] },
+            SEQERA_RUNS_DUMP.out.run_dump.collect {  -> it[0].group },
             aws_cur_report,
-            params.remove_failed_tasks
+            params.remove_failed_tasks,
         )
         ch_versions = ch_versions.mix(BENCHMARK_REPORT.out.versions)
     }
@@ -77,28 +73,32 @@ workflow NF_AGGREGATE {
     //
     ch_versions
         .unique()
-        .map { getProcessVersions(it) }
+        .map {  -> getProcessVersions(it) }
         .mix(Channel.of(getWorkflowVersions()))
         .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'collated_software_mqc_versions.yml', newLine: true)
-        .set { ch_collated_versions }
+        .set {  -> ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
     ch_multiqc_report = Channel.empty()
     if (!skip_multiqc) {
-        ch_multiqc_config = Channel.fromPath("$projectDir/workflows/nf_aggregate/assets/multiqc_config.yml", checkIfExists: true)
+        ch_multiqc_config = Channel.fromPath("${projectDir}/workflows/nf_aggregate/assets/multiqc_config.yml", checkIfExists: true)
         summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
         ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
-        ch_multiqc_files = ch_multiqc_files.mix(SEQERA_RUNS_DUMP.out.run_dump.collect{it[1]})
-        MULTIQC (
+        ch_multiqc_files = ch_multiqc_files.mix(SEQERA_RUNS_DUMP.out.run_dump.collect {  -> it[1] })
+
+        MULTIQC(
             ch_multiqc_files.collect(),
             ch_multiqc_config.toList(),
             multiqc_custom_config.toList(),
-            multiqc_logo.toList()
+            multiqc_logo.toList(),
+            [],
+            [],
         )
+
         ch_multiqc_report = MULTIQC.out.report
     }
 

From 9c20761905a471dde3640dfb06c9bc178320c39e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 18:04:28 +0100
Subject: [PATCH 12/20] no need for first()

---
 workflows/nf_aggregate/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
index 9d662dc..aaa5819 100644
--- a/workflows/nf_aggregate/main.nf
+++ b/workflows/nf_aggregate/main.nf
@@ -37,7 +37,7 @@ workflow NF_AGGREGATE {
         java_truststore_path ?: '',
         java_truststore_password ?: '',
     )
-    ch_versions = ch_versions.mix(SEQERA_RUNS_DUMP.out.versions.first())
+    ch_versions = ch_versions.mix(SEQERA_RUNS_DUMP.out.versions)
 
     //
     // MODULE: Generate Gantt chart for workflow execution
@@ -51,7 +51,7 @@ workflow NF_AGGREGATE {
     PLOT_RUN_GANTT(
         ch_runs_for_gantt
     )
-    ch_versions = ch_versions.mix(PLOT_RUN_GANTT.out.versions.first())
+    ch_versions = ch_versions.mix(PLOT_RUN_GANTT.out.versions)
 
     //
     // MODULE: Generate benchmark report

From 1caf696e71c5dc5cc2317aea58c3985f707a19bd Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 18:16:48 +0100
Subject: [PATCH 13/20] update CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0193d3e..33876ff 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,7 +21,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #73](https://github.com/seqeralabs/nf-aggregate/pull/73) - Add process for generating Benchmark reports
 - [PR #74](https://github.com/seqeralabs/nf-aggregate/pull/74) - Add process for generating Benchmark reports
 - [PR #75](https://github.com/seqeralabs/nf-aggregate/pull/75) - Skip failed jobs in benchmarking report
-- [PR #76](https://github.com/seqeralabs/nf-aggregate/pull/76) - Sync with nf-core tools 3.2.0
+- [PR #78](https://github.com/seqeralabs/nf-aggregate/pull/78) - Sync with nf-core tools 3.2.0
 
 ## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-11-12
 

From 1a280d629066366502c1f5ba38061a990f4a117a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 18:28:39 +0100
Subject: [PATCH 14/20] fix INITIALISATION

---
 main.nf                                       | 21 +++++++--------
 subworkflows/local/utils_nf_aggregate/main.nf | 27 ++++++++-----------
 2 files changed, 21 insertions(+), 27 deletions(-)

diff --git a/main.nf b/main.nf
index 3d354e1..33a5d4c 100644
--- a/main.nf
+++ b/main.nf
@@ -13,8 +13,6 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-ch_multiqc_logo          = params.multiqc_logo   ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.fromPath("$projectDir/assets/seqera_logo_colour.png", checkIfExists: true )
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -29,16 +27,23 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nf_aggregat
 // WORKFLOW: Execute a single named workflow for the pipeline
 //
 workflow {
+    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.fromPath("${projectDir}/assets/seqera_logo_colour.png", checkIfExists: true)
 
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
-    PIPELINE_INITIALISATION ()
+    PIPELINE_INITIALISATION(
+        params.version,
+        params.validate_params,
+        params.outdir,
+        params.input,
+    )
 
     //
     // WORKFLOW: Run primary workflows for the pipeline
     //
-    NF_AGGREGATE (
+    NF_AGGREGATE(
         PIPELINE_INITIALISATION.out.ids,
         ch_multiqc_custom_config,
         ch_multiqc_logo,
@@ -46,12 +51,6 @@ workflow {
         params.skip_run_gantt,
         params.skip_multiqc,
         params.java_truststore_path,
-        params.java_truststore_password
+        params.java_truststore_password,
     )
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
diff --git a/subworkflows/local/utils_nf_aggregate/main.nf b/subworkflows/local/utils_nf_aggregate/main.nf
index 92cf80d..4951320 100644
--- a/subworkflows/local/utils_nf_aggregate/main.nf
+++ b/subworkflows/local/utils_nf_aggregate/main.nf
@@ -24,6 +24,11 @@ include { samplesheetToList       } from 'plugin/nf-schema'
 */
 
 workflow PIPELINE_INITIALISATION {
+    take:
+    version           // boolean: Display version and exit
+    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
+    outdir            //  string: The output directory where the results will be saved
+    input             //  string: Path to input samplesheet
 
     main:
 
@@ -31,31 +36,21 @@ workflow PIPELINE_INITIALISATION {
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
     UTILS_NEXTFLOW_PIPELINE (
-        params.version,
+        version,
         true,
-        params.outdir,
+        outdir,
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-    //
-    // Validate parameters and generate parameter summary to stdout
-    //
-    def pre_help_text = ''
-    def post_help_text = ''
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.txt --outdir <OUTDIR>"
-
     UTILS_NFSCHEMA_PLUGIN (
-        params.help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
-        params.validate_params,
-        "nextflow_schema.json"
+        workflow,
+        validate_params,
+        null
     )
 
     // Read in ids from --input file
     Channel
-        .fromList(samplesheetToList(params.input, "assets/schema_input.json"))
+        .fromList(samplesheetToList(input, "assets/schema_input.json"))
         .flatten()
         .set { ch_ids }
 

From 029c9a14521d5557dad47152f3132d3a111b34f0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 18:43:24 +0100
Subject: [PATCH 15/20] fix tests

---
 subworkflows/local/utils_nf_aggregate/tests/main.nf.test | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
index 77d5de7..953376e 100644
--- a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
+++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
@@ -15,10 +15,17 @@ nextflow_workflow {
     test("Should run without failures") {
 
         when {
+            params {
+                outdir = "$outputDir"
+                }
+
             workflow {
                 """
                 // define inputs of the workflow here. Example:
-                // input[0] = file("test-file.txt")
+                input[0] = false
+                input[1] = false
+                input[2] = params.outdir
+                input[3] = "${projectDir}/workflows/nf_aggregate/assets/test_run_ids.csv"
                 """
             }
         }

From 2dcee33fca3b60f6e8eaec6d5a4a9e66c42f9114 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 18:55:48 +0100
Subject: [PATCH 16/20] remove stabby operator from langage server

---
 workflows/nf_aggregate/main.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
index aaa5819..ea75eee 100644
--- a/workflows/nf_aggregate/main.nf
+++ b/workflows/nf_aggregate/main.nf
@@ -43,10 +43,10 @@ workflow NF_AGGREGATE {
     // MODULE: Generate Gantt chart for workflow execution
     //
     SEQERA_RUNS_DUMP.out.run_dump
-        .filter { meta, run_dir ->
+        .filter { meta, _run_dir ->
             meta.fusion && !skip_run_gantt
         }
-        .set {  -> ch_runs_for_gantt }
+        .set { ch_runs_for_gantt }
 
     PLOT_RUN_GANTT(
         ch_runs_for_gantt
@@ -60,8 +60,8 @@ workflow NF_AGGREGATE {
         aws_cur_report = params.benchmark_aws_cur_report ? Channel.fromPath(params.benchmark_aws_cur_report) : []
 
         BENCHMARK_REPORT(
-            SEQERA_RUNS_DUMP.out.run_dump.collect {  -> it[1] },
-            SEQERA_RUNS_DUMP.out.run_dump.collect {  -> it[0].group },
+            SEQERA_RUNS_DUMP.out.run_dump.collect { it[1] },
+            SEQERA_RUNS_DUMP.out.run_dump.collect { it[0].group },
             aws_cur_report,
             params.remove_failed_tasks,
         )
@@ -73,10 +73,10 @@ workflow NF_AGGREGATE {
     //
     ch_versions
         .unique()
-        .map {  -> getProcessVersions(it) }
+        .map { getProcessVersions(it) }
         .mix(Channel.of(getWorkflowVersions()))
         .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'collated_software_mqc_versions.yml', newLine: true)
-        .set {  -> ch_collated_versions }
+        .set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
@@ -88,7 +88,7 @@ workflow NF_AGGREGATE {
         ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
-        ch_multiqc_files = ch_multiqc_files.mix(SEQERA_RUNS_DUMP.out.run_dump.collect {  -> it[1] })
+        ch_multiqc_files = ch_multiqc_files.mix(SEQERA_RUNS_DUMP.out.run_dump.collect { it[1] })
 
         MULTIQC(
             ch_multiqc_files.collect(),

From 62d6944d9db9f642571a3463c129fd4f0f28814a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Feb 2025 19:04:36 +0100
Subject: [PATCH 17/20] update CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 33876ff..795b35a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,11 +13,13 @@ Special thanks to the following for their contributions to the release:
 - [Edmund Miller](https://github.com/edmundmiller)
 - [Florian Wuennemann](https://github.com/FloWuenne)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
+- [PR #71](https://github.com/seqeralabs/nf-aggregate/pull/71) - Reduce stuttering in nextflow_schema.json
 - [PR #73](https://github.com/seqeralabs/nf-aggregate/pull/73) - Add process for generating Benchmark reports
 - [PR #74](https://github.com/seqeralabs/nf-aggregate/pull/74) - Add process for generating Benchmark reports
 - [PR #75](https://github.com/seqeralabs/nf-aggregate/pull/75) - Skip failed jobs in benchmarking report

From 9724c4969e47970980ad19258587fa6f2484b989 Mon Sep 17 00:00:00 2001
From: Florian Wuennemann <flowuenne@gmail.com>
Date: Wed, 26 Feb 2025 14:50:00 -0500
Subject: [PATCH 18/20] Update CHANGELOG.md

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 795b35a..c6df445 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,7 +20,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [PR #71](https://github.com/seqeralabs/nf-aggregate/pull/71) - Reduce stuttering in nextflow_schema.json
-- [PR #73](https://github.com/seqeralabs/nf-aggregate/pull/73) - Add process for generating Benchmark reports
 - [PR #74](https://github.com/seqeralabs/nf-aggregate/pull/74) - Add process for generating Benchmark reports
 - [PR #75](https://github.com/seqeralabs/nf-aggregate/pull/75) - Skip failed jobs in benchmarking report
 - [PR #78](https://github.com/seqeralabs/nf-aggregate/pull/78) - Sync with nf-core tools 3.2.0

From 8e9b33c11a412ab4c65c0b882805ad83175f0a85 Mon Sep 17 00:00:00 2001
From: Florian Wuennemann <flowuenne@gmail.com>
Date: Wed, 26 Feb 2025 15:52:10 -0500
Subject: [PATCH 19/20] Update nextflow.config

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 23bfe35..b20d022 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -228,7 +228,6 @@ manifest {
     name            = 'seqeralabs/nf-aggregate'
     author          = 'SciDev Team'
     contributors    = [
-        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
             name: 'SciDev Team',
             affiliation: 'Seqera',

From 2966417ad444a06bfdea0f1df802c6d6bf7335fc Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.miller@seqera.io>
Date: Wed, 26 Feb 2025 15:25:50 -0600
Subject: [PATCH 20/20] fix: Add quotes around author

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index b20d022..f14bfca 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -233,7 +233,7 @@ manifest {
             affiliation: 'Seqera',
             email: '',
             github: '',
-            contribution: [author],
+            contribution: ['author'],
             orcid: ''
         ],
         [