diff --git a/Poster SWAT4HCLS.pdf b/Poster SWAT4HCLS.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..adec009a0871ab59aa1b1f08cebe1d63e7751b9b
Binary files /dev/null and b/Poster SWAT4HCLS.pdf differ
diff --git a/README.md b/README.md
index 00caf69729489d03aa966efae985767405b06970..d286e58b408ff038b715bd2c819d4a2eedd725fa 100644
--- a/README.md
+++ b/README.md
@@ -1,93 +1,289 @@
# SWAT4HCLS 2024
+# Workflow RO-Crate profile 2.0
+> This README provides an overview of the poster created and presented at the [SWAT4HCLS 2024](https://www.swat4ls.org/) conference. The poster can be found in the `poster.pdf` file specified at the root.
-## Getting started
+> This README is highly inspired by [this page](https://about.workflowhub.eu/Workflow-RO-Crate/) which describes the *Workflow RO-Crate profile 1.0* and [this page](https://www.researchobject.org/ro-crate/1.1/workflows.html).
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+* Authors:
+ * [George Marchment](https://orcid.org/0000-0002-4565-3940)
+ * Marie Schmit
+* Title: Workflow RO-Crate profile 2.0
+* Version: 2.0
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+_Workflow RO-Crates_ are a specialization of [_RO-Crate_](https://researchobject.github.io/ro-crate/) for packaging an executable workflow with all necessary documentation. It extends the more general [Bioschemas ComputationalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE).
-## Add your files
+## Table of Contents
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+- [SWAT4HCLS 2024](#swat4hcls-2024)
+- [Workflow RO-Crate profile 2.0](#workflow-ro-crate-profile-20)
+ - [Table of Contents](#table-of-contents)
+ - [Concepts](#concepts)
+ - [Context](#context)
+ - [Metadata File Descriptor](#metadata-file-descriptor)
+ - [Main Workflow File](#main-workflow-file)
+ - [Main Workflow](#main-workflow)
+ - [Subworkflow](#subworkflow)
+ - [Process](#process)
+ - [Describing inputs and outputs](#describing-inputs-and-outputs)
+ - [Complete Workflow Example](#complete-workflow-example)
-```
-cd existing_repo
-git remote add origin https://gitlab.liris.cnrs.fr/sharefair/posters/swat4hcls-2024.git
-git branch -M main
-git push -uf origin main
-```
+## Concepts
-## Integrate with your tools
+This section uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1).
-- [ ] [Set up project integrations](https://gitlab.liris.cnrs.fr/sharefair/posters/swat4hcls-2024/-/settings/integrations)
+### Context
-## Collaborate with your team
+The _Crate_ JSON-LD MUST be valid according to [RO-Crate 1.1](https://w3id.org/ro/crate/1.1) and SHOULD use the RO-Crate 1.1 `@context` [https://w3id.org/ro/crate/1.1/context](https://w3id.org/ro/crate/1.1/context)
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
+### Metadata File Descriptor
-## Test and Deploy
+The [Metadata File Descriptor](https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#ro-crate-metadata-file-descriptor) `conformsTo` SHOULD be an array that contains at least [https://w3id.org/ro/crate/1.1](https://w3id.org/ro/crate/1.1) and [https://w3id.org/workflowhub/workflow-ro-crate/1.0](https://w3id.org/workflowhub/workflow-ro-crate/1.0)
-Use the built-in continuous integration in GitLab.
+### Main Workflow File
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
+The _Crate_ MUST contain a data entity of type `["File", "SoftwareSourceCode"]` as the _Main Workflow File_ entry point. This is the file which contains the main of the workflow.
-***
+The _Crate_ MUST refer to the _Main Workflow_ via `mainEntity`.
-# Editing this README
+The _Main Workflow File_ MUST refers to all the elements which are defined in the file.
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
+### Main Workflow
-## Suggestions for a good README
+The _Main Workflow File_ refers to the data entity *Main Workflow* of type `["SoftwareSourceCode", "ComputationalWorkflow"]`. This is the entity which describes the main of the workflow.
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+The _Main Workflow_ MUST refers to all the elements which are called in the main.
-## Name
-Choose a self-explaining name for your project.
+### Subworkflow
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+The *Subworkflow* entity is essentially a specialised version of the *Main Workflow*. The only difference is that instead of describing the main of the workflow, it describes the subworkflow.
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+The _Subworkflow_ MUST refers to all the elements which are called in the subworkflow.
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
+### Process
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
+The *Process* entity describes an individual step of a workflow. Depending on the workflow system used, it can be interchanged with *Module* or *Rule*. Its type is `["SoftwareSourceCode", "Script"]`.
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+The _Process_ MUST refers to all the tools which are used.
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
+### Describing inputs and outputs
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+The input and output _parameters_ for a *Subworkflow* or *Process* can be given with `input` and `output` to [FormalParameter](https://bioschemas.org/types/FormalParameter/0.1-DRAFT-2020_07_21) contextual entities. Note that this entity usually represent a _potential_ input/output value in a reusable workflow, much like [function parameter definitions](https://en.wikipedia.org/wiki/Parameter_(computer_programming)) in general programming.
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+If complying with the Bioschemas [FormalParameter profile](https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21), the _contextual entities_ for [FormalParameter](https://bioschemas.org/types/FormalParameter/0.1-DRAFT-2020_07_21), referenced by `input` or `output`, MUST describe: [name](http://schema.org/name), [additionalType](http://schema.org/additionalType), [encodingFormat](http://schema.org/encodingFormat)
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
+The Bioschemas [FormalParameter profile](https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21) explains the above and lists additional properties that can be used, including [description](http://schema.org/description), [valueRequired](http://schema.org/valueRequired), [defaultValue](http://schema.org/defaultValue) and [identifier](http://schema.org/identifier).
-## License
-For open source projects, say how it is licensed.
+A contextual entity conforming to the [FormalParameter profile](https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21) SHOULD declare the versioned profile URI using [conformsTo](http://purl.org/dc/terms/conformsTo), e.g.:
+
+```json
+{
+ "@id": "#36aadbd4-4a2d-4e33-83b4-0cbf6a6a8c5b",
+ "@type": "FormalParameter",
+ "conformsTo":
+ {"@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/"},
+ "..": ""
+}
+```
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+> `input`, `output` and `FormalParameter` are at time of writing proposed by Bioschemas and not yet integrated in Schema.org
+
+## Complete Workflow Example
+
+```json
+{
+ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@id": "ro-crate-metadata-exampleWF.json",
+ "@type": "CreativeWork",
+ "about": {
+ "@id": "./"
+ },
+ "conformsTo": [
+ {
+ "@id": "https://w3id.org/ro/crate/1.1"
+ }
+ ]
+ },
+ {
+ "@id": "./",
+ "@type": "Dataset",
+ "name": "exampleWF",
+ "datePublished": "2024-02-19",
+ "description": "Description of ExampleWF",
+ "mainEntity": {
+ "@id": "main.nf"
+ },
+ "license": {
+ "@id": "mit"
+ },
+ "author": [
+ {
+ "@id": "George"
+ }
+ ],
+ "maintainer": [
+ {
+ "@id": "George"
+ }
+ ],
+ "hasPart": [
+ {
+ "@id": "main.nf"
+ },
+ {
+ "@id": "sub.nf"
+ },
+ {
+ "@id": "main.nf",
+ "name": "main.nf",
+ "@type": [
+ "File",
+ "SoftwareSourceCode"
+ ],
+ "programmingLanguage": {
+ "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+ },
+ "contentSize": 1.718,
+ "dateCreated": "2024-02-19",
+ "dateModified": "2024-02-19",
+ "creator": [
+ {
+ "@id": "George"
+ }
+ ],
+ "isPartOf": [],
+ "hasPart": [
+ {
+ "@id": "sub.nf"
+ },
+ {
+ "@id": "main.nf/MAIN"
+ }
+ ]
+ },
+ {
+ "@id": "sub.nf",
+ "name": "sub.nf",
+ "@type": [
+ "File",
+ "SoftwareSourceCode"
+ ],
+ "programmingLanguage": {
+ "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+ },
+ "contentSize": 6.114,
+ "dateCreated": "2024-02-19",
+ "dateModified": "2024-02-19",
+ "creator": [
+ {
+ "@id": "George"
+ }
+ ],
+ "isPartOf": [
+ {
+ "@id": "main.nf"
+ }
+ ],
+ "hasPart": [
+ {
+ "@id": "sub.nf/subworkflow"
+ },
+ {
+ "@id": "sub.nf/process"
+ }
+ ]
+ },
+ {
+ "@id": "sub.nf/subworkflow",
+ "name": "Subworkflow",
+ "@type": [
+ "SoftwareSourceCode",
+ "ComputationalWorkflow"
+ ],
+ "input": [],
+ "output": [],
+ "isPartOf": [
+ {
+ "@id": "sub.nf"
+ }
+ ],
+ "hasPart": [
+ {
+ "@id": "sub.nf/process"
+ }
+ ]
+ },
+ {
+ "@id": "sub.nf/process",
+ "name": "Process",
+ "@type": [
+ "SoftwareSourceCode",
+ "Script"
+ ],
+ "input": [
+ {
+ "@id": "in"
+ }
+ ],
+ "output": [
+ {
+ "@id": "out"
+ }
+ ],
+ "isPartOf": [
+ {
+ "@id": "sub.nf"
+ },
+ {
+ "@id": "sub.nf/subworkflow"
+ }
+ ],
+ "hasPart": [
+ {
+ "@id": "tool1"
+ }
+ ]
+ },
+ {
+ "@id": "in",
+ "@type": "FormalParameter"
+ },
+ {
+ "@id": "out",
+ "@type": "FormalParameter"
+ },
+ {
+ "@id": "tool1",
+ "name": "Tool",
+ "url": "https://some-url.org"
+ },
+ {
+ "@id": "main.nf/MAIN",
+ "name": "Main Workflow",
+ "@type": [
+ "SoftwareSourceCode",
+ "ComputationalWorkflow"
+ ],
+ "input": [],
+ "output": [],
+ "isPartOf": [
+ {
+ "@id": "main.nf"
+ }
+ ],
+ "hasPart": [
+ {
+ "@id": "sub.nf/subworkflow"
+ }
+ ]
+ }
+ ]
+ }
+ ]
+}
+```
\ No newline at end of file