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2 changes: 1 addition & 1 deletion About-WorkflowHub.md
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* [WorkflowHub](https://workflowhub.eu) is a new workflow registry designed around [FAIR principles](https://workflows.community/groups/fair/).
* WorkflowHub allows workflows to be FAIR, citable, have managed *metadata* profiles, and be openly available for review and analytics.
* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more.
* Workflows are packaged, registered, downloaded and exchanged as [workflow-centric Research Objects](/Workflow-RO-Crate/) using the [RO-Crate](https://w3id.org/ro/crate) specification, with test and example data, managed metadata profiles, citations and more.
* A [schema.org](https://schema.org/) based Bioschemas profile describes the metadata about a workflow and use of the [Common Workflow Language](https://www.commonwl.org/) is encouraged, providing a canonical description of the workflow itself.
* Popular workflow management systems such as [Galaxy](https://galaxyproject.org/), [Nextflow](https://nextflow.io/), and [Snakemake](https://snakemake.readthedocs.io/) are working with the Hub to seamlessly and automatically support object packaging, registration and exchange.
* WorkflowHub is *workflow management system agnostic*: workflows may remain in their native repositories in their native forms.
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4 changes: 3 additions & 1 deletion How-to-join-a-team.md
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---
title: Joining and creating WorkflowHub teams
redirect_from:
- /How-to-join-a-project/
---

# Terminology
Expand Down Expand Up @@ -52,4 +54,4 @@ Once submitted, relevant administrators will be notified who will then review an

If you are creating a Team within a Space you administer, then there is no approval step. You will be shown a page to review the details and then can create straight away.

Otherwise, an appropriate administrator will be notified by email about your request. They will also be notified directly within WorkflowHub. The administrator will be shown a page that allows them to quickly review the details and either accept or reject the request, and in either case you will be notified by email. During the working day (according to the timezone of the member notified) this will normally be a quick process.
Otherwise, an appropriate administrator will be notified by email about your request. They will also be notified directly within WorkflowHub. The administrator will be shown a page that allows them to quickly review the details and either accept or reject the request, and in either case you will be notified by email. During the working day (according to the timezone of the member notified) this will normally be a quick process.
6 changes: 3 additions & 3 deletions How-to-make-a-workflow-RO-crate.md
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title: How to make a workflow RO-crate?
---

More info about workflow RO-crate specification can be found in our [Workflow-RO-Crate](../Workflow-RO-Crate) section.
More info about workflow RO-crate specification can be found in our [Workflow-RO-Crate](Workflow-RO-Crate/index.md) section.

### 1. Using the WorkflowHub website

The most convenient way to make a workflow RO-crate at this moment is by making use of WorkflowHub capabilities. The website is able to generate RO-crates based on an uploaded/referenced workflow file and some general metadata that is requested through a form. After the workflow is registered (click [here](../How-to-register-your-workflow%28s%29-in-WorkflowHub) for more info about this topic) it is possible to download the RO-crate with the download button. The generated RO-crate, basically a zip file, will contain these elements:
The most convenient way to make a workflow RO-crate at this moment is by making use of WorkflowHub capabilities. The website is able to generate RO-crates based on an uploaded/referenced workflow file and some general metadata that is requested through a form. After the workflow is [registered](How-to-register-your-workflow(s)-in-WorkflowHub.md) for more info about this topic) it is possible to download the RO-crate with the download button. The generated RO-crate, basically a zip file, will contain these elements:

- **JSONLD file**\
JSONLD serving machine readable metadata including:
Expand Down Expand Up @@ -42,4 +42,4 @@ The most convenient way to make a workflow RO-crate at this moment is by making
### 2. Making one offline yourself

We are working on a python package at this moment to wrap your own RO-crates. This will allow you to not be bounded by the file limitations of the WorkflowHub website (workflow + CWL abstract and/or diagram), and will make it possible to automate the RO-Crate generation.
The python package can be found in this [repo](https://github.com/ResearchObject/ro-crate-py).
The python package can be found in [ResearchObject/ro-crate-py](https://github.com/ResearchObject/ro-crate-py).
13 changes: 6 additions & 7 deletions How-to-register-your-workflow(s)-in-WorkflowHub.md
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Expand Up @@ -5,16 +5,15 @@ tite: How to register your workflow(s) in WorkflowHub?
### Prerequisites

Before you register a workflow, you need to ensure that you
* are [logged into](../Logging-in) WorkflowHub
* are part of a suited project for your registration (Find more information on how to join a project [here](../How-to-join-a-project))
* are [logged into](Logging-in.md) WorkflowHub
* are part of a suited team for your registration (Find more information on how to [join a team](How-to-join-a-team.md))
* know the type of the workflow
* have decided which [projects](../Browsing-projects) to assign the workflow to

### Get started

To register a workflow, you can either click on the "contribute" icon on the WorkflowHub homepage, or in the "Workflow" option of the "Create" menu from any page of the application.

![](images/ug_link_to_wf_upload.PNG)
![](/images/ug_link_to_wf_upload.PNG)


### Supported workflow types
Expand Down Expand Up @@ -76,14 +75,14 @@ It is also possible to upload workflows from another type (for ex. bash scripts)

After clicking on the "Contribute" icon or selecting "Create" and then "Workflow" from the navigation menu bar, you have 2 options for registering your workflow. For more information on the these options, please go to the corresponding pages:

#### - [The simple and recommended way: registering a workflow-file](../Registering-a-workflow-with-a-diagram-and-abstract-CWL)
#### - [The simple and recommended way: registering a workflow-file](Registering-a-workflow-with-a-diagram-and-abstract-CWL.md)

Using the UI of WorkflowHub you upload or reference a workflow file along with optionally a CWL Description and/or a diagram.

#### - [The advanced way: registering a workflow RO-crate](../Registering-an-existing-Workflow-RO-Crate)
#### - [The advanced way: registering a workflow RO-crate](Registering-an-existing-Workflow-RO-Crate.md)

When you have created a workflow RO-crate of your workflow using the [python package](https://github.com/ResearchObject/ro-crate-py), and want to upload or reference it.

#### - [In development] Registering a workflow RO-crate using the API

We are working on a WorkflowHub API that will allow the user to automatically register workflow RO-crates. Not all features are yet developed, but a glimpse of the API can be found [here](https://workflowhub.eu/api).
We are working on a WorkflowHub API that will allow the user to automatically register workflow RO-crates. Not all features are yet developed, but have a glimpse of the [API documentation](https://workflowhub.eu/api).
6 changes: 3 additions & 3 deletions How-to-register.md
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---

> Which WorkflowHub instance?
> * Use <https://dev.workflowhub.eu/> for testing - this testing instance may occasionally be wiped
> * (TODO) Use <http://covid19.workflowhub.eu/> for long-lived workflow registrations - this will become the production instance
> * Use <https://dev.workflowhub.eu/> for testing - this _testing instance_ may occasionally be wiped
> * Use <https://workflowhub.eu/> for actual workflow registrations - this is the _production instance_
In order to register yourself in WorkflowHub, you need to click Register button in the top right hand corner of WorkflowHub.

Expand All @@ -26,7 +26,7 @@ You will then be taken to a screen where you will enter further information. We

It is recommended that you also add

* ORCID ID - if you do not have an ORCID you will need to register for one here http://orcid.org/
* ORCID ID - if you do not have an ORCID you will need to register for one at <http://orcid.org/>

Information that is required is indicated with a red star.

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2 changes: 1 addition & 1 deletion Registering-a-workflow-with-a-diagram-and-abstract-CWL.md
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Expand Up @@ -40,7 +40,7 @@ If the workflow came from an external repository (i.e. GitHub), you can include

- **Maturity**: This field can be used to specify in which maturity state the workflow is. The two available options are *work-in-progress* and *stable*.

- **Projects\***: Every workflow registration is linked to one or more projects. If you can not select the correct project, please go to [Joining a project](../How-to-join-a-project).
- **Teams\***: Every workflow registration is linked to one or more teams. If you can not select the correct team, please go to [Joining a team](How-to-join-a-team.md).

- **License**: The standard license is [Apache Software License 2.0](https://opensource.org/licenses/Apache-2.0). If you did not make the workflow yourself, be sure that the license corresponds to the license where you took the workflow from (for example [github licenses](https://help.github.com/en/github/creating-cloning-and-archiving-repositories/licensing-a-repository) ).

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4 changes: 2 additions & 2 deletions Registering-an-existing-Workflow-RO-Crate.md
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title: "**Advanced** - Registering a Workflow RO-Crate"
---

Creating workflow RO-crates can be done using the [ro-crate-py ](https://github.com/ResearchObject/ro-crate-py) package. This gives you the advantage that you are not bound by the file limitations the workflow registration can give you.
Creating workflow RO-crates can be done using the [ro-crate-py](https://github.com/ResearchObject/ro-crate-py) package. This gives you the advantage that you are not bound by the file limitations the workflow registration can give you.

## Referring or uploading the RO-Crate

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- **Maturity**: This field can be used to specify in which maturity state the workflow is. The two available options are *work-in-progress* and *stable*.

- **Projects\***: Every workflow registration is linked to one or more projects. If you can not select the correct project, please go to [Joining a project](../How-to-join-a-project).
- **Teams\***: Every workflow registration is linked to one or more teams. If you can not select the correct team, please go to [Joining a team](How-to-join-a-team.md).

- **License**: The standard license is [Apache Software License 2.0](https://opensource.org/licenses/Apache-2.0). If you did not make the workflow yourself, be sure that the license corresponds to the license where you took the workflow from (for example [github licenses](https://help.github.com/en/github/creating-cloning-and-archiving-repositories/licensing-a-repository) )

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2 changes: 1 addition & 1 deletion Updating-a-registered-workflow.md
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Expand Up @@ -6,7 +6,7 @@ title: Updating a registered workflow
## Prerequisites

Before you update a registered workflow, you need to ensure that you
* are [logged into](../Logging-in) WorkflowHub.
* are [logged into](Logging-in.md) WorkflowHub.
* have the rights to change the workflow.
* are on the workflow page of the workflow.

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2 changes: 1 addition & 1 deletion Workflow-RO-Crate/0.2/index.md
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*Please note* this is a draft spec and subject to change. Please leave any suggestions and comments here: [https://github.com/seek4science/seek/issues/183](https://github.com/seek4science/seek/issues/183)

_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 is aligned with, and intends to strictly extend, the more general [Bioschemas ComputatioonalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/).
_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 is aligned with, and intends to strictly extend, the more general [Bioschemas ComputatioonalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE).

WorkflowHub uses _Workflow RO-Crates_ as an exchange format for users to upload a packaged workflow.

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2 changes: 1 addition & 1 deletion Workflow-RO-Crate/1.0/index.md
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Expand Up @@ -55,7 +55,7 @@ title: Workflow RO-Crate profile 1.0

Please leave any suggestions and comments here: <https://github.com/seek4science/seek/issues/183>

_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/).
_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).

WorkflowHub uses _Workflow RO-Crates_ as an exchange format for users to upload a packaged workflow.

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13 changes: 13 additions & 0 deletions Workflow-RO-Crate/1.0/languages/index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="refresh" content="0; url=../ro-crate-preview.html#languages" />
<title>Moved</title>
</head>
<body>
<h1>Moved</h1>
<p>This page <a href="../ro-crate-preview.html#languages">redirect</a> to the new location.
</body>
</html>

13 changes: 13 additions & 0 deletions Workflow-RO-Crate/1.0/licenses/index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="refresh" content="0; url=../ro-crate-preview.html#licenses" />
<title>Moved</title>
</head>
<body>
<h1>Moved</h1>
<p>This page <a href="../ro-crate-preview.html#licenses">redirect</a> to the new location.
</body>
</html>

10 changes: 5 additions & 5 deletions Workflow-RO-Crate/1.0/ro-crate-metadata.json
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"@id": "https://orcid.org/0000-0001-9842-9718"
}
],
"datePublished": "2021-11-18T14:17:00Z",
"datePublished": "2022-02-11T14:35:50Z",
"description": "This is the Profile Crate for Workflow RO-Crate. Workflow RO-Crates are a specialization of RO-Crate for packaging an executable workflow with all necessary documentation. It is aligned with, and intends to strictly extend, the more general Bioschemas ComputationalWorkflow profile.\n\nWorkflowHub uses Workflow RO-Crates as an exchange format for users to upload a packaged workflow.",
"hasPart": [
{
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"subjectOf": {
"@id": "ro-crate-preview.html"
},
"version": "1.0.1",
"version": "1.0.2",
"workExample": {
"@id": "example/"
}
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"subjectOf": {
"@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE"
},
"url": "https://bioschemas.org/types/ComputationalWorkflow/1.0-RELEASE/",
"url": "https://bioschemas.org/types/ComputationalWorkflow/1.0-RELEASE",
"version": "1.0-RELEASE"
},
{
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"description": "A FormalParameter is an identified variable used to stand for the actual value(s) that are consumed/produced by a set of steps.",
"name": "Formal Parameter",
"termCode": "FormalParameter",
"url": "https://bioschemas.org/types/FormalParameter/1.0-RELEASE/",
"url": "https://bioschemas.org/types/FormalParameter/1.0-RELEASE",
"subjectOf": {
"@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE"
},
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}

]
}
}
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