new structure

workflowhub-eu · Mar 3, 2022 · 306dd18 · 306dd18
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diff --git a/Workflow-RO-Crate/0.2/index.md b/Workflow-RO-Crate/0.2/index.md
@@ -34,7 +34,7 @@
 <link href="http://schema.org/ImageObject" rel="item" />
 <link href="https://github.com/KockataEPich/CheckMyCrate/blob/master/CheckMyCrate/profile_library/ro_crate_1.1_basic.json" rel="item" />
 
-![Workflow RO-Crate](logo/ro-crate-workflow.svg)
+![Workflow RO-Crate](/assets/img/ro-crate-workflow.svg)
 
 * Permalink: `TODO`
 * Version: [0.2.0](https://github.com/workflowhub-eu/about/releases/tag/workflow-ro-crate-0.2.0)

diff --git a/_config.yml b/_config.yml
@@ -11,18 +11,32 @@ permalink: pretty
 defaults:
   -
     scope:
-      path: ""
+      path: "project"
       type: "pages"
     values:
       layout: "page"
-      sidebar: documentation
+      sidebar: about
   -
     scope:
-      path: "about"
+      path: "docs"
       type: "pages"
     values:
       layout: "page"
-      sidebar: about
+      sidebar: docs
+  -
+    scope:
+      path: "developer"
+      type: "pages"
+    values:
+      layout: "page"
+      sidebar: docs
+  -
+    scope:
+      path: "Workflow-RO-Crate"
+      type: "pages"
+    values:
+      layout: "page"
+      sidebar: docs
 
 theme_variables: 
   theme_color: 1f8787

diff --git a/_data/events.yml b/_data/events.yml
@@ -0,0 +1,7 @@
+- name: Contentathon
+  startDate: 2021-06-23
+  startTime: '9:00'
+  endDate: 2021-06-24
+  endTime: 13:30 CET
+  description: We would like to invite you to highlight your set of data management tools as a tool assembly in the RDMkit and describe how to use it, so others can do the same (two half days). [Sign up here](https://nettskjema.no/a/rdmkit-tool-assemblies#/page/1).
+  location: Online
diff --git a/_data/footer.yml b/_data/footer.yml
@@ -21,6 +21,6 @@ columns:
   - type: image
     image_width: 120px
     width: 3
-    src: '/assets/img/workflowhub_logo__square.svg'
+    src: '/assets/img/workflowhub-square.svg'
     alt: workflowhub logo square
 
diff --git a/_data/sidebars/about.yml b/_data/sidebars/about.yml
@@ -1,8 +1,16 @@
 subitems:
   - title: About
-    url: /about/About-WorkflowHub/
+    url: /project/
+  - title: Acknowledgements
+    url: /project/acknowledgements/
+  - title: Community
+    url: /project/community/
+  - title: Events
+    url: /project/events/
+  - title: Outreach
+    url: /project/outreach/
   - title: Roadmap
-    url: /about/roadmap/
-  - title: Usability Review
-    url: /about/UsabilityReview/
+    url: /project/roadmap/
+  - title: Usability review
+    url: /project/usability-review/
 
diff --git a/_data/sidebars/docs.yml b/_data/sidebars/docs.yml
@@ -0,0 +1,39 @@
+subitems:
+  - title: Docs
+    url: /docs/
+  - title: Prerequisites 
+    subitems:
+    - title: How to register
+      url: /docs/how-to-register/
+    - title: Logging in
+      url: /docs/logging-in/
+    - title: What is a team
+      url: /docs/what-is-a-team/
+    - title: Joining a team
+      url: /docs/how-to-join-a-team/
+  - title: Start guide
+    url: /docs/registering-workflows/
+  - title: Citable workflows
+    url: /docs/citable/
+  - title: Finding workflows
+    url: /docs/how-to-find-and-retrieve-workflows/
+  - title: Registering workflows (old)
+    url: /docs/how-to-register-your-workflow/
+    subitems:
+    - title: Existing Workflow RO-Crate
+      url: /docs/registering-an-existing-workflow-ro-crate/
+    - title: Workflow + diagram and abstract CWL
+      url: /docs/registering-a-workflow-with-a-diagram-and-abstract-cwl/
+  - title: Updating a registered workflow
+    url: /docs/updating-a-registered-workflow/
+  - title: For developers
+    subitems:
+      - title: How to make a workflow RO-Crate
+        url: /developer/how-to-make-a-workflow-ro-crate/
+      - title: RO-Crate API
+        url: /developer/ro-crate-api/
+      - title: TRS
+        url: /developer/trs/
+      - title: Workflow RO-Crate
+        url: /Workflow-RO-Crate/
+
diff --git a/_data/sidebars/documentation.yml b/_data/sidebars/documentation.yml
diff --git a/_data/topnav.yml b/_data/topnav.yml
@@ -3,7 +3,7 @@
 subitems:
   - title: Home
     url: /
-  - title: Documentation
-    url: /Workflow-RO-Crate/
   - title: About
-    url: /about/About-WorkflowHub/
+    url: /project/
+  - title: Docs
+    url: /docs/
diff --git a/assets/css/style.scss b/assets/css/style.scss
diff --git a/assets/img/workflowhub_logo__square.svg → assets/img/workflowhub-square.svg b/assets/img/workflowhub_logo__square.svg → assets/img/workflowhub-square.svg
diff --git a/How-to-make-a-workflow-RO-crate.md → developer/how-to-make-a-workflow-ro-crate.md b/How-to-make-a-workflow-RO-crate.md → developer/how-to-make-a-workflow-ro-crate.md
diff --git a/ro-crate-api.md → developer/ro-crate-api.md b/ro-crate-api.md → developer/ro-crate-api.md
diff --git a/TRS.md → developer/trs.md b/TRS.md → developer/trs.md
diff --git a/citable.md → docs/citable.md b/citable.md → docs/citable.md
diff --git a/...-retrieve-workflow(s)-from-WorkflowHub.md → docs/how-to-find-and-retrieve-workflows.md b/...-retrieve-workflow(s)-from-WorkflowHub.md → docs/how-to-find-and-retrieve-workflows.md
diff --git a/How-to-join-a-team.md → docs/how-to-join-a-team.md b/How-to-join-a-team.md → docs/how-to-join-a-team.md
diff --git a/...gister-your-workflow(s)-in-WorkflowHub.md → docs/how-to-register-your-workflow.md b/...gister-your-workflow(s)-in-WorkflowHub.md → docs/how-to-register-your-workflow.md
@@ -2,21 +2,21 @@
 tite: How to register your workflow(s) in WorkflowHub?
 ---
 
-### Prerequisites
+## Prerequisites
 
 Before you register a workflow, you need to ensure that you
 * 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
 
-### Get started
+## 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)
 
 
-### Supported workflow types
+## Supported workflow types
 
 Following workflow types are tested to work well with WorkflowHub, click on them to find out more. 
 
@@ -71,18 +71,18 @@ It is also possible to upload workflows from another type (for ex. bash scripts)
 
 <br>
 
-### Registering your workflow on WorkflowHub 
+## Registering your workflow on WorkflowHub 
 
 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.md) 
+### - [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.md)
+### - [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
+### - [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 have a glimpse of the [API documentation](https://workflowhub.eu/api).
diff --git a/How-to-register.md → docs/how-to-register.md b/How-to-register.md → docs/how-to-register.md
@@ -8,15 +8,15 @@ title: How to register
 
 In order to register yourself in WorkflowHub, you need to click Register button in the top right hand corner of WorkflowHub.
 
-![](images/register-1.PNG)
+![](/images/register-1.PNG)
 
 It will take you to a screen where you need to provide
 
 * A Login name (can be your real name, or another appropriate name)
 * An email address
 * A password for your account. When complete click the Register button in the bottom left hand corner.
 
-![](images/register-2.PNG)
+![](/images/register-2.PNG)
 
 You will then be taken to a screen where you will enter further information. We require the following information:
 
@@ -34,6 +34,6 @@ If your project is already in WorkflowHub please select it from the dropdown men
 
 If you don't join any listed project during registration, you can request to join a project or create your own project after the registration.  
 
-![](images/register-3.PNG)
+![](/images/register-3.PNG)
 
 After you have registered the rest of your information, you will need to activate your account. You will receive an email in the email account you have provided.
diff --git a/docs/index.md b/docs/index.md
@@ -0,0 +1,3 @@
+---
+title: Documentation
+---
diff --git a/Logging-in.md → docs/logging-in.md b/Logging-in.md → docs/logging-in.md
@@ -6,8 +6,8 @@ Before you log in, you must have already [registered](../How-to-register) on Wor
 
 To log in you need to click the login button in the top right hand corner of WorkflowHub.
 
-![](images/login-1.PNG)
+![](/images/login-1.PNG)
 
 This will take you to a page where you need to enter your username, and password.
 
-![](images/login-2.PNG)
+![](/images/login-2.PNG)
diff --git a/...rkflow-with-a-diagram-and-abstract-CWL.md → ...rkflow-with-a-diagram-and-abstract-cwl.md b/...rkflow-with-a-diagram-and-abstract-CWL.md → ...rkflow-with-a-diagram-and-abstract-cwl.md
@@ -60,7 +60,7 @@ If the workflow came from an external repository (i.e. GitHub), you can include
     3. **If anyone not registered with WorkflowHub assisted creating this Workflow, you can specify them below.**\
     Use this field to fill in the remaining creators.
 
-![](images/creators_metadata.PNG)
+![](/images/creators_metadata.PNG)
 
 
 ##  Check the uploaded workflow
@@ -69,7 +69,7 @@ Make sure that all the metadata you filled in previously is showed properly and
 
 You can also Click **Download RO-Crate** where metadata files (JSONLD and HTML) have been generated based on the information fill
 
-![](images/result_diagram_CWLabstract.PNG)
+![](/images/result_diagram_CWLabstract.PNG)
 
 ## Minting a DOI
 

diff --git a/Registering-an-existing-Workflow-RO-Crate.md → ...istering-an-existing-workflow-ro-crate.md b/Registering-an-existing-Workflow-RO-Crate.md → ...istering-an-existing-workflow-ro-crate.md
@@ -52,10 +52,10 @@ If the workflow came from an external repository (i.e. GitHub), you can include
     3. **If anyone not registered with WorkflowHub assisted creating this Workflow, you can specify them below.**\
     Use this field to fill in the remaining creators.
 
-![](images/creators_metadata.PNG)
+![](/images/creators_metadata.PNG)
 
 ##  Check the uploaded RO-crate
 
 Make sure that all the metadata that is parsed/ filled is showed properly and is correct.
 
-![](images/uploaded-galaxy-workflow.PNG)
+![](/images/uploaded-galaxy-workflow.PNG)
diff --git a/registering-workflows.md → docs/registering-workflows.md b/registering-workflows.md → docs/registering-workflows.md
@@ -2,10 +2,8 @@
 title: Registering a workflow on WorkflowHub
 ---
 
-## How-to-Guide
 
-
-### Before you start!
+## Before you start!
 
 1. [Login to WorkflowHub](Logging-in.md)
 2. Make sure you have [joined a team](How-to-join-a-team.md)
@@ -17,7 +15,7 @@ title: Registering a workflow on WorkflowHub
 8. Prepare your [metadata](#metadata-list)
 9. See the [Glossary](#glossary) for more details.
 
-# What is the overall process for registration?
+## What is the overall process for registration?
 
 
 ![Remote files URLs, Git Repository, Local Files, Zipped RO-Crate are Imported, then Register workflow, Add Metadata and Finalize Registration with review](/images/registration-01-overview.svg "Registration Overview")

diff --git a/Updating-a-registered-workflow.md → docs/updating-a-registered-workflow.md b/Updating-a-registered-workflow.md → docs/updating-a-registered-workflow.md
diff --git a/what-is-a-team.md → docs/what-is-a-team.md b/what-is-a-team.md → docs/what-is-a-team.md
diff --git a/fair-computational-workflows/index.html b/fair-computational-workflows/index.html
@@ -10,15 +10,13 @@
 <title>Page moved to https://workflows.community/groups/fair/ | WorkflowHub project</title>
 <link rel="canonical" href="https://workflows.community/groups/fair/" />
 <meta http-equiv="refresh" content="0;url=https://workflows.community/groups/fair/"/>
-    <link rel="stylesheet" href="/assets/css/style.css?v=eac51af1e45c952eef0587a818e39ed96f2e02f9">
   </head>
   <body>
     <div class="wrapper">
       <header>
         <h1><a href="https://about.workflowhub.eu/">WorkflowHub project</a></h1>
-
 
-          <img src="/logo/workflowhub-square.svg" alt="Logo" />
+          <img src="/assets/img/workflowhub-square.svg" alt="Logo" />
 
       </header>
       <section>

diff --git a/how-to/index.md b/how-to/index.md
diff --git a/assets/img/BioExcel_logo_payoff_cropped.svg → images/BioExcel_logo_payoff_cropped.svg b/assets/img/BioExcel_logo_payoff_cropped.svg → images/BioExcel_logo_payoff_cropped.svg
diff --git a/images/ELIXIR_logo_white_background.png b/images/ELIXIR_logo_white_background.png
diff --git a/assets/img/fair-workflows.png → images/fair-workflows.png b/assets/img/fair-workflows.png → images/fair-workflows.png
diff --git a/assets/img/fairdom-logo-fixed-colours.svg → images/fairdom-logo-fixed-colours.svg b/assets/img/fairdom-logo-fixed-colours.svg → images/fairdom-logo-fixed-colours.svg
diff --git a/assets/img/fairplus-logo.png → images/fairplus-logo.png b/assets/img/fairplus-logo.png → images/fairplus-logo.png
diff --git a/assets/img/ibisba-logo.png → images/ibisba-logo.png b/assets/img/ibisba-logo.png → images/ibisba-logo.png
diff --git a/assets/img/seek.svg → images/seek.svg b/assets/img/seek.svg → images/seek.svg
diff --git a/assets/img/synthesys-plus-logo-white.png → images/synthesys-plus-logo-white.png b/assets/img/synthesys-plus-logo-white.png → images/synthesys-plus-logo-white.png
diff --git a/index.md b/index.md
@@ -1,9 +1,9 @@
 ---
-title: WorkflowHub
+title: WorkflowHub project
 hide_sidebar: true
-sidebar: none
 ---
-## WorkflowHub project
+
+
 
 [WorkflowHub](https://workflowhub.eu/) is a new FAIR **workflow registry** sponsored by the European RI Cluster EOSC-Life and the European Research Infrastructure ELIXIR. It is workflow management system agnostic: workflows may remain in their native repositories in their native forms.