workflowhub-eu · fbacall · Jul 30, 2024 · Jul 29, 2024 · Jul 29, 2024 · Jul 29, 2024
diff --git a/_data/sidebars/documentation.yml b/_data/sidebars/documentation.yml
@@ -6,6 +6,8 @@ subitems:
     url: /docs/guide-to-using-workflowhub
   - title: Detailed documentation
     subitems:
+    - title: WorkflowHub instances
+      url: /docs/workflowhub_instances/
     - title: How to register
       url: /docs/how-to-register/
     - title: Logging in
@@ -15,18 +17,18 @@ subitems:
     - title: Join or set up Teams & Spaces
       url: /docs/join-create-teams-spaces/
     - title: Registering workflows
-      url: /docs/registering-a-workflow/
+      url: /docs/registering_workflows/registering-a-workflow/
       subitems:
       - title: Register and login
-        url: /docs/register-and-login/
+        url: /docs/registering_workflows/register-and-login/
       - title: Adding files
-        url: /docs/adding-files/
+        url: /docs/registering_workflows/adding-files/
       - title: Complete workflow metadata
-        url: /docs/complete-workflow-metadata/
+        url: /docs/registering_workflows/complete-workflow-metadata/
       - title: Check uploaded workflow
-        url: /docs/check-uploaded-workflow/
+        url: /docs/registering_workflows/check-uploaded-workflow/
       - title: Supported workflow types
-        url: /docs/supported-workflow-types/
+        url: /docs/registering_workflows/supported-workflow-types/
     - title: Organising your workflows on WorkflowHub
       url: /docs/organising-workflows/
     - title: Maintaining your workflow

diff --git a/docs/guide-to-using-workflowhub.md b/docs/guide-to-using-workflowhub.md
@@ -1,6 +1,5 @@
 ---
 title:  A guide to using WorkflowHub
-toc: false
 ---
 
 **If your research project is producing workflows, they should be registered in WorkflowHub:**
@@ -191,7 +190,7 @@ Note that you need to use Manage workflow to change its permissions or team owne
 
 ### Update the workflow version manually
 
-#### If the workflow was imported via Git
+#### If the workflow was uploaded manually, or via an RO-Crate
 
 Files can be added/removed/modified via the `Files` tab if the current version is `Open`.
 
@@ -208,7 +207,7 @@ A version must be `Frozen` before a new version can be created, or before a DOI
 2. Click `New Version`
 3. Decide either to continue managing the files on WorkflowHub (`Upload/Import files`), or switch to using a Git repository (`Import Git Version`).
 
-#### If the workflow was uploaded manually, or via an RO-Crate
+#### If the workflow was imported via Git
 
 1. Go to the `Actions` dropdown menu 
 2. Click `New Version` 

diff --git a/docs/join-create-teams-spaces.md b/docs/join-create-teams-spaces.md
@@ -73,12 +73,16 @@ The steps for creating a Team are outlined here:
 - If you already administer an existing Space, a dropdown box will be shown instead allowing you to select it. 
 - Only the title is required at this stage, and further details can be added once the Team has been created.
 
+{:start="2"}
+
 2. You next need to define the `Team`. The minimum requirement is a Title, but you can also provide a:
    - Description, and 
    - Webpage URL 
 
 {% include callout.html type="note" content="Once created you can edit and add additional details and add members." %}    
 
+{:start="3"}
+
 3. You then need to define **your** Organization. 
 4. Start to type the name of your Organization, and existing options will be displayed that contain the text you type (or information related to the Organization such as city or country). 
    - Hopefully, your Organization is found, and you can then select it, or 

diff --git a/docs/organising-workflows.md b/docs/organising-workflows.md
@@ -5,7 +5,7 @@ title: A guide to organising your workflows on WorkflowHub
 The documentation below provides guidance on the relationship between a given workflow and the structural elements of the WorkflowHub registry: `Spaces`, `Teams` and `Collections`. 
 We also provide examples of how to structure larger consortia and projects on WorkflowHub that accommodates recognition of multiple `Organisations` and `Teams`, potentially across multiple `Spaces`.
 
-[More information on Spaces, Teams and Organisations](https://about.workflowhub.eu/docs/joining-a-team/).
+[More information on Spaces, Teams and Organisations](https://about.workflowhub.eu/docs/space-team-organisation/).
 
 {% include image.html file="workflows_teams_spaces_1.png" caption="Fig 1. Example WorkflowHub Space structures." %}
 

diff --git a/docs/adding-files.md → docs/registering_workflows/adding-files.md b/docs/adding-files.md → docs/registering_workflows/adding-files.md
diff --git a/docs/check-uploaded-workflow.md → ...ring_workflows/check-uploaded-workflow.md b/docs/check-uploaded-workflow.md → ...ring_workflows/check-uploaded-workflow.md
diff --git a/docs/complete-workflow-metadata.md → ...g_workflows/complete-workflow-metadata.md b/docs/complete-workflow-metadata.md → ...g_workflows/complete-workflow-metadata.md
diff --git a/docs/register-and-login.md → ...gistering_workflows/register-and-login.md b/docs/register-and-login.md → ...gistering_workflows/register-and-login.md
diff --git a/docs/registering-a-workflow.md → ...ering_workflows/registering-a-workflow.md b/docs/registering-a-workflow.md → ...ering_workflows/registering-a-workflow.md
@@ -10,16 +10,16 @@ redirect_from:
 
 ## What is the overall process for registration?
 
-Using the WorkflowHub registration wizard:
-
-1. Import a workflow file. These can be:
-   1. A local file, or files
-   2. A remote file URL
-   3. A git repository
-   4. A zipped Research Object Crate (RO-crate)
-2. Register the workflow
-3. Add relevant metadata
-4. Review the entry and finalise registration
+1. Register and log-in
+2. Make sure you are a member of a Team
+3. Using the WorkflowHub registration wizard, import and add a workflow file. These files can be:
+   - A local file, or files 
+   - A remote file URL 
+   - A git repository 
+   - A zipped [Research Object Crate (RO-crate)](https://about.workflowhub.eu/Workflow-RO-Crate/)
+4. Register the workflow
+5. Add relevant metadata
+6. Review the entry and finalise registration
 
 {% include callout.html type="important" content="You can also register your workflow using a Research Object Crate (RO-Crate). This is an option for advanced users, and  further instructions can be found here. The advanced way: registering a workflow RO-crate When you have created a workflow RO-Crate of your workflow  using the python package, and want to upload or reference it." %}
 

diff --git a/docs/supported-workflow-types.md → ...ing_workflows/supported-workflow-types.md b/docs/supported-workflow-types.md → ...ing_workflows/supported-workflow-types.md
diff --git a/docs/workflowhub_instances.md b/docs/workflowhub_instances.md
@@ -0,0 +1,12 @@
+---
+title: WorkflowHub instances
+---
+
+The main WorkflowHub registry for workflows is available here: [https://workflowhub.eu/](https://workflowhub.eu/).
+
+But, did you know that WorkflowHub also operates a development instance? [https://dev.workflowhub.eu/](https://dev.workflowhub.eu/)
+
+You can use this development instance if you want to test WorkflowHub. For example, before contributing to the registry, or as part of testing integration of your systems with WorkflowHub.
+
+{% include callout.html type="warning" content="The _development instance_ may occasionally be wiped!" %}
+
diff --git a/project/roadmap.md b/project/roadmap.md
@@ -29,23 +29,34 @@ See also:
 * Search/filtering improvements
 -->
 
-## Spring 2023
-* Improved workflow branding
-* Extended execution link support (additional Galaxy instances, Jupyter/Binder, Nextflow Tower, etc.)
-* GitHub app for automated workflow submission
-* Improved curation support
-* Workflow/WorkflowHub best-practice guide
+## 2024 activities
 
-## Late 2023
-* Support for linking together workflows to variants and subworkflows
-* Better RO-Crate support for additional Workflow Management Systems (e.g. Snakemake, Nextflow)
-* Working with Workflow Management Systems to improve how tool metadata is exposed in their native formats
+* GitHub app for automated workflow submission and synchronisation
 * Closer collaboration with journals
-* Targeting additional workflow communities on GitHub, GitLab etc. (in addition to IWC, nf-core)
-* Collecting basic workflow execution metrics
+* Better RO-Crate support for additional Workflow Management Systems (e.g. Snakemake, Nextflow)
+* Collaborating with additional workflow communities (Galaxy Training Network)
+* Collaborating with additional workflow communities (Snakemake)
+* WorkflowHub manuscript
+* Documentation site updates and streamlining
+
+
+## Future work (i.e. 2025 onwards)
 
-## 2024 onwards
+* Collecting basic workflow execution metrics
+* Workflow / WorkflowHub best-practice guide
+* Improved workflow branding
+* Support for linking together workflows to variants and subworkflows
+* Working with Workflow Management Systems to improve how tool metadata is exposed in their native formats
+* Improved curation support
 * One-click publish of workflows to LifeMonitor
 * Curation campaign
 * OpenEBench integration
 * Registering as a trusted registry and adhering to the TRUST principles
+
+
+## Completed activities
+
+* Extended execution link support (additional Galaxy instances, Jupyter/Binder, Nextflow Tower, etc.)
+* Generic guides and customised consortium specific guides for WorkflowHub
+* Collaborating with additional workflow communities (Nf-core automatic registration and annotation)
+