workflowhub-eu · fbacall · Feb 11, 2025 · Nov 29, 2024 · Nov 29, 2024 · Dec 5, 2024
diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.event.inputs.branch }}
 
@@ -30,7 +30,7 @@ jobs:
 
       - name: Setup Pages
         id: pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v5
 
       - name: Install dependencies
         run: |
@@ -46,4 +46,4 @@ jobs:
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
diff --git a/_config.yml b/_config.yml
@@ -4,7 +4,7 @@ description: >
   Project pages for developing and running WorkflowHub, 
   a registry of scientific workflows.
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@2.5.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
 
 permalink: pretty
 

diff --git a/_data/glossary.yml b/_data/glossary.yml
@@ -0,0 +1,25 @@
+- title: "Team"
+  description: Project, also called “Team”
+  url:
+- title: "Workflow type"
+  description: See <a href="{{ '/docs/supported-workflow-types' | relative_url }}">supported workflow types</a>
+- title: "Organisation"
+  description:
+  url:
+- title: "Space"
+  description:
+  url:
+- title: "Main workflow file"
+  description: This is the main workflow file that has to be uploaded/referenced. Specify the Workflow type of the main workflow in the dropdown list (i.e. Common Workflow Language ".cwl", Galaxy ".ga", KNIME ".knwf", Nextflow ".nf", Snakemake ".snake". If your workflow type is not listed, please choose "other".
+- title: "Git repository"
+  description:
+  url:
+- title: "Remote file URL"
+  description:
+- title: "CWL abstract"
+  description: The CWL abstract is used as a summary of the workflow to parse for example the description (doc) if provided or to generate a svg diagram. If you have a Galaxy workflow you can generate the CWL abstract with <a href="https://github.com/workflowhub-eu/galaxy2cwl">galaxy2cwl</a>. If your main workflow is a CWL workflow, you can skip this step. In the future it will also be possible to convert other workflow types to CWL abstract.
+- title: "Diagram"
+  description: If your main workflow file is CWL or you give a CWL abstract, the diagram is automatically generated by the WorkflowHub website. In any other case, you will have to supply a diagram yourself, which will then be included in the workflow entry on WorkflowHub (and by extension in the RO-Crate). During registration, you can use the upload / reference fields to attach a diagram in .svg (preferred) or .jpeg/.png format.
+- title: "RO-Crate"
+  description: Research Object Crate (RO-crate)
+  url: https://www.researchobject.org/ro-crate/
diff --git a/_data/resources.yml b/_data/resources.yml
@@ -0,0 +1,15 @@
+- title: "Common Workflow Language (.cwl)"
+  url: https://www.commonwl.org/
+  url_community_workflows: https://github.com/common-workflow-library
+  url_community: https://www.commonwl.org/community/
+- title: "Nextflow (.nf)"
+  url: https://www.nextflow.io/
+  url_community_workflows: https://nf-co.re/pipelines/
+  url_community: https://nf-co.re/
+- title: "SnakeMake (.snake)"
+  url: https://snakemake.github.io/
+  url_community_workflows: https://snakemake.github.io/snakemake-workflow-catalog/
+- title: "KNIME (.knwf)"
+  url: https://www.knime.com/
+  url_community_workflows: https://hub.knime.com/
+
diff --git a/_data/sidebars/documentation.yml b/_data/sidebars/documentation.yml
@@ -1,49 +1,44 @@
 title: Documentation
 subitems:
-  - title: Quick start guide
+  - title: Getting started
     url: /docs/index
   - title: Complete guide to using WorkflowHub
     url: /docs/guide-to-using-workflowhub
-  - title: Detailed documentation
+  - title: Finding workflows
+    url: /docs/finding-workflows/
+  - title: Test submissions to WorkflowHub
+    url: /docs/workflowhub_instances/
+  - title: Getting set up on WorkflowHub
+    url: /docs/organising-and-setup/
+    subitems:
+      - title: How to register with WorkflowHub
+        url: /docs/how-to-register/
+      - title: Logging in
+        url: /docs/logging-in/
+      - title: Join or set up Teams & Spaces
+        url: /docs/join-create-teams-spaces/
+      - title: What are Teams, Spaces and Organizations?
+        url: /docs/space-team-organisation/
+  - title: Contributing workflows
+    url: /docs/registering_workflows/registering-a-workflow/
     subitems:
-    - title: WorkflowHub instances
-      url: /docs/workflowhub_instances/
-    - title: How to register
-      url: /docs/how-to-register/
-    - title: Logging in
-      url: /docs/logging-in/
-    - title: What are Teams, Spaces and Organizations?
-      url: /docs/space-team-organisation/
-    - title: Join or set up Teams & Spaces
-      url: /docs/join-create-teams-spaces/
-    - title: Registering workflows
-      url: /docs/registering_workflows/registering-a-workflow/
-      subitems:
       - title: Register and login
         url: /docs/registering_workflows/register-and-login/
       - title: Adding files
         url: /docs/registering_workflows/adding-files/
       - title: Complete workflow metadata
         url: /docs/registering_workflows/complete-workflow-metadata/
-      - title: Check uploaded workflow
+      - title: Finalise registration
         url: /docs/registering_workflows/check-uploaded-workflow/
       - title: Supported workflow types
         url: /docs/registering_workflows/supported-workflow-types/
-    - title: Organising your workflows on WorkflowHub
-      url: /docs/organising-workflows/
-    - title: Maintaining your workflow
-      url: /docs/maintaining-your-workflow/
-    - title: Mint a DOI for your workflow
-      url: /docs/citable/
-    - title: Finding workflows
-      url: /docs/finding-workflows/
-    - title: Metadata list
-      url: /docs/metadata-list/
-    - title: Glossary
-      url: /docs/glossary/
-    - title: For developers
-      url: /developer/
-      subitems:
+  - title: Maintain your workflows
+    url: /docs/maintaining-your-workflow/
+  - title: Mint a workflow DOI
+    url: /docs/citable/
+  - title: For developers
+    url: /developer/
+    subitems:
       - title: Bioschemas.org
         url: /developer/bioschemas/
       - title: Workflow RO-Crate
@@ -52,5 +47,11 @@ subitems:
         url: /developer/how-to-make-a-workflow-ro-crate/
       - title: RO-Crate API
         url: /developer/ro-crate-api/
-      - title: TRS
+      - title: TRS API
         url: /developer/trs/
+  - title: FAQ
+    url: /docs/faq/
+  - title: Metadata list
+    url: /docs/metadata-list/
+  - title: Glossary
+    url: /docs/glossary/
diff --git a/_includes/glossary.html b/_includes/glossary.html
@@ -0,0 +1,34 @@
+{%- if include.tag %}
+{%- assign tools = site.data.glossary | add_related_pages | where:"related_pages", include.tag  | sort_natural: "name" %}
+{%- else %}
+{%- assign tools = site.data.glossary | add_related_pages  | sort_natural: "name" %}
+{%- endif %}
+{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
+{%- unless tools.size == 0 or tools == nil %}
+<a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
+<div class="table-responsive mt-4 mb-5">
+    <table class="tooltable table display">
+        <thead>
+            <tr class="text-nowrap">
+                <th>Term</th>
+                <th>Description</th>
+            </tr>
+        </thead>
+        <tbody>
+            {%- for tool in tools %}
+            <tr>
+                {% if tool.url %}
+                <td><a href="{{tool.url}}">{{tool.title}}</a></td>
+                {%- else %}
+                <td>{{tool.title}}</td>
+                {%- endif %}
+                {% if tool.description %}
+                <td>{{tool.description}}</td>
+                {%- endif %}
+            </tr>
+            {%- endfor %}
+        </tbody>
+    </table>
+</div>
+{%- endunless %}
+<div id="skip-tool-table"></div>
diff --git a/_includes/resources.html b/_includes/resources.html
@@ -0,0 +1,43 @@
+{%- if include.tag %}
+{%- assign tools = site.data.resources | add_related_pages | where:"related_pages", include.tag  | sort_natural: "name" %}
+{%- else %}
+{%- assign tools = site.data.resources | add_related_pages  | sort_natural: "name" %}
+{%- endif %}
+{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
+{%- unless tools.size == 0 or tools == nil %}
+<a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
+<div class="table-responsive mt-4 mb-5">
+    <table class="tooltable table display">
+        <thead>
+            <tr class="text-nowrap">
+                <th>WfMS</th>
+                <th>Links to related information {%- if include.tag -%}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="Links">
+                        <i class="fa-solid fa-info-circle"></i>
+                    </a>{%- endif %}
+                </th>
+            </tr>
+        </thead>
+        <tbody>
+            {%- for tool in tools %}
+            <tr>
+                {% if tool.url %}
+                <td><a href="{{tool.url}}">{{tool.title}}</a></td>
+                {%- else %}
+                <td>{{tool.title}}</td>
+                {%- endif %}
+                <td>
+                    {%- if tool.url_community %}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="Community" href="{{tool.url_community}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-info me-2"></i>Community</span></a>
+                    {%- endif %}
+                    {%- if tool.url_community_workflows %}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="Community workflows" href="{{tool.url_community_workflows}}"><span class="badge bg-dark text-white hover-primary"><i class="fa-solid fa-database me-2"></i>Community workflows</span></a>
+                    {%- endif %}
+                </td>
+            </tr>
+            {%- endfor %}
+        </tbody>
+    </table>
+</div>
+{%- endunless %}
+<div id="skip-tool-table"></div>
diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss
@@ -1,3 +1,24 @@
+/*-----Navigation tiles-----*/
+/*-----From https://github.com/elixir-europe/infectious-diseases-toolkit/blob/main/_sass/_custom_classes.scss-----*/
+
+.navigation-tiles {
+    .card {
+        background-color: $light;
+        color: $dark;
+    }
+    .card:hover {
+        box-shadow: $box-shadow;
+        background-color: $primary;
+    }
+
+    .card-body {
+        h3 {
+            color: $dark;
+            font-size: 1.2rem;
+        }
+    }
+}
+
 /*-----Top navigation-----*/
 header .navbar {
     .navbar-brand {

diff --git a/_sass/_custom_variables.scss b/_sass/_custom_variables.scss
@@ -3,3 +3,8 @@ $topnav-bg: $light;
 $topnav-title-color: $primary;
 $topnav-brand-height: 80px;
 
+/*-----Section navigation tiles-----*/
+$nav-card-bg: $primary;
+$nav-card-color: $dark;
+$nav-card-bg-hover: $primary;
+$nav-card-color-hover: $white;
diff --git a/developer/how-to-make-a-workflow-ro-crate.md b/developer/how-to-make-a-workflow-ro-crate.md
@@ -1,16 +1,17 @@
 ---
-title: How to make a workflow RO-crate?
+title: How to make a workflow RO-crate
 redirect_from: /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.
 
-### 1. Using the WorkflowHub website
+## 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](/docs/registering-a-workflow) 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](/docs/registering-a-workflow) for more info about this topic) it is possible to download the RO-crate with the download button. 
 
-- **JSONLD file**\
-  JSONLD serving machine readable metadata including: 
+The generated RO-crate, basically a zip file, will contain these elements:
+
+- **JSONLD file**: JSONLD serving machine-readable metadata including: 
   - Author
   - Contents and structure
   - Project
@@ -24,23 +25,19 @@ The most convenient way to make a workflow RO-crate at this moment is by making
 
   The metadata properties are based on the [BioSchemas workflow profile](https://bioschemas.org/profiles/Workflow)  .
 
-- **HTML file**\
-  A web page serving the metadata in a human readable way.
+- **HTML file**: A web page serving the metadata in a human-readable way.
   - Original URL
   - Author (creators)
   - License
   - Contents
 
-- **Main Workflow file**\
-  The workflow file itself if uploaded.
+- **Main Workflow file**: The workflow file itself, if uploaded.
 
-- **Main Workflow Diagram (optional)**\
-  A diagram visualizing the steps in the workflow if uploaded or generated out of the CWL.
+- **Main Workflow Diagram (optional)**: A diagram visualizing the steps in the workflow, if uploaded or generated from CWL.
 
-- **Main Workflow CWL Description (optional)**\
-  This file can be included if supplied by the user.
+- **Main Workflow CWL Description (optional)**: This file can be included if supplied by the user.
 
-### 2. Making one offline yourself
+## 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 [ResearchObject/ro-crate-py](https://github.com/ResearchObject/ro-crate-py).
diff --git a/developer/index.md b/developer/index.md
@@ -1,5 +1,8 @@
 ---
-title: For developers
+title: Documentation for developers
+description: Documentation for developers, including bioschemas, RO-crate, and APIs.
+page_id: developer
+toc: false
 ---
 
 Programmatic access to WorkflowHub is based on [FAIRDOM-SEEK](https://seek4science.org/) and [RO-Crate](https://www.researchobject.org/ro-crate/):
@@ -9,3 +12,14 @@ Programmatic access to WorkflowHub is based on [FAIRDOM-SEEK](https://seek4scien
 * [Workflow RO-Crate](../Workflow-RO-Crate) including [How to make Workflow RO-Crate](how-to-make-a-workflow-ro-crate/) and [RO-Crate API](ro-crate-api/)
 * [FAIR Signposting](signposting/) and FAIR Digital Objects (FDO)
 * [GA4GH’s Tool Registry Service API](trs/) for iterating over every workflow
+
+
+### Reference material
+
+WorkflowHub is based on the [SEEK framework](https://docs.seek4science.org/). Below is a map between WorkflowHub terms and the underlying SEEK definitions and documentation.
+
+|WorkflowHub term|FAIRDOM SEEK term|Explanation|Link|
+|-----|-----|-----|-----|
+|Team|Project|Set up for a specific activity or group|<https://docs.seek4science.org/help/user-guide/create-a-project.html>|
+|Space|Programme|Set up for a funded piece of work, project or consortium|<https://docs.seek4science.org/help/user-guide/programme-creation-and-management.html>|
+