Merge branch 'subdomain_unification' of https://github.com/nomadscien…

…tist/galaxy_codex into subdomain_unification

subdomains/singlecell/base.yml

@@ -28,15 +28,15 @@ terms_url: https://usegalaxy.org/static/terms.html
 help_links:
   - title: General Galaxy support
     url: https://galaxyproject.org/support/
-  - title: Single Cell community help forum
-    url: https://usegalaxy-eu.github.io/scrna
+  - title: Single Cell help forum
+    url: https://help.galaxyproject.org/tag/single-cell
   - title: General Galaxy help forum
     url: https://help.galaxyproject.org
-  - title: Galaxy Training Network Slack Forum
+  - title: Galaxy Training Network Slack workspace
     url: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-2llyx6p8j-LmpEIsJu0t4MQkBctkN8qg
-  - title: Single cell Galaxy user community chat room - on Slack!
+  - title: Single cell Slack channel (#single-cell-users)
     url: https://gtnsmrgsbord.slack.com/archives/C06PBRR40D7
-  - title: Single cell Galaxy user community chat room
+  - title: Single cell user community chat room (Same channel but using Matrix/Element)
     url: https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im
   - title: Galaxy Training Community chat
     url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im

subdomains/singlecell/sections/1_beginner.yml

@@ -115,7 +115,6 @@ tabs:
     content:
       - title_md: <code>Plot with Scanpy</code>
         description_md: >
-          <code>Plot with Scanpy</code>
           This tool allows you to generate many plots, from scatterplots, to violin plots, to gene heatplots.
         inputs:
           - anndata
@@ -125,7 +124,6 @@ tabs:
         button_tip: Run tool
       - title_md: <code>Scanpy PlotEmbed</code>
         description_md: >
-          <code>Scanpy PlotEmbed</code>
           This tool allows you to plot embeddings like UMAPs.
         inputs:
           - anndata
@@ -135,7 +133,6 @@ tabs:
         button_tip: Run tool
       - title_md: <code>Scanpy PlotTrajectory</code>
         description_md: >
-          <code>Scanpy PlotTrajectory</code>
           This tool allows you to plot trajectory data, such as PAGA, pre-calculated in an AnnData object.
         inputs:
           - anndata
@@ -145,7 +142,6 @@ tabs:
         button_tip: Run tool
       - title_md: <code>Scanpy Plot dimension reduction</code>
         description_md: >
-          <code>Scanpy Plot dimension reduction</code>
           This tool allows you to plot embeddings such as PCA, UMAP, and tSNE.
         inputs:
           - RDS with a Seurat Object
@@ -158,7 +154,6 @@ tabs:
         button_tip: Run tool
       - title_md: <code>Plot with Seurat</code>
         description_md: >
-          <code>Plot with Seurat</code>
           This tool allows you to plot gene expressions, such as with Violin Plots.
         inputs:
           - RDS with a Seurat Object
@@ -177,18 +172,18 @@ tabs:
         description_md: >
           <iframe src="https://oembed.apps.galaxyproject.eu/oembed?style=gtn&format=iframe-embed&url=https://training.galaxyproject.org/training-material/topics/single-cell/faqs/user_community_join.html#how-can-i-talk-with-other-users.html"
           width="100%"
-          height="600px">
+          height="430px">
           </iframe>
+      - title_md: Is there a help forum?
+        description_md: >
+          <i class="far fa-question-circle" aria-hidden="true"></i>
+          [Single cell help forum](https://help.galaxyproject.org/tag/scrna)
       - title_md: How can I troubleshoot?
         description_md: >
             <iframe src="https://oembed.apps.galaxyproject.eu/oembed?style=gtn&format=iframe-embed&url=https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html#troubleshooting-errors.html"
             width="100%"
             height="600px">
             </iframe>
-      - title_md: Is there a help forum?
-        description_md: >
-          <i class="far fa-question-circle" aria-hidden="true"></i>
-          [Single cell help forum](https://help.galaxyproject.org/tag/scrna)
       - title_md: Can I upload sensitive data?
         description_md: >
           No, please do not upload personal or sensitive, such as human health or clinical data. Please see our

subdomains/singlecell/sections/3_advanced.yml

@@ -4,17 +4,18 @@ tabs:
   - id: workflows1
     title: Workflow Best Practices
     heading_md: >
-      Workflows are chains of of tools that can be run together at the click of a button. The following tabs contain both peer reviewed and community submitted workflows.
-      Common workflow tags for our community are:
-                    - <code>single-cell</code>
-                    - <code>training</code> (for workflows that correspond to the Galaxy Training Network's tutorials)
-                    - <code>data interoperability</code>
-                    - <code>deconvolution</code>
-                    - <code>spatial omics</code>
+      Workflows are chains of of tools that can be run together at the click of a button.
+      <p>The above tabs contain both peer reviewed and community submitted workflows.</p>
       <p class="alert alert-success">
         <a href="https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_annotate.html">Tag your workflows</a>
         with <b>#single-cell</b> and share publicly with other users!
       </p>
+      Additional common workflow tags for our community are:
+                    <li><code>training</code> (for workflows that correspond to the Galaxy Training Network's tutorials)</li>
+                    <li><code>data interoperability</code></li>
+                    <li><code>deconvolution</code></li>
+                    <li><code>spatial omics</code></li>
+
     content:
       - title_md: How to tag a workflow
         description_md: >
@@ -27,11 +28,11 @@ tabs:
   - id: workflows2
     title: Peer-reviewed workflows
     heading_md: >
-      You can see workflows before that have been reviewed by scientists.
+      You can browse through workflows before that have been reviewed by scientists.
     content:
       - title_md: IWC
         description_md: >
-          IWC is a label given to peer-reviewed workflows within Galaxy.
+          IWC is an **owner** of peer-reviewed workflows within Galaxy.
           <iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?all=single-cell+IWC" height="300px" width="100%" frameborder="0"></iframe>
       - title_md: WorkflowHub
         description_md: >
@@ -41,34 +42,38 @@ tabs:
   - id: workflows3
     title: Community workflows
     heading_md: >
-      Anyone on Galaxy can share their workflow publicly - if your workflow is running well, share it with others! You can search these community workflows below.
+      Anyone on Galaxy can share their workflow publicly - if your workflow is running well, share it with others!
+      <p>You can search these community workflows below.</p>
     content:
       - title_md: Community Workflows
         description_md: >
-          The GTN's
-          {gtn modal}[Pan-Galactic Workflow Search](https://training.galaxyproject.org/training-material/workflows/list.html)
-          allows you to search for workflows across all of Galaxy!
-
-          It's even possible to do an
-          {gtn modal}[advanced search](https://training.galaxyproject.org/training-material/news/2023/11/20/workflow-search.html)
-          to find exactly what you need.
+          Search through community workflows tagged with #single-cell.
+          <iframe src="https://training.galaxyproject.org/training-material/workflows/embed.html?all=single-cell&none=training+IWC"
+                  width="100%"
+                  height="600px"
+                  style="border:none;">
+          </iframe>
 
       - title_md: Bespoke workflow search
         description_md: >
           The GTN's
           {gtn modal}[Pan-Galactic Workflow Search](https://training.galaxyproject.org/training-material/workflows/list.html)
           allows you to search for workflows across all of Galaxy!
 
+        button_icon: run
+        button_tip: Launch site in tutorial-mode
+
           It's even possible to do an
           {gtn modal}[advanced search](https://training.galaxyproject.org/training-material/news/2023/11/20/workflow-search.html)
           to find exactly what you need.
 
+        button_icon: tutorial
+        button_tip: Launch tutorial
+
       - title_md: How to share your workflow
         description_md: >
-          The GTN's
-          {gtn modal}[Pan-Galactic Workflow Search](https://training.galaxyproject.org/training-material/workflows/list.html)
-          allows you to search for workflows across all of Galaxy!
-
-          It's even possible to do an
-          {gtn modal}[advanced search](https://training.galaxyproject.org/training-material/news/2023/11/20/workflow-search.html)
-          to find exactly what you need.
+          <iframe src="https://oembed.apps.galaxyproject.eu/oembed?style=gtn&format=iframe-embed&url=https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_publish.html"
+                  width="100%"
+                  height="350px"
+                  style="border:none;">
+          </iframe>

subdomains/singlecell/sections/4_community.yml

@@ -8,32 +8,40 @@ tabs:
         description_md: >
           <iframe src="https://oembed.apps.galaxyproject.eu/oembed?style=gtn&format=iframe-embed&url=https://training.galaxyproject.org/training-material/topics/single-cell/faqs/user_community_join.html#how-can-i-talk-with-other-users.html"
           width="100%"
-          height="600px">
+          height="430px">
           </iframe>
       - title_md: Join our community!
         description_md: >
-          This Galaxy space is the result of seemingly infinite hours of hard work by a number of people. It is maintained by the [Galaxy Single-cell & sPatial Omics **(SPOC)** Community of Practice])(https://galaxyproject.org/community/sig/singlecell/). This group unites scientists like yourself with software developers and bioinformaticians to create, share and test resources to make single-cell & spatial omics analysis easier.
+
+          This Galaxy space is the result of hard, collaborative work by many contributors .
+
+          It is maintained by the [Galaxy Single-cell & sPatial Omics **SPOC** Community of Practice](https://galaxyproject.org/community/sig/singlecell/).
+
+          This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make single-cell & spatial omics analysis easier.
+
           Check out our site and join our community!
-          [Galaxy Single-cell & sPatial Omics **(SPOC)** Community of Practice])(https://galaxyproject.org/community/sig/singlecell/)
+
         button_link: "https://galaxyproject.org/community/sig/singlecell/"
         button_icon: run
         button_tip: Visit SPOC
       - title_md: Contributors
         description_md: >
           ### Contributors
 
-          - also Gareth & Cameron!
+          - [Wendi Bacon](https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/)
+
+          - [Cameron Hyde](https://github.com/neoformit)
 
           - [Mehmet Tekman](https://github.com/mtekman)
 
           - [Pavankumar Videm](https://github.com/pavanvidem)
 
-          - [Wendi Bacon](https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/)
-
           - [Pablo Moreno](https://github.com/pcm32)
 
           - [José Domínguez](https://github.com/kysrpex)
 
+          - [Gareth Price](https://github.com/GarethPrice-Aus)
+
           - [Alex Ostrovsky](https://github.com/astrovsky01)
 
           - [Andrey Solovyev](https://github.com/a-solovyev12)
@@ -81,7 +89,7 @@ tabs:
     heading_md: >
       <iframe src="https://oembed.apps.galaxyproject.eu/oembed?style=gtn&format=iframe-embed&url=https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html"
               width="100%"
-              height="600px"
+              height="620px"
               style="border:none;">
       </iframe>
     content: []

subdomains/singlecell/templates/intro.html

@@ -7,7 +7,9 @@
     Access Single Cell Omics analysis tutorials, tools, and workflows that let you analyse data without programming experience or private infrastructure.
   </p>
 
-  <img class="w-100 my-3 mx-auto" style="max-width: 400px;" src="https://github.com/galaxyproject/galaxy_codex/blob/main/results/spoc/tools_wordcloud.png?raw=true" alt="Word cloud of common single cell tools including Seurat and Scanpy">
+    <div style="text-align: center;">
+      <img class="w-100 my-3 mx-auto" style="max-width: 400px;" src="https://github.com/galaxyproject/galaxy_codex/blob/main/results/spoc/tools_wordcloud.png?raw=true" alt="Word cloud of common single cell tools including Seurat and Scanpy">
+    </div>
 
   <p>
     <a