From 69b1829e5492deae75a41d89741964e9be7227ea Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 16:24:44 +0000 Subject: [PATCH 01/17] Add news widget to main page --- topics/single-cell/index.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index a7d9d0ba06f5f6..a8fac47525469d 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -9,7 +9,7 @@ topic_name: single-cell Check out workflows shared by users like you! - + ## Want to contribute? @@ -18,3 +18,11 @@ If you want to help us behind the scenes, from testing workflows and tutorials t - {% icon point-right %} [Community of Practice](https://galaxyproject.org/projects/singlecell/) - {% icon feedback %} [Matrix Chat Forum](https://matrix.to/#/#spoc3:matrix.org) - {% icon email %} [Mailing List](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) + +## News & Events +
+

News and Events

+
+ +
+
From 2453fc051eff973e0f9f0ef38c84c575c29f7dd5 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 16:32:45 +0000 Subject: [PATCH 02/17] ToC attempt 1 --- topics/single-cell/metadata.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/topics/single-cell/metadata.yaml b/topics/single-cell/metadata.yaml index 56d84d08957db2..f51d51c48c94c0 100644 --- a/topics/single-cell/metadata.yaml +++ b/topics/single-cell/metadata.yaml @@ -8,6 +8,16 @@ summary: | What else do you want to see? You can submit tool and/or tutorial request on our [Single Cell Community Tool Request Spreadsheet](https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing). {: .alert.alert-success} + +> +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + #docker_image: "quay.io/galaxy/transcriptomics-training" learning_path_cta: intro_single_cell From 2cd954a41c9a3096a302cc200748acda3571e8b8 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 16:38:31 +0000 Subject: [PATCH 03/17] move ToC --- topics/single-cell/metadata.yaml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/topics/single-cell/metadata.yaml b/topics/single-cell/metadata.yaml index f51d51c48c94c0..067afbb9a1bedc 100644 --- a/topics/single-cell/metadata.yaml +++ b/topics/single-cell/metadata.yaml @@ -9,15 +9,6 @@ summary: | What else do you want to see? You can submit tool and/or tutorial request on our [Single Cell Community Tool Request Spreadsheet](https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing). {: .alert.alert-success} -> -> -> In this tutorial, we will cover: -> -> 1. TOC -> {:toc} -> -{: .agenda} - #docker_image: "quay.io/galaxy/transcriptomics-training" learning_path_cta: intro_single_cell @@ -78,3 +69,13 @@ references: title: "User-friendly, scalable tools and workflows for single-cell RNA-seq analysis" link: "https://www.nature.com/articles/s41592-021-01102-w" summary: "" + +--- +> +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} From c176d19ddbbc293bff94b28c758bf9e7100e8e37 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 16:43:37 +0000 Subject: [PATCH 04/17] testing news columns --- topics/single-cell/index.md | 38 ++++++++++++++++++++++++++++--------- 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index a8fac47525469d..ee47eab175fc32 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -7,10 +7,38 @@ topic_name: single-cell ## Want to explore analysis beyond our tutorials? -Check out workflows shared by users like you! + +## News & Events +
+
+

Publicly shared workflow

+ "Check out workflows shared by users like you!" + +

News and Events

+ +
+
+ +
+
+ +
+

Publicly Shared Workflow

+

Check out workflows shared by users like you!

+ +
+ + +
+

News and Events

+ +
+
+
+ ## Want to contribute? If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single-cell & sPatial Omics Community of Practice! @@ -18,11 +46,3 @@ If you want to help us behind the scenes, from testing workflows and tutorials t - {% icon point-right %} [Community of Practice](https://galaxyproject.org/projects/singlecell/) - {% icon feedback %} [Matrix Chat Forum](https://matrix.to/#/#spoc3:matrix.org) - {% icon email %} [Mailing List](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) - -## News & Events -
-

News and Events

-
- -
-
From 3bd390389dd9416816f35b0e748a0834795c82f8 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 16:51:57 +0000 Subject: [PATCH 05/17] try 3 on news columns --- topics/single-cell/index.md | 31 ++++++++++++------------------- 1 file changed, 12 insertions(+), 19 deletions(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index ee47eab175fc32..b4cb7c01e4138a 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -7,37 +7,30 @@ topic_name: single-cell ## Want to explore analysis beyond our tutorials? - - ## News & Events
-
-

Publicly shared workflow

- "Check out workflows shared by users like you!" -

News and Events

-
-
+
-
-

Publicly Shared Workflow

-

Check out workflows shared by users like you!

- -
+
+

Publicly Shared Workflow

+

Check out workflows shared by users like you!

+ +
- -
-

News and Events

- -
+ +
+

News and Events

+
-
+ + ## Want to contribute? From 1213b44cb9d9e7913016f94cf82ec48b9a5b3add Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 17:18:16 +0000 Subject: [PATCH 06/17] Specify tests --- topics/single-cell/index.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index b4cb7c01e4138a..ed793e63e3592c 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -9,13 +9,15 @@ topic_name: single-cell -## News & Events +## News & Events - new testing

News and Events

+## News & Events - ROW +
From 0c39d893016f3bcffca6d034447ad39cc807e411 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 17:35:53 +0000 Subject: [PATCH 07/17] fix workflows --- topics/single-cell/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index ed793e63e3592c..e14bec53c26385 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -23,7 +23,7 @@ topic_name: single-cell

Publicly Shared Workflow

Check out workflows shared by users like you!

- +
From e3c56cdafa1877a1ec5fcf1087a1257b4b78fff6 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 17:37:34 +0000 Subject: [PATCH 08/17] metadata order change? --- topics/single-cell/metadata.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/topics/single-cell/metadata.yaml b/topics/single-cell/metadata.yaml index 067afbb9a1bedc..5f5f5e23fb30f6 100644 --- a/topics/single-cell/metadata.yaml +++ b/topics/single-cell/metadata.yaml @@ -3,6 +3,10 @@ name: single-cell type: use topic_type: technology title: Single Cell + +learning_path_cta: intro_single_cell +gitter: Galaxy-Training-Network_galaxy-single-cell:gitter.im + summary: | Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!). When you generate your lovely gene lists for your cells, consider checking out our Transcriptomics tutorials for further network analysis! @@ -11,9 +15,6 @@ summary: | #docker_image: "quay.io/galaxy/transcriptomics-training" -learning_path_cta: intro_single_cell -gitter: Galaxy-Training-Network_galaxy-single-cell:gitter.im - requirements: - type: "internal" From 9875bb76a7e9489cb0e0296430f3d8fc3e7f5623 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 17:56:47 +0000 Subject: [PATCH 09/17] try again --- topics/single-cell/index.md | 30 +++++++++++++++++++++--------- topics/single-cell/metadata.yaml | 4 ++-- 2 files changed, 23 insertions(+), 11 deletions(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index e14bec53c26385..2d0ccb3a35fa3c 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -3,6 +3,15 @@ layout: topic topic_name: single-cell --- +> +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + {% snippet faqs/galaxy/analysis_troubleshooting.md sc=true %} ## Want to explore analysis beyond our tutorials? @@ -16,21 +25,24 @@ topic_name: single-cell
-## News & Events - ROW +## News & Events - ROW2
- -
-

Publicly Shared Workflow

-

Check out workflows shared by users like you!

- -
- - +

News and Events

+ +
+

Want to Contribute?

+

If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single-cell & Spatial Omics Community of Practice!

+
    +
  • {% icon point-right %} [Community of Practice](https://galaxyproject.org/projects/singlecell/)
    • +
  • {% icon feedback %} [Matrix Chat Forum](https://matrix.to/#/#spoc3:matrix.org)
    • +
  • {% icon email %} [Mailing List](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/)
    • +
+
diff --git a/topics/single-cell/metadata.yaml b/topics/single-cell/metadata.yaml index 5f5f5e23fb30f6..ba3ac5f5b65e1d 100644 --- a/topics/single-cell/metadata.yaml +++ b/topics/single-cell/metadata.yaml @@ -8,9 +8,9 @@ learning_path_cta: intro_single_cell gitter: Galaxy-Training-Network_galaxy-single-cell:gitter.im summary: | - Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!). When you generate your lovely gene lists for your cells, consider checking out our Transcriptomics tutorials for further network analysis! + Training material and practicals for all kinds of single cell analysis (particularly scRNA-seq!). - What else do you want to see? You can submit tool and/or tutorial request on our [Single Cell Community Tool Request Spreadsheet](https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing). + What else do you want to see? You can submit tool or tutorial requests, or upvote other requests, on our [Single-Cell & Spatial Omics Tool Request Spreadsheet](https://docs.google.com/spreadsheets/d/15hqgqA-RMDhXR-ylKhRF-Dab9Ij2arYSKiEVoPl2df4/edit?usp=sharing). {: .alert.alert-success} #docker_image: "quay.io/galaxy/transcriptomics-training" From d6384647620ad87aee79ce2825f9f6f29ae62022 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 18:02:39 +0000 Subject: [PATCH 10/17] trying to use the event horizon --- topics/single-cell/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index 2d0ccb3a35fa3c..669f3e65e12971 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -45,6 +45,8 @@ topic_name: single-cell
+## Try event horizon +{{event.title}}{% if event.draft %} (draft, will be hidden) {% endif %} ## Want to contribute? From d7d543dfa39a171ad9d49c4303e2683095f68554 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 18:10:58 +0000 Subject: [PATCH 11/17] event horizon try 2 --- topics/single-cell/index.md | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index 669f3e65e12971..f3d73467fc395e 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -38,9 +38,9 @@ topic_name: single-cell

Want to Contribute?

If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single-cell & Spatial Omics Community of Practice!

@@ -48,6 +48,23 @@ topic_name: single-cell ## Try event horizon {{event.title}}{% if event.draft %} (draft, will be hidden) {% endif %} +## Try event horizon 2 +{% assign upcoming_events = site | get_upcoming_events_for_this: new_material %} +{% assign upcoming_event_count = upcoming_events | size %} +{% if upcoming_event_count > 0 %} +
+
+ +
+ +

Want to learn more with a live instructor? Check out these upcoming events:

+ {% include _includes/event-table.html events=upcoming_events campaign="via-tutorial" %} +
+{% endif %} + ## Want to contribute? If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single-cell & sPatial Omics Community of Practice! From fc3d23e2939e396773eb15cd639a42fa8a6127a7 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 18:15:58 +0000 Subject: [PATCH 12/17] fix optimising --- topics/single-cell/index.md | 57 ++++--------------------------------- 1 file changed, 6 insertions(+), 51 deletions(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index f3d73467fc395e..9a8a2f8054921e 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -3,68 +3,23 @@ layout: topic topic_name: single-cell --- -> -> -> In this tutorial, we will cover: -> -> 1. TOC -> {:toc} -> -{: .agenda} - {% snippet faqs/galaxy/analysis_troubleshooting.md sc=true %} ## Want to explore analysis beyond our tutorials? - - -## News & Events - new testing -
-

News and Events

- - -
- -## News & Events - ROW2 -
- +
+ +

Public workflows

+ +
+

News and Events

- -
-

Want to Contribute?

-

If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single-cell & Spatial Omics Community of Practice!

- -
-## Try event horizon -{{event.title}}{% if event.draft %} (draft, will be hidden) {% endif %} - -## Try event horizon 2 -{% assign upcoming_events = site | get_upcoming_events_for_this: new_material %} -{% assign upcoming_event_count = upcoming_events | size %} -{% if upcoming_event_count > 0 %} -
-
- -
- -

Want to learn more with a live instructor? Check out these upcoming events:

- {% include _includes/event-table.html events=upcoming_events campaign="via-tutorial" %} -
-{% endif %} - ## Want to contribute? If you want to help us behind the scenes, from testing workflows and tutorials to building tools, join our Galaxy Single-cell & sPatial Omics Community of Practice! From e1373cf0b5ff97e5faccc5e3a02b37fb0767a972 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 18:19:10 +0000 Subject: [PATCH 13/17] change heading levels --- topics/single-cell/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index 9a8a2f8054921e..3974bf1884dc58 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -10,12 +10,12 @@ topic_name: single-cell
-

Public workflows

+

Public workflows

-

News and Events

+

News and Events

From ee8f976fdf34cc54a065c55747a963f038e4ffef Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 19:08:59 +0000 Subject: [PATCH 14/17] change to daily digest --- topics/single-cell/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index 3974bf1884dc58..d84369e3dd6d5e 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -16,7 +16,7 @@ topic_name: single-cell

News and Events

- +
From 4cb7b5e76afac824465326e0a448303494cbdb13 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Mon, 2 Dec 2024 19:11:59 +0000 Subject: [PATCH 15/17] Revert "change to daily digest" This reverts commit ee8f976fdf34cc54a065c55747a963f038e4ffef. --- topics/single-cell/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/single-cell/index.md b/topics/single-cell/index.md index d84369e3dd6d5e..3974bf1884dc58 100644 --- a/topics/single-cell/index.md +++ b/topics/single-cell/index.md @@ -16,7 +16,7 @@ topic_name: single-cell

News and Events

- +
From 00e2438409dcd7cb25a016b2b158bae9c8bc2d2f Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Wed, 4 Dec 2024 12:53:02 +0100 Subject: [PATCH 16/17] add topic toc option --- _layouts/topic.html | 14 ++++++++++++++ topics/single-cell/metadata.yaml | 10 +--------- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/_layouts/topic.html b/_layouts/topic.html index 6c60dacafed55c..059d2b75076dc4 100644 --- a/_layouts/topic.html +++ b/_layouts/topic.html @@ -45,6 +45,20 @@

Not sure where to start?

{% endif %}

Material

+ + {% if topic.toc %} +

+

+
Jump to a section!
+ +
+

+ {% endif %} + You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides ({% icon slides %}) and tutorial ({% icon tutorial %}) buttons below. {% if topic.draft %} diff --git a/topics/single-cell/metadata.yaml b/topics/single-cell/metadata.yaml index ba3ac5f5b65e1d..b0dadc8ca676e8 100644 --- a/topics/single-cell/metadata.yaml +++ b/topics/single-cell/metadata.yaml @@ -25,6 +25,7 @@ editorial_board: - mtekman - pavanvidem +toc: true # create table of contents for the subtopics subtopics: - id: scintroduction title: "Introduction" @@ -71,12 +72,3 @@ references: link: "https://www.nature.com/articles/s41592-021-01102-w" summary: "" ---- -> -> -> In this tutorial, we will cover: -> -> 1. TOC -> {:toc} -> -{: .agenda} From 3d10cf84d8d93ff16087e07bdbdf9e2b24cdf0b9 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Wed, 4 Dec 2024 13:02:08 +0100 Subject: [PATCH 17/17] add toc to schema --- bin/schema-topic.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/bin/schema-topic.yaml b/bin/schema-topic.yaml index f3d36b8a715565..2f96b1a51290eb 100644 --- a/bin/schema-topic.yaml +++ b/bin/schema-topic.yaml @@ -66,6 +66,11 @@ mapping: The image ID for an image which contains all of the tools and data for this topic. _examples: - quay.io/galaxy/sequence-analysis-training + toc: + type: bool + required: false + description: + For large topics with many subtopics, set this to true to generate a table of contents above the tutorial table to support quickly jumping to a subtopic. subtopics: type: seq required: false @@ -219,7 +224,7 @@ mapping: type: str description: | The alt text for the logo (MANDATORY). - learning_path_cta: + learning_path_cta: type: str description: | The specific learning path you wish to reference as a call-to-action for views who aren't sure where to get started.