Merge branch 'main' into edit_CUTnRUN

galaxyproject · Dec 7, 2024 · 3c41b9e · 3c41b9e
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diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -51,6 +51,7 @@ awspolly:
 
 # our real contributors <3 (please add yourself in alphabetical order)
 
+
 a-asai:
     name: Atsushi Asai
     email: [email protected]
@@ -86,6 +87,14 @@ abueg:
     orcid: 0000-0002-6879-3954
     joined: 2022-01
 
+adya29:
+    name: Adya Shreya
+    email: [email protected]
+    joined: 2024-12
+    linkedin: adya-shreya
+    location:
+      country: SG
+
 adairama:
     name: Adaikalavan Ramasamy
     email: [email protected]
@@ -95,6 +104,7 @@ adairama:
     location:
       country: SG
 
+
 ahmedhamidawan:
     name: Ahmed Hamid Awan
     email: [email protected]

diff --git a/events/2022-07-08-gat.md b/events/2022-07-08-gat.md
@@ -119,7 +119,7 @@ program:
         topic: admin
       - name: tool-integration
         topic: dev
-      - name: processing-many-samples-at-once
+      - name: collections
         topic: galaxy-interface
       - name: upload-rules
         topic: galaxy-interface

diff --git a/events/2023-04-17-gat-gent.md b/events/2023-04-17-gat-gent.md
@@ -223,7 +223,7 @@ program:
         time: "11:30 - 11:45"
       - name: tool-integration
         topic: dev
-      - name: processing-many-samples-at-once
+      - name: collections
         topic: galaxy-interface
       - name: upload-rules
         topic: galaxy-interface

diff --git a/faqs/galaxy/visualisations_igv.md b/faqs/galaxy/visualisations_igv.md
@@ -4,6 +4,7 @@ area: visualisation
 box_type: tip
 layout: faq
 contributors: [shiltemann]
+redirect_from: [/topics/galaxy-interface/tutorials/processing-many-samples-at-once/faqs/visualisations_igv]
 ---
 
 You can send data from your Galaxy history to IGV for viewing as follows:

diff --git a/learning-pathways/admin-training.md b/learning-pathways/admin-training.md
@@ -88,7 +88,7 @@ pathway:
         topic: admin
       - name: tool-integration
         topic: dev
-      - name: processing-many-samples-at-once
+      - name: collections
         topic: galaxy-interface
       - name: upload-rules
         topic: galaxy-interface

diff --git a/news/_posts/2024-12-06-spoc_cofest.md b/news/_posts/2024-12-06-spoc_cofest.md
@@ -0,0 +1,19 @@
+---
+title: "SPOC CoFest 2024: How did it go?"
+contributions:
+  authorship: [nomadscientist]
+tags: [gtn, single-cell]
+layout: news
+cover: "news/images/2023_dec_sc.png"
+coveralt: "swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)"
+---
+
+# First SPOC CoFest
+
+We held our first 🖖🏾[SPOC CoFest]({% link events/2024-12-06-spoc-cofest-2024.md %}), in the great tradition of the excellent CoFests organised in the GTN that welcomed @gtn:nomadscientist and many others into the community.
+
+We welcomed a diverse group of participants, from experienced Galaxy trainers to bioinformaticians with little to no Galaxy experience whatsoever. We also were lucky enough to be joined by a 5-strong outpost from Singapore, prompting a Pacific-time-zone kick-off session prior to our day-long event.
+
+🎉A big thank you to all the participants for their hard work!🎉
+
+![Chart showing: 14 new participants, 5 experienced SPOC members, 60% attendance rate, 12 PRs made, 5 tutorials tested on different servers, 2 workflows updated, 8 issues raised, 2 new tutorials WIP, 5 slide decks updated, 1 trained trainer]({% link news/images/2024-12-06-spoc-cofest_outputs.png %} "SPOC CoFest: By the numbers")
diff --git a/news/images/2024-12-06-spoc-cofest_outputs.png b/news/images/2024-12-06-spoc-cofest_outputs.png
diff --git a/topics/admin/tutorials/monitoring/tutorial.md b/topics/admin/tutorials/monitoring/tutorial.md
@@ -364,7 +364,7 @@ Setting up Telegraf is again very simple. We just add a single role to our playb
 >    +  - plugin: disk
 >    +  - plugin: kernel
 >    +  - plugin: processes
->    +  - plugin: io
+>    +  - plugin: diskio
 >    +  - plugin: mem
 >    +  - plugin: system
 >    +  - plugin: swap

diff --git a/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.md b/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.md
@@ -86,7 +86,7 @@ publishable as a real Data Paper giving recognition to all the people that helpe
 >
 > 1. Create a new history for this tutorial
 > 2. Import this metadata file from [Zenodo]({{ page.zenodo_link }}) to test it
->     -> Training Data for "Creating Quality FAIR assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS"):
+>     -> Training Data for "Creating Quality FAIR assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS":
 >    ```
 >    https://zenodo.org/record/8130567/files/Kakila_database_marine_mammal.xml
 >    ```
@@ -109,7 +109,7 @@ you want to use.
 
 ![Interface when file is selected](./Images/upload_1.png){:width="500"}
 
-After uploading the file, or if you have indicate it as input data if the tool, you just have to click on **Execute** to launch the tool with the file.
+After uploading the file, or if you have indicated it as input data in the tool form, you just have to click on **Execute** to launch MetaShRIMPS jobs with the file.
 
 # Outputs
 

diff --git a/topics/galaxy-interface/metadata.yaml b/topics/galaxy-interface/metadata.yaml
@@ -5,6 +5,11 @@ title: "Using Galaxy and Managing your Data"
 summary: "A collection of microtutorials explaining various features of the Galaxy user interface and manipulating data within Galaxy."
 docker_image:
 requirements:
+  -
+    type: "internal"
+    topic_name: introduction
+    tutorials:
+      - galaxy-intro-101
 
 subtopics:
   - id: upload

diff --git a/topics/galaxy-interface/tutorials/collections/faqs/index.md b/topics/galaxy-interface/tutorials/collections/faqs/index.md
@@ -1,3 +1,5 @@
 ---
 layout: faq-page
+redirect_from:
+- /topics/galaxy-interface/tutorials/processing-many-samples-at-once/faqs/index
 ---
diff --git a/...amples-at-once/faqs/visualisations_igv.md → ...ls/collections/faqs/visualisations_igv.md b/...amples-at-once/faqs/visualisations_igv.md → ...ls/collections/faqs/visualisations_igv.md
diff --git a/topics/galaxy-interface/tutorials/collections/tutorial.md b/topics/galaxy-interface/tutorials/collections/tutorial.md
@@ -2,6 +2,8 @@
 layout: tutorial_hands_on
 redirect_from:
   - /topics/galaxy-data-manipulation/tutorials/collections/tutorial
+  - /topics/galaxy-data-manipulation/tutorials/processing-many-samples-at-once/tutorial
+  - /topics/galaxy-interface/tutorials/processing-many-samples-at-once/tutorial
 
 title: "Using dataset collections"
 zenodo_link: "https://doi.org/10.5281/zenodo.5119008"
@@ -46,6 +48,7 @@ recordings:
 
 Here we will show Galaxy features designed to help with the analysis of large numbers of samples. When you have just a few samples - clicking through them is easy. But once you've got hundreds - it becomes very annoying. In Galaxy we have introduced **Dataset collections** that allow you to combine numerous datasets in a single entity that can be easily manipulated.
 
+
 # Getting data
 
 First, we need to upload datasets. Cut and paste the following URLs to Galaxy upload tool (see a {% icon tip %} **Tip** on how to do this [below](#tip-upload-fastqsanger-datasets-via-links)).

diff --git a/topics/galaxy-interface/tutorials/processing-many-samples-at-once/faqs/index.md b/topics/galaxy-interface/tutorials/processing-many-samples-at-once/faqs/index.md
diff --git a/topics/galaxy-interface/tutorials/processing-many-samples-at-once/tutorial.md b/topics/galaxy-interface/tutorials/processing-many-samples-at-once/tutorial.md
diff --git a/topics/single-cell/metadata.yaml b/topics/single-cell/metadata.yaml
@@ -24,6 +24,9 @@ editorial_board:
   - nomadscientist
   - mtekman
   - pavanvidem
+  - hexhowells
+  - MarisaJL
+  - heylf
 
 toc: true  # create table of contents for the subtopics
 subtopics:

diff --git a/...s/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md b/...s/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md
@@ -6,11 +6,6 @@ subtopic: single-cell-CS
 priority: 3
 zenodo_link: 'https://zenodo.org/record/7053673'
 
-input_histories:
-  - label: "UseGalaxy.eu"
-    history: https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data
-
-
 questions:
 - Is my single cell dataset a quality dataset?
 - How do I pick thresholds and parameters in my analysis? What’s a “reasonable” number, and will the world collapse if I pick the wrong one?

diff --git a/topics/single-cell/tutorials/scrna-intro/slides.html b/topics/single-cell/tutorials/scrna-intro/slides.html
@@ -98,9 +98,9 @@
 
 |Attribute| Summary |
 |-:|:-|
-| Resolution| Individual cells within tissues |
-| Signal | Individual gene expression per cell |
-| Differential Expression | Some cells express the same set of genes in the same way; comparing one set of cells against another |
+|Resolution| Individual cells within tissues |
+|Signal | Individual gene expression per cell |
+|Differential Expression | Some cells express the same set of genes in the same way; comparing one set of cells against another |
 
 ]
 ]
@@ -186,7 +186,7 @@
 
 --
 
-__Biological Replicates__
+
 
 .center[
 .reduce90[