Merge branch 'main' into sujaikumar-lotus2-identifying-fungi

.github/workflows/ci-main.yml

@@ -66,8 +66,8 @@ jobs:
 
       - name: Check Tutorial Formatting
         run: |
-          find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review
-          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-on-error
+          find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review -fail-level=any
+          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-level=any
         env:
             REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

Gemfile.lock

@@ -110,7 +110,7 @@ GEM
     typhoeus (1.4.0)
       ethon (>= 0.9.0)
     unicode-display_width (2.5.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
     yell (2.2.2)
     zeitwerk (2.6.12)
 

_config.yml

@@ -166,6 +166,7 @@ icon-tag:
   galaxy-toggle: fas fa-toggle-on
   galaxy-upload: fas fa-upload
   galaxy-download: fas fa-download
+  galaxy-wf-best-practices: fas fa-wand-magic-sparkles
   galaxy-wf-connection: fas fa-arrows-alt-h
   galaxy-wf-edit: fa fa-edit
   galaxy-wf-new: fas fa-plus

_layouts/event.html

@@ -502,14 +502,15 @@ <h3>Promote the Event</h3>
 
         // on load of the page: switch to the currently selected tab
         var hash = window.location.hash;
-
-        var potential_tab = $('#myTab button[data-target="' + hash + '"]')
-        if (potential_tab.length != 0) {
-            potential_tab.tab('show');
-        } else {
-            var target_tab = '#' + $(`${hash}`).closest(".tab-pane").attr("id")
-            $('#myTab button[data-target="' + target_tab + '"]').tab('show');
-            $(hash).get(0).scrollIntoView();
+        if (hash){
+        	var potential_tab = $('#myTab button[data-target="' + hash + '"]')
+        	if (potential_tab.length != 0) {
+            	potential_tab.tab('show');
+        	} else {
+            	var target_tab = '#' + $(`${hash}`).closest(".tab-pane").attr("id")
+            	$('#myTab button[data-target="' + target_tab + '"]').tab('show');
+            	$(hash).get(0).scrollIntoView();
+        	}
         }
     });
 })(window, document);

_plugins/jekyll-jsonld.rb

@@ -3,6 +3,7 @@
 require 'json'
 require './_plugins/gtn'
 require './_plugins/gtn/git'
+require './_plugins/util'
 
 module Jekyll
   # Generate JSON-LD metadata for the GTN.
@@ -794,12 +795,35 @@ def generate_material_jsonld(material, topic, site)
 
       data['isPartOf'] = topic_desc
 
+      data['abstract'] = material
+        .fetch('content', '')
+        .strip
+        .split("\n")
+        .first
+
+      if ! data['abstract'].nil?
+        data['abstract'] = data['abstract']
+          .gsub(/\{\{\s*site.baseurl\s*\}\}/, url_prefix(site))
+          .gsub(/\[{{\s*site.url\s*}}/, '[' + url_prefix(site))
+          .gsub(/{% link (topics[^%]*).md %}/, url_prefix(site) + '\1.html')
+          .gsub(/{% link (topics[^%]*).html %}/, url_prefix(site) + '\1.html')
+          .gsub(/\s*\(?{%\s*cite [^}]+\s*%}\)?/, '')
+          .gsub('{{ site.github_repository }}', safe_site_config(site, 'github_repository', 'https://example.com'))
+          .gsub(/{% snippet ([^%]*) %}/, '')
+          .gsub(/{% include ([^%]*) %}/, '')
+      end
+
+      description.push("## Abstract\n\n#{data['abstract']}\n\n")
+
       if (material['name'] == 'tutorial.md') || (material['name'] == 'slides.html')
-        data['learningResourceType'] = if material['name'] == 'tutorial.md'
-                                         'hands-on tutorial'
-                                       else
-                                         'slides'
-                                       end
+
+        if material['name'] == 'tutorial.md'
+          data['learningResourceType'] = 'e-learning'
+          description.push("## About This Material\n\nThis is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.\n\n")
+        else
+          data['learningResourceType'] = 'slides'
+        end
+
         data['name'] = material['title']
         data['url'] = "#{site['url']}#{site['baseurl']}#{material['url']}"
 
@@ -817,8 +841,8 @@ def generate_material_jsonld(material, topic, site)
           description.push("## Questions this #{material['type']} will address\n\n - #{questions}\n\n")
         end
         if material.key?('objectives') && !material['objectives'].nil? && material['objectives'].length.positive?
-          objectives = material['objectives'].join("\n - ")
-          description.push("## Learning Objectives\n\n - #{objectives}\n\n")
+          objectives = material['objectives'].map{|x| "- #{x}"}.join("\n")
+          description.push("## Learning Objectives\n\n#{objectives}\n\n")
           data['teaches'] = objectives
         end
         if material.key?('keypoints') && !material['keypoints'].nil? && material['keypoints'].length.positive?
@@ -844,12 +868,41 @@ def generate_material_jsonld(material, topic, site)
                         name: "Associated Workflows"
                       })
       end
-      if actual_material.key?('zenodo_link')
-        mentions.push({
-                        '@type': 'Thing',
-                        url: (actual_material['zenodo_link']).to_s,
-                        name: "Associated Training Datasets"
-                      })
+
+      # Notebooks
+      if actual_material.key?('notebook')
+        if actual_material['notebook']['language'] != 'r'
+          # Python, Bash, SQL (all via jupyter)
+          url = "#{site['url']}#{site['baseurl']}#{material['dir']}#{material['topic_name']}-#{material['tutorial_name']}.ipynb"
+          mentions.push({
+                          '@type': 'Thing',
+                          url: url,
+                          name: "Jupyter Notebook (with Solutions)"
+                        })
+          mentions.push({
+                          '@type': 'Thing',
+                          url: url.gsub(/\.ipynb$/, '-course.ipynb'),
+                          name: "Jupyter Notebook (without Solutions)"
+                        })
+        elsif actual_material['notebook']['language'] == 'r' # Actual R
+          url = "#{site['url']}#{site['baseurl']}#{material['dir']}#{material['topic_name']}-#{material['tutorial_name']}.Rmd"
+          mentions.push({
+                          '@type': 'Thing',
+                          url: url,
+                          name: "Quarto/RMarkdown Notebook"
+                        })
+        end
+      end
+
+      # Zenodo link out
+      if actual_material.key?('zenodo_link') && ! actual_material['zenodo_link'].nil?
+        if actual_material['zenodo_link'].length.positive?
+          mentions.push({
+                          '@type': 'Thing',
+                          url: (actual_material['zenodo_link']).to_s,
+                          name: "Associated Training Datasets"
+                        })
+        end
       end
 
       if description.empty?
@@ -905,7 +958,7 @@ def generate_material_jsonld(material, topic, site)
                             '@context': 'http://schema.org',
                             '@type': 'LearningResource',
                             url: (page['hands_on_url']).to_s,
-                            learningResourceType: 'hands-on tutorial',
+                            learningResourceType: 'e-learning',
                             interactivityType: 'expositive',
                           }
                         )
@@ -921,7 +974,7 @@ def generate_material_jsonld(material, topic, site)
                                "/#{tuto}/tutorial.html",
                           name: (page['title']).to_s,
                           description: "Hands-on for '#{page['title']}' tutorial",
-                          learningResourceType: 'hands-on tutorial',
+                          learningResourceType: 'e-learning',
                           interactivityType: 'expositive',
                           provider: GTN
                         }
@@ -991,7 +1044,6 @@ def generate_material_jsonld(material, topic, site)
 
       data['educationalLevel'] = material.key?('level') ? eduLevel[material['level']] : 'Beginner'
       data['mentions'] = mentions
-      data['abstract'] = material.fetch('content', '').strip.split("\n").first
 
       data
     end

_plugins/util.rb

@@ -27,3 +27,26 @@ def collapse_event_date_pretty(event)
     "#{s.strftime('%B')} #{s.day}, #{s.year}#{dash}#{e.strftime('%B')} #{e.day}, #{e.year}"
   end
 end
+
+def safe_site_config(site, key, default)
+  if !site.config.nil? && site.config.key?(key)
+    site.config[key]
+  else
+    default
+  end
+end
+
+
+def url_prefix(site)
+  if !site.config.nil? && site.config.key?('url')
+    "#{site.config['url']}#{site.config['baseurl']}"
+  else
+    'http://localhost:4000/training-material/'
+  end
+end
+
+def markdownify(site, text)
+  site.find_converter_instance(
+    Jekyll::Converters::Markdown
+  ).convert(text.to_s)
+end

faqs/galaxy/workflows_best_practices.md

@@ -3,17 +3,23 @@ title: Ensuring Workflows meet Best Practices
 area: workflows
 box_type: tip
 layout: faq
-contributors: [hexylena]
+contributors: [hexylena, elichad]
 ---
 
 When you are editing a workflow, there are a number of additional steps you can take to ensure that it is a Best Practice workflow and will be more reusable.
 
 1. Open a workflow for editing
-1. In the workflow menu bar, you'll find the {% icon galaxy-wf-options %} Workflow Options dropdown menu.
-1. Click on it and select "Best Practices" from the dropdown menu.
+1. In the workflow menu bar, you'll find the {% icon galaxy-wf-options %} **Workflow Options** dropdown menu.
+1. Click on it and select {% icon galaxy-wf-best-practices %} **Best Practices** from the dropdown menu.
 
    ![screenshot showing the best practices menu item in the gear dropdown.]({% link faqs/galaxy/images/best-practices1.png %})
 
 1. This will take you to a new side panel, which allows you to investigate and correct any issues with your workflow.
 
    ![screenshot showing the best practices side panel. several issues are raised like a missing annotation with a link to add that, and non-optional inputs that are unconnected. Additionally several items already have green checks like the workflow defining creator information and a license.]({% link faqs/galaxy/images/best-practices2.png %})
+
+The Galaxy community also has a [guide on best practices for maintaining workflows](https://planemo.readthedocs.io/en/latest/best_practices_workflows.html). This guide includes the best practices from the Galaxy workflow panel, plus:
+
+* adding tests to the workflow
+* publishing the workflow on GitHub, a public GitLab server, or another public version-controlled repository
+* registering the workflow with a workflow registry such as WorkflowHub or Dockstore

topics/assembly/tutorials/assembly-decontamination/tutorial.md

@@ -1,6 +1,5 @@
 ---
 layout: tutorial_hands_on
-
 title: Decontamination of a genome assembly
 zenodo_link: https://zenodo.org/records/13367433
 questions:
@@ -11,14 +10,27 @@ objectives:
 - Remove Mitochondrial DNA from an assembly
 time_estimation: 1H30M
 key_points:
-- Assembly decontamination is important to avoid false identification of genes, blast hits...
+- Assembly decontamination is important to avoid false identification of genes, blast
+  hits...
 contributions:
   authorship:
-    - delphine-l
+  - delphine-l
+recordings:
+- youtube_id: -5oxfNnNwoA
+  length: 29M
+  galaxy_version: 24.1.2.dev0
+  date: '2024-09-20'
+  speakers:
+  - delphine-l
+  captioners:
+  - delphine-l
+  bot-timestamp: 1726801100
+
 
 ---
 
 
+
 When sequencing a genome, it is common that contamination from a foreign organism get mixed with the genomic material of our species of interest. For instance, if you are processing a whole body sample of an insect then you will sequence not only the insect, but everything on and inside of it. When building a reference genome, it is important to separate these contaminants from the genome of our species. Foreign DNA sequences could cause false positive identification when running BLAST analyses, the misidentification of genes that don't actually belong to the species, or they can be incorporated as 'reference' sequence for that species in the public archives when those sequences did not actually belong to that species.
 
 

topics/assembly/tutorials/mitochondrion-assembly/tutorial.md

@@ -1,22 +1,34 @@
 ---
 layout: tutorial_hands_on
-
 title: Assembly of the mitochondrial genome from PacBio HiFi reads
-zenodo_link: 'https://zenodo.org/records/13345315'
+zenodo_link: https://zenodo.org/records/13345315
 questions:
 - How to assemble the mitochondrial genome from PacBio Hifi Reads
 objectives:
 - Generate Mitochondrial assembly
 - Understand the outputs of MitoHifi
 time_estimation: 1H
 key_points:
-- MitoHifi generates the assembly and annotation of the Mitochondrial Genome using a reference sequence.
+- MitoHifi generates the assembly and annotation of the Mitochondrial Genome using
+  a reference sequence.
 contributors:
 - delphine-l
+recordings:
+- youtube_id: 0ehAZ0DZsFU
+  length: 11M
+  galaxy_version: " 24.1.2.dev0"
+  date: '2024-09-20'
+  speakers:
+  - delphine-l
+  captioners:
+  - delphine-l
+  bot-timestamp: 1726861719
+
 
 ---
 
 
+
 # Introduction
 
 This tutorial will show you how to assemble a mitochondrial genome from PacBio HiFi data using MitoHiFi {% cite uliano2023 %}.