Create a new learning path from the Nanopore Workshop

_data/contributors.yml

@@ -0,0 +1,14 @@
+- name: Nils Kleinbölting
+  ORCID: https://orcid.org/0000-0001-9124-5203
+
+- name: Dilfuza Djamalova
+  ORCID: https://orcid.org/0009-0004-7782-2894
+
+- name: Sebastian Jünemann
+  ORCID: https://orcid.org/0000-0002-3714-0328
+
+- name: Alexander Sczyrba
+  ORCID: https://orcid.org/0000-0002-4405-3847
+
+- name: Abhijeet Shah
+  ORCID: https://orcid.org/0000-0002-0467-4884

_data/tutorial_groups.yml

@@ -28,6 +28,8 @@
     - basicsAmpliconQC
     - nanopore
     - mgtk_short
+    - genome-annotation
+    - genome-assembly
 
 - title: Data Management on the Cloud
   description: Tutorials focused on data management best practices, solutions on the Cloud, including how to adapt a solution to the cloud (Kubernetes and S3 storage)

_includes/attributions.html

@@ -23,12 +23,34 @@
 <div class="faq-container">
     <div class="faq-summary">Contributions</div>
     <div class="faq-answer">
-        {% if authors %}
-            <p><strong>Author(s):</strong> {{ authors | join: ", " }}</p>
-        {% endif %}
+    {% if authors %}
+        <p>
+            <strong>Author(s):</strong>
+            {% for author in authors %}
+                {% assign author_data = site.data.contributors | where: "name", author | first %}
+                {% if author_data and author_data.ORCID %}
+                    <a href="{{ author_data.ORCID }}" target="_blank" rel="noopener" style="color: #0e0e0e; text-decoration: none;">{{ author }}</a>
+                {% else %}
+                    {{ author }}
+                {% endif %}
+                {% unless forloop.last %}, {% endunless %}
+            {% endfor %}
+        </p>
+    {% endif %}
 
     {% if editors %}
-        <p><strong>Editor(s):</strong> {{ editors | join: ", " }}</p>
+        <p>
+            <strong>Editor(s):</strong>
+            {% for editor in editors %}
+                {% assign editor_data = site.data.contributors | where: "name", editor | first %}
+                {% if editor_data and editor_data.ORCID %}
+                    <a href="{{ editor_data.ORCID }}" target="_blank" rel="noopener" style="color: #0e0e0e; text-decoration: none;">{{ editor }}</a>
+                {% else %}
+                    {{ editor }}
+                {% endif %}
+                {% unless forloop.last %}, {% endunless %}
+            {% endfor %}
+        </p>
     {% endif %}
     </div>
 </div>

_includes/pathway_lifecycle.html

@@ -0,0 +1,29 @@
+{% comment %}
+    Display learning path's lifecycle.
+    Possible values: "under development", "active", "archived".
+    If not set, the learning path is considered "under development".
+{% endcomment %}
+
+{% if page.life_cycle == nil %}
+{% assign life_cycle = include.life_cycle %}
+{% else %}
+{% assign life_cycle = page.life_cycle %}
+{% endif %}
+
+{% if life_cycle == "under development" %}
+<div class="lifecycle lifecycle-draft">
+  <strong>Under development</strong>: This learning path is in an early stage of development and may change significantly.
+</div>
+{% elsif life_cycle == "active" %}
+<div class="lifecycle lifecycle-active">
+  <strong>Active</strong>: This learning path is actively maintained and updated.
+</div>
+{% elsif life_cycle == "archived" %}
+<div class="lifecycle lifecycle-archived">
+  <strong>Archived</strong>: This learning path is no longer actively maintained.
+</div>
+{% else %}
+<div class="lifecycle lifecycle-unknown">
+  <strong>Unknown</strong>: The lifecycle status of this learning path is not defined. Please <a href="mailto:{{ site.email }}">contact us</a> for more information.
+</div>
+{% endif %} 

_includes/tutorial_feedback.html

@@ -3,8 +3,8 @@
 {% endcomment %}
 
 <div class="alert alert-info">
-  <strong>💬 Feedback</strong>: Found something unclear or want to suggest an improvement? <a href="https://github.com/deKCD/Training-Materials/issues/new?template=feedback.yml" target="_blank">Open a feedback issue.</a>
+  <strong>💬 Feedback</strong>: Found something unclear or want to suggest an improvement? <a href="https://github.com/deKCD/Training-Materials/issues/new?template=feedback.yml" target="_blank"><b>Open a feedback issue.</b></a>
   <p></p>
   <strong>👥 Contribution</strong>: We also welcome contributions when you spot an opportunity to improve the training materials.
-  Please review the <a href="{{ '/CONTRIBUTING/' | relative_url }}">contribution page</a> first. Then, <a href="{{ site.repository_url }}/edit/main/{{ page.path }}" target="_blank" rel="noopener">edit this material on GitHub</a> to suggest your improvements.
+  Please review the <a href="{{ '/CONTRIBUTING/' | relative_url }}"><b>contribution page</b></a> first. Then, <a href="{{ site.repository_url }}/edit/main/{{ page.path }}" target="_blank" rel="noopener"><b>edit this material on GitHub</b></a> to suggest your improvements.
 </div>

_layouts/pathway.html

@@ -12,6 +12,7 @@
     <script async="" src="https://piwik.cebitec.uni-bielefeld.de/matomo.js"></script>
     <script src="{{ '/assets/js/jquery/jquery-3.7.1.min.js' | relative_url }}"></script>
     <script src="{{ '/assets/js/bootstrap5/bootstrap.bundle.min.js' | relative_url }}"></script>
+    <script src="{{ '/assets/js/lesson.js' | relative_url }}"></script>
     <!-- Bootstrap core CSS -->
     <link href="{{ '/assets/css/bootstrap5/bootstrap.min.css' | relative_url }}" rel="stylesheet">
     <link href="{{ '/assets/css/dekcd_styles.css' | relative_url }}" rel="stylesheet">
@@ -131,6 +132,7 @@
         <div class="my-1">
           <h2 class="text-center" style="margin: 2rem 0;">{{ page.title }}</h2>
           <p class="text-center" style="font-size: large; margin-bottom: 2rem;"> {{ page.description }}</p>
+          {% include _includes/pathway_lifecycle.html %}
           <div class="mx-auto p-2 width-padder my-1">
             <div class="pathway-content tutorial-grop container">    
 
@@ -143,14 +145,16 @@ <h2>{{ section.section }}</h2>
                   <col style="width: 20%;">
                   <col style="width: 5%;">
                   <col style="width: 25%;">
-                  <col style="width: 50%;">
+                  <col style="width: 40%;">
+                  <col style="width: 10%;">
                 </colgroup>
                 <thead>
                   <tr>
                     <th>Tutorial</th>
                     <th>Slides</th>
                     <th>Description</th>
-                    <th>Learning Objectives</th>  
+                    <th>Learning Objectives</th>
+                    <th>Estimated Time</th>    
                   </tr>
                 </thead>
                 <tbody>
@@ -191,6 +195,7 @@ <h2>{{ section.section }}</h2>
                                   {% endfor %}
                               </ul>
                           </td>
+                          <td>{{ tutorial.time_estimation }}</td>
                       </tr>
                     {% else %}
                     <tr>
@@ -201,21 +206,9 @@ <h2>{{ section.section }}</h2>
                 </tbody>
               </table>
               {% endfor %}
-
-              <p>This material is reviewed by our Editorial Board:</p>
-                  <ul>
-                      {% for editor in page.editorial_board %}
-                          {% if editor.orcid %}
-                          <a href="https://orcid.org/{{ editor.orcid }}" target="_blank">{{ editor.name }}</a>
-                          {% else %}
-                          {{ editor.name }}
-                          {% endif %}
-                      {% endfor %}
-                  </ul>
-
-                  {% include _includes/tutorial_feedback.html %}
-
-              </div>
+              {% include _includes/attributions.html %}
+              {% include _includes/tutorial_feedback.html %}
+              </div> 
             </div>
           </div>
         </div>

_pathways/nanopore-workshop.md

@@ -0,0 +1,50 @@
+---
+layout: pathway
+title: "ONT Sequencing: From Reads to Annotation"
+description: "This learning path introduces the complete workflow for analyzing isolate genome sequencing data generated with Oxford Nanopore Technologies (ONT) and Illumina platforms. Starting from raw ONT signal data, you will learn how to perform basecalling, quality control, genome assembly, polishing, hybrid assembly, genome annotation, and downstream analysis of long-read metagenomic data."
+keywords: [ONT, Nanopore, Basecalling, dorado, flye, SPAdes, QUAST, polypolish, hybrid assembly, binning, prokka, bakta, EDGAR]
+level: intermediate
+life_cycle: under development
+
+pathway:
+  - section: "Module 1: Introduction to basic Unix commands"
+    description: "This module introduces essential Unix shell commands and concepts required for working in computational environments. You will learn how to navigate file systems, manipulate files, and execute basic commands commonly used in bioinformatics workflows."
+    tutorials:
+      - name: unix-course
+        version: main
+
+  - section: "Module 2: Basecalling ONT data"
+    description: "This module introduces the preprocessing workflow for Oxford Nanopore Technologies (ONT) sequencing data, starting from raw signal files. You will learn how to perform basecalling, assess read quality, and prepare high-quality sequencing reads for downstream genome analysis."
+    tutorials:
+      - name: nanopore
+        version: main
+
+  - section: "Module 3: Metagenomics assembly"
+    description: "This module introduces genome assembly approaches for long-read and short-read sequencing data. You will learn how to assemble prokaryotic genomes from ONT and Illumina reads, evaluate assembly quality, improve assemblies through polishing and hybrid assembly strategies, and assess the final assembly results. The module also provides an introduction to metagenome assembly workflows using dedicated bioinformatics tools."
+    tutorials:
+      - name: mgworkshop_assembly
+        version: main
+
+      - name: genome-assembly
+        version: main
+
+  - section: "Module 4: Genome annotation"
+    description: "This module covers the functional annotation of bacterial genomes. You will learn how to identify genomic features, predict genes, assign functional information, and interpret genome annotations using commonly used annotation tools."
+    tutorials:
+      - name: genome-annotation
+        version: main
+
+  - section: "Module 5: Long-Read Metagenomics using the Metagenomics-Toolkit"
+    description: "This module introduces long-read metagenomics analysis using the Metagenomics-Toolkit. You will learn how to prepare ONT sequencing data, run the initial analysis workflow, and explore the first steps of metagenomic data processing and interpretation."
+    tutorials:
+      - name: mgtk_short
+        version: main
+
+contributions:
+  authorship:
+  - Nils Kleinbölting
+  editing:
+  - Dilfuza Djamalova 
+  funding:
+---
+