quarto setup file

_quarto.yml

@@ -1,63 +1,63 @@
-project:
-  type: website
-
-website:
-  title: 'Introduction to NGS data analysis'
-  google-analytics: 
-    tracking-id: "G-EXW13D5861"
-    anonymize-ip: true
-  open-graph:
-    locale: en_US
-    site-name: Introduction to NGS data analysis
-  navbar:
-    logo: /images/NGSlogo.png
-    left:
-      - href: index.qmd
-        text: Home
-      - href: slides.qmd
-        text: Slides
-#      - href: access/index.qmd
-#        text: HPC access
-#      - href: modules/index.qmd
-#        text: Modules
-#      - href: workshop/workshop_april2024.qmd
-#        text: Workshop
-      - text: Access
-        menu:
-          - href: access/UCloud.qmd
-            text: UCloud
-          - href: access/genomedk.qmd
-            text: GenomeDK
-#          - href: datasets/synthdata.qmd
-      - href: galaxy/galaxy.qmd
-        text: Galaxy
-      - text: Tutorials
-        menu:
-          - href: nb/align.ipynb
-            text: Alignment
-          - href: nb/vcf.ipynb
-            text: Variant analysis
-          - href: nb/bulk.ipynb
-            text: bulkRNA analysis
-          - href: nb/scrna.html
-            text: scRNA analysis
-#          - href: datasets/synthdata.qmd
-
-#      - href: about/about.qmd
-#        text: About
-#      - href: contact/contact.qmd
-#        text: Contact
-
-    right: 
-      - icon: github
-        href: https://github.com/hds-sandbox
-        aria-label: GitHub
-
-format:
-  html:
-    theme: 
-      light: [materia, css/materialight.scss]
-      dark: darkly
-    toc: true
-    include-in-header:
+project:
+  type: website
+
+website:
+  title: 'Introduction to NGS data analysis'
+  google-analytics: 
+    tracking-id: "G-EXW13D5861"
+    anonymize-ip: true
+  open-graph:
+    locale: en_US
+    site-name: Introduction to NGS data analysis
+  navbar:
+    logo: /images/NGSlogo.png
+    left:
+      - href: index.qmd
+        text: Home
+      - href: slides.qmd
+        text: Slides
+#      - href: access/index.qmd
+#        text: HPC access
+#      - href: modules/index.qmd
+#        text: Modules
+#      - href: workshop/workshop_april2024.qmd
+#        text: Workshop
+      - text: Access
+        menu:
+          - href: access/UCloud.qmd
+            text: UCloud
+          - href: access/genomedk.qmd
+            text: GenomeDK
+#          - href: datasets/synthdata.qmd
+      - href: galaxy/galaxy.qmd
+        text: Galaxy
+      - text: Tutorials
+        menu:
+          - href: nb/01_raw_data_alignment.ipynb
+            text: Alignment
+          - href: nb/02_VCF_variant_calling_analysis.ipynb
+            text: Variant analysis
+          - href: nb/03_bulk_RNA_analysis.ipynb
+            text: bulkRNA analysis
+          - href: nb/04_scRNAseq_analysis.ipynb
+            text: scRNA analysis
+#          - href: datasets/synthdata.qmd
+
+#      - href: about/about.qmd
+#        text: About
+#      - href: contact/contact.qmd
+#        text: Contact
+
+    right: 
+      - icon: github
+        href: https://github.com/hds-sandbox
+        aria-label: GitHub
+
+format:
+  html:
+    theme: 
+      light: [materia, css/materialight.scss]
+      dark: darkly
+    toc: true
+    include-in-header:
       - file: "resources/bioschema.html"