Moved output format from config to rmd files

NBISweden · Aug 15, 2023 · c5cf97c · c5cf97c
1 parent 233d11b
commit c5cf97c
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Showing 23 changed files with 373 additions and 18 deletions.
diff --git a/_site.yml b/_site.yml
@@ -24,24 +24,7 @@ navbar:
       href: home_content.html
     - text: Precourse
       href: home_precourse.html
-output:
-  bookdown::html_document2:
-    highlight: textmate
-    toc: true
-    toc_float:
-      collapsed: true
-      smooth_scroll: true
-      print: false
-    toc_depth: 4
-    number_sections: true
-    df_print: default
-    code_folding: none
-    self_contained: false
-    keep_md: false
-    encoding: 'UTF-8'
-    css: "assets/lab.css"
-    include:
-      after_body: assets/footer-lab.html
+
 # r packages needed for the workshop
 # used in home_precourse.Rmd
 # split into cran and bioc packages

diff --git a/home_content.Rmd b/home_content.Rmd
@@ -2,8 +2,22 @@
 title: "Content"
 output:
   bookdown::html_document2:
+    highlight: textmate
     toc: false
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
     number_sections: false
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/home_info.Rmd b/home_info.Rmd
@@ -2,8 +2,22 @@
 title: "Info"
 output:
   bookdown::html_document2:
+    highlight: textmate
     toc: false
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
     number_sections: false
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/home_precourse.Rmd b/home_precourse.Rmd
@@ -2,8 +2,22 @@
 title: "Precourse"
 output:
   bookdown::html_document2:
+    highlight: textmate
     toc: false
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
     number_sections: false
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/home_schedule.Rmd b/home_schedule.Rmd
@@ -2,8 +2,22 @@
 title: "Schedule"
 output:
   bookdown::html_document2:
+    highlight: textmate
     toc: false
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
     number_sections: false
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/index.Rmd b/index.Rmd
@@ -2,8 +2,22 @@
 title: "&nbsp;"
 output:
   bookdown::html_document2:
+    highlight: textmate
     toc: false
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
     number_sections: false
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_annotation.Rmd b/lab_annotation.Rmd
@@ -1,6 +1,24 @@
 ---
 title: "Transcriptome annotation"
 subtitle: "Workshop on RNA-Seq"
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_assembly.Rmd b/lab_assembly.Rmd
@@ -1,6 +1,24 @@
 ---
 title: "Transcriptome assembly"
 subtitle: "Workshop on RNA-Seq"
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_dge.Rmd b/lab_dge.Rmd
@@ -3,6 +3,24 @@ title: "Differential Gene Expression"
 subtitle: "Workshop on RNA-Seq"
 editor_options: 
   chunk_output_type: console
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_download.Rmd b/lab_download.Rmd
@@ -1,6 +1,24 @@
 ---
 title: "Annotation data"
 subtitle: Workshop on RNA-Seq
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_eda.Rmd b/lab_eda.Rmd
@@ -3,6 +3,24 @@ title: "PCA and Clustering"
 subtitle: "Workshop on RNA-Seq"
 editor_options:
   chunk_output_type: console
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_functional.Rmd b/lab_functional.Rmd
@@ -3,6 +3,24 @@ title: "Gene Function Annotation"
 subtitle: Workshop on RNA-Seq
 editor_options:
   chunk_output_type: console
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_geoquery.Rmd b/lab_geoquery.Rmd
@@ -3,6 +3,24 @@ title: "Online Repositories"
 subtitle: "Workshop on RNA-Seq"
 editor_options:
   chunk_output_type: console
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_igv.Rmd b/lab_igv.Rmd
@@ -1,6 +1,24 @@
 ---
 title: "Using IGV"
 subtitle: "Workshop on RNA-Seq"
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_kallisto.Rmd b/lab_kallisto.Rmd
@@ -1,6 +1,24 @@
 ---
 title: 'Kallisto '
 subtitle: Workshop on RNA-Seq
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}

diff --git a/lab_mapping.Rmd b/lab_mapping.Rmd
@@ -1,6 +1,24 @@
 ---
 title: "Mapping"
 subtitle: "Workshop on RNA-Seq"
+output:
+  bookdown::html_document2:
+    highlight: textmate
+    toc: true
+    toc_float:
+      collapsed: true
+      smooth_scroll: true
+      print: false
+    toc_depth: 4
+    number_sections: true
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html
 ---
 
 ```{r,child="assets/header-lab.Rmd"}