update student-guide config and add student-guide.Rmd

Author: KatherineCox

resources/dictionary.txt

@@ -22,6 +22,7 @@ deconvolved
 der
 differentially
 dimensionality
+docx
 doi
 downregulated
 downregulation
@@ -78,6 +79,7 @@ PMC
 preprint
 QC
 Res
+Rmd
 RNA
 RNA-seq
 scanpy

student-guide.Rmd

@@ -0,0 +1,20 @@
+
+# Student Guide
+
+## Activity One
+
+Many of the AnVIL books that are designed for teaching a class or workshop contain information aimed at the instructor.
+
+You might want to create a "student guide" that contains a different subset of Rmd files from your book, or renders to a different output format (e.g. word document). You can specify the output and Rmd files that will be used for the student guide using the `_output.yml` and `_bookdown.yml` files in the `student-guide` directory.
+
+By default, repositories based on `AnVIL_Template` create a docx file containing this chapter as an example. Once you have adjusted `student-guide/bookdown.yml` to include the chapters you want in your student guide, you can link to it by replacing `{repo-name}` in the following URL:
+
+`https://github.com/jhudsl/{repo-name}/raw/main/student-guide/docs/Student_Guide.docx`
+
+When someone clicks this link, they will download the docx file. For example, here is the link for the student guide from `AnVIL_Template`:
+
+https://github.com/jhudsl/AnVIL_Template/raw/main/student-guide/docs/Student_Guide.docx
+
+## Activity Two
+
+Steps of the guide could go here.

student-guide/_bookdown.yml

@@ -1,13 +1,14 @@
-book_filename: "Student_Guide"
 chapter_name: "Chapter "
-repo: https://github.com/jhudsl/AnVIL_Template/
+repo: https://github.com/jhudsl/GDSCN_Book_Statistics_for_Genomics_scRNA-seq/
 rmd_files: ["index.Rmd",
-            "09-student_guide.Rmd",
+            "student-guide.Rmd",
+            "About.Rmd",
             "References.Rmd"]
 new_session: yes
 bibliography: [book.bib]
 delete_merged_file: true
 language:
   ui:
     chapter_name: "Chapter"
-output_dir: "student-guide"
+book_filename: "Student_Guide" # Do not change
+output_dir: "student-guide/docs" # Do not change

student-guide/_output.yml

@@ -0,0 +1,2 @@
+bookdown::word_document2:
+  toc: true