Merge branch 'main' into cansavvy/google-porting

.github/automatic-issues/add-feedback-method.md

@@ -1,4 +1,8 @@
 
 To help users report issues or areas of improvement for your course, you should provide a clear method of feedback for your users to route their concerns through.
 
-[Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html).
+- [ ] [Read this chapter from an OTTR-made course about how to obtain user feedback](https://jhudatascience.org/Documentation_and_Usability/obtaining-user-feedback.html).
+
+It's also a good idea to collect passive feedback via Google Analytics.
+
+- [ ] [Read our guide to Google Analytics here](https://www.ottrproject.org/more_features.html#google-analytics).

.github/course_README_template.md

@@ -0,0 +1,24 @@
+# {Course Name}
+
+This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).
+
+You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.}
+
+If you would like to contribute to this course material, take a look at the [OTTR documentation](https://www.ottrproject.org/).
+
+## About this course
+
+This course introduces {info on what this course introduces}
+
+## Learning Objectives
+
+This course will teach learners to:  
+
+- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here}
+- {More learning objectives}
+
+## Encountering problems?
+
+If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}.
+
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />All materials in this course are licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> unless noted otherwise.

.github/sync.yml

@@ -29,7 +29,6 @@ group:
       jhudsl/Documentation_and_Usability
       jhudsl/Informatics_Research_Leadership
       jhudsl/Data_Management_for_Cancer_Research
-      jhudsl/Ethical_Data_Handling_for_Cancer_Research
       jhudsl/Computing_for_Cancer_Informatics
       jhudsl/Adv_Reproducibility_in_Cancer_Informatics
       jhudsl/Reproducibility_in_Cancer_Informatics
@@ -47,13 +46,20 @@ group:
       fhdsl/NIH_Data_Sharing
       fhdsl/FH_Cluster_Guide
       fhdsl/Using_Leanpub
-      fhdsl/Overleaf_Tutorial
+      fhdsl/Ethical_Data_Handling_for_Cancer_Research
+      fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles
       fhdsl/Design_of_Data_Analysis
       fhdsl/Tools_for_Reproducible_Workflows_in_R
       fhdsl/Introduction_to_reproducible_research
       mccoy-lab/hgv_modules
       griffithlab/pVACtools_Intro_Course
       griffithlab/CIVIC_SVI_Course
+      PracticalGenomics/cogaps-on-sciserver
+      fhdsl/AI_for_software
+      griffithlab/Immuno_Workflow_Course
+      fhdsl/S1_Intro_to_R
+      fhdsl/S1_Intro_to_Command_Line
+      fhdsl/S1_Intro_to_Git_GitHub
 
 ###ADD NEW REPO HERE following the format above#
 
@@ -109,3 +115,25 @@ group:
       dest: style-sets/fhdasl/
     repos: |
       jhudsl/AnVIL_Template
+
+  - files:
+    - source: config_automation.yml
+      dest: config_automation.yml
+    - source: .github/workflows/
+      dest: .github/workflows/
+      deleteOrphaned: true
+    - source: .github/switch_sync_repo.R
+      dest: .github/switch_sync_repo.R
+    - source: .github/automatic-issues/
+      dest: .github/automatic-issues/
+    - source: assets/box_images/
+      dest: assets/box_images/
+    - source: assets/style.css
+      dest: assets/style.css
+    - source: assets/toc_close.css
+      dest: assets/toc_close.css
+    - source: scripts/
+      dest: scripts/
+      deleteOrphaned: true
+    repos: |
+      C-MOOR/C-MOOR_Template

.github/workflows/render-all.yml

@@ -10,6 +10,7 @@ on:
     paths:
       - '**.Rmd'
       - assets/*
+      - quizzes/*
 
 jobs:
 

.github/workflows/starting-course.yml

@@ -30,6 +30,7 @@ jobs:
       - name: Cleanup
         run: |
           # Cleanup
+          mv .github/course_README_template.md README.md
           rm -rf \
             .github/workflows/report-maker.yml \
             .github/workflows/send-updates.yml \

README.md

@@ -1,5 +1,3 @@
-<!--Delete this section below upon using the template-->
-
 ## Open-source Tools for Training Resources - OTTR
 
 Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:
@@ -29,34 +27,7 @@ _This template and guide helps you_:
 ## To Get Started
 - Go to the [ottrproject.org](https://www.ottrproject.org/).
 - Check out the [rendered version of the template](https://jhudatascience.org/OTTR_Template/).
+- Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform.
 - Please take a look at the [code of conduct](./code_of_conduct.md).
 - If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated.
 
-<!--Delete everything above this line upon using the template-->
-
-# {Course Name}
-
-[![Render Bookdown and Coursera](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-all.yml/badge.svg)](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-all.yml)
-
-This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).
-
-You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.}
-
-If you would like to contribute to this course material, take a look at the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki).
-
-## About this course
-
-This course introduces {info on what this course introduces}
-
-## Learning Objectives
-
-This course will teach learners to:  
-
-- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here}
-- {More learning objectives}
-
-## Encountering problems?
-
-If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}.
-
-<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />All materials in this course are licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> unless noted otherwise.