ottrproject · padmashris · Mar 19, 2026 · Mar 20, 2026 · Mar 20, 2026 · Mar 24, 2026
diff --git a/_quarto.yml b/_quarto.yml
@@ -13,34 +13,44 @@ website:
         menu:
           - text: "Getting Started"
             href: getting_started.qmd
-          - text: "Next Steps"
-            href: next_steps.qmd
-      - text: "Customization"
+          - text: "Example use cases"
+            href: examples.qmd
+      - text: "Build with OTTR"
         menu:
-          - text: "Customizing checks {{< fa robot title='A robot' >}}"
-            href: customize-robots.qmd
-          - text: "Customizing style {{< fa palette title='A palette' >}}"
+          - text: "Templates"
+            href: getting_started.qmd
+          - text: "Setup steps"
+            href: next_steps.qmd
+          - text: "Enroll for sync updates"
+            href: enroll_sync.qmd
+          - text: "OTTR-fy existing repo"
+            href: ottr-fy.qmd
+          - text: "---"
+          - text: "Customize"
+          - text: "Style {{< fa palette title='A palette' >}}"
             href: customize-style.qmd
-          - text: "Customizing Docker {{< fa gears title='gears' >}}"
+          - text: "Checks {{< fa robot title='A robot' >}}"
+            href: customize-robots.qmd
+          - text: "Docker {{< fa gears title='gears' >}}"
             href: customize-docker.qmd
+      - text: "Advanced / Integrations"
+        menu:
+          - text: "Google Analytics {{< fa chart-line title='a line chart' >}}"
+            href: more_features_ganalytic.qmd
           - text: "Citing sources {{< fa quote-left title='A left quotation mark' >}}"
             href: more_features_sources.qmd
           - text: "Giving credits {{< fa award title='An award' >}}"
             href: more_features_credits.qmd
+          - text: "Google Docs {{< fa file title='a file folder' >}}"
+            href: more_features_gdoc.qmd
           - text: "Borrowing chapters {{< fa bookmark title='A bookmark' >}}"
             href: more_features_borrowing.qmd
-          - text: "Compatibility with Google Docs {{< fa file title='a file folder' >}}"
-            href: more_features_gdoc.qmd
-          - text: "Google Analytics {{< fa chart-line title='a line chart' >}}"
-            href: more_features_ganalytic.qmd
-          - text: "OTTR-fying an existing repository"
-            href: ottr-fy.qmd
-          - text: "About OTTR babies"
-            href: examples.qmd
-      - text: "Troubleshooting {{< fa tools title='tools' >}}"
-        href: faqs.qmd
-      - text: "Contact {{< fa envelope title='An envelope' >}}"
-        href: contact.qmd
+      - text: "Help"
+        menu:
+          - text: "Troubleshooting {{< fa tools title='tools' >}}"
+            href: faqs.qmd
+          - text: "Contact {{< fa envelope title='An envelope' >}}"
+            href: contact.qmd
       - text: "{{< fa brands github title='The GitHub logo' >}}"
         href: https://github.com/ottrproject/OTTR_Template
 

diff --git a/contact.qmd b/contact.qmd
@@ -4,8 +4,10 @@ output:
   html_document
 ---
 
+If you have questions please contact:
 
+-   Carrie Wright (cwright2@fredhutch.org)
 
-If you have questions please contact:
+---
 
-* Carrie Wright (cwrigh60@jhu.edu)
+← [Troubleshooting](faqs.qmd) &emsp; [Home](index.qmd)
diff --git a/customize-docker.qmd b/customize-docker.qmd
@@ -220,3 +220,7 @@ If you do choose to use the action manually, then you can use this by going to `
 ![](resources/images/docker-gha.png)
 
 For more guidance on how to personalize Docker images, we taking our [Containers for Scientist course](https://hutchdatascience.org/Containers_for_Scientists/). Or file a GitHub issue on the relevant repository.
+
+---
+
+← [Customizing Checks](customize-robots.qmd) &emsp; [Next Steps](next_steps.qmd) →
diff --git a/customize-robots.qmd b/customize-robots.qmd
@@ -216,3 +216,7 @@ To investigate why a GitHub action has failed, go to `Actions` and click on the
 See our [FAQ's section](./faqs.html) for the most commonly encountered errors and how to address them.
 
 If you are unsure what the error message means and have trouble addressing it, please [file an issue on the OTTR_Template repository to get help](https://github.com/ottrproject/OTTR_Template/issues/new?assignees=cansavvy&labels=bug&template=course-template-problem-report.md).
+
+---
+
+← [Customizing Style](customize-style.qmd) &emsp; [Customizing Docker](customize-docker.qmd) →
diff --git a/customize-style.qmd b/customize-style.qmd
@@ -103,3 +103,7 @@ If you would like to change the current light blue color to be a different color
 If you would like to change the image at the top of the Bookdown version of the course, you need to do the following steps:
 * Add a new image file to the `assets` directory
 * Modify the `assets/big-image.html` file on line 11. Change out `src = "assets/dasl_thin_main_image.png"` so that `dasl_thin_main_image.png` is replaced with the name of your image file.
+
+---
+
+← [Next Steps](next_steps.qmd) &emsp; [Customizing Checks](customize-robots.qmd) →
diff --git a/enroll_sync.qmd b/enroll_sync.qmd
@@ -0,0 +1,57 @@
+---
+title: "Enroll for Sync Updates"
+---
+
+The OTTR templates are always a work in progress. New features are added and bugs are smoothed out over time. [Your feedback is greatly appreciated](https://github.com/ottrproject/OTTR_Template/issues/new/choose). When updates are made to non-content files (checks, automation), pull requests are automatically filed to downstream repositories made from the template.
+
+## Add `jhudsl-robot` as a collaborator
+
+*You can skip this step if your course is in the `jhudsl` organization.*
+
+To enable the full functionality of GitHub Actions, add `jhudsl-robot` as a collaborator with write access:
+
+1. In your repository, go to **Settings** > **Collaborators & Teams** and click **Add people**.
+2. Search for and add `jhudsl-robot`.
+3. If prompted, choose the **Write** option, then click **Add jhudsl-robot to this repository**.
+
+<img src="https://github.com/ottrproject/OTTR_Template/raw/main/resources/screenshots/add-jhudsl-robot.png" width="400">
+
+## Which sync file should you edit?
+
+Add your repository name to the `.github/sync.yml` file of the OTTR template you created your repository from:
+
+- [OTTR_Template sync file](https://github.com/ottrproject/OTTR_Template/blob/main/.github/sync.yml) — for R Markdown courses
+- [OTTR_Template_Website sync file](https://github.com/ottrproject/OTTR_Template_Website/blob/main/.github/sync.yml) — for websites
+- [OTTR_Quizzes sync file](https://github.com/ottrproject/OTTR_Quizzes/blob/main/.github/sync.yml) — for quizzes
+
+## If you are part of the jhudsl GitHub organization
+
+1. Open the relevant sync file above and click the pencil icon to edit.
+2. Add your repository name where it says `#NEW REPO HERE#`, indented to match the other entries.
+
+![](https://raw.githubusercontent.com/ottrproject/OTTR_Template/main/resources/screenshots/edit-sync.yml.png)
+
+3. Click **Commit changes...**, type `Add new repository to sync` as the commit message, and choose **Create a new branch**.
+4. Click **Propose changes**, then open a pull request and request `@kweav` as a reviewer.
+
+## If you are not part of the jhudsl GitHub organization
+
+Use one of these options:
+
+- **Google Form** — submit your organization/username and repo name in the [OTTR Feedback Google Form](https://forms.gle/jGQnd5oemHWyuUq28) and we'll make the edit for you.
+- **Open an issue** — use the links in the table below and provide your repo info; we'll update `sync.yml` for you.
+- **Fork and PR** — fork the template repo, edit `sync.yml` on a new branch adding your repo name where it says `#NEW REPO HERE#`, commit, and open a pull request. Add a comment tagging `@kweav` so we see it.
+
+| Repository | Issue Links |
+|:---:|:---|
+| OTTR_Template | [General issue](https://github.com/ottrproject/OTTR_Template/issues/new/choose) · [Add new repo to sync](https://github.com/ottrproject/OTTR_Template/issues/new?assignees=kweav&labels=&projects=&template=new-course-add-to-sync.md&title=) · [Update repo info in sync](https://github.com/ottrproject/OTTR_Template/issues/new?assignees=kweav&labels=&projects=&template=update-course-info-for-sync.md&title=) |
+| OTTR_Quizzes | [Open an issue](https://github.com/jhudsl/OTTR_Quizzes/issues/new/choose) |
+| OTTR_Template_Website | [General issue](https://github.com/ottrproject/OTTR_Template_Website/issues/new/choose) · [Add new repo to sync](https://github.com/ottrproject/OTTR_Template_Website/issues/new?assignees=kweav&labels=&projects=&template=new-website-add-to-sync.md&title=) |
+
+<p class="comment">
+_If you have any questions about these updates or files, please tag `@kweav` or `@carriewright11`._
+</p>
+
+---
+
+← [Next Steps](next_steps.qmd) &emsp; [Customizing Style](customize-style.qmd) →
diff --git a/examples.qmd b/examples.qmd
@@ -1,7 +1,8 @@
 ---
 title: "Examples of OTTR in the Wild"
 output:
-  html_document
+  html_document:
+    toc-depth: 3
 ---
 
 # OTTR spinoff babies
@@ -36,6 +37,18 @@ This template shows basics for how you can display metrics collected from:
 
 And more websites being added. [See metricminer.org for more details!](https://www.metricminer.org/)
 
+## DaSEH Instructor Guide
+
+A course instructor guide built with OTTR for the Data Science for the Experience of Health (DaSEH) program.
+
+- [View the course](https://hutchdatascience.org/daseh_instructor_guide/index.html)
+
+## Baltimore Community Course
+
+A community-focused data science course built with OTTR.
+
+- [View the course](https://jhudatascience.org/Baltimore_Community_Course/)
+
 ## AnVIL template
 
 This is a template (made from our main OTTR Template) that is used for a set of courses being made for the [AnVIL set of cloud tools](https://anvilproject.org/)
@@ -53,3 +66,7 @@ This is a template (made from our main OTTR Template) that will be used for a se
 Courses will look similar to this [link](https://datatrail-jhu.github.io/DataTrail_Template/introduction.html).
 
 <br>
+
+---
+
+Ready to build your own? [Get Started](getting_started.qmd) →
diff --git a/faqs.qmd b/faqs.qmd
@@ -150,8 +150,32 @@ Then look at the `GA_Script.Rhtml` file and remove the following `html` frontmat
 Check that the config file is up-to-date. It should look like this: https://github.com/ottrproject/OTTR_Template/blob/main/config_automation.yml.
 (be careful to keep your selections for the configuration you would like).
 
+### `could not read Username for 'https://github.com': terminal prompts disabled`: GitHub authentication failure
+
+_Error example:_
+```
+The process '/usr/bin/git' failed with exit code 128
+could not read Username for 'https://github.com': terminal prompts disabled
+could not read Username for 'https://github.com': terminal prompts disabled
+could not read Username for 'https://github.com': terminal prompts disabled
+```
+
+_What does this mean?:_
+
+This error occurs when the GitHub Action workflow does not have the necessary permissions to authenticate with GitHub. This is typically caused by missing or insufficient repository permissions for the workflow's `GITHUB_TOKEN`.
+
+To fix this, see the [OTTR token cheatsheet](https://www.ottrproject.org/cheatsheets/ottr_token.html) for detailed instructions, or follow these steps:
+
+1) Go to your repository's **Settings** > **Actions** > **General**.
+2) Under **Workflow permissions**, select `Read and write permissions`.
+3) Click **Save**, then re-run the failed workflow.
+
 ## Contact Info
 
 If you have a question that's not addressed by this website or just wanna chat with us about something else, please email us at itcrtrainingnetwork@gmail.com OR you can [leave a GitHub issue here](https://github.com/ottrproject/OTTR_Template/issues/new) and assign or "at" a team member in the description/a comment (`@carriewright11`, `@kweav`, or `@avahoffman`).
 
 We greatly appreciate any feedback! We are always looking for ways to improve OTTR so more open source courses can be made!
+
+---
+
+**Still need help?** [Contact us](contact.qmd) →