OTTR Pull Requests
Writing New Content

Download cheatsheet
Last updated: May 13, 2026

All OTTR content development revolves around pull requests where proposed changes trigger automated checks before publishing.

⚠️ Never edit the docs folder directly or push rendered files. Automation handles those files.


Writing Your Content

Option A: Browser (Entry Level)

  • On your repo page, click the branch button and create a new branch
  • Navigate to a file, click the pencil icon to edit
  • Scroll down and Commit directly to your new branch
  • Return to the main repo page and click Compare & pull request
  • Add a description and click Create Pull Request

Option B: Local (Advanced)

  • Clone your repo using GitKraken or Git
  • Create a new branch for your changes
  • Edit files locally, then stage and commit in GitKraken
  • Push your branch to GitHub
  • Go to GitHub and click Compare & pull request
  • Add a description and click Create Pull Request

⚠️ Do not push rendered files (e.g. files in docs/). OTTR’s automation renders and manages these files automatically. Pushing rendered files can cause conflicts and break the automated workflow.


OTTR Automated Checks

Once your PR is open, checks run automatically and post results as comments on the PR.

Check What it does
URL check Verifies all links are valid
Spell check Flags spelling errors
Style check Checks code formatting
Preview render Generates a rendered preview
Quiz check Validates quiz formatting (if applicable)

If a check result looks unexpected, refresh the page or make a new commit to re-trigger.


Adding a New Chapter

Quarto

  • Add a new .qmd file to your branch
  • Add the filename to _quarto.yml under navar:
navbar:
    left:
    - text: ""
      href: index.qmd
      icon: fa-home
    - text: 1. Setup
      href: setup.qmd
    - text: 2. New Chapter
      href: new_chapter.qmd ## new!
  • Commit the updated _quarto.yml
  • Check your PR for any new automated check results

R Markdown

  • Add a new .Rmd file to your branch
  • Add the filename to _bookdown.yml under rmd_files:
rmd_files: ["index.Rmd",
            "01-intro.Rmd",
            "02-new_chapter.Rmd"]  ## new!
  • Commit the updated _bookdown.yml
  • Check your PR for any new automated check results

Ensure you have checked that the quotation marks and commas align with the YAML and that you have the correct file names!




Authors: Padmashri Saravanan from BioData Sage created the cheatsheet content. Carrie Wright reviewed the material. Kate Isaac created the original styling, Carrie Wright did the css styling and Carrie Wright and Candace Savonen did the publishing engineering for the cheatsheet. OTTR was created and or is maintained by the following team: Candace Savonen, Carrie Wright, Kate Isaac, Ava Hoffman, Adam Coffman, Katherine Cox, Federick Tan, John Muschelli, Howard Baek, and Jeffrey Leek.