fhdsl/anvil_data_subsetting

Tutorial for running the fastq_subsample WDL workflow on AnVIL!

anvil_data_subsetting's Issues

Reminder - Add user feedback method

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.

A feedback method (Google Form) has already been provided for AnVIL and GDSCN courses. When users give you feedback they can enter the name of your course. You can make it easier for them by adding the course to form:

• Add your course name here: https://forms.gle/AK12iVXTjsB7yCUUA.

See these instructions for more suggestions on how to add a feedback method for this course.

New Course - Set Repository Settings

For more information on these settings see instructions in the getting started GitHub wiki pages.

• This course repository is set to public.

• Add the jhudsl-robot as a collaborator to your repository..

• GH_PAT has been set up as a GitHub secret

• GitHub pages is turned on

  • Go to Settings > Pages. Underneath Source, choose main for the branch and select the docs folder. Then click Save.
  • Check Enforce HTTPS.

• Github secret GH_PAT has been set
  Name: GH_PAT
value: A personal access token following these instructions.
  Underneath Select scopes, check both repo and workflow.
  Then copy the PAT and save as the value.

• Set branch protections settings

  • main branch has been set up:
    • Require pull request reviews before merging box is checked.
    • Require status checks to pass before merging box is checked.
      • Underneath that Require branches to be up to date before merging box is checked.
  • Click Save at the bottom of the page!

• Customize GitHub actions for what you will need in this course.

New Course - Add Repo to AnVIL Collection

If you want this repository to be added to the AnVIL Collection, make sure you do the following:

• Click the gear icon on the top right of the "Code" page next to "About"
• Create a repository description
• Add the homepage where your course will be rendered
• Add a description of your course/content
• Add the topic tag anvil or gdscn. You should also supply any other relevant tags.

Following these steps will also automatically add this repository to the AnVIL Collection if this repository is owned by one of the DaSL organizations.

For more information on these settings see instructions in the wiki pages.

For more information about adding repositories to the DaSL Collection, see the AnVIL Collection README.

New Course - Template Update Enrollment

The original template: https://github.com/jhudsl/OTTR_Template is always a work in progress.
We are working on adding more features and smoothing out bugs as we go. The AnVIL Template collects these and can pass them along to this repository.

If you want to receive updates from the AnVIL template to your course template, you will need to enroll this repository to the template updates by adding it to the sync.yml file.

• Follow these instructions to enroll your course repository to receive these updates.

• Ensure that you have followed these instructions to add the jhudsl-robot as a collaborator to your repository.

New Course - Templates to Edit

Follow the Wiki instructions here for details on how to complete the items in this issue.

The following files need to be edited to get this new course started!

Files that need edited upon creating a new course.

• README.md - Fill in all the { }.
• index.Rmd - title: should be updated.
• 01-intro.Rmd - replace the information there with information pertinent to this new course.
• 02-chapter_of_course.Rmd - This Rmd has examples of how to set things up, if you don't need it as a reference, it can be deleted.

Files that need to be edited upon adding each new chapter (including upon creating a new course):

• _bookdown.yml - The list of Rmd files that need to be rendered needs to be updated. See instructions.
• book.bib - any citations need to be added. See instructions.

Picking a style

See more about customizing style on this page in the guide.
By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.

Using a style set

Read more about the style sets here.

• On a new branch, copy the style-sets/<set-name>/index.Rmd and style-sets/<set-name>/_output.yml to the top of the repository to overwrite the default index.Rmd and _output.yml.
• Copy over all the files in the style-sets/<set-name>/copy-to-assets to the assets folder in the top of the repository.
• Create a pull request with these changes, and double check the rendered preview to make sure that the style is what you are looking for.

Files that need to be edited upon adding new packages that the book's code uses:

• docker/Dockerfile needs to have the new package added so it will be installed. See instructions.
• The code chunk in index.Rmd should be edited to add the new package.