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Exercise 03: GitHub Actions & Static Releases

GitHub Actions

  1. Navigate to the .github/workflows/test.yml file to understand the automated tests implemented for this repository.

    • Based on this file, consider if the changes we made to add gc-calculation and reporting to fastq-peek.sh would pass this test.

  2. Navigate to the pull request made in the Week 2 Exercise and see if these changes pass the automated test defined in .github/workflows/test.yml

    • If the checks have failed, click "Details" to investigate further.

  1. Propose solutions to resolve these failed tests and implement your proposed solution on your dev branch.

    • NOTE: Workflow files within GitHub require elevated authentication to modify. If you're using a personal access token (PAT), ensure that you have the required workflow scope to modify files in the .github/workflows/ directory. Otherwise, you may encounter the following error Tried to add this file and got : > git push origin main:main To https://github.com/theiagen/Western-WFD-2024.git ! [remote rejected] main -> main (refusing to allow an OAuth App to create or update workflow .github/workflows/test.yml without workflow scope) error: failed to push some refs to 'https://github.com/theiagen/Western-WFD-2024.git'

    • Solution: Generate a new PAT with the necessary scopes (repo and workflow).

      • Go to GitHub and generate a new token with repo and workflow scopes.
      • First, from github.com, click on your profile photo in the upper-right hand corner and clieck Settings from the drop down menu
      • From Settings, select "Developer Spaces" on the bottom of the left-hand menu.
      • Click the "Personal access token" drop down and select "Tokens (clasic)"
      • Select "Generate new token (classic)" and ensure the "workflow" scope is selected and then click "Generate token" at the bottom of the screen.

  • Update your Git remote URL to use the new token:

    git remote set-url origin https://<your-token>@github.com/theiagen/Northeast-SDP4PHB-2025.git
    • Replace <your-token> with your new PAT.
  1. Commit any changes you've made to resolve these issues. If done correctly, you should see that all automated checks now pass:

  1. Once this PR is merged, as a group, we will make a version release with our new code changes!
Exercise 3 Solution

A modified test.yml file to account for gc-count reporting can be found in the back of the book.