template-issues.md

Task Template: [Specify Task Title Here]

(Copy and fill out this section for each new task)

Task Details

• Repository: amitkarpe/setup (https://github.com/amitkarpe/setup)
• Local Workspace: /home/ec2-user/git/github/setup
• Task Title: [Re-state the concise title for the task/issue]
• Goal: [Describe the primary objective of this task in 1-2 sentences. e.g., Add support to install Nextflow and nf-core tools via the main setup scripts.]
• References:
  • [Link/Path to relevant code to reference, e.g., https://github.com/amitkarpe/gitlab/tree/main/docs]
  • [Link to official documentation, e.g., https://nf-co.re/usage/installation]
  • [Any other relevant files, issues, or URLs]
• Preferences/Constraints: [Specify any preferences, e.g., Add installation steps to scripts/devops.sh, Use a Makefile if appropriate for build/test steps, Follow existing script style.]

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(Instructions for Cursor AI - Do not modify below this line for the task)

AI Workflow Instructions

Okay Cursor, let's tackle the task defined above. Please follow this workflow precisely:

1. Acknowledge & Plan:

   • Read the "Task Details" section above carefully.
   • State that you are starting the task: "[Task Title]".
   • Briefly outline your plan, including the main files you expect to modify or create and the general sequence of steps (e.g., "1. Analyze reference scripts. 2. Add installation commands to scripts/devops.sh. 3. Create a test function/script. 4. Update README.").

2. Branch Creation:

   • Suggest a suitable branch name based on the task title (e.g., feature/add-nextflow-support).
   • Ask me to create this branch locally using a git checkout -b [suggested-branch-name] command. Wait for confirmation or execution.

3. Implementation:

   • Based on your plan and the provided references, proceed with the necessary code changes.
   • Request specific file edits (using edit_file) or provide code snippets incrementally.
   • Consult the reference links/paths provided in "Task Details" as needed.
   • If Makefiles are preferred and suitable, propose additions or modifications to a Makefile.
   • Commit changes locally frequently after logical steps are completed. Propose clear commit messages (e.g., "feat: Add Nextflow installation command").

4. Documentation:

   • Identify or create relevant documentation (e.g., update README.md, add comments in scripts).
   • Propose specific changes to documentation to explain the new functionality or installation steps.
   • Commit documentation changes.

5. Testing:

   • Create a test script (e.g., scripts/test_nextflow.sh) or add a test function/target (e.g., in a Makefile) to verify the installation or functionality.
   • The test should perform a basic check (e.g., run nextflow --version, nf-core --version).
   • Propose the content for the test script/function.
   • Commit testing additions.

6. Push Branch:

   • Once implementation, documentation, and testing additions are committed locally, propose the command to push the feature branch to the remote repository: git push -u origin [feature-branch-name].

7. Create Pull Request:

   • Propose using the GitHub tool (mcp_github_create_pull_request) to create a Draft Pull Request.
   • Specify the head branch (your feature branch), base branch (main), owner (amitkarpe), repo (setup).
   • Suggest a clear PR Title (e.g., "feat: Add Nextflow and nf-core Installation").
   • Suggest a brief PR body summarizing the changes and linking to this issue (if this issues.md is tracked as a GitHub issue, otherwise just summarize).
   • Set draft: true.

8. Pause for User Review:

   • State clearly: "The feature branch [feature-branch-name] has been pushed and a draft Pull Request has been created. I will now pause and wait for you (Amit Karpe) to review the code, test the changes thoroughly, and provide feedback or approval."
   • Do not proceed further until explicitly told to.

9. Final Steps (After User Confirmation):

   • Wait for explicit confirmation from me (Amit Karpe) that the PR has been reviewed, tested, approved, and merged into main.
   • Once confirmation of merge is received, if this task corresponds to a GitHub Issue, propose closing that specific issue using mcp_github_update_issue with state: closed.
   • Conclude the task: "Task '[Task Title]' is complete and the corresponding issue (if applicable) has been closed."

Remember to follow the general Cursor best practices: Be specific in your requests, break down complex edits, and use the available tools appropriately.