Issues — Tracking Bugs and Ideas

A user tries the pipeline and finds a bug. Instead of emailing, they open an Issue:

On GitHub:

1. Click "Issues" → "New issue"
2. Title: Error in QC filtering with empty cells
3. Description:

      ## Bug description
      When running `qc_filtering.py` on a dataset with empty droplets, 
      the script crashes with:
   

   IndexError: list index out of range

      ## Steps to reproduce
      1. Load dataset with empty cells: `adata = load_data("empty_drops.h5ad")`
      2. Run: `qc_filtering.py --min-genes 200`
   
      ## Expected behavior
      Should filter out empty cells without crashing
   
      ## System info
      - Python 3.9
      - scanpy 1.9.1
   

4. Add labels: bug, priority:high
5. Submit issue (#15)

Dr. X sees the issue, creates a branch fix-empty-cells, fixes the bug, and references it in the commit:

git commit -m "Fix QC filtering for empty cells (fixes #15)"

When merged, issue #15 automatically closes!

flowchart LR
  A[User finds bug] --> B[Open Issue #15]
  B --> C[Dr. X creates fix-empty-cells branch]
  C --> D[Commit: 'fixes #15']
  D --> E[Pull Request]
  E --> F[Merge to main]
  F --> G[Issue #15 auto-closes]

  style B fill:#ffe6e6,stroke:#f00
  style G fill:#e6ffe6,stroke:#0a0