Update student instructions with interactive script workflow

- Added STEP 3: python3 answer_assignment.py
- Added STEP 4: git add/commit/push workflow
- Clarified class dataset (everyone analyzes same data)
- Added auto-grading check instructions (Actions tab)
- Updated both README.md and start_here.md
- Complete 4-step workflow clearly documented

Now students know:
1. Run tutorial
2. Run analysis
3. Answer questions interactively
4. Push to GitHub for auto-grading

Author: cosmelab

README.md

@@ -40,10 +40,16 @@ See **[start_here.md](start_here.md)** for the complete beginner's guide.
 # STEP 1: Learn with test data (15 min)
 ./tutorial.sh
 
-# STEP 2: Analyze YOUR mosquito sequences (5 min)
+# STEP 2: Analyze the class mosquito sequences (5 min)
 ./run-analysis.sh
 
-# STEP 3: Fill out assignment.md
+# STEP 3: Answer questions interactively (10 min)
+python3 answer_assignment.py
+
+# STEP 4: Submit to GitHub (auto-graded!)
+git add answers.json results/
+git commit -m "Complete assignment"
+git push origin main
 ```
 
 ### For Instructors

start_here.md

@@ -84,12 +84,9 @@ This teaches you all 5 steps using example data. **DO NOT SKIP THIS!**
 
 ---
 
-### STEP 2: Analyze Your Own Mosquito Sequences
+### STEP 2: Analyze the Class Mosquito Sequences
 
-**Put your .ab1 files in the data folder:**
-```bash
-cp ~/Desktop/*.ab1 data/student_sequences/
-```
+**Important:** Everyone analyzes the **same class dataset**. The .ab1 files are already in `data/student_sequences/`
 
 **Run the complete analysis:**
 ```bash
@@ -107,23 +104,49 @@ Your results will be in: `results/my_analysis/`
 
 ---
 
-### STEP 3: Fill Out Assignment
+### STEP 3: Answer Assignment Questions
+
+**Run the interactive question script:**
+```bash
+python3 answer_assignment.py
+```
+
+This script will:
+- Guide you through your analysis results
+- Ask questions about QC, BLAST, and phylogeny
+- Save your answers to `answers.json`
+
+It's interactive and easy - just follow the prompts!
+
+---
+
+### STEP 4: Submit to GitHub
 
-Open these files and answer the questions in `assignment.md`:
+**Commit and push your work:**
+```bash
+git add answers.json results/
+git commit -m "Complete DNA barcoding analysis"
+git push origin main
+```
 
-- `results/my_analysis/01_qc/qc_report.html` - How many sequences passed?
-- `results/my_analysis/04_phylogeny/tree.png` - What species cluster together?
-- `results/my_analysis/05_blast/identification_report.html` - What species did you find?
+**Check auto-grading:**
+1. Go to your GitHub repository
+2. Click the "Actions" tab
+3. Look for ✅ (passed) or ❌ (failed)
+4. If failed, click on it to see feedback
 
 ---
 
 ## That's It!
 
-**The workflow in 3 commands:**
+**The complete workflow:**
 ```bash
-./tutorial.sh              # Learn (15 min)
-./run-analysis.sh          # Analyze your data (5 min)
-# Fill out assignment.md
+./tutorial.sh              # STEP 1: Learn (15 min)
+./run-analysis.sh          # STEP 2: Analyze class data (5 min)
+python3 answer_assignment.py  # STEP 3: Answer questions (10 min)
+git add answers.json results/
+git commit -m "Complete assignment"
+git push origin main       # STEP 4: Submit (auto-graded!)
 ```
 
 **Need help?**