Test Nextflow Example Script

Test a Nextflow example script and verify it matches the documentation.

See ../shared/repo-conventions.md for directory mapping.

Working Directory

This skill works in two phases:

1. Initial phase: Start from repository root for finding scripts and reading documentation
2. Execution phase: Change to the script's directory for running Nextflow (ensures relative paths work)

Return to repository root after testing for final documentation checks.

Tasks to Perform

1. Identify the Script

   • Ask user which script to test (or find recently modified .nf files)
   • Read the script to understand what it does
   • Note any params. definitions for testing

2. Find Related Documentation

   • Search docs/ for markdown files referencing this script
   • Identify what the documentation claims about outputs and behavior

3. Run the Script

   • Change to the script's directory
   • Run: env -u CLAUDECODE NXF_AGENT_MODE=false nextflow run [script.nf] — see Console Output Mode: without this override, Nextflow 26.04+ renders in agent mode and the captured output will not match what learners see
   • Capture console output
   • Note the work directory hash

4. Verify Outputs

   • Check work directory for outputs
   • If publishDir used, check results/ directory
   • Compare actual output files with what documentation describes
   • Verify file contents match expectations

5. Test with Resume

   • Run: env -u CLAUDECODE NXF_AGENT_MODE=false nextflow run [script.nf] -resume
   • Verify processes show as "cached"
   • Confirm work directory hash is reused

6. Test with Parameters (if applicable)

   • Identify parameters from script
   • Run with different parameter values
   • Verify outputs change appropriately

7. Compare with Documentation

   • Check console output matches documented examples
   • Verify commands shown in docs are correct
   • Ensure file paths referenced are accurate
   • Confirm expected outputs match reality

Output Format

Provide a comprehensive test report:

# Test Report: [script.nf]

## Script Understanding
- Purpose: [what it does]
- Parameters: [list]
- Expected outputs: [list]

## Test Results

### Basic Run
✓ Script executed successfully
✓ Output files created: [list]
✓ Console output as expected

### Resume Test
✓ All processes cached
✓ Work directory reused

### Parameter Tests
✓ --param1 value: works correctly
[or issues found]

## Documentation Comparison

### Accurate
- Console output examples match
- File paths correct
- Command syntax verified

### Issues Found
- Line 123: Console output shows v25.04 but docs show v24.10
- Example missing --param flag
[or none]

## Recommendations
[Suggested documentation updates or script fixes]

Notes

• Always run from the script's directory
• Save work directory paths for verification
• Test both success and documented failure cases
• If script doesn't work, report why but don't fail - that's useful information