Test Nextflow Example Script

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

Working Directory

IMPORTANT: This skill works with directories in two phases:

1. Initial phase - Start from repository root

- Repository root is the directory containing mkdocs.yml, docs/, and .github/ - Verify you are in the correct directory (check for these files/folders) - Use this for finding scripts and reading documentation - All Grep and Glob operations use repository root paths

1. Execution phase - Change to the script's directory for running Nextflow

- Use cd to the script's directory before running nextflow run - This ensures relative paths in the script work correctly

After testing, return to repository root or use absolute paths 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

1. Find Related Documentation

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

1. Run the Script

- Change to the script's directory - Run: nextflow run [script.nf] - Capture console output - Note the work directory hash

1. 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

1. Test with Resume

- Run: nextflow run [script.nf] -resume - Verify processes show as "cached" - Confirm work directory hash is reused

1. Test with Parameters (if applicable)

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

1. 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