Test a Nextflow script by running it, verifying outputs, testing resume functionality, and comparing results with documentation. Use when validating that example scripts work correctly and match their documentation.
Content & Writing
210 Stars
263 Forks
Updated Jan 18, 2026, 06:34 PM
Why Use This
This skill provides specialized capabilities for nextflow-io's codebase.
Use Cases
Developing new features in the nextflow-io repository
Refactoring existing code to follow nextflow-io standards
Understanding and working with nextflow-io's codebase structure
---
name: Test Nextflow Example Script
description: Test a Nextflow script by running it, verifying outputs, testing resume functionality, and comparing results with documentation. Use when validating that example scripts work correctly and match their documentation.
---
# Test Nextflow Example Script
Test a Nextflow example script and verify it matches the documentation.
See [../shared/repo-conventions.md](../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: `nextflow run [script.nf]`
- 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: `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
