test-nextflow-example-script

# 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: `env -u CLAUDECODE NXF_AGENT_MODE=false nextflow run [script.nf]` — see [Console Output Mode](../shared/repo-conventions.md#console-output-mode-critical): 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