Find TODO and FIXME Comments

Search the training materials codebase for TODO and FIXME comments to identify pending work.

Working Directory

IMPORTANT: All commands in this skill must be executed from the repository root directory.

• The repository root is the directory containing mkdocs.yml, docs/, and .github/
• Verify you are in the correct directory before running any commands (check for these files/folders)
• All file paths in this skill are relative to the repository root
• Do not change directories during skill execution
• Use paths relative to repository root only

Tasks to Perform

1. Search Markdown Files

   • Use Grep to find TODO and FIXME in docs/**/*.md
   • Capture file path, line number, and full comment
   • Note context (which module/lesson)

2. Search Nextflow Scripts

   • Find TODO/FIXME in **/*.nf files
   • Distinguish between training examples and solution code
   • Note if in core examples or side-quests

3. Search Configuration Files

   • Check mkdocs.yml
   • Check .github/**/*.yml and .github/**/*.py
   • Check CONTRIBUTING.md

4. Categorize Results

   • High Priority: Marked as FIXME, TODO(urgent), or blocking
   • Documentation: TODOs in markdown files
   • Code: TODOs in .nf or .py files
   • Configuration: TODOs in config files

5. Check Known Issues

   • Read CONTRIBUTING.md for any documented TODOs
   • Note which are tracked vs untracked

Output Format

Provide an organized report:

# TODO/FIXME Report

## Summary
- Total items: 23
- High priority: 3
- Documentation: 15
- Code: 4
- Configuration: 1

## High Priority Items

### docs/hello_nextflow/03_hello_workflow.md:156
```markdown
<!-- FIXME: Update this example for DSL2 syntax -->

Documentation TODOs

By File

docs/side_quests/debugging.md (5 items)

• Line 45: TODO: Add example of common error message
• Line 89: TODO: Include screenshot of trace report
• ...

docs/nf4_science/genomics/01_per_sample_variant_calling.md (3 items)

• Line 234: TODO: Verify this command works with latest GATK
• ...

Code TODOs

nf-training/script7.nf:23

// TODO: Add error handling for missing files

Configuration TODOs

CONTRIBUTING.md:204

Known limitation documented - needs upstream fix in mkdocs plugin

Recommendations

1. Immediate attention (3 items):

   • Fix blocking issues in hello_nextflow
   • Update genomics examples for latest tools

2. Next sprint (8 items):

   • Complete debugging module exercises
   • Add missing screenshots

3. Low priority (12 items):

   • Style improvements
   • Nice-to-have features

Files with Most TODOs

1. docs/side_quests/debugging.md (5)
2. docs/nf4_science/genomics/01_per_sample_variant_calling.md (3)
3. nf-training/script7.nf (2)

## Notes

- Use Grep tool with pattern `TODO|FIXME` (case insensitive)
- Show enough context to understand what needs doing
- Distinguish between legitimate TODOs and example comments in training materials
- Provide actionable priorities, not just a list