find-todo-and-fixme-comments

name	Find TODO and FIXME Comments
description	Search markdown files, Nextflow scripts, and config files for TODO/FIXME comments, categorize by priority, and provide actionable recommendations. Use when you need to identify pending work or track technical debt.

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