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Find TODO and FIXME Comments

Productivity
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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.

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How to use this skill

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  2. Copy the prompt below and paste it into your agent.
  3. Review the proposed files and risks before you approve installation.
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I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/analysis/find-todos-nextflow-io-training/SKILL.md

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Find TODO and FIXME Comments

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

Execute from repository root. See ../shared/repo-conventions.md for directory structure.

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