// 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.
| 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. |
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.
Search Markdown Files
docs/**/*.mdSearch Nextflow Scripts
**/*.nf filesSearch Configuration Files
docs/en/mkdocs.yml.github/**/*.yml and .github/**/*.pyCONTRIBUTING.mdCategorize Results
Check Known Issues
# TODO/FIXME Report
## Summary
Total items, High priority count, by category (Documentation/Code/Configuration)
## High Priority Items
[List FIXME and urgent items with file:line and context]
## Documentation TODOs
[Group by file with line numbers]
## Code TODOs
[Group by file with line numbers]
## Recommendations
1. Immediate attention: [blocking items]
2. Next sprint: [significant items]
3. Low priority: [nice-to-haves]
## Files with Most TODOs
[Top 3-5 files]
TODO|FIXME (case insensitive)Run comprehensive validation and review checks including heading numbering, TODO/FIXME comments, Nextflow script conventions, orphaned files, admonition syntax, lesson structure, formatting, content accuracy, and teaching effectiveness. Use when validating, reviewing, or checking training materials quality, lesson quality, or before committing changes.
Walk through a training tutorial as a user would, progressively building examples exactly as instructed, running all commands, and verifying results against solutions. Use when testing tutorials end-to-end or validating that instructions are correct and complete.
Add an interactive exercise with solution to an existing lesson. Creates properly formatted exercise and solution admonition blocks. Use when a lesson needs hands-on practice.
Verify that hl_lines attributes in markdown code blocks correctly highlight the intended lines. Use when reviewing documentation with code examples, especially Before/After comparisons, or when highlights seem incorrect.
Review inline code in markdown files for proper formatting and syntax highlighting. Check for missing backticks on CLI flags, filenames, and code elements. Verify that inline syntax highlighting (#!groovy) is used appropriately. Use when reviewing documentation or quiz questions.
Set up a Docker container for running Nextflow training examples. Handles basic setup, Docker-outside-of-Docker (DooD) for containerized processes, ARM Mac platform emulation, and troubleshooting. Use when you need to run Nextflow examples in a consistent environment.