training

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.

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.

Create a new numbered lesson page within an existing training module. Use when adding a new topic like '05_error_handling.md' to an existing course.

Scaffold a complete new training module with standard directory structure, index, orientation, lessons, survey, and next-steps files. Use when creating a new course like 'Advanced Pipelines' or a new domain module.

Start local MkDocs preview server to view training material changes. Use when editing documentation, checking formatting, or testing how content renders before committing.

Stop a running MkDocs preview server. Use when port 8000 is busy, switching tasks, or done editing documentation.

Test a Nextflow script by running it, verifying outputs, testing resume functionality, and comparing results with documentation. Use when validating that example scripts work correctly and match their documentation.