// 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.
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.
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.
| name | Check Inline Code Formatting |
| description | 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. |
Review inline code in markdown files for proper formatting and appropriate use of syntax highlighting.
See ../shared/repo-conventions.md for file conventions.
The following should always be wrapped in backticks:
CLI flags and options:
-resume, -profile, -params-file, --input, etc.Filenames and paths:
nextflow.config, .command.sh, work/, modules/, etc.Commands:
nextflow run, nextflow log, docker run, etc.Code elements:
params.input, outputDirSAYHELLOcollect(), map(), view()container, publishDir, memoryUse `#!groovy code` for Groovy/Nextflow code that benefits from syntax colouring.
DO use #!groovy for:
`#!groovy ${variable}``#!groovy { meta.id }` or `#!groovy .map { it * 2 }``#!groovy channel.of(1,2,3).map { it * 2 }``#!groovy "${greeting}-output.txt"``#!groovy param: String = 'value'`DO NOT use #!groovy for:
`outputDir` not `#!groovy outputDir``container 'uri'` not `#!groovy container 'uri'``processName.out` not `#!groovy processName.out``include` not `#!groovy include`The rule: Only use #!groovy when there's meaningful syntax structure (braces, interpolation, operators) that highlighting will visually enhance. A single word or simple expression gains nothing from syntax highlighting.
Run the workflow with `nextflow run main.nf -resume`.
The `#!groovy ${greeting}` variable is interpolated into the string.
Set memory with `#!groovy process { withName: 'FOO' { memory = '4.GB' } }`.
The `container` directive specifies the Docker image.
Access outputs with `processName.out.outputName`.
<!-- Missing backticks -->
Run the workflow with nextflow run main.nf -resume.
<!-- Unnecessary #!groovy on single word -->
The `#!groovy container` directive specifies the image.
<!-- Missing #!groovy on closure -->
Transform with `.map { it.toUpperCase() }`.