check-inline-code-formatting

# Check Inline Code Formatting Review inline code in markdown files for proper formatting and appropriate use of syntax highlighting. See [../shared/repo-conventions.md](../shared/repo-conventions.md) for file conventions. ## What to Check ### 1. Missing Backticks 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:** - Variable names: `params.input`, `outputDir` - Process names: `SAYHELLO` - Operators and methods: `collect()`, `map()`, `view()` - Directives: `container`, `publishDir`, `memory` ### 2. Inline Syntax Highlighting Use `` `#!groovy code` `` for Groovy/Nextflow code that benefits from syntax colouring. **DO use `#!groovy` for:** - Variable interpolation: `` `#!groovy ${variable}` `` - Closures: `` `#!groovy { meta.id }` `` or `` `#!groovy .map { it * 2 }` `` - Method chains with closures: `` `#!groovy channel.of(1,2,3).map { it * 2 }` `` - String interpolation: `` `#!groovy "${greeting}-output.txt"` `` - Type declarations: `` `#!groovy param: String = 'value'` `` **DO NOT use `#!groovy` for:** - Single words or identifiers: use `` `outputDir` `` not `` `#!groovy outputDir` `` - Simple directives: use `` `container 'uri'` `` not `` `#!groovy container 'uri'` `` - Plain dot notation: use `` `processName.out` `` not `` `#!groovy processName.out` `` - Keywords alone: use `` `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. ### 3. Consistency - Similar code references should be formatted the same way throughout a document - Quiz answer options should have consistent formatting ## Examples ### Good inline code formatting ```markdown 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`. ``` ### Bad inline code formatting ```markdown <!-- 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() }`. ```