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

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

<!-- 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() }`.