Writing docs

Sources

Information is pulled from multiple sources (each only if available):

Source	Content
`README.md`	Pipeline overview
`nextflow_schema.json`	Typed input parameters with validation rules
`nextflow.config`	Runtime configuration defaults
Language Server	Processes, workflows, functions with Groovydoc comments
`meta.yml`	nf-core module metadata (tools, keywords, authors)

Groovydoc comments

nf-docs reads Groovydoc-style /** ... */ comments on processes, workflows, and functions.

/**
 * Align reads to a reference genome using BWA MEM.
 *
 * Handles both single-end and paired-end reads automatically.
 *
 * @param reads  Tuple of sample ID and FASTQ files
 * @param index  BWA index files
 * @return       Tuple of sample ID and aligned BAM file
 */
process BWA_MEM {
    input:
    tuple val(sample_id), path(reads)
    path index

    output:
    tuple val(sample_id), path("*.bam"), emit: bam

    // ...
}

Supported tags: @param, @return.

Input parameters

Input parameters are sourced from nextflow_schema.json ( nf-schema format). Use description for a short label and help_text for extended detail.

{
  "$defs": {
    "input_output_options": {
      "properties": {
        "input": {
          "type": "string",
          "format": "file-path",
          "description": "Path to the sample sheet",
          "help_text": "CSV file with columns: sample, fastq_1, fastq_2"
        }
      }
    }
  }
}