nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com//master/nextflow_schema.json",
  "title": " pipeline parameters",
  "description": "",
  "type": "object",
  "definitions": {
    "parameters": {
      "title": "Parameters",
      "type": "object",
      "description": "Parameters for nf-hello-gatk pipeline",
      "default": "",
      "properties": {
        "reads_bam": {
          "type": "string",
          "description": "Path to BAM input files (.bam)",
          "format": "path"
        },
        "outdir": {
          "type": "string",
          "description": "Output directory to write results to.",
          "default": "results",
          "format": "path"
        },
        "reference": {
          "type": "string",
          "description": "Path to genome FASTA file (.fasta)",
          "format": "file-path"
        },
        "reference_index": {
          "type": "string",
          "description": "Path to genome FASTA index (.fai)",
          "format": "file-path"
        },
        "reference_dict": {
          "type": "string",
          "description": "Path to genome GATK dictionary file (.dict)",
          "format": "file-path"
        },
        "intervals": {
          "type": "string",
          "description": "Path to intervals for variant calling in BED format (.bed)",
          "format": "file-path"
        },
        "cohort_name": {
          "type": "string",
          "description": "Name of cohort to be used as output file"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/parameters"
    }
  ]
}