nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/nextflow-io/rnaseq-nf/master/nextflow_schema.json",
  "title": "rnaseq-nf pipeline parameters",
  "description": "Proof of concept of a RNA-seq pipeline implemented with Nextflow",
  "type": "object",
  "definitions": {
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Define where the pipeline should find input data and save output data.",
      "properties": {
        "outdir": {
          "type": "string",
          "format": "directory-path",
          "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
          "fa_icon": "fas fa-folder-open",
          "default": "results"
        },
        "reads": {
          "type": "string",
          "description": "The input read-pair files",
          "fa_icon": "fas fa-folder-open",
          "default": "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
        },
        "transcriptome": {
          "type": "string",
          "description": "The input transcriptome file",
          "fa_icon": "fas fa-folder-open",
          "default": "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
        },
        "multiqc": {
          "type": "string",
          "fa_icon": "fas fa-folder-open",
          "default": "${projectDir}/multiqc"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_output_options"
    }
  ]
}