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",
  "properties": {
    "publishDir": {
      "type": "string",
      "default": "results",
      "format": "directory-path"
    },
    "bam_g1": {
      "type": "array"
    },
    "bam_g2": {
      "type": "array"
    },
    "gtf": {
      "type": "string",
      "format": "file-path"
    },
    "is_single_end": {
      "type": "boolean"
    },
    "readLength": {
      "type": "integer"
    },
    "nthread": {
      "type": "integer",
      "default": 1
    },
    "out_dir": {
      "type": "string"
    },
    "lib_type": {
      "type": "string",
      "default": "fr-unstranded"
    },
    "variable_read_length": {
      "type": "boolean"
    },
    "anchorLength": {
      "type": "integer"
    },
    "tstat": {
      "type": "integer",
      "default": 1
    },
    "cstat": {
      "type": "number",
      "default": 0.0001
    },
    "statoff": {
      "type": "boolean"
    },
    "paired_stats": {
      "type": "boolean"
    },
    "darts_model": {
      "type": "boolean"
    },
    "darts_cutoff": {
      "type": "number",
      "default": 0.05
    },
    "novelSS": {
      "type": "boolean"
    },
    "mil": {
      "type": "integer",
      "default": 50
    },
    "mel": {
      "type": "integer",
      "default": 500
    },
    "allow_clipping": {
      "type": "boolean"
    },
    "individual_counts": {
      "type": "boolean"
    },
    "machine_mem_gb": {
      "type": "integer",
      "default": 4
    },
    "rmats_version": {
      "type": "string",
      "default": "v4.3.0"
    }
  },
  "required": ["publishDir", "bam_g1", "gtf", "readLength", "out_dir"]
}