nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/TamaraNaboulsi/nextflow-filedump/main/nextflow_schema.json",
  "title": "FileDump Nextflow Pipeline Parameters",
  "description": "",
  "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": {
        "email": {
          "type": "string",
          "description": "Email address for completion summary.",
          "fa_icon": "fas fa-envelope",
          "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`    ~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
          "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
        },
        "registry": {
          "type": "string",
          "description": "Registry file.",
          "fa_icon": "fas fa-database",
          "help_text": "Set this parameter to the path of the registry file, in which defined are the details for connecting to the registry.",
          "pattern": ".+"
        },
        "dump_dir": {
          "type": "string",
          "description": "File dump directory.",
          "fa_icon": "fas fa-folder",
          "help_text": "Set this parameter to the path of the directory where you want the dumped files to be stored.",
          "pattern": ".+"
        },
        "pipeline_dir": {
          "type": "string",
          "description": "Pipeline directory.",
          "fa_icon": "fas fa-code",
          "help_text": "Set this parameter to the path of the directory containing the run_process.pl script.",
          "pattern": ".+"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_output_options"
    }
  ],
  "properties": {
    "pipeline_dir": {
      "type": "string",
      "default": ""
    },
    "user": {
      "type": "string",
      "default": ""
    },
    "core_dump": {
      "type": "integer",
      "default": 0
    },
    "species": {
      "type": "string",
      "default": ""
    },
    "antispecies": {
      "type": "string",
      "default": ""
    },
    "division": {
      "type": "string",
      "default": ""
    },
    "run_all": {
      "type": "integer",
      "default": 0
    },
    "dbname": {
      "type": "string",
      "default": ""
    },
    "meta_filters": {
      "type": "string",
      "default": ""
    },
    "dump_dir": {
      "type": "string",
      "default": ""
    },
    "ftp_root": {
      "type": "string",
      "default": ""
    },
    "genome_types": {
      "type": "string",
      "default": ""
    },
    "geneset_types": {
      "type": "string",
      "default": "Geneset_EMBL,Geneset_FASTA,Xref_TSV"
    },
    "rnaseq_types": {
      "type": "string",
      "default": "RNASeq_Exists"
    },
    "dump_metadata": {
      "type": "integer",
      "default": 0
    },
    "dump_mysql": {
      "type": "integer",
      "default": 0
    },
    "overwrite": {
      "type": "integer",
      "default": 1
    },
    "per_chromosome": {
      "type": "integer",
      "default": 0
    },
    "rnaseq_email": {
      "type": "string",
      "default": ""
    },
    "run_datachecks": {
      "type": "integer",
      "default": 0
    },
    "datacheck_groups": {
      "type": "string",
      "default": "rapid_release"
    },
    "config_file": {
      "type": "string",
      "default": ""
    },
    "history_file": {
      "type": "string",
      "default": ""
    },
    "output_dir": {
      "type": "string",
      "default": ""
    },
    "datacheck_names": {
      "type": "string",
      "default": ""
    },
    "datacheck_types": {
      "type": "string",
      "default": ""
    },
    "blastdb_exe": {
      "type": "string",
      "default": "makeblastdb"
    },
    "gtf_to_genepred_exe": {
      "type": "string",
      "default": "gtfToGenePred"
    },
    "genepred_check_exe": {
      "type": "string",
      "default": "genePredCheck"
    },
    "gt_gff3_exe": {
      "type": "string",
      "default": "gt gff3"
    },
    "gt_gff3validator_exe": {
      "type": "string",
      "default": "gt gff3validator"
    },
    "blast_index": {
      "type": "integer",
      "default": 0
    },
    "chain_ucsc": {
      "type": "integer",
      "default": 1
    },
    "dna_per_chromosome": {
      "type": "integer",
      "default": 0
    },
    "embl_per_chromosome": {
      "type": "integer",
      "default": 0
    },
    "gff3_per_chromosome": {
      "type": "integer",
      "default": 0
    },
    "gtf_per_chromosome": {
      "type": "integer",
      "default": 0
    },
    "xref_external_dbs": {
      "type": "string",
      "default": ""
    },
    "run_assembly_chain": {
      "type": "integer",
      "default": 0
    },
    "run_chromosome_tsv": {
      "type": "integer",
      "default": 0
    },
    "run_genome_fasta": {
      "type": "integer",
      "default": 0
    },
    "run_geneset_embl": {
      "type": "integer",
      "default": 1
    },
    "run_geneset_fasta": {
      "type": "integer",
      "default": 1
    },
    "run_geneset_gff3": {
      "type": "integer",
      "default": 0
    },
    "run_geneset_gtf": {
      "type": "integer",
      "default": 0
    },
    "run_xref_tsv": {
      "type": "integer",
      "default": 1
    },
    "run_rnaseq_exists": {
      "type": "integer",
      "default": 1
    }
  }
}