nextflow_schema.json

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/oma-browser-build/master/nextflow_schema.json",
  "title": "oma-browser-build pipeline parameters",
  "description": "Convert OMA run into OMA Browser release",
  "type": "object",
  "definitions": {
    "generic_options": {
      "title": "Generic options",
      "type": "object",
      "fa_icon": "fas fa-file-import",
      "description": "Less common options for the pipeline, typically set in a config file.",
      "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
      "properties": {
        "help": {
          "type": "boolean",
          "description": "Display help text.",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/generic_options"
    }
  ],
  "properties": {
    "hog_orthoxml": {
      "type": "string"
    },
    "matrix_file": {
      "type": "string"
    },
    "pairwise_orthologs_folder": {
      "type": "string"
    },
    "genomes_dir": {
      "type": "string"
    },
    "known_domains": {
      "type": "string"
    },
    "cath_names_path": {
      "type": "string",
      "default": "http://download.cathdb.info/cath/releases/latest-release/cath-classification-data/cath-names.txt"
    },
    "pfam_names_path": {
      "type": "string",
      "default": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
    },
    "xref_uniprot_swissprot": {
      "type": "string",
      "default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz"
    },
    "xref_uniprot_trembl": {
      "type": "string",
      "default": "/dev/null"
    },
    "xref_refseq": {
      "type": "string"
    },
    "go_obo": {
      "type": "string",
      "default": "http://purl.obolibrary.org/obo/go/go-basic.obo"
    },
    "go_gaf": {
      "type": "string",
      "default": "https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz"
    },
    "oma_browser_data_dir": {
      "type": "string",
      "default": "test/bla"
    },
    "nr_medium_procs": {
      "type": "integer",
      "default": 10
    },
    "outputDir": {
      "type": "string",
      "default": "./results"
    }
  }
}