parabricks-nextflow/nextflow_schema.json at main · Elembio/parabricks-nextflow · GitHub

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{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com//master/nextflow_schema.json",
  "title": " pipeline parameters",
  "description": "",
  "type": "object",
  "$defs": {
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Define where the pipeline should find input data and save output data.",
      "required": ["input", "outdir"],
      "properties": {
        "input": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "schema": "assets/schema_input.json",
          "mimetype": "text/csv",
          "pattern": "^\\S+\\.csv$",
          "description": "Path to comma-separated file containing information about the samples in the experiment.",
          "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
          "fa_icon": "fas fa-file-csv"
        },
        "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"
        },
        "ignore_samples": {
          "type": "string",
          "default": "['Unassigned', 'PhiX', 'phiX', 'CBPhiX', 'Undetermined']"
        }
      }
    },
    "parabricks": {
      "title": "Parabricks",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "assay": {
          "type": "string",
          "default": "WGS"
        },
        "target_region_bed": {
          "type": "string"
        },
        "known_sites": {
          "type": "string"
        },
        "proposed_variants": {
          "type": "string"
        },
        "model_file": {
          "type": "string"
        }
      }
    },
    "reference": {
      "title": "Reference",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "genome": {
          "type": "string"
        },
        "igenomes_base": {
          "type": "string",
          "default": "s3://ngi-igenomes/igenomes"
        }
      }
    },
    "infrastructure": {
      "title": "Infrastructure",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "batch_size": {
          "type": "integer",
          "default": 12
        },
        "max_cpus": {
          "type": "integer",
          "default": 48,
          "hidden": true
        },
        "max_memory": {
          "type": "string",
          "default": "192.GB",
          "hidden": true
        },
        "max_time": {
          "type": "string",
          "default": "4.h",
          "hidden": true
        }
      }
    },
    "multiqc": {
      "title": "MultiQC",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "multiqc_config": {
          "type": "string"
        },
        "max_multiqc_email_size": {
          "type": "string",
          "default": "25.MB"
        },
        "multiqc_title": {
          "type": "string"
        },
        "multiqc_logo": {
          "type": "string"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/input_output_options"
    },
    {
      "$ref": "#/$defs/parabricks"
    },
    {
      "$ref": "#/$defs/reference"
    },
    {
      "$ref": "#/$defs/infrastructure"
    },
    {
      "$ref": "#/$defs/multiqc"
    }
  ],
  "properties": {
    "publish_dir_mode": {
      "type": "string",
      "default": "copy",
      "hidden": true
    },
    "igenomes_ignore": {
      "type": "boolean",
      "hidden": true
    },
    "fasta": {
      "type": "string",
      "hidden": true
    },
    "fasta_fai": {
      "type": "string",
      "hidden": true
    },
    "bwa_index": {
      "type": "string",
      "hidden": true
    },
    "custom_config_version": {
      "type": "string",
      "default": "master",
      "hidden": true
    },
    "custom_config_base": {
      "type": "string",
      "default": "https://raw.githubusercontent.com/nf-core/configs/master",
      "hidden": true
    },
    "config_profile_description": {
      "type": "string",
      "hidden": true
    },
    "config_profile_contact": {
      "type": "string",
      "hidden": true
    },
    "config_profile_url": {
      "type": "string",
      "hidden": true
    },
    "config_profile_name": {
      "type": "string",
      "hidden": true
    }
  }
}