nextflow_schema.json

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/elembio/base2fastq/master/nextflow_schema.json",
  "title": "elembio/base2fastq pipeline parameters",
  "description": "FASTQ generation using Bases2Fastq for Element AVITI System",
  "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": ["run_dir", "outdir"],
      "properties": {
        "run_dir": {
          "type": "string",
          "description": "Input run directory"
        },
        "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": "."
        },
        "run_manifest": {
          "type": "string",
          "description": "(optional) path to custom RunManifest.csv"
        }
      }
    },
    "bases2fastq": {
      "title": "Bases2Fastq",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "legacy_fastq": {
          "type": "boolean",
          "description": "Apply a legacy file naming convention to FASTQ files, such as SampleName_S1_L001_R1_001.fastq.gz. Some secondary analysis software might require this naming convention."
        },
        "detect_adapters": {
          "type": "boolean",
          "description": "Detect adapter sequences and override any sequences present in the run manifest."
        },
        "force_index_orientation": {
          "type": "boolean",
          "description": "Perform demultiplexing without detecting the index sequence orientation. When used, Bases2Fastq applies the orientation recorded in the run manifest."
        },
        "num_unassigned": {
          "type": "number",
          "description": "Indicates the maximum number of unassigned sequences to support.",
          "minimum": 1,
          "maximum": 1000
        },
        "qc_only": {
          "type": "boolean",
          "description": "Enable QC-only mode, which generates a representative view of run metrics on one tile and no FASTQ files. Executions in QC-only mode are faster than executions with demultiplexing."
        },
        "split_lanes": {
          "type": "boolean",
          "description": "Divide FASTQ files by flow cell lane."
        },
        "settings": {
          "type": "string",
          "default": "[]",
          "description": "Overwrite run manifest settings. May be applies more than once."
        },
        "flowcell_id": {
          "type": "string",
          "description": "Overwrite the flow cell ID in RunParameters.json with another flow cell ID. You can use this argument to add a missing flow cell ID."
        },
        "filter_mask": {
          "type": "string",
          "description": "\"Apply a custom base mask to specify the cycles that determine if a read passes filter. Separate each read section with a hyphen. The argument is only compatible with Cloudbreak or Cloudbreak Freestyle chemistry"
        }
      }
    },
    "bases2fastq_advanced_settings": {
      "title": "Bases2Fastq Advanced Settings",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "exclude_tile": {
          "type": "string",
          "default": "[]",
          "description": "Specify subset of tiles to exclude from processing. Use a regex to identify the tiles (e.g. 'L1R..C..S.')"
        },
        "include_tile": {
          "type": "string",
          "default": "[]",
          "description": "Specify subset of tiles to include in processing. Use a regex to identify the tiles (e.g. 'L1R..C..S.'). To include specific tiles, you must first exclude all tiles with the exclude-tile parameter"
        },
        "no_error_on_invalid": {
          "type": "boolean",
          "description": "Skip non-critical files that Bases2Fastq identifies as invalid"
        },
        "b2f_args": {
          "type": "string",
          "description": "Send a string of arguments to Bases2Fastq. Recommended for local testing & development only."
        }
      }
    },
    "infrastructure": {
      "title": "Infrastructure",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "max_cpus": {
          "type": "integer",
          "default": 48
        },
        "max_memory": {
          "type": "string",
          "default": "192.GB"
        },
        "max_time": {
          "type": "string",
          "default": "8.h"
        },
        "b2f_container_url": {
          "type": "string",
          "default": "docker.io/elembio/bases2fastq"
        },
        "b2f_container_tag": {
          "type": "string",
          "default": "latest"
        },
        "tracedir": {
          "type": "string",
          "default": "./pipeline_info"
        },
        "enable_conda": {
          "type": "boolean"
        },
        "publish_dir_mode": {
          "type": "string",
          "default": "copy"
        },
        "custom_config_version": {
          "type": "string",
          "default": "master"
        },
        "custom_config_base": {
          "type": "string",
          "default": "https://raw.githubusercontent.com/nf-core/configs/master"
        },
        "config_profile_description": {
          "type": "string"
        },
        "config_profile_contact": {
          "type": "string"
        },
        "config_profile_url": {
          "type": "string"
        },
        "config_profile_name": {
          "type": "string"
        }
      }
    },
    "multiqc": {
      "title": "MultiQC",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "multiqc_title": {
          "type": "string"
        },
        "max_multiqc_email_size": {
          "type": "string",
          "default": "25.MB"
        },
        "multiqc_logo": {
          "type": "string"
        },
        "multiqc_config": {
          "type": "string"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/input_output_options"
    },
    {
      "$ref": "#/$defs/bases2fastq"
    },
    {
      "$ref": "#/$defs/bases2fastq_advanced_settings"
    },
    {
      "$ref": "#/$defs/infrastructure"
    },
    {
      "$ref": "#/$defs/multiqc"
    }
  ],
  "properties": {
    "projects": {
      "type": "boolean",
      "default": true
    }
  }
}