nextflow_schema.json

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com//master/nextflow_schema.json",
  "title": " pipeline parameters",
  "description": "",
  "type": "object",
  "properties": {
    "experiment_name": {
      "type": "string",
      "description": "Name of the experiment, used for reports (title and filename)."
    },
    "data_dir": {
      "type": "string",
      "description": "Path to the directory containing POD5 files.",
      "format": "directory-path"
    },
    "sample_data": {
      "type": "string",
      "default": "input/samples.csv",
      "format": "file-path",
      "schema": "/assets/samples_data_schema.json",
      "mimetype": "text/csv",
      "description": "Path to the CSV file containing the sample data (if not provided, will not perform demultiplexing)."
    },
    "output_dir": {
      "type": "string",
      "default": "results/",
      "description": "Directory for saving results."
    },
    "fastq_output": {
      "type": "boolean",
      "default": true,
      "description": "Generates FASTQ files if `true`; otherwise, generates UBAM files."
    },
    "qscore_filter": {
      "type": "integer",
      "default": 10,
      "description": "Minimum QScore threshold for \"pass\" data, used in demultiplexing."
    },
    "dorado_basecalling_model": {
      "type": "string",
      "default": "sup",
      "description": "Model used for basecalling. Check Dorado help for available options."
    },
    "dorado_basecalling_gpus": {
      "type": "integer",
      "default": 1,
      "description": "Number of GPUs to allocate for basecalling."
    },
    "dorado_demux_kit": {
      "type": "string",
      "default": "SQK-NBD114-96",
      "description": "Kit identifier used for demultiplexing."
    },
    "dorado_demux_both_ends": {
      "type": "boolean",
      "description": "Demultiplexes using barcodes on both ends (5' and 3') if `true`."
    },
    "use_dorado_container": {
      "type": "boolean",
      "default": true,
      "description": "Uses Dorado via container if `true`; expects a local installation if `false`."
    },
    "qc_tools": {
      "type": "array",
      "items": {
        "type": "string",
        "enum": ["nanoq", "nanoplot", "fastqc", "toulligqc", "pycoqc"]
      },
      "description": "Specifies which QC tools to run."
    }
  },
  "required": ["data_dir"]
}