{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "cellranger_atac_count",
  "description": "Align fastq files using Cell Ranger ATAC count.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "The fastq.gz files to align",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"sample_S1_L001_R1_001.fastq.gz\";\"sample_S1_L001_R2_001.fastq.gz\"]`. "
        },
        "reference": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "The path to Cell Ranger reference tar.gz file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"reference.tar.gz\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The folder to store the alignment results.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/output\"`. ",
          "default": "$id.$key.output"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "description": {
          "type": "string",
          "description": "Sample description to embed in output files",
          "help_text": "Type: `string`, multiple: `False`, default: `\"\"`. ",
          "default": ""
        },
        "force_cells": {
          "type": "integer",
          "description": "Define the top N barcodes with the most fragments overlapping peaks as cells and override the cell calling algorithm",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "peaks": {
          "type": "string",
          "format": "path",
          "description": "Override peak caller: specify peaks to use in downstream analyses from supplied 3-column BED file",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"peaks.bed\"`. "
        },
        "dim_reduce": {
          "type": "string",
          "description": "Dimensionality reduction mode for clustering",
          "help_text": "Type: `string`, multiple: `False`, default: `\"lsa\"`, choices: ``lsa`, `pca`, `plsa``. ",
          "enum": [
            "lsa",
            "pca",
            "plsa"
          ],
          "default": "lsa"
        },
        "subsample_rate": {
          "type": "number",
          "description": "Downsample to preserve this fraction of reads",
          "help_text": "Type: `double`, multiple: `False`, example: `0.1`. "
        },
        "lanes": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "bcl2fastq option",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"1,3\"]`. "
        }
      }
    },
    "nextflow input-output arguments": {
      "title": "Nextflow input-output arguments",
      "type": "object",
      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
      "properties": {
        "publish_dir": {
          "type": "string",
          "description": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
