{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "falco",
  "description": "A C++ drop-in replacement of FastQC to assess the quality of sequence read data",
  "type": "object",
  "$defs": {
    "input arguments": {
      "title": "Input arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "input fastq files",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input1.fastq;input2.fastq\"]`. "
        }
      }
    },
    "run arguments": {
      "title": "Run arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "nogroup": {
          "type": "boolean",
          "description": "Disable grouping of bases for reads >50bp",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "contaminents": {
          "type": "string",
          "format": "path",
          "description": "Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "adapters": {
          "type": "string",
          "format": "path",
          "description": "Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "limits": {
          "type": "string",
          "format": "path",
          "description": "Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "subsample": {
          "type": "integer",
          "description": "[Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads).\n",
          "help_text": "Type: `integer`, multiple: `False`, example: `10`. "
        },
        "bisulfite": {
          "type": "boolean",
          "description": "[Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "reverse_complement": {
          "type": "boolean",
          "description": "[Falco only] The input is a \nreverse-complement",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "allow_empty_input": {
          "type": "boolean",
          "description": "Allow empty input files and generate empty output files without an error state.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "output arguments": {
      "title": "Output arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "outdir": {
          "type": "string",
          "format": "path",
          "description": "Create all output files in the specified \noutput directory",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.outdir\"`, direction: `output`, example: `\"output\"`. ",
          "default": "$id.$key.outdir"
        },
        "format": {
          "type": "string",
          "description": "Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format",
          "help_text": "Type: `string`, multiple: `False`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. ",
          "enum": [
            "bam",
            "sam",
            "bam_mapped",
            "sam_mapped",
            "fastq",
            "fq",
            "fastq.gz",
            "fq.gz"
          ]
        },
        "data_filename": {
          "type": "string",
          "format": "path",
          "description": "[Falco only] Specify filename for FastQC \ndata output (TXT)",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.data_filename\"`, direction: `output`. ",
          "default": "$id.$key.data_filename"
        },
        "report_filename": {
          "type": "string",
          "format": "path",
          "description": "[Falco only] Specify filename for FastQC \nreport output (HTML)",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.report_filename\"`, direction: `output`. ",
          "default": "$id.$key.report_filename"
        },
        "summary_filename": {
          "type": "string",
          "format": "path",
          "description": "[Falco only] Specify filename for the short \nsummary output (TXT)",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.summary_filename\"`, direction: `output`. ",
          "default": "$id.$key.summary_filename"
        }
      }
    },
    "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/input arguments"
    },
    {
      "$ref": "#/$defs/run arguments"
    },
    {
      "$ref": "#/$defs/output arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
