{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bwa_samse",
  "description": "BWA samse - generate single-end alignment in SAM format from BWA aln SAI files.",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "index": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "BWA index base name (prefix of .amb, .ann, .bwt, .pac, .sa files).",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"reference.fasta\"`. "
        },
        "sai": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input SAI file generated by BWA aln.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"alignment.sai\"`. "
        },
        "reads": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input FASTQ file with single-end reads.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"reads.fastq\"`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output SAM file",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.sam\"`, direction: `output`, example: `\"output.sam\"`. ",
          "default": "$id.$key.output.sam"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "max_occ": {
          "type": "integer",
          "description": "Maximum occurrences for read mapping",
          "help_text": "Type: `integer`, multiple: `False`, example: `3`. "
        },
        "read_group": {
          "type": "string",
          "description": "Read group header line such as '@RG\\tID:foo\\tSM:bar'.",
          "help_text": "Type: `string`, multiple: `False`, example: `\"@RG\\tID:sample1\\tSM:sample1\"`. "
        }
      }
    },
    "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"
    },
    {
      "$ref": "#/$defs/output"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
