{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "alignment_quantification",
  "description": "Align reads to the genome using STAR and quantify gene expression using\nSalmon\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_r1": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "FASTQ file containing read 1",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "input_r2": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "FASTQ file containing read 2",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "input_transcript_fasta": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "FASTA file containing transcript sequences",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "input_gtf": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "GTF file containing sequence annotations",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "input_star_genome_dir": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "STAR genome index directory",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output_star_bam_genome": {
          "type": "string",
          "format": "path",
          "description": "BAM file containing reads aligned to the genome using STAR",
          "help_text": "Type: `file`, multiple: `False`, default: `\"star/aligned_genome.bam\"`, direction: `output`. ",
          "default": "star/aligned_genome.bam"
        },
        "output_star_bam_transcriptome": {
          "type": "string",
          "format": "path",
          "description": "BAM file containing reads aligned to the transcriptome using STAR",
          "help_text": "Type: `file`, multiple: `False`, default: `\"star/aligned_transcriptome.bam\"`, direction: `output`. ",
          "default": "star/aligned_transcriptome.bam"
        },
        "output_star_junctions": {
          "type": "string",
          "format": "path",
          "description": "Tabular file containing splice junctions identified by STAR",
          "help_text": "Type: `file`, multiple: `False`, default: `\"star/splice_junctions.tab\"`, direction: `output`. ",
          "default": "star/splice_junctions.tab"
        },
        "output_star_log": {
          "type": "string",
          "format": "path",
          "description": "STAR execution log file",
          "help_text": "Type: `file`, multiple: `False`, default: `\"star/log.out\"`, direction: `output`. ",
          "default": "star/log.out"
        },
        "output_salmon": {
          "type": "string",
          "format": "path",
          "description": "salmon alignment mode quantification output directory",
          "help_text": "Type: `file`, multiple: `False`, default: `\"salmon\"`, direction: `output`. ",
          "default": "salmon"
        }
      }
    },
    "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/nextflow input-output arguments"
    }
  ]
}