{
  "parameters": [
    {
      "name": "reads",
      "label": "Single or pair-end reads",
      "usage": "Workflow input data.",
      "type": "string",
      "render": "file",
      "default_value": "path/to/reads.fastq.gz",
      "pattern": ".*(\\.fastq$|\\.fastq\\.gz$)",
      "group": "input"
    },
    {
      "name": "profile",
      "label": "Profile",
      "usage": "HPC profile",
      "type": "string",
      "render": "textfield",
      "default_value": "",
      "group": "input"
    },
    {
      "name": "singleEnd",
      "label": "Sequencing strategy",
      "usage": "Flag if input data is of type singleEnd.",
      "type": "boolean",
      "render": "check-box",
      "default_value": false,
      "group": "input"
    },
    {
      "name": "genome",
      "label": "Sequencing strategy",
      "usage": "Flag if input data is of type singleEnd.",
      "type": "boolean",
      "render": "check-box",
      "default_value": false,
      "group": "reference"
    },
    {
      "name": "fasta",
      "label": "FASTA reference",
      "usage": "Path to custom FASTA reference.",
      "type": "string",
      "render": "textfield",
      "default_value": "",
      "group": "reference"
    },
    {
      "name": "gtf",
      "label": "GTF annotation",
      "usage": "Path to custom GTF annotation.",
      "type": "string",
      "render": "textfield",
      "default_value": "",
      "group": "reference"
    },
    {
      "name": "star_index",
      "label": "STAR index",
      "usage": "Path to STAR index.",
      "type": "string",
      "render": "textfield",
      "default_value": "",
      "group": "reference"
    },
    {
      "name": "star_fusion",
      "label": "STAR-Fusion",
      "usage": "Enable STAR-Fusion.",
      "type": "boolean",
      "render": "check-box",
      "default_value": true,
      "group": "star_fusion"
    },
    {
      "name": "star_fusion_ref",
      "label": "STAR-Fusion reference",
      "usage": "Path to STAR-Fusion reference.",
      "type": "string",
      "render": "text-field",
      "default_value": "",
      "group": "star_fusion"
    },
    {
      "name": "fusioncatcher",
      "label": "Fusioncatcher",
      "usage": "Enable Fusioncatcher.",
      "type": "boolean",
      "render": "check-box",
      "default_value": true,
      "group": "fusioncatcher"
    },
    {
      "name": "fc_extra_options",
      "label": "Fusioncatcher",
      "usage": "Fusioncatcher extra params.",
      "type": "string",
      "render": "textbox",
      "default_value": "",
      "group": "fusioncatcher"
    },
    {
      "name": "fusioncatcher_ref",
      "label": "Fusioncatcher reference",
      "usage": "Path to Fusioncatcher reference.",
      "type": "string",
      "render": "textbox",
      "default_value": "",
      "group": "fusioncatcher"
    },
    {
      "name": "ericscript",
      "label": "Ericscript",
      "usage": "Enable Fusioncatcher.",
      "type": "boolean",
      "render": "check-box",
      "default_value": true,
      "group": "ericscript"
    },
    {
      "name": "ericscript_ref",
      "label": "Ericscript reference",
      "usage": "Path to Ericscript reference.",
      "type": "string",
      "render": "textbox",
      "default_value": "",
      "group": "ericscript"
    },
    {
      "name": "pizzly",
      "label": "Pizzly",
      "usage": "Enable Pizzly.",
      "type": "boolean",
      "render": "check-box",
      "default_value": true,
      "group": "pizzly"
    },
    {
      "name": "pizzly_fasta",
      "label": "Pizzly FASTA reference",
      "usage": "Path to Pizzly FASTA reference.",
      "type": "string",
      "render": "textbox",
      "default_value": "",
      "group": "pizzly"
    },
    {
      "name": "pizzly_gtf",
      "label": "Pizzly GTF annotation",
      "usage": "Path to Pizzly GTF annotation.",
      "type": "string",
      "render": "textbox",
      "default_value": "",
      "group": "pizzly"
    },
    {
      "name": "fusion_inspector",
      "label": "FusionInspector",
      "usage": "Enable FusionInspector.",
      "type": "boolean",
      "render": "check-box",
      "default_value": true,
      "group": "visualization"
    },
    {
      "name": "read_length",
      "label": "Average read length",
      "usage": "The length is used to generate STAR index.",
      "type": "integer",
      "render": "textfield",
      "default_value": 100,
      "group": "other"
    },
    {
      "name": "tool_cutoff",
      "label": "Detection tool cutoff",
      "usage": "Number of tools required to detect fusion (used as filter in summary report.)",
      "type": "integer",
      "render": "textfield",
      "default_value": 2,
      "group": "other"
    }
  ]
}