parameters.settings.json

{
  "parameters": [
    {
      "name": "samplePlan",
      "label": "Input files",
      "usage": "Path to sample plan (csv format)",
      "type": "path",
      "choices": [],
      "nargs": "+",
      "default_value": null,
      "pattern": ".*\\*.*",
      "render": "textfield",
      "arity": 0,
      "group": "Mandatory arguments"
    },
    {
      "name": "profile",
      "label": "Configuration profile(s)",
      "usage": "Configuration profile to use. Can use multiple (comma separated).",
      "type": "string",
      "choices": [
        "conda", "cluster", "docker", "multiconda", "conda", "path", "multipath", "singularity"
      ],
      "nargs": "+",
      "default_value": null,
      "pattern": ".*",
      "render": "textfield",
      "arity": 0,
      "group": "Mandatory arguments"
    },
    {
      "name": "genome",
      "label": "Reference genome",
      "usage": "Name of the reference genome.",
      "type": "string",
      "nargs": "1",
      "choices": [],
      "default_value": false,
      "pattern": "",
      "render": "textfield",
      "arity": 0,
      "group": "Mandatory arguments"
    },

    {
      "name": "genomeAnnotationPath",
      "label": "Annotation path",
      "usage": "Path to genome annotations folder",
      "type": "path",
      "choices": [],
      "nargs": "+",
      "default_value": null,
      "pattern": ".*\\*.*",
      "render": "textfield",
      "arity": 0,
      "group": "References"
    },

    {
      "name": "outDir",
      "label": "Output directory",
      "usage": "The output directory where the results will be saved",
      "type": "path",
      "nargs": 1,
      "choices": [],
      "default_value": null,
      "pattern": ".*",
      "render": "file",
      "arity": 0,
      "group": "Other options"
    },
  
    {
      "name": "metadata",
      "label": "MultiQC metadata file",
      "usage": "Specify a custom metadata file for MultiQC",
      "type": "path",
      "nargs": 1,
      "choices": [],
      "default_value": null,
      "pattern": ".*",
      "render": "file",
      "arity": 0,
      "group": "Other options"
    },
    {
      "name": "name",
      "label": "Name for the pipeline run",
      "usage": "Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic",
      "type": "string",
      "nargs": 1,
      "choices": [],
      "default_value": "25.MB",
      "pattern": ".*",
      "render": "textfield",
      "arity": 0,
      "group": "Other options"
    }
  ]
}