nextflow_schema.json

{
	"$schema": "http://json-schema.org/draft-07/schema",
	"$id": "https://raw.githubusercontent.com/CNIC-Proteomics/nf-SearchEngine/main/nextflow_schema.json",
	"title": "SearchEngine",
	"description": "Nextflow for the SearchEngine pipeline.",
	"url": "https://github.com/CNIC-Proteomics/nf-SearchEngine",
	"revision": "main",
	"icon": "",
	"status": 0,
	"type": "object",
	"definitions": {
			"input_output_options": {
					"title": "Input/Output options",
					"type": "object",
					"fa_icon": "pi pi-box",
					"description": "Inputs and outputs required for the pipeline",
					"required": [
							"raw_files",
							"database",
							"add_decoy",
							"decoy_prefix"
					],
					"properties": {
							"raw_files": {
									"title": "MS data",
									"description": "MS data files (.raw format)",
									"help_text": "Under construction...",
									"fa_icon": "pi pi-folder",
									"type": "string",
									"format": "directory-path",
									"default": "",
									"mimetype": "text/plain"
							},
							"database": {
									"title": "Protein database",
									"description": "The fasta protein database used during database search",
									"help_text": "Under construction...",
									"fa_icon": "pi pi-database",
									"type": "string",
									"format": "file-path",
									"default": "",
									"pattern": "^\\S+\\.(?:fasta|fa)$"
	
							},
							"add_decoys": {
									"title": "Add decoys",
									"description": "Generate and append decoys to the given protein database",
									"help_text": "Under construction...",
									"fa_icon": "pi pi-pen-to-square",
									"type": "boolean",
									"format": "boolean",
									"default": true
							},
							"decoy_prefix": {
									"title": "Decoy prefix",
									"description": "Pre- or suffix of decoy proteins in their accession",
									"help_text": "Under construction...",
									"fa_icon": "pi pi-pen-to-square",
									"type": "string",
									"format": "string",
									"default": "DECOY_"
							}
					}
			},
			"parameter_options": {
					"title": "Parameter options",
					"type": "object",
					"fa_icon": "pi pi-table",
					"description": "Outputs required for the pipeline",
					"required": [
							"msf_params_file"
					],
					"properties": {
							"msf_params_file": {
									"title": "MSFragger parameter file",
									"description": "File with the parameters for the MSFragger program",
									"help_text": "Under construction...",
									"fa_icon": "pi pi-file-import",
									"type": "string",
									"format": "file-path",
									"mimetype": "text/plain"
							},
							"reporter_ion_isotopic": {
									"title": "Ion isotopic reporter file",
									"description": "The ion isotopic reporter file",
									"help_text": "Under construction...",
									"fa_icon": "pi pi-file-import",
									"type": "string",
									"format": "file-path",
									"mimetype": "text/plain"
							}
					}
			},
			"output_options": {
					"title": "Output options",
					"type": "object",
					"fa_icon": "fas fa-terminal",
					"description": "Outputs required for the pipeline",
					"required": [
						"outdir"
					],
					"properties": {
							"outdir": {
									"title": "Output directory",
									"description": "The output directory where the results will be saved.",
									"help_text": "Under construction...",
									"fa_icon": "fas fa-folder-open",
									"type": "string",
									"format": "directory-path"
							}
					}
			}
	},
	"allOf": [
			{
					"$ref": "#/definitions/input_output_options"
			},
			{
					"$ref": "#/definitions/parameter_options"
			}
	]
}