nextflow_schema_recom.json

{
	"$schema": "http://json-schema.org/draft-07/schema",
	"$id": "https://raw.githubusercontent.com/CNIC-Proteomics/nf-PTM-compass/main/nextflow_schema.json",
	"title": "PTM-compass",
	"description": "Nextflow for the PTM-compass pipeline using ReCom as input",
	"url": "https://github.com/CNIC-Proteomics/nf-PTM-compass",
	"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": [
					"recom_files",
					"exp_table",
					"database",
					"decoy_prefix",
					"outdir"
			],
			"properties": {
				"recom_files": {
					"title": "ReCom results",
					"description": "ReCom result files",
					"help_text": "Under construction...",
					"fa_icon": "pi pi-folder",
					"type": "string",
					"format": "directory-path",
					"mimetype": "text/plain",
					"default": ""
				},
				"exp_table": {
					"title": "Experimental table",
					"description": "Experimental table file",
					"help_text": "Under construction...",
					"fa_icon": "pi pi-file",
					"type": "string",
					"format": "file-path",
					"default": ""
				},
				"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",
					"pattern": "^\\S+\\.(?:fasta|fa)$",
					"default": ""
				},
				"decoy_prefix": {
					"title": "Decoy prefix",
					"description": "Pre- or suffix of decoy proteins in their accession",
					"help_text": "Under construction...",
					"fa_icon": "pi pi-pen-to-square",
					"type": "string",
					"format": "string",
					"default": "DECOY_"
				}
			}
		},
		"parameter_options": {
			"title": "Parameter options",
			"type": "object",
			"fa_icon": "pi pi-table",
			"description": "Outputs required for the pipeline",
			"required": [
				"params_file"
			],
			"properties": {
				"params_file": {
					"title": "Parameter file",
					"description": "File with the parameter for the programs in INI format",
					"help_text": "Under construction...",
					"fa_icon": "pi pi-file-import",
					"type": "string",
					"format": "file-path",
					"mimetype": "text/plain"
				},
				"sitelist_file": {
					"title": "Sitelist file",
					"description": "File with the Sitelist info",
					"help_text": "Under construction...",
					"fa_icon": "pi pi-file-import",
					"type": "string",
					"format": "file-path",
					"mimetype": "text/plain"
				},
				"groupmaker_file": {
					"title": "Groupmaker file",
					"description": "File with the group maker",
					"help_text": "Under construction...",
					"fa_icon": "pi pi-file-import",
					"type": "string",
					"format": "file-path",
					"mimetype": "text/plain"
				}
			}
		},
		"output_options": {
			"title": "Output options",
			"type": "object",
			"fa_icon": "fas fa-terminal",
			"description": "Outputs required for the pipeline",
			"required": [
				"outdir"
			],
			"properties": {
				"outdir": {
					"title": "Output directory",
					"description": "The output directory where the results will be saved.",
					"help_text": "Under construction...",
					"fa_icon": "fas fa-folder-open",
					"type": "string",
					"format": "directory-path"
				}
			}
		}
	},
	"allOf": [{
			"$ref": "#/definitions/input_output_options"
		},{
			"$ref": "#/definitions/parameter_options"
		}
	]
}