parameters.settings.json

{
	"parameters": [
		{
			"name": "reads",
			"label": "Path to fastq reads",
			"usage": "The path to the fastq files must be wrapped in single quotes.",
			"type": "string",
			"renderer": "file",
			"group": "invisible",
			"required": true

		},
		{
			"name": "genomes_base",
			"label": "Reference genome base path",
			"usage": "Bio-Rad formatted refence genomes and annotations",
			"type": "string",
			"renderer": "file",
			"group": "invisible",
			"required": true
		},
		{
			"name": "outDir",
			"label": "Output path",
			"usage": "Indicate the output directory to write to",
			"type": "string",
			"renderer": "file",
			"default_value": "./results",
			"group": "invisible"
		},
		{
			"name": "skipUmi",
			"label": "Skip UMI processing",
			"usage": "Indicate no UMI processing is required",
			"type": "boolean",
			"renderer": "check-box",
			"default_value": false,
			"group": "options"
		},
		{
			"name": "genome",
			"label": "Species",
			"usage": "Genome to align to and annotate against",
			"type": "string",
			"renderer": "drop-down",
			"group": "options",
			"choices": ["hg38", "mm10", "rnor6","tair10","sacCer3","dm6","danRer11","ce11"],
			"required": true
		},
		{
			"name": "spikeType",
			"label": "Spike in type",
			"usage": "The type of spike in used, if any",
			"type": "string",
			"renderer": "drop-down",
			"default_value": "NONE",
			"group": "advanced",
			"choices": ["NONE", "ercc"]
		},
		{
			"name": "minMapqToCount",
			"label": "Minimum MapQ score to count",
			"usage": "The minimum MapQ socre for an aligned read to count toward a feature count",
			"type": "integer",
			"renderer": "range",
			"default_value": "1",
			"group": "advanced",
			"choices": [0, 255]
		},
		{
			"name": "minBp",
			"label": "Min base pairs per read",
			"usage": "Reads with fewer base pairs will be rejected",
			"type": "intger",
			"renderer": "range",
			"default_value": 15,
			"group": "advanced",
			"choices": [0, 500]
		},
		{
			"name": "validateInputs",
			"label": "Validate Input Reads",
			"usage": "Ensure input meets standards and is below 500 million reads",
			"type": "boolean",
			"renderer": "check-box",
			"default_value": true,
			"group": "invisible"
		},
		{
			"name": "reverseStrand",
			"label": "Is the libarary reverse stranded?",
			"usage": "Indicate if your library is reverse stranded",
			"type": "boolean",
			"renderer": "check-box",
			"default_value": false,
			"group": "invisible"
		},
		{
			"name": "noTrim",
			"label": "Skip read trimming?",
			"usage": "Indicates whether or not trimming skipped on the reads",
			"type": "boolean",
			"renderer": "check-box",
			"default_value": false,
			"group": "advanced"
		},
		{
			"name": "fivePrimeQualCutoff",
			"label": "5' read quality cutoff",
			"usage": "The read quality below which bases will be trimmed on the 5' end",
			"type": "integer",
			"renderer": "range",
			"default_value": 0,
			"group": "advanced",
			"choices": [0, 42]
		},
		{
			"name": "threePrimeQualCutoff",
			"label": "3' read quality cutoff",
			"usage": "The read quality below which bases will be trimmed on the 3' end",
			"type": "integer",
			"renderer": "range",
			"default_value": 0,
			"group": "advanced",
			"choices": [0, 42]
		},
		{
			"name": "minGeneCutoff",
			"label": "Option to define minium threshold for what genes are reported",
			"usage": "Provide double value to cutoff how many reads are minimally required for a gene to be counted",
			"type": "double",
			"renderer": "range",
			"defualt_value": 0, 
			"group": "advanced",
			"choices": [0, 9e7]
		},
		{
			"name": "minGeneType",
			"label": "Option to define minium threshold type for genes are reported",
			"usage": "Provide metric to be used for quantifying gene expression",
			"type": "string",
			"renderer": "check-box",
			"defualt_value": "none", 
			"group": "advanced",
			"choices": ["none","reads","RPKM","TPM"]

		},
		{
			"name": "seqType",
			"label": "Option to define type of sequencing used (Paired vs Single end)",
			"usage": "Provide sequencing method used, if using SE provided deduplication will not occur",
			"type": "string",
			"renderer": "check-box",
			"defualt_value": "PE", 
			"group": "advanced",
			"choices": ["SE","PE"]

		},
		{
			"name": "max_cpus",
			"label": "Max CPUs",
			"usage": "The max number of cpus the pipeline may use. Defaults provided by -profile.",
			"type": "integer",
			"renderer": "range",
			"group": "invisible"
		},
		{
			"name": "max_memory",
			"label": "Max Memory",
			"usage": "The max memory in GB that the pipeline may use. Defaults provided by -profile.",
			"type": "integer",
			"renderer": "range",
			"group": "invisible"
		}
	]
}