{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "parallel_map",
"description": "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
"type": "object",
"definitions": {

    
    
    "input arguments" : {
    "title": "Input arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input_r1": {
                "type":
                "string",
                "description": "Type: List of `file`, required, multiple_sep: `\";\"`. ",
                "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. "
            
            }
    

        ,
                "input_r2": {
                "type":
                "string",
                "description": "Type: List of `file`, required, multiple_sep: `\";\"`. ",
                "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. "
            
            }
    

        ,
                "genomeDir": {
                "type":
                "string",
                "description": "Type: `file`, required. STAR reference directory",
                "help_text": "Type: `file`, required. STAR reference directory"
            
            }
    

        ,
                "barcodes": {
                "type":
                "string",
                "description": "Type: List of `string`, required, multiple_sep: `\";\"`. The barcodes/wells to process",
                "help_text": "Type: List of `string`, required, multiple_sep: `\";\"`. The barcodes/wells to process"
            
            }
    

}
},
    
    
    "barcode arguments" : {
    "title": "Barcode arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "wellBarcodesLength": {
                "type":
                "integer",
                "description": "Type: `integer`, required. The length of the well barcodes",
                "help_text": "Type: `integer`, required. The length of the well barcodes"
            
            }
    

        ,
                "umiLength": {
                "type":
                "integer",
                "description": "Type: `integer`, required. The length of the UMIs",
                "help_text": "Type: `integer`, required. The length of the UMIs"
            
            }
    

        ,
                "limitBAMsortRAM": {
                "type":
                "string",
                "description": "Type: `string`, default: `10000000000`. ",
                "help_text": "Type: `string`, default: `10000000000`. "
            ,
                "default": "10000000000"
            }
    

}
},
    
    
    "runtime arguments" : {
    "title": "Runtime arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "runThreadN": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution",
                "help_text": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution."
            ,
                "default": "1"
            }
    

}
},
    
    
    "output arguments" : {
    "title": "Output arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\";\"`. Location of the output folders, 1 folder per barcode",
                "help_text": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\";\"`. Location of the output folders, 1 folder per barcode. The value used\nfor this argument must contain a \u0027*\u0027, which will be replaced with the\nbarcode to form the final output location for that barcode.\n"
            ,
                "default": "$id.$key.output_*./*"
            }
    

        ,
                "joblog": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs",
                "help_text": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs."
            ,
                "default": "$id.$key.joblog.txt"
            }
    

}
},
    
    
    "nextflow input-output arguments" : {
    "title": "Nextflow input-output arguments",
    "type": "object",
    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
    "properties": {
    
        
                "publish_dir": {
                "type":
                "string",
                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
            
            }
    

        ,
                "param_list": {
                "type":
                "string",
                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
                "hidden": true
            
            }
    

}
}
},
"allOf": [

    {
    "$ref": "#/definitions/input arguments"
    },

    {
    "$ref": "#/definitions/barcode arguments"
    },

    {
    "$ref": "#/definitions/runtime arguments"
    },

    {
    "$ref": "#/definitions/output arguments"
    },

    {
    "$ref": "#/definitions/nextflow input-output arguments"
    }
]
}
