{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "runner",
"description": "Runner for HT RNA-seq pipeline",
"type": "object",
"definitions": {

    
    
    "input arguments" : {
    "title": "Input arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input": {
                "type":
                "string",
                "description": "Type: `file`, required. Base directory of the form `s3:/\u003cbucket\u003e/Sequencing/\u003cSequencer\u003e/\u003cRunID\u003e/\u003cdemultiplex_dir\u003e`",
                "help_text": "Type: `file`, required. Base directory of the form `s3:/\u003cbucket\u003e/Sequencing/\u003cSequencer\u003e/\u003cRunID\u003e/\u003cdemultiplex_dir\u003e`"
            
            }
    

        ,
                "barcodesFasta": {
                "type":
                "string",
                "description": "Type: `file`, required. ",
                "help_text": "Type: `file`, required. "
            
            }
    

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

        ,
                "annotation": {
                "type":
                "string",
                "description": "Type: `file`, required. ",
                "help_text": "Type: `file`, required. "
            
            }
    

}
},
    
    
    "metadata arguments" : {
    "title": "Metadata arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "id": {
                "type":
                "string",
                "description": "Type: `string`. Unique identifier for the run",
                "help_text": "Type: `string`. Unique identifier for the run"
            
            }
    

        ,
                "project_id": {
                "type":
                "string",
                "description": "Type: `string`, required. Project ID",
                "help_text": "Type: `string`, required. Project ID"
            
            }
    

        ,
                "experiment_id": {
                "type":
                "string",
                "description": "Type: `string`, required. Experiment ID",
                "help_text": "Type: `string`, required. Experiment ID"
            
            }
    

}
},
    
    
    "annotation flags" : {
    "title": "Annotation flags",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "plain_output": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/\u003cdate_time\u003e_demultiplex_\u003cversion\u003e/",
                "help_text": "Type: `boolean_true`, default: `false`. Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/\u003cdate_time\u003e_demultiplex_\u003cversion\u003e/.\n"
            ,
                "default":false
            }
    

}
},
    
    
    "publish arguments" : {
    "title": "Publish arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "fastq_publish_dir": {
                "type":
                "string",
                "description": "Type: `string`, required. ",
                "help_text": "Type: `string`, required. "
            
            }
    

        ,
                "results_publish_dir": {
                "type":
                "string",
                "description": "Type: `string`, required. ",
                "help_text": "Type: `string`, required. "
            
            }
    

}
},
    
    
    "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/metadata arguments"
    },

    {
    "$ref": "#/definitions/annotation flags"
    },

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

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