{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "bgzip",
"description": "Block compression/decompression utility",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input": {
                "type":
                "string",
                "description": "Type: `file`, required. file to be compressed or decompressed",
                "help_text": "Type: `file`, required. file to be compressed or decompressed"
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output`. compressed or decompressed output",
                "help_text": "Type: `file`, required, default: `$id.$key.output`. compressed or decompressed output"
            ,
                "default":"$id.$key.output"
            }
    

        ,
                "index_name": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.index_name`. name of BGZF index file [file",
                "help_text": "Type: `file`, default: `$id.$key.index_name`. name of BGZF index file [file.gz.gzi]"
            ,
                "default":"$id.$key.index_name"
            }
    

}
},
    
    
    "arguments" : {
    "title": "Arguments",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "offset": {
                "type":
                "integer",
                "description": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)",
                "help_text": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)"
            
            }
    

        ,
                "decompress": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. decompress the input file",
                "help_text": "Type: `boolean_true`, default: `false`. decompress the input file"
            ,
                "default":false
            }
    

        ,
                "rebgzip": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file",
                "help_text": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file"
            ,
                "default":false
            }
    

        ,
                "index": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. compress and create BGZF index",
                "help_text": "Type: `boolean_true`, default: `false`. compress and create BGZF index"
            ,
                "default":false
            }
    

        ,
                "compress_level": {
                "type":
                "integer",
                "description": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]",
                "help_text": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]"
            
            }
    

        ,
                "reindex": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. (re)index the output file",
                "help_text": "Type: `boolean_true`, default: `false`. (re)index the output file"
            ,
                "default":false
            }
    

        ,
                "size": {
                "type":
                "integer",
                "description": "Type: `integer`. decompress INT bytes (uncompressed size)",
                "help_text": "Type: `integer`. decompress INT bytes (uncompressed size)"
            
            }
    

        ,
                "test": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. test integrity of compressed file",
                "help_text": "Type: `boolean_true`, default: `false`. test integrity of compressed file"
            ,
                "default":false
            }
    

        ,
                "binary": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines",
                "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines"
            ,
                "default":false
            }
    

}
},
    
    
    "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/inputs"
    },

    {
    "$ref": "#/definitions/outputs"
    },

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

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