{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "multiqc",
"description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\u0027s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input": {
                "type":
                "string",
                "description": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report",
                "help_text": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report.\n"
            
            }
    

}
},
    
    
    "ouput" : {
    "title": "Ouput",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output_report": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report",
                "help_text": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report.\n"
            ,
                "default":"$id.$key.output_report.html"
            }
    

        ,
                "output_data": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files",
                "help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n"
            ,
                "default":"$id.$key.output_data.output_data"
            }
    

        ,
                "output_plots": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots",
                "help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n"
            ,
                "default":"$id.$key.output_plots.output_plots"
            }
    

}
},
    
    
    "modules and analyses to run" : {
    "title": "Modules and analyses to run",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "include_modules": {
                "type":
                "string",
                "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module",
                "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module"
            
            }
    

        ,
                "exclude_modules": {
                "type":
                "string",
                "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules",
                "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules"
            
            }
    

        ,
                "ignore_analysis": {
                "type":
                "string",
                "description": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. ",
                "help_text": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. "
            
            }
    

        ,
                "ignore_samples": {
                "type":
                "string",
                "description": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. ",
                "help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. "
            
            }
    

        ,
                "ignore_symlinks": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files",
                "help_text": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files"
            ,
                "default":false
            }
    

}
},
    
    
    "sample name handling" : {
    "title": "Sample name handling",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "dirs": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames",
                "help_text": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames"
            ,
                "default":false
            }
    

        ,
                "dirs_depth": {
                "type":
                "integer",
                "description": "Type: `integer`. Prepend n directories to sample names",
                "help_text": "Type: `integer`. Prepend n directories to sample names. Negative number to take from start of path."
            
            }
    

        ,
                "full_names": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)",
                "help_text": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)"
            ,
                "default":false
            }
    

        ,
                "fn_as_s_name": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name",
                "help_text": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name"
            ,
                "default":false
            }
    

        ,
                "replace_names": {
                "type":
                "string",
                "description": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation",
                "help_text": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation"
            
            }
    

}
},
    
    
    "report customisation" : {
    "title": "Report Customisation",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "title": {
                "type":
                "string",
                "description": "Type: `string`. Report title",
                "help_text": "Type: `string`. Report title. Printed as page header, used for filename if not otherwise specified.\n"
            
            }
    

        ,
                "comment": {
                "type":
                "string",
                "description": "Type: `string`. Custom comment, will be printed at the top of the report",
                "help_text": "Type: `string`. Custom comment, will be printed at the top of the report.\n"
            
            }
    

        ,
                "template": {
                "type":
                "string",
                "description": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use",
                "help_text": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use.\n",
                "enum": ["default", "gathered", "geo", "highcharts", "sections", "simple"]
            
            
            }
    

        ,
                "sample_names": {
                "type":
                "string",
                "description": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report",
                "help_text": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report.\n"
            
            }
    

        ,
                "sample_filters": {
                "type":
                "string",
                "description": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n",
                "help_text": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n"
            
            }
    

        ,
                "custom_css_file": {
                "type":
                "string",
                "description": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n",
                "help_text": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n"
            
            }
    

        ,
                "profile_runtime": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n",
                "help_text": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n"
            ,
                "default":false
            }
    

}
},
    
    
    "multiqc behaviour" : {
    "title": "MultiQC behaviour",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "verbose": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Increase output verbosity",
                "help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n"
            ,
                "default":false
            }
    

        ,
                "quiet": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Only show log warnings\n",
                "help_text": "Type: `boolean_true`, default: `false`. Only show log warnings\n"
            ,
                "default":false
            }
    

        ,
                "strict": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development",
                "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development.\n"
            ,
                "default":false
            }
    

        ,
                "development": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Development mode",
                "help_text": "Type: `boolean_true`, default: `false`. Development mode. Do not compress and minimise JS, export uncompressed plot data.\n"
            ,
                "default":false
            }
    

        ,
                "require_logs": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files",
                "help_text": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.\n"
            ,
                "default":false
            }
    

        ,
                "no_megaqc_upload": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found",
                "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found.\n"
            ,
                "default":false
            }
    

        ,
                "no_ansi": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Disable coloured log output",
                "help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n"
            ,
                "default":false
            }
    

        ,
                "cl_config": {
                "type":
                "string",
                "description": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection",
                "help_text": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection.\n"
            
            }
    

}
},
    
    
    "output format" : {
    "title": "Output format",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "flat": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use only flat plots (static images)",
                "help_text": "Type: `boolean_true`, default: `false`. Use only flat plots (static images).\n"
            ,
                "default":false
            }
    

        ,
                "interactive": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript)",
                "help_text": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript).\n"
            ,
                "default":false
            }
    

        ,
                "data_dir": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created",
                "help_text": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created.\n"
            ,
                "default":false
            }
    

        ,
                "no_data_dir": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created",
                "help_text": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created.\n"
            ,
                "default":false
            }
    

        ,
                "zip_data_dir": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Compress the data directory",
                "help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n"
            ,
                "default":false
            }
    

        ,
                "data_format": {
                "type":
                "string",
                "description": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027",
                "help_text": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027.\n",
                "enum": ["tsv", "csv", "json", "yaml"]
            
            
            }
    

        ,
                "pdf": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template",
                "help_text": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template. Requires Pandoc to be installed.\n"
            ,
                "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/input"
    },

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

    {
    "$ref": "#/definitions/modules and analyses to run"
    },

    {
    "$ref": "#/definitions/sample name handling"
    },

    {
    "$ref": "#/definitions/report customisation"
    },

    {
    "$ref": "#/definitions/multiqc behaviour"
    },

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

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