{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "snpeff",
"description": "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n",
"type": "object",
"definitions": {

    
    
    "inputs" : {
    "title": "Inputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "input": {
                "type":
                "string",
                "description": "Type: `file`, required, example: `test.vcf`. Input variants file",
                "help_text": "Type: `file`, required, example: `test.vcf`. Input variants file."
            
            }
    

        ,
                "genome_version": {
                "type":
                "string",
                "description": "Type: `string`, required, example: `GRCh37.75`. Reference genome version",
                "help_text": "Type: `string`, required, example: `GRCh37.75`. Reference genome version."
            
            }
    

}
},
    
    
    "outputs" : {
    "title": "Outputs",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.output.vcf`, example: `out.vcf`. The output file",
                "help_text": "Type: `file`, required, default: `$id.$key.output.vcf`, example: `out.vcf`. The output file."
            ,
                "default": "$id.$key.output.vcf"
            }
    

        ,
                "summary": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory",
                "help_text": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory."
            ,
                "default": "$id.$key.summary.summary"
            }
    

        ,
                "genes": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory",
                "help_text": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory."
            ,
                "default": "$id.$key.genes.genes"
            }
    

}
},
    
    
    "options" : {
    "title": "Options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "chr": {
                "type":
                "string",
                "description": "Type: `string`. Prepend \u0027string\u0027 to chromosome name (e",
                "help_text": "Type: `string`. Prepend \u0027string\u0027 to chromosome name (e.g. \u0027chr1\u0027 instead of \u00271\u0027). Only on TXT output.\n"
            
            }
    

        ,
                "classic": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use old style annotations instead of Sequence Ontology and Hgvs",
                "help_text": "Type: `boolean_true`, default: `false`. Use old style annotations instead of Sequence Ontology and Hgvs."
            ,
                "default": "False"
            }
    

        ,
                "csv_stats": {
                "type":
                "string",
                "description": "Type: `file`. Create CSV summary file",
                "help_text": "Type: `file`. Create CSV summary file."
            
            }
    

        ,
                "download": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Download reference genome if not available",
                "help_text": "Type: `boolean_true`, default: `false`. Download reference genome if not available."
            ,
                "default": "False"
            }
    

        ,
                "input_format": {
                "type":
                "string",
                "description": "Type: `string`. Input format [ vcf, bed ]",
                "help_text": "Type: `string`. Input format [ vcf, bed ]. Default: VCF.\nexample: \"VCF\"\n"
            
            }
    

        ,
                "file_list": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Input actually contains a list of files to process",
                "help_text": "Type: `boolean_true`, default: `false`. Input actually contains a list of files to process."
            ,
                "default": "False"
            }
    

        ,
                "output_format": {
                "type":
                "string",
                "description": "Type: `string`, example: `VCF`. Output format [ vcf, gatk, bed, bedAnn ]",
                "help_text": "Type: `string`, example: `VCF`. Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n"
            
            }
    

        ,
                "stats": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Create HTML summary file",
                "help_text": "Type: `boolean_true`, default: `false`. Create HTML summary file."
            ,
                "default": "False"
            }
    

        ,
                "no_stats": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not create stats (summary) file",
                "help_text": "Type: `boolean_true`, default: `false`. Do not create stats (summary) file."
            ,
                "default": "False"
            }
    

}
},
    
    
    "results filter options" : {
    "title": "Results filter options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "fi": {
                "type":
                "string",
                "description": "Type: `file`. Only analyze changes that intersect with the intervals \nspecified in this file",
                "help_text": "Type: `file`. Only analyze changes that intersect with the intervals \nspecified in this file. This option can be used several times.\n"
            
            }
    

        ,
                "no_downstream": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not show DOWNSTREAM changes",
                "help_text": "Type: `boolean_true`, default: `false`. Do not show DOWNSTREAM changes"
            ,
                "default": "False"
            }
    

        ,
                "no_intergenic": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not show INTERGENIC changes",
                "help_text": "Type: `boolean_true`, default: `false`. Do not show INTERGENIC changes."
            ,
                "default": "False"
            }
    

        ,
                "no_intron": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not show INTRON changes",
                "help_text": "Type: `boolean_true`, default: `false`. Do not show INTRON changes."
            ,
                "default": "False"
            }
    

        ,
                "no_upstream": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not show UPSTREAM changes",
                "help_text": "Type: `boolean_true`, default: `false`. Do not show UPSTREAM changes."
            ,
                "default": "False"
            }
    

        ,
                "no_utr": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not show 5_PRIME_UTR or 3_PRIME_UTR changes",
                "help_text": "Type: `boolean_true`, default: `false`. Do not show 5_PRIME_UTR or 3_PRIME_UTR changes."
            ,
                "default": "False"
            }
    

        ,
                "no": {
                "type":
                "string",
                "description": "Type: `string`. Do not show \u0027EffectType\u0027",
                "help_text": "Type: `string`. Do not show \u0027EffectType\u0027. This option can be used several times.\n"
            
            }
    

}
},
    
    
    "annotations options" : {
    "title": "Annotations options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "cancer": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Perform \u0027cancer\u0027 comparisons (Somatic vs Germline)",
                "help_text": "Type: `boolean_true`, default: `false`. Perform \u0027cancer\u0027 comparisons (Somatic vs Germline)."
            ,
                "default": "False"
            }
    

        ,
                "cancer_samples": {
                "type":
                "string",
                "description": "Type: `file`. Two column TXT file defining \u0027original \\t derived\u0027 samples",
                "help_text": "Type: `file`. Two column TXT file defining \u0027original \\t derived\u0027 samples."
            
            }
    

        ,
                "fastaprot": {
                "type":
                "string",
                "description": "Type: `file`. Create an output file containing the resulting protein sequences",
                "help_text": "Type: `file`. Create an output file containing the resulting protein sequences.\n"
            
            }
    

        ,
                "format_eff": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use \u0027EFF\u0027 field compatible with older versions (instead of \u0027ANN\u0027)",
                "help_text": "Type: `boolean_true`, default: `false`. Use \u0027EFF\u0027 field compatible with older versions (instead of \u0027ANN\u0027).\n"
            ,
                "default": "False"
            }
    

        ,
                "gene_id": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use gene ID instead of gene name (VCF output)",
                "help_text": "Type: `boolean_true`, default: `false`. Use gene ID instead of gene name (VCF output)."
            ,
                "default": "False"
            }
    

        ,
                "hgvs": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use HGVS annotations for amino acid sub-field",
                "help_text": "Type: `boolean_true`, default: `false`. Use HGVS annotations for amino acid sub-field."
            ,
                "default": "False"
            }
    

        ,
                "hgvs_old": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use old HGVS notation",
                "help_text": "Type: `boolean_true`, default: `false`. Use old HGVS notation."
            ,
                "default": "False"
            }
    

        ,
                "hgvs1_letter_aa": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use one letter Amino acid codes in HGVS notation",
                "help_text": "Type: `boolean_true`, default: `false`. Use one letter Amino acid codes in HGVS notation."
            ,
                "default": "False"
            }
    

        ,
                "hgvs_tr_id": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use transcript ID in HGVS notation",
                "help_text": "Type: `boolean_true`, default: `false`. Use transcript ID in HGVS notation."
            ,
                "default": "False"
            }
    

        ,
                "lof": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Add loss of function (LOF) and Nonsense mediated decay (NMD) tags",
                "help_text": "Type: `boolean_true`, default: `false`. Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n"
            ,
                "default": "False"
            }
    

        ,
                "-no_hgvs": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not add HGVS annotations",
                "help_text": "Type: `boolean_true`, default: `false`. Do not add HGVS annotations."
            ,
                "default": "False"
            }
    

        ,
                "no_lof": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not add LOF and NMD annotations",
                "help_text": "Type: `boolean_true`, default: `false`. Do not add LOF and NMD annotations."
            ,
                "default": "False"
            }
    

        ,
                "no_shift_hgvs": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not shift variants according to HGVS notation (most 3prime end)",
                "help_text": "Type: `boolean_true`, default: `false`. Do not shift variants according to HGVS notation (most 3prime end).\n"
            ,
                "default": "False"
            }
    

        ,
                "oicr": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Add OICR tag in VCF file",
                "help_text": "Type: `boolean_true`, default: `false`. Add OICR tag in VCF file."
            ,
                "default": "False"
            }
    

        ,
                "sequence_ontology": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms",
                "help_text": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms."
            ,
                "default": "False"
            }
    

}
},
    
    
    "generic options" : {
    "title": "Generic options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "config": {
                "type":
                "string",
                "description": "Type: `file`. Specify config file",
                "help_text": "Type: `file`. Specify config file"
            
            }
    

        ,
                "config_option": {
                "type":
                "string",
                "description": "Type: `string`. Override a config file option (name=value)",
                "help_text": "Type: `string`. Override a config file option (name=value)."
            
            }
    

        ,
                "debug": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)",
                "help_text": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)."
            ,
                "default": "False"
            }
    

        ,
                "data_dir": {
                "type":
                "string",
                "description": "Type: `file`. Override data_dir parameter from config file",
                "help_text": "Type: `file`. Override data_dir parameter from config file."
            
            }
    

        ,
                "no_download": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not download a SnpEff database, if not available locally",
                "help_text": "Type: `boolean_true`, default: `false`. Do not download a SnpEff database, if not available locally."
            ,
                "default": "False"
            }
    

        ,
                "no_log": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not report usage statistics to server",
                "help_text": "Type: `boolean_true`, default: `false`. Do not report usage statistics to server."
            ,
                "default": "False"
            }
    

        ,
                "quiet": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Quiet mode (do not show any messages or errors)",
                "help_text": "Type: `boolean_true`, default: `false`. Quiet mode (do not show any messages or errors)"
            ,
                "default": "False"
            }
    

        ,
                "verbose": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Verbose mode",
                "help_text": "Type: `boolean_true`, default: `false`. Verbose mode."
            ,
                "default": "False"
            }
    

}
},
    
    
    "database options" : {
    "title": "Database options",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "canon": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Only use canonical transcripts",
                "help_text": "Type: `boolean_true`, default: `false`. Only use canonical transcripts."
            ,
                "default": "False"
            }
    

        ,
                "canon_list": {
                "type":
                "string",
                "description": "Type: `file`. Only use canonical transcripts, replace some transcripts using the \u0027gene_id         \ntranscript_id\u0027 entries in \u003cfile\u003e",
                "help_text": "Type: `file`. Only use canonical transcripts, replace some transcripts using the \u0027gene_id         \ntranscript_id\u0027 entries in \u003cfile\u003e.\n"
            
            }
    

        ,
                "tag": {
                "type":
                "string",
                "description": "Type: `string`. Only use transcript having a tag \u0027tagName\u0027",
                "help_text": "Type: `string`. Only use transcript having a tag \u0027tagName\u0027. This option can be used multiple times.\n"
            
            }
    

        ,
                "no_tag": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Filter out transcript having a tag \u0027tagName\u0027",
                "help_text": "Type: `boolean_true`, default: `false`. Filter out transcript having a tag \u0027tagName\u0027. This option can be used multiple times.\n"
            ,
                "default": "False"
            }
    

        ,
                "interaction": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Annotate using interactions (requires interaction database)",
                "help_text": "Type: `boolean_true`, default: `false`. Annotate using interactions (requires interaction database)."
            ,
                "default": "False"
            }
    

        ,
                "interval": {
                "type":
                "string",
                "description": "Type: `file`. Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)",
                "help_text": "Type: `file`. Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).\n"
            
            }
    

        ,
                "max_tsl": {
                "type":
                "integer",
                "description": "Type: `integer`. Only use transcripts having Transcript Support Level lower than \u003cTSL_number\u003e",
                "help_text": "Type: `integer`. Only use transcripts having Transcript Support Level lower than \u003cTSL_number\u003e."
            
            }
    

        ,
                "motif": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Annotate using motifs (requires Motif database)",
                "help_text": "Type: `boolean_true`, default: `false`. Annotate using motifs (requires Motif database)."
            ,
                "default": "False"
            }
    

        ,
                "nextprot": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Annotate using NextProt (requires NextProt database)",
                "help_text": "Type: `boolean_true`, default: `false`. Annotate using NextProt (requires NextProt database)."
            ,
                "default": "False"
            }
    

        ,
                "no_genome": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Do not load any genomic database (e",
                "help_text": "Type: `boolean_true`, default: `false`. Do not load any genomic database (e.g. annotate using custom files)."
            ,
                "default": "False"
            }
    

        ,
                "no_expand_iub": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Disable IUB code expansion in input variants",
                "help_text": "Type: `boolean_true`, default: `false`. Disable IUB code expansion in input variants."
            ,
                "default": "False"
            }
    

        ,
                "no_interaction": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Disable inteaction annotations",
                "help_text": "Type: `boolean_true`, default: `false`. Disable inteaction annotations."
            ,
                "default": "False"
            }
    

        ,
                "no_motif": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Disable motif annotations",
                "help_text": "Type: `boolean_true`, default: `false`. Disable motif annotations."
            ,
                "default": "False"
            }
    

        ,
                "no_nextprot": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Disable NextProt annotations",
                "help_text": "Type: `boolean_true`, default: `false`. Disable NextProt annotations."
            ,
                "default": "False"
            }
    

        ,
                "only_reg": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Only use regulation tracks",
                "help_text": "Type: `boolean_true`, default: `false`. Only use regulation tracks."
            ,
                "default": "False"
            }
    

        ,
                "only_protein": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Only use protein coding transcripts",
                "help_text": "Type: `boolean_true`, default: `false`. Only use protein coding transcripts."
            ,
                "default": "False"
            }
    

        ,
                "only_tr": {
                "type":
                "string",
                "description": "Type: `file`, example: `file.txt`. Only use the transcripts in this file",
                "help_text": "Type: `file`, example: `file.txt`. Only use the transcripts in this file. Format: One transcript ID per line.\n"
            
            }
    

        ,
                "reg": {
                "type":
                "string",
                "description": "Type: `string`. Regulation track to use (this option can be used add several times)",
                "help_text": "Type: `string`. Regulation track to use (this option can be used add several times)."
            
            }
    

        ,
                "ss": {
                "type":
                "integer",
                "description": "Type: `integer`. Set size for splice sites (donor and acceptor) in bases",
                "help_text": "Type: `integer`. Set size for splice sites (donor and acceptor) in bases. Default: 2.\n"
            
            }
    

        ,
                "splice_region_exon_size": {
                "type":
                "integer",
                "description": "Type: `integer`. Set size for splice site region within exons",
                "help_text": "Type: `integer`. Set size for splice site region within exons. Default: 3 bases.\n"
            
            }
    

        ,
                "splice_region_intron_min": {
                "type":
                "integer",
                "description": "Type: `integer`. Set minimum number of bases for splice site region within intron",
                "help_text": "Type: `integer`. Set minimum number of bases for splice site region within intron. Default: 3 bases.\n"
            
            }
    

        ,
                "splice_region_intron_max": {
                "type":
                "integer",
                "description": "Type: `integer`. Set maximum number of bases for splice site region within intron",
                "help_text": "Type: `integer`. Set maximum number of bases for splice site region within intron. Default: 8 bases.\n"
            
            }
    

        ,
                "strict": {
                "type":
                "boolean",
                "description": "Type: `boolean_true`, default: `false`. Only use \u0027validated\u0027 transcripts (i",
                "help_text": "Type: `boolean_true`, default: `false`. Only use \u0027validated\u0027 transcripts (i.e. sequence has been checked)."
            ,
                "default": "False"
            }
    

        ,
                "ud": {
                "type":
                "integer",
                "description": "Type: `integer`. Set upstream downstream interval length (in bases)",
                "help_text": "Type: `integer`. Set upstream downstream interval length (in bases)."
            
            }
    

}
},
    
    
    "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/options"
    },

    {
    "$ref": "#/definitions/results filter options"
    },

    {
    "$ref": "#/definitions/annotations options"
    },

    {
    "$ref": "#/definitions/generic options"
    },

    {
    "$ref": "#/definitions/database options"
    },

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