{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "sortmerna",
"description": "Local sequence alignment tool for filtering, mapping and clustering. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "paired": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Are the reads single-end or paired-end",
                "help_text": "Type: `boolean`. Are the reads single-end or paired-end"
            
            }
    

        ,
                "input": {
                "type":
                "string",
                "description": "Type: List of `file`, multiple_sep: `\",\"`. Input fastq",
                "help_text": "Type: List of `file`, multiple_sep: `\",\"`. Input fastq"
            
            }
    

        ,
                "ribo_database_manifest": {
                "type":
                "string",
                "description": "Type: List of `file`, multiple_sep: `\";\"`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA",
                "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA."
            
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "sortmerna_log": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file",
                "help_text": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file."
            ,
                "default":"$id.$key.sortmerna_log.log"
            }
    

        ,
                "fastq_1": {
                "type":
                "string",
                "description": "Type: `file`, required, default: `$id.$key.fastq_1.gz`. Output file for read 1",
                "help_text": "Type: `file`, required, default: `$id.$key.fastq_1.gz`. Output file for read 1."
            ,
                "default":"$id.$key.fastq_1.gz"
            }
    

        ,
                "fastq_2": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.fastq_2.gz`. Output file for read 2",
                "help_text": "Type: `file`, default: `$id.$key.fastq_2.gz`. Output file for read 2."
            ,
                "default":"$id.$key.fastq_2.gz"
            }
    

}
},
    
    
    "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/output"
    },

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