{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "rsem_calculate_expression",
"description": "Calculate expression with RSEM.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "id": {
                "type":
                "string",
                "description": "Type: `string`. Sample ID",
                "help_text": "Type: `string`. Sample ID."
            
            }
    

        ,
                "strandedness": {
                "type":
                "string",
                "description": "Type: `string`, choices: ``forward`, `reverse`, `unstranded``. Sample strand-specificity",
                "help_text": "Type: `string`, choices: ``forward`, `reverse`, `unstranded``. Sample strand-specificity. Must be one of unstranded, forward, reverse",
                "enum": ["forward", "reverse", "unstranded"]
            
            
            }
    

        ,
                "paired": {
                "type":
                "boolean",
                "description": "Type: `boolean`. Paired-end reads or not?",
                "help_text": "Type: `boolean`. Paired-end reads or not?"
            
            }
    

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

        ,
                "index": {
                "type":
                "string",
                "description": "Type: `file`. RSEM index",
                "help_text": "Type: `file`. RSEM index."
            
            }
    

        ,
                "extra_args": {
                "type":
                "string",
                "description": "Type: `string`. Extra rsem-calculate-expression arguments in addition to the defaults",
                "help_text": "Type: `string`. Extra rsem-calculate-expression arguments in addition to the defaults."
            
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "counts_gene": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `sample.genes.results`. Expression counts on gene level",
                "help_text": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `sample.genes.results`. Expression counts on gene level"
            ,
                "default": "$id.$key.counts_gene.results"
            }
    

        ,
                "counts_transcripts": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `sample.isoforms.results`. Expression counts on transcript level",
                "help_text": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `sample.isoforms.results`. Expression counts on transcript level"
            ,
                "default": "$id.$key.counts_transcripts.results"
            }
    

        ,
                "stat": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.stat.stat`, example: `sample.stat`. RSEM statistics",
                "help_text": "Type: `file`, default: `$id.$key.stat.stat`, example: `sample.stat`. RSEM statistics"
            ,
                "default": "$id.$key.stat.stat"
            }
    

        ,
                "logs": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.logs.log`, example: `sample.log`. RSEM logs",
                "help_text": "Type: `file`, default: `$id.$key.logs.log`, example: `sample.log`. RSEM logs"
            ,
                "default": "$id.$key.logs.log"
            }
    

        ,
                "bam_star": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `sample.STAR.genome.bam`. BAM file generated by STAR (optional)",
                "help_text": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `sample.STAR.genome.bam`. BAM file generated by STAR (optional)"
            ,
                "default": "$id.$key.bam_star.bam"
            }
    

        ,
                "bam_genome": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `sample.genome.bam`. Genome BAM file (optional)",
                "help_text": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `sample.genome.bam`. Genome BAM file (optional)"
            ,
                "default": "$id.$key.bam_genome.bam"
            }
    

        ,
                "bam_transcript": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `sample.transcript.bam`. Transcript BAM file (optional)",
                "help_text": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `sample.transcript.bam`. Transcript BAM file (optional)"
            ,
                "default": "$id.$key.bam_transcript.bam"
            }
    

}
},
    
    
    "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"
    }
]
}
