{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "pseudo_alignment_and_quant",
"description": "A viash sub-workflow for pseudo alignment and quantification stage of nf-core/rnaseq pipeline.\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "id": {
                "type":
                "string",
                "description": "Type: `string`, required, example: `foo`. ID of the sample",
                "help_text": "Type: `string`, required, example: `foo`. ID of the sample."
            
            }
    

        ,
                "fastq_1": {
                "type":
                "string",
                "description": "Type: `file`, required, example: `input.fastq.gz`. Path to the sample (or read 1 of paired end sample)",
                "help_text": "Type: `file`, required, example: `input.fastq.gz`. Path to the sample (or read 1 of paired end sample)."
            
            }
    

        ,
                "fastq_2": {
                "type":
                "string",
                "description": "Type: `file`. Path to read 2 of the sample",
                "help_text": "Type: `file`. Path to read 2 of the sample."
            
            }
    

        ,
                "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, or reverse",
                "enum": ["forward", "reverse", "unstranded"]
            
            
            }
    

        ,
                "gtf": {
                "type":
                "string",
                "description": "Type: `file`. GTF file",
                "help_text": "Type: `file`. GTF file"
            
            }
    

        ,
                "transcript_fasta": {
                "type":
                "string",
                "description": "Type: `file`. Fasta file of the reference transcriptome",
                "help_text": "Type: `file`. Fasta file of the reference transcriptome."
            
            }
    

        ,
                "pseudo_aligner": {
                "type":
                "string",
                "description": "Type: `string`, default: `false`, choices: ``salmon`, `kallisto``. Specifies the pseudo aligner to use - available options are \u0027salmon\u0027",
                "help_text": "Type: `string`, default: `false`, choices: ``salmon`, `kallisto``. Specifies the pseudo aligner to use - available options are \u0027salmon\u0027. Runs in addition to \u0027--aligner\u0027.",
                "enum": ["salmon", "kallisto"]
            
            ,
                "default":"false"
            }
    

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

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

        ,
                "lib_type": {
                "type":
                "string",
                "description": "Type: `string`, default: ``. Override library type inferred based on strandedness defined in meta object",
                "help_text": "Type: `string`, default: ``. Override library type inferred based on strandedness defined in meta object"
            ,
                "default":""
            }
    

        ,
                "kallisto_quant_fragment_length": {
                "type":
                "number",
                "description": "Type: `double`. For single-end mode only, the estimated average fragment length to use for quantification with Kallisto",
                "help_text": "Type: `double`. For single-end mode only, the estimated average fragment length to use for quantification with Kallisto."
            
            }
    

        ,
                "kallisto_quant_fragment_length_sd": {
                "type":
                "number",
                "description": "Type: `double`. For single-end mode only, the estimated standard deviation of the fragment length for quantification with Kallisto",
                "help_text": "Type: `double`. For single-end mode only, the estimated standard deviation of the fragment length for quantification with Kallisto."
            
            }
    

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

        ,
                "quant_out_dir": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.quant_out_dir.quant`. ",
                "help_text": "Type: `file`, default: `$id.$key.quant_out_dir.quant`. "
            ,
                "default":"$id.$key.quant_out_dir.quant"
            }
    

        ,
                "salmon_quant_results_file": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.salmon_quant_results_file.sf`. ",
                "help_text": "Type: `file`, default: `$id.$key.salmon_quant_results_file.sf`. "
            ,
                "default":"$id.$key.salmon_quant_results_file.sf"
            }
    

        ,
                "kallisto_quant_results_file": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.kallisto_quant_results_file.tsv`. ",
                "help_text": "Type: `file`, default: `$id.$key.kallisto_quant_results_file.tsv`. "
            ,
                "default":"$id.$key.kallisto_quant_results_file.tsv"
            }
    

}
},
    
    
    "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"
    }
]
}
