{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "deseq2_qc",
"description": "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "counts": {
                "type":
                "string",
                "description": "Type: `file`, required. Count file matrix where rows are genes and columns are samples",
                "help_text": "Type: `file`, required. Count file matrix where rows are genes and columns are samples."
            
            }
    

        ,
                "vst": {
                "type":
                "boolean",
                "description": "Type: `boolean`, default: `false`. Use vst transformation instead of rlog with ",
                "help_text": "Type: `boolean`, default: `false`. Use vst transformation instead of rlog with .DESeq2"
            ,
                "default":false
            }
    

        ,
                "count_col": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `3`. First column containing sample count data",
                "help_text": "Type: `integer`, default: `3`. First column containing sample count data."
            ,
                "default":3
            }
    

        ,
                "id_col": {
                "type":
                "integer",
                "description": "Type: `integer`, default: `1`. Column containing identifiers to be used",
                "help_text": "Type: `integer`, default: `1`. Column containing identifiers to be used."
            ,
                "default":1
            }
    

        ,
                "sample_suffix": {
                "type":
                "string",
                "description": "Type: `string`, default: ``. Suffix to remove after sample name in columns e",
                "help_text": "Type: `string`, default: ``. Suffix to remove after sample name in columns e.g. \u0027.rmDup.bam\u0027 if \u0027DRUG_R1.rmDup.bam\u0027."
            ,
                "default":""
            }
    

        ,
                "outprefix": {
                "type":
                "string",
                "description": "Type: `string`, default: `deseq2`. Output prefix",
                "help_text": "Type: `string`, default: `deseq2`. Output prefix"
            ,
                "default":"deseq2"
            }
    

        ,
                "label": {
                "type":
                "string",
                "description": "Type: `string`. Label to used in MultiQC report",
                "help_text": "Type: `string`. Label to used in MultiQC report"
            
            }
    

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

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

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