rnaseq/target/nextflow/picard_markduplicates/nextflow_schema.json

{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "picard_markduplicates",
"description": "Locate and tag duplicate reads in a BAM file\n",
"type": "object",
"definitions": {

    
    
    "input" : {
    "title": "Input",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "bam": {
                "type":
                "string",
                "description": "Type: `file`. Input BAM file",
                "help_text": "Type: `file`. Input BAM file"
            
            }
    

        ,
                "fasta": {
                "type":
                "string",
                "description": "Type: `file`. Reference genome FASTA file",
                "help_text": "Type: `file`. Reference genome FASTA file"
            
            }
    

        ,
                "fai": {
                "type":
                "string",
                "description": "Type: `file`. Reference genome FASTA index",
                "help_text": "Type: `file`. Reference genome FASTA index"
            
            }
    

        ,
                "extra_picard_args": {
                "type":
                "string",
                "description": "Type: `string`, default: `--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Additional argument to be passed to Picard MarkDuplicates",
                "help_text": "Type: `string`, default: `--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Additional argument to be passed to Picard MarkDuplicates"
            ,
                "default":"--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
            }
    

}
},
    
    
    "output" : {
    "title": "Output",
    "type": "object",
    "description": "No description",
    "properties": {
    
        
                "output_bam": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.output_bam.bam`. BAM file with duplicate reads marked/removed",
                "help_text": "Type: `file`, default: `$id.$key.output_bam.bam`. BAM file with duplicate reads marked/removed"
            ,
                "default":"$id.$key.output_bam.bam"
            }
    

        ,
                "bai": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.bai.bai`. An optional BAM index file",
                "help_text": "Type: `file`, default: `$id.$key.bai.bai`. An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag"
            ,
                "default":"$id.$key.bai.bai"
            }
    

        ,
                "metrics": {
                "type":
                "string",
                "description": "Type: `file`, default: `$id.$key.metrics.txt`. Duplicate metrics file generated by picard",
                "help_text": "Type: `file`, default: `$id.$key.metrics.txt`. Duplicate metrics file generated by picard"
            ,
                "default":"$id.$key.metrics.txt"
            }
    

}
},
    
    
    "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"
    }
]
}