nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/IARCbioinfo/RNAseq-fusion-nf/master/nextflow_schema.json",
    "title": "IARCbioinfo RNAseq-fusion-nf pipeline parameters",
    "description": "This pipeline performs fusion-gene discovery from junction reads identified by STAR during alignment.",
    "type": "object",
    "definitions": {
        "input_output_params": {
            "title": "Input_output_params",
            "type": "object",
            "description": "Input and output parameters",
            "default": "",
            "properties": {
                "input_folder": {
                    "type": "string",
                    "description": "Folder containing fastq files and STAR junction files",
                    "default": "."
                },
                "input_file": {
                    "type": "string",
                    "description": "Input file (comma-separated) with 4 columns: SM(sample name), pair1 (path to fastq pair 1), pair2 (path to fastq pair 2), and junction (path to junction file)"
                },
                "fastq_ext": {
                    "type": "string",
                    "description": "Extension of fastq files",
                    "default": "fq.gz"
                },
                "suffix1": {
                    "type": "string",
                    "description": "Suffix of 1st element of fastq files pair",
                    "default": "_1"
                },
                "suffix2": {
                    "type": "string",
                    "description": "Suffix of 2nd element of fastq files pair",
                    "default": "_2"
                },
                "junction_suffix": {
                    "type": "string",
                    "description": "Suffix of STAR chimeric junction files",
                    "default": "Chimeric.SJ.out.junction"
                },
                "output_folder": {
                    "type": "string",
                    "description": "Output folder",
                    "default": "results_fusion"
                }
            }
        },
        "computing_params": {
            "title": "Computing_params",
            "type": "object",
            "description": "Computing parameters",
            "default": "",
            "properties": {
                "cpu": {
                    "type": "integer",
                    "description": "Number of cpu used by bwa mem and sambamba",
                    "default": 2
                },
                "mem": {
                    "type": "string",
                    "description": "Size of memory used for mapping (in GB)",
                    "default": "2"
                }
            }
        },
        "ref_params": {
            "title": "Ref_params",
            "type": "object",
            "description": "Reference parameters",
            "default": "",
            "properties": {
                "CTAT_folder": {
                    "type": "string",
                    "description": "Folder with STAR-Fusion bundle (CTAT)",
                    "default": "."
                },
                "starfusion_path": {
                    "type": "string",
                    "description": "Path to STAR-fusion executable; note that the default is set to the location in the singularity container",
                    "default": "/usr/local/src/STAR-Fusion/STAR-Fusion"
                }
            }
        },
        "pipeline_params": {
            "title": "Pipeline_params",
            "type": "object",
            "description": "Pipeline parameters",
            "default": "",
            "properties": {
                "junctions": {
                    "type": "boolean",
                    "description": "Option to use STAR junction files already generated"
                },
                "help": {
                    "type": "boolean",
                    "description": "Display help"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_params"
        },
        {
            "$ref": "#/definitions/computing_params"
        },
        {
            "$ref": "#/definitions/ref_params"
        },
        {
            "$ref": "#/definitions/pipeline_params"
        }
    ]
}