nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/IARCbioinfo/abra-nf/master/nextflow_schema.json",
    "title": "IARCbioinfo abra-nf pipeline parameters",
    "description": "Nextflow pipeline for ABRA2 to realign next generation sequencing data using localized assembly in a set of BAM files",
    "type": "object",
    "definitions": {
        "input_output_params": {
            "title": "Input_output_params",
            "type": "object",
            "description": "Input and output parameters",
            "default": "",
            "properties": {
                "tumor_bam_folder": {
                    "type": "string",
                    "description": "Folder containing tumor BAM files"
                },
                "normal_bam_folder": {
                    "type": "string",
                    "description": "Folder containing matched normal BAM files"
                },
                "bam_folder": {
                    "type": "string",
                    "description": "Folder containing BAM files"
                },
                "suffix_tumor": {
                    "type": "string",
                    "default": "_T",
                    "description": "Suffix identifying tumor bam"
                },
                "suffix_normal": {
                    "type": "string",
                    "default": "_N",
                    "description": "Suffix identifying normal bam"
                },
                "output_folder": {
                    "type": "string",
                    "default": "abra_BAM",
                    "description": "Output folder containing the realigned BAM"
                }
            }
        },
        "computing_params": {
            "title": "Computing_params",
            "type": "object",
            "description": "Computing parameters",
            "default": "",
            "properties": {
                "mem": {
                    "type": "integer",
                    "default": 16,
                    "description": "Maximum RAM used"
                },
                "cpu": {
                    "type": "integer",
                    "default": 4,
                    "description": "Number of threads used"
                }
            }
        },
        "ref_params": {
            "title": "Ref_params",
            "type": "object",
            "description": "Reference parameters",
            "default": "",
            "properties": {
                "ref": {
                    "type": "string",
                    "description": "Path to Reference fasta file indexed"
                },
                "bed": {
                    "type": "string",
                    "description": "Bed file containing intervals (without header)"
                },
                "gtf": {
                    "type": "string",
                    "description": "GTF file containing junction annotations"
                },
                "abra_path": {
                    "type": "string",
                    "default": "/opt/conda/envs/abra-nf/share/abra2*/abra2.jar",
                    "description": "Path to abra.jar (not needed if you use docker or singularity container)"
                }
            },
            "required": [
                "ref"
            ]
        },
        "pipeline_params": {
            "title": "Pipeline_params",
            "type": "object",
            "description": "Pipeline parameters",
            "default": "",
            "properties": {
                "single": {
                    "type": "boolean",
                    "description": "Switch to single-end sequencing mode"
                },
                "rna": {
                    "type": "boolean",
                    "description": "Add RNA-specific recommended ABRA2 parameters"
                },
                "junctions": {
                    "type": "boolean",
                    "description": "Use STAR identified junctions"
                },
                "help": {
                    "type": "boolean",
                    "description": "Display help"
                }
            }
            
        }
   },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_params"
        },
        {
            "$ref": "#/definitions/computing_params"
        },
        {
            "$ref": "#/definitions/ref_params"
        },
        {
            "$ref": "#/definitions/pipeline_params"
        }
    ]
   
}