gatk4-germline-snps-indels/nextflow_schema.json at master · human-nature-lab/gatk4-germline-snps-indels · GitHub

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{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/seqeralabs/gatk4-germline-snps-indels/master/nextflow_schema.json",
    "title": "seqeralabs/gatk4-germline-snps-indels pipeline parameters",
    "description": "Workflow for germline short variant discovery using GATK4 written in Nextflow.",
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input/Output options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "input_fofn": {
                    "type": "string",
                    "fa_icon": "fas fa-table",
                    "default": "${projectDir}/resources/seqera_nf_tower_data/manifest-2samples.txt",
                    "description": "The location of input samplesheet, by default it uses 2 samples."
                },
                "unmapped_bams_list": {
                    "type": "string",
                    "fa_icon": "fas fa-bars",
                    "default": "${projectDir}/resources/seqera_nf_tower_data/unmapped_bams.tsv",
                    "description": "The location of input samplesheet for bam files, by default it uses 2 samples."
                },
                "outdir": {
                    "type": "string",
                    "fa_icon": "fas fa-folder-open",
                    "default": "s3://nf-tower-bucket/scratch/gatk4-germline-snps-indels-nf/results",
                    "description": "The output directory for the results of the analysis."
                }
            },
            "required": [
                "input_fofn",
                "unmapped_bams_list",
                "outdir"
            ],
            "fa_icon": "fas fa-terminal"
        },
        "reference_files_options": {
            "title": "Reference file options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "fasta": {
                    "type": "string",
                    "fa_icon": "fas fa-file-code",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/references/Homo_sapiens_assembly38.fasta",
                    "description": "The location of input reference fasta file."
                },
                "known_indels_dbSNP": {
                    "type": "string",
                    "fa_icon": "fas fa-file-archive",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/references/Homo_sapiens_assembly38.known_indels.vcf.gz",
                    "description": "The location of reference known indels database archive."
                },
                "known_indels_mills": {
                    "type": "string",
                    "fa_icon": "far fa-file-archive",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/references/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
                    "description": "The location of Mills and 1000G gold standard database archive."
                },
                "dbSNP_vcf": {
                    "type": "string",
                    "fa_icon": "far fa-file-alt",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/references/Homo_sapiens_assembly38.dbsnp138.vcf",
                    "description": "The location variant calling file for the SNP database (dbSNP)."
                },
                "scattered_calling_interval": {
                    "type": "string",
                    "fa_icon": "fas fa-file-alt",
                    "default": "${projectDir}/resources/seqera_nf_tower_data/hg38_wgs_scattered_calling_intervals.txt",
                    "description": "The location of target chromosome interval definition file."
                }
            },
            "required": [
                "fasta",
                "known_indels_dbSNP",
                "known_indels_mills",
                "dbSNP_vcf",
                "scattered_calling_interval"
            ],
            "fa_icon": "fas fa-anchor",
            "help_text": ""
        },
        "chromosome_grouping_files_options": {
            "title": "Chromosome grouping files options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "sequence_grouping_unmapped": {
                    "type": "string",
                    "fa_icon": "fas fa-stream",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/sequence_grouping_with_unmapped.txt",
                    "description": "The location of chromosome sequences with unmapped tag."
                },
                "sequence_grouping": {
                    "type": "string",
                    "fa_icon": "fas fa-clipboard-list",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/sequence_grouping.txt",
                    "description": "The location of chromosome sequences."
                }
            },
            "required": [
                "sequence_grouping_unmapped",
                "sequence_grouping"
            ],
            "fa_icon": "fas fa-object-ungroup"
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_files_options"
        },
        {
            "$ref": "#/definitions/chromosome_grouping_files_options"
        }
    ]
}