quartet_dna_quality_control_wes_big_pipeline/schema.json

{
    "formMode": "batch",
    "fields": [
        {
            "tmplType": "sample_id",
            "type": "number",
            "label": "Sample ID",
            "name": "sample_id",
            "question": "How many samples? For auto generating sample id.",
            "placeholder": "How many samples? For auto generating sample id.",
            "model": "sample_id",
            "disabled": false,
            "min": 1,
            "max": 100,
            "config": {
                "initialValue": 1,
                "rules": [
                    {
                        "type": "number",
                        "required": true,
                        "message": "Please input a number."
                    }
                ]
            }
        },
        {
            "tmplType": "radio",
            "label": "Platform?",
            "model": "pl",
            "options": [
                {
                    "label": "BGI",
                    "value": "BGI"
                },
                {
                    "label": "ILLUMINA",
                    "value": "ILLUMINA"
                }
            ],
            "config": {
                "rules": [
                    {
                        "type": "string",
                        "required": true,
                        "message": "Please select a platform."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "Reference Bed Dict",
            "model": "reference_bed_dict",
            "readOnly": false,
            "multiple": false,
            "filterType": ".dict",
            "question": "A sequence dictionary for a reference sequence.",
            "placeholder": "A sequence dictionary for a reference sequence.",
            "config": {
                "initialValue": "oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.dict",
                "rules": [
                    {
                        "required": true,
                        "message": "Please select a bed file."
                    }
                ]
            }
        },
        {
            "tmplType": "radio",
            "label": "FASTQ/VCF File?",
            "model": "fastq_or_vcf",
            "options": [
                {
                    "label": "FASTQ",
                    "value": "fastq"
                },
                {
                    "label": "VCF",
                    "value": "vcf"
                }
            ],
            "config": {
                "rules": [
                    {
                        "type": "string",
                        "required": true,
                        "message": "Please select a file type."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "D5 VCF Files",
            "model": "vcf_D5",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "vcf",
            "filterType": "vcf",
            "placeholder": "Select files for D5 vcf.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for D5 vcf."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "D5 Read1 Files",
            "model": "fastq_1_D5",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for D5 read1.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for D5 read1."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "D5 Read2 Files",
            "model": "fastq_2_D5",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for D5 read2.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for D5 read2."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "D6 VCF Files",
            "model": "vcf_D6",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "vcf",
            "filterType": "vcf",
            "placeholder": "Select files for D6 vcf.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for D6 vcf."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "D6 Read1 Files",
            "model": "fastq_1_D6",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for D6 read1.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for D6 read1."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "D6 Read2 Files",
            "model": "fastq_2_D6",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for D6 read2.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for D6 read2."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "F7 VCF Files",
            "model": "vcf_F7",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "vcf",
            "filterType": "vcf",
            "placeholder": "Select files for F7 vcf.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for F7 vcf."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "F7 Read1 Files",
            "model": "fastq_1_F7",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for F7 read1.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for F7 read1."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "F7 Read2 Files",
            "model": "fastq_2_F7",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for F7 read2.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for F7 read2."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "M8 VCF Files",
            "model": "vcf_M8",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "vcf",
            "filterType": "vcf",
            "placeholder": "Select files for M8 vcf.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for M8 vcf."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "M8 Read1 Files",
            "model": "fastq_1_M8",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for M8 read1.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for M8 read1."
                    }
                ]
            }
        },
        {
            "tmplType": "file",
            "label": "M8 Read2 Files",
            "model": "fastq_2_M8",
            "readOnly": false,
            "multiple": true,
            "visibleVariable": "fastq_or_vcf",
            "expectedValue": "fastq",
            "filterType": "_R[12].fastq.gz|_R[12].fq.gz",
            "placeholder": "Select files for M8 read2.",
            "config": {
                "rules": [
                    {
                        "type": "array",
                        "required": true,
                        "message": "Please select files for M8 read2."
                    }
                ]
            }
        },
        {
            "tmplType": "actions",
            "buttons": [
                {
                    "type": "cancel",
                    "buttonType": "default",
                    "buttonLabel": "Previous Step"
                },
                {
                    "type": "submit",
                    "buttonType": "primary",
                    "buttonLabel": "Next Step",
                    "validate": true
                }
            ]
        }
    ]
}