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quartet_dna_quality_control_wes_big_pipeline
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Add schema & manifest files.

tags/v0.1.0
YJC 1 year ago
parent
d9e69f66f9
commit
a9504990ce
2 changed files with 371 additions and 0 deletions
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  1. +21
    -0
      manifest.json
  2. +350
    -0
      schema.json

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manifest.json View File

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{
"name": "WES QC for Quartet",
"short_name": "quartet_dna_quality_control_wes_big_pipeline",
"description": "Quality control of germline variants calling results using a Chinese Quartet family",
"home": "http://apps.clinico-omics.org/renluyao/quartet_dna_quality_control_wes_big_pipeline",
"hidden": false,
"icons": [
{
"src": "",
"type": "image/png",
"sizes": "192x192"
},
{
"src": "",
"type": "image/png",
"sizes": "192x192"
}
],
"category": "Pipeline",
"source": "PGx"
}

+ 350
- 0
schema.json View File

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{
"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
}
]
}
]
}

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