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maxulyssemaxulysse
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update schema_input
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-124
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Diff for: ‎assets/schema_input.json

+34-124
Original file line numberDiff line numberDiff line change
@@ -23,16 +23,8 @@
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"errorMessage": "Sex cannot contain spaces",
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"meta": ["sex"],
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"default": "NA",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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]
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"type": "string",
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"pattern": "^\\S+$"
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},
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"status": {
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"type": "integer",
@@ -48,183 +40,101 @@
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"meta": ["lane"]
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},
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"fastq_1": {
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"errorMessage": "Gzipped FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz$",
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"format": "file-path",
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"exists": true
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},
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"fastq_2": {
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"errorMessage": "Gzipped FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz$",
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"format": "file-path",
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"exists": true
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},
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"spring_1": {
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"errorMessage": "Gzipped and spring-compressed FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz.spring' or '.fastq.gz.spring'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$",
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"format": "file-path",
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"exists": true
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},
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"spring_2": {
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"errorMessage": "Gzipped and spring-compressed FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz.spring' or '.fastq.gz.spring'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$",
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"format": "file-path",
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"exists": true
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},
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"table": {
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"errorMessage": "Recalibration table cannot contain spaces and must have extension '.table'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.table$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.table$",
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"format": "file-path",
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"exists": true
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},
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"cram": {
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"errorMessage": "CRAM file cannot contain spaces and must have extension '.cram'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.cram$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.cram$",
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"format": "file-path",
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"exists": true
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},
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"crai": {
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"errorMessage": "CRAM index file cannot contain spaces and must have extension '.crai'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.crai$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.crai$",
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"format": "file-path",
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"exists": true
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},
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"bam": {
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"errorMessage": "BAM file cannot contain spaces and must have extension '.bam'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.bam$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.bam$",
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"format": "file-path",
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"exists": true
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},
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"bai": {
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"errorMessage": "BAM index file cannot contain spaces and must have extension '.bai'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.bai$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.bai$",
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"format": "file-path",
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"exists": true
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},
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"vcf": {
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"errorMessage": "VCF file for reads 1 cannot contain spaces and must have extension '.vcf' or '.vcf.gz'",
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"anyOf": [
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{
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"type": "string",
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"pattern": "^\\S+\\.vcf(\\.gz)?$"
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},
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{
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"type": "string",
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"maxLength": 0
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}
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],
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"type": "string",
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"pattern": "^\\S+\\.vcf(\\.gz)?$",
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"format": "file-path",
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"exists": true
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},
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"variantcaller": {
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"type": "string"
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}
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},
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"required": ["patient", "sample"],
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"uniqueEntries": ["patient", "sample"],
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"anyOf": [
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{
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"dependentRequired": {
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"fastq_2": ["fastq_1"],
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"spring_2": ["spring_1"],
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"lane": ["bam"]
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"lane": ["fastq_1"]
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}
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},
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{
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"dependentRequired": {
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"fastq_2": ["fastq_1"],
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"spring_2": ["spring_1"],
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"lane": ["fastq_1"]
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"lane": ["spring_1"]
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}
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},
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{
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"dependentRequired": {
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"fastq_2": ["fastq_1"],
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"spring_2": ["spring_1"],
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"lane": ["spring_1"]
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"lane": ["bam"]
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}
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}
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]
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],
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"dependentRequired": {
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"fastq_2": ["fastq_1"],
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"spring_2": ["spring_1"]
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},
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"required": ["patient", "sample"],
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"uniqueEntries": ["lane", "patient", "sample"]
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}
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}

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