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schema_input.json
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{
"$schema": "https://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/phac-nml/snvphylnfc/main/assets/schema_input.json",
"title": "phac-nml/snvphylnfc pipeline - params.input schema",
"description": "Schema for the file provided with params.input",
"type": "array",
"items": {
"type": "object",
"properties": {
"sample": {
"type": "string",
"pattern": "^\\S+$",
"meta": ["irida_id"],
"unique": true,
"errorMessage": "Sample must be provided and cannot contain spaces"
},
"sample_name": {
"type": "string",
"meta": ["id", "id_alt"],
"errorMessage": "Sample name is optional, if provided will replace sample for filenames and outputs"
},
"fastq_1": {
"type": "string",
"pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
"format": "file-path",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have the extension: '.fq', '.fastq', '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have the extension: '.fq', '.fastq', '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q(\\.gz)?$"
},
{
"type": "string",
"maxLength": 0
}
]
},
"reference_assembly": {
"errorMessage": "Reference assembly file associated with this sample and must have the extension: '.fa', '.fasta', '.fa.gz' or '.fasta.gz'",
"anyOf": [
{
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?a(\\.gz)?$"
},
{
"type": "string",
"maxLength": 0
}
]
},
"metadata_1": {
"type": "string",
"meta": ["metadata_1"],
"errorMessage": "Metadata associated with the sample (metadata_1).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_2": {
"type": "string",
"meta": ["metadata_2"],
"errorMessage": "Metadata associated with the sample (metadata_2).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_3": {
"type": "string",
"meta": ["metadata_3"],
"errorMessage": "Metadata associated with the sample (metadata_3).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_4": {
"type": "string",
"meta": ["metadata_4"],
"errorMessage": "Metadata associated with the sample (metadata_4).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_5": {
"type": "string",
"meta": ["metadata_5"],
"errorMessage": "Metadata associated with the sample (metadata_5).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_6": {
"type": "string",
"meta": ["metadata_6"],
"errorMessage": "Metadata associated with the sample (metadata_6).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_7": {
"type": "string",
"meta": ["metadata_7"],
"errorMessage": "Metadata associated with the sample (metadata_7).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
},
"metadata_8": {
"type": "string",
"meta": ["metadata_8"],
"errorMessage": "Metadata associated with the sample (metadata_8).",
"default": "",
"pattern": "^[^\\n\\t\"]+$"
}
},
"required": ["sample", "fastq_1"]
}
}