ampliseq/assets/schema_input.json at 94c0c519664a9202f0e6d6a80ddbb48d86de7ee4 · d4straub/ampliseq · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/ampliseq/master/assets/schema_input.json",
    "title": "nf-core/ampliseq pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "pattern": "^[a-zA-Z][a-zA-Z0-9_]+$",
                "errorMessage": "Unique sample ID must be provided: Must start with a letter, and can only contain letters, numbers or underscores; Regex: '^[a-zA-Z][a-zA-Z0-9_]+$'",
                "meta": ["sample"]
            },
            "fastq_1": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
            },
            "fastq_2": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
            },
            "run": {
                "type": ["string", "integer"],
                "pattern": "^\\S+$",
                "errorMessage": "Run name cannot contain spaces",
                "meta": ["run"],
                "default": "1"
            },
            "control": {
                "type": ["string"],
                "enum": ["control", "sample"],
                "errorMessage": "Must be 'control' or 'sample'",
                "meta": ["control"]
            },
            "quant_reading": {
                "type": ["number"],
                "errorMessage": "Quantification must be a number",
                "meta": ["quant_reading"]
            }
        },
        "required": ["sample", "fastq_1"]
    },
    "uniqueEntries": ["sample"]
}