smallvariants/assets/schema_input.json at 717340e7fb5d8ad7141d102c14967b6ebcd67d27 · nf-cmgg/smallvariants · 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
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-cmgg/smallvariants/main/assets/schema_input.json",
    "title": "nf-cmgg/smallvariants 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-Z0-9_\\.]+$",
                "meta": ["id", "sample"],
                "errorMessage": "Sample name should be a string that may contain underscores (_) and dots (.)",
                "default": ""
            },
            "family": {
                "type": "string",
                "pattern": "^[a-zA-Z0-9_\\.]+$",
                "meta": ["family"],
                "errorMessage": "Family name should be a string that may contain underscores (_) and dots (.)"
            },
            "cram": {
                "type": "string",
                "pattern": "^\\S+\\.(b|cr)am$",
                "format": "file-path",
                "exists": true
            },
            "crai": {
                "type": "string",
                "pattern": "^\\S+\\.(b|cr)am\\.(bai|csi|crai)$",
                "format": "file-path",
                "exists": true
            },
            "gvcf": {
                "type": "string",
                "pattern": "^\\S+\\.g\\.vcf(\\.gz)?$",
                "format": "file-path",
                "exists": true
            },
            "gtbi": {
                "type": "string",
                "pattern": "^\\S+\\.g\\.vcf\\.gz\\.tbi$",
                "format": "file-path",
                "exists": true
            },
            "vcf": {
                "type": "string",
                "pattern": "^\\S+\\.vcf(\\.gz)?$",
                "format": "file-path",
                "exists": true
            },
            "tbi": {
                "type": "string",
                "pattern": "^\\S+\\.vcf\\.gz\\.tbi$",
                "format": "file-path",
                "exists": true
            },
            "roi": {
                "type": "string",
                "pattern": "^\\S+\\.bed(\\.gz)?$",
                "format": "file-path",
                "exists": true
            },
            "ped": {
                "type": "string",
                "pattern": "^\\S+\\.ped$",
                "format": "file-path",
                "exists": true
            },
            "truth_vcf": {
                "type": "string",
                "pattern": "^\\S+\\.vcf\\.gz$",
                "format": "file-path",
                "exists": true
            },
            "truth_tbi": {
                "type": "string",
                "pattern": "^\\S+\\.tbi$",
                "format": "file-path",
                "exists": true
            },
            "truth_bed": {
                "type": "string",
                "pattern": "^\\S+\\.bed$",
                "format": "file-path",
                "exists": true
            },
            "vardict_min_af": {
                "type": "number",
                "meta": ["vardict_min_af"]
            },
            "msi": {
                "type": "boolean",
                "default": false,
                "meta": "msi"
            },
            "sex": {
                "type": "string",
                "default": null,
                "meta": "sex",
                "enum": ["male", "female"]
            }
        },
        "anyOf": [
            {
                "required": ["sample", "cram"]
            },
            {
                "required": ["sample", "gvcf"]
            },
            {
                "required": ["family", "vcf"]
            }
        ]
    },
    "dependentRequired": {
        "truth_tbi": ["truth_vcf"],
        "truth_bed": ["truth_vcf"],
        "gtbi": ["gvcf"],
        "tbi": ["vcf"],
        "crai": ["cram"]
    }
}