-
Notifications
You must be signed in to change notification settings - Fork 0
/
dxapp.json
executable file
·170 lines (170 loc) · 4.24 KB
/
dxapp.json
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
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
{
"name": "eggd_vcf_rescue",
"title": "VCF Rescue",
"summary": "Filter in low support variants on specified locations or recover filtered out variants",
"dxapi": "1.0.0",
"version": "1.2.0",
"inputSpec": [
{
"name": "gvcf",
"label": "genomic vcf",
"class": "file",
"optional": true,
"group": "files",
"patterns": [
"*.vcf"
],
"help": "Input genomic vcf - to be used with rescue_non_pass mode"
},
{
"name": "filtered_vcf",
"label": "Filtered VCF",
"class": "file",
"optional": true,
"group": "files",
"patterns": [
"*.vcf",
"*.vcf.gz"
],
"help": "vcf of filtered variants - to be used with rescue_filtered mode"
},
{
"name": "unfiltered_vcf",
"label": "Unfiltered VCF",
"class": "file",
"optional": true,
"group": "files",
"patterns": [
"*.vcf",
"*.vcf.gz"
],
"help": "vcf of unfiltered variants - to be used with rescue_filtered mode"
},
{
"name": "rescue_vcf",
"class": "file",
"optional": false,
"group": "files",
"patterns": [
"*vcf.gz"
],
"help": "vcf of variants to rescue from given input vcf"
},
{
"name": "fasta_tar",
"label": "Reference genome fasta and index",
"class": "file",
"optional": false,
"group": "files",
"patterns": ["*.fasta-index.tar.gz"],
"help": "tar.gz containing genome.fa and genome.fa.fai. Must match reference genome build used.",
"default":{
"$dnanexus_link": {
"project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
"id": "file-F3zxG0Q4fXX9YFjP1v5jK9jf"
}
}
},
{
"name": "rescue_non_pass",
"label": "non pass rescue",
"class": "boolean",
"optional": true,
"group": "mode",
"help": "determines if to run as non-pass rescue, must be used with gvcf input"
},
{
"name": "rescue_filtered",
"label": "rescue filtered",
"class": "boolean",
"optional": true,
"group": "mode",
"help": "determines if to run as rescuing filtered out variants, must be used with filtered and unfiltered vcf inputs"
},
{
"name": "strip_chr",
"label": "strip chr prefix",
"class": "boolean",
"optional": true,
"group": "optional",
"help": "determines if to strip chr prefix from input vcfs, should be determined by presence of chr prefixes in reference fasta"
},
{
"name": "filter_tag",
"label": "filter tag",
"class": "string",
"default": "rescued",
"group": "optional",
"help": "tag to apply to FILTER field of rescued variants"
},
{
"name": "filter_tag_description",
"label": "filter tag description",
"class": "string",
"optional": true,
"group": "optional",
"help": "extra description to append to FILTER field in vcf header for given filter_tag"
},
{
"name": "filter_string",
"label": "BCFtools filter command",
"class": "string",
"optional": true,
"group": "optional",
"help": "filters variants that meet string input. The type of filterings that can be used by bcftools are listed here: https://samtools.github.io/bcftools/bcftools.html"
}
],
"outputSpec": [
{
"name": "output_vcf",
"class": "file",
"patterns": [
"*.vcf.gz"
],
"help": ""
}
],
"runSpec": {
"execDepends": [
],
"distribution" : "Ubuntu",
"release": "20.04",
"version": "0",
"file": "src/eggd_vcf_rescue.sh",
"interpreter": "bash",
"timeoutPolicy": {
"*": {
"hours": 1
}
},
"assetDepends": [
{
"name": "htslib",
"project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
"folder": "/app_assets/htslib/htslib_v1.15.0",
"version": "1.15.0"
}
]
},
"developers":[
"org-emee_1"
],
"authorizedUsers": [
"org-emee_1"
],
"access": {
"allProjects":"UPLOAD",
"network": [
"*"
]
},
"regionalOptions": {
"aws:eu-central-1": {
"systemRequirements": {
"*": {
"instanceType": "mem1_ssd1_v2_x2"
}
}
}
}
}