-
Notifications
You must be signed in to change notification settings - Fork 50
/
Copy pathoutput_definition.json
228 lines (228 loc) · 9.03 KB
/
output_definition.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
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
{
"files": {
"workflow-alignment-stats-report": {
"filepath": "{{ alias }}.wf-human-alignment-report.html",
"title": "Report of the alignment statistics",
"description": "Report summarising the results of the alignment statistics for the sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"metrics-json": {
"filepath": "{{ alias }}.stats.json",
"title": "JSON file of some base statistics",
"description": "This JSON file contains base statistics on the reads, mappings, SNPs and SVs for the sample.",
"mime-type": "application/json",
"optional": false,
"type": "per-sample"
},
"workflow-snv-report": {
"filepath": "{{ alias }}.wf-human-snp-report.html",
"title": "Report of the SNP workflow",
"description": "Report summarising the results of the SNP subworkflow for the sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"workflow-sv-report": {
"filepath": "{{ alias }}.wf-human-sv-report.html",
"title": "Report of the SV workflow",
"description": "Report summarising the results of the SV subworkflow for the sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"workflow-cnv-report": {
"filepath": "{{ alias }}.wf-human-cnv-report.html",
"title": "Report of the CNV workflow",
"description": "Report summarising the results of the CNV subworkflow for the sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"workflow-str-report": {
"filepath": "{{ alias }}.wf-human-str-report.html",
"title": "Report of the STR workflow",
"description": "Report summarising the results of the short tandem repeat subworkflow for the sample.",
"mime-type": "text/html",
"optional": true,
"type": "per-sample"
},
"snp-vcf": {
"filepath": "{{ alias }}.wf_snp.vcf.gz",
"title": "Short variant VCF",
"description": "VCF file with the SNPs for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"sv-vcf": {
"filepath": "{{ alias }}.wf_sv.vcf.gz",
"title": "Structural variant VCF",
"description": "VCF file with the SVs for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"sv-snf": {
"filepath": "{{ alias }}.wf_sv.snf",
"title": "Structural variant SNF",
"description": "SNF file with the SVs for the sample, for onward multi-sample SV calling.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"cnv-vcf": {
"filepath": "{{ alias }}.wf_cnv.vcf.gz",
"title": "Copy number variants VCF",
"description": "VCF file with the CNV for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"mod-bedmethyl": {
"filepath": "{{ alias }}.wf_mods.bedmethyl.gz",
"title": "Modified bases BEDMethyl",
"description": "BED file with the aggregated modification counts for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"mod-bedmethyl-hap1": {
"filepath": "{{ alias }}.wf_mods.1.bedmethyl.gz",
"title": "Modified bases BEDMethyl (haplotype 1)",
"description": "BED file with the aggregated modification counts for haplotype 1 of the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"mod-bedmethyl-hap2": {
"filepath": "{{ alias }}.wf_mods.2.bedmethyl.gz",
"title": "Modified bases BEDMethyl (haplotype 2)",
"description": "BED file with the aggregated modification counts for haplotype 2 of the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"mod-bedmethyl-ungroup": {
"filepath": "{{ alias }}.wf_mods.ungrouped.bedmethyl.gz",
"title": "Modified bases BEDMethyl (ungrouped)",
"description": "BED file with the aggregated modification counts of non-haplotagged reads for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"str-vcf": {
"filepath": "{{ alias }}.wf_str.vcf.gz",
"title": "Short tandem repeat VCF",
"description": "VCF file with the STR sites for the sample.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment": {
"filepath": "{{ alias }}.cram",
"title": "Alignment file",
"description": "CRAM or BAM file with the aligned reads for the sample, generated when the input file is unaligned.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-index": {
"filepath": "{{ alias }}.cram.crai",
"title": "Alignment file index",
"description": "The index of the resulting CRAM or BAM file with the reads for the sample, generated when the input file is unaligned.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"haplotagged-alignment": {
"filepath": "{{ alias }}.haplotagged.cram",
"title": "Haplotagged alignment file",
"description": "CRAM or BAM file of all input reads with haplotags added by phasing.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"haplotagged-alignment-index": {
"filepath": "{{ alias }}.haplotagged.cram.crai",
"title": "Haplotagged alignment file index",
"description": "The index of the resulting CRAM or BAM file produced when haplotags have been added by phasing.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"coverage-by-region": {
"filepath": "{{ alias }}.regions.bed.gz",
"title": "Mean coverage for each region",
"description": "The mean coverage in the individual regions of the genome in BED format.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"coverage-by-threshold": {
"filepath": "{{ alias }}.thresholds.bed.gz",
"title": "Coverage per region above the given thresholds",
"description": "The BED reporting the number of bases in each region that are covered at or above each threshold values (1x, 10x, 20x and 30x).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"distribution-of-coverage": {
"filepath": "{{ alias }}.mosdepth.global.dist.txt",
"title": "Distribution of the proportion of total bases covered by a given coverage value",
"description": "The cumulative distribution indicating the proportion of total bases covered by a given coverage value, both genome-wide and by sequence.",
"mime-type": "text/plain",
"optional": false,
"type": "per-sample"
},
"coverage-summary": {
"filepath": "{{ alias }}.mosdepth.summary.txt",
"title": "Mean coverage per sequence and target region",
"description": "The summary of mean depths per chromosome and within specified regions per chromosome.",
"mime-type": "text/plain",
"optional": false,
"type": "per-sample"
},
"coverage-per-base": {
"filepath": "{{ alias }}.per-base.bedgraph.gz",
"title": "BEDgraph of the single-base coverage",
"description": "The single-base coverage of the genome in BED graph format.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"gene-summary": {
"filepath": "SAMPLE.gene_summary.tsv",
"title": "Gene level coverage summary",
"description": "A table where each gene of the input BED file has columns describing the percentage of positions along the gene region that are covered to a given threshold, and a column with the average coverage.",
"mime-type": "text/tsv",
"optional": true,
"type": "per-sample"
},
"haplocheck_output": {
"filepath": "{{ alias }}.haplocheck.tsv",
"title": "Haplocheck contamination summary",
"description": "A table generated by [haplocheck](https://mitoverse.readthedocs.io/haplocheck/haplocheck/), with estimate of contamination from the MT genome.",
"mime-type": "text/tsv",
"optional": true,
"type": "per-sample"
},
"reference-fai-index": {
"filepath": "{{ ref }}.fai",
"title": "FAI index of the reference FASTA file",
"description": "FAI Index of the reference FASTA file.",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "aggregated"
},
"reference-gzi-index": {
"filepath": "{{ ref }}.gzi",
"title": "GZI index of the reference FASTA file",
"description": "GZI Index of the reference FASTA file.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "aggregated"
}
}
}