-
Notifications
You must be signed in to change notification settings - Fork 14
/
pepatac_output_schema.yaml
359 lines (359 loc) · 8.88 KB
/
pepatac_output_schema.yaml
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
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
title: An example Pipestat output schema
description: objects produced by PEPATAC pipeline.
type: object
properties:
pipeline_name: PEPATAC
samples:
type: object
properties:
smooth_bw:
type: string
description: "Smoothed signal track"
exact_bw:
type: string
description: "Nucleotide-resolution signal track"
aligned_bam:
type: string
description: "Coordinate sorted deduplicated, aligned BAM file"
peak_file:
type: string
description: "Sample peak file"
coverage_file:
type: string
description: "Sample peak coverage table"
summits_bed:
type: string
description: "Peak summit file"
File_mb:
type: number
description: "size of file"
Read_type:
type: string
description: "read_type"
Genome:
type: string
description: "e.g. hg38"
Raw_reads:
type: string
description: "raw reads"
Fastq_reads:
type: number
description: "fastq_reads"
Trimmed_reads:
type: number
description: "trimmed_reads"
Trimmed_loss_rate:
type: number
description: "trimmed loss rate"
FastQC report r1:
title: "FastQC report r1"
description: "FastQC report r1"
type: object
object_type: file
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
FastQC report r2:
title: "FastQC report r2"
description: "FastQC report r2"
type: object
object_type: file
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
Aligned_reads_rCRSd:
type: number
description: "Aligned_reads_rCRSd"
Alignment_rate_rCRSd:
type: number
description: "Alignment_rate_rCRSd"
Mapped_reads:
type: string
description: "mapped_reads"
QC_filtered_reads:
type: number
description: "QC_filtered_reads"
Aligned_reads:
type: string
description: "Aligned_reads"
Alignment_rate:
type: number
description: "Alignment_rate"
Total_efficiency:
type: number
description: "Total_efficiency"
Mitochondrial_reads:
type: number
description: "Mitochondrial_reads"
NRF:
type: number
description: "NRF"
PBC1:
type: number
description: "PBC1"
PBC2:
type: number
description: "PBC1"
Unmapped_reads:
type: number
description: "Unmapped_reads"
Duplicate_reads:
type: string
description: "Duplicate_reads"
Dedup_aligned_reads:
type: number
description: "Dedup_aligned_reads"
Dedup_alignment_rate:
type: number
description: "Dedup_alignment_rate"
Dedup_total_efficiency:
type: number
description: "Dedup_total_efficiency"
NFR_frac:
type: number
description: "NFR_frac"
mono_frac:
type: number
description: "mono_frac"
di_frac:
type: number
description: "di_frac"
tri_frac:
type: number
description: "tri_frac"
poly_frac:
type: number
description: "poly_frac"
Read_length:
type: number
description: "Read_length"
Genome_size:
type: number
description: "Read_length"
Frac_exp_unique_at_10M:
type: number
description: "Frac_exp_unique_at_10M"
TSS_score:
type: number
description: "TSS_score"
Fragment distribution:
title: "Fragment distribution"
description: "Fragment distribution"
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
Peak_count:
type: number
description: "Peak_count"
FRiP:
type: number
description: "FRiP"
Peak chromosome distribution:
title: "Peak chromosome distribution"
description: "Peak chromosome distribution"
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
TSS distance distribution:
title: "TSS distance distribution"
description: "TSS distance distribution"
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
Peak partition distribution:
title: "Peak partition distribution"
description: "Peak partition distribution"
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
cFRiF:
title: "cFRiF"
description: "cFRiF"
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
FRiF:
title: "FRiF"
description: "FRiF"
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
Time:
type: string
description: "time"
Success:
type: string
description: "success"
project:
type: object
properties:
alignment_percent_file:
title: "Alignment percent file"
description: "Plots percent of total alignment to all pre-alignments and primary genome."
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
alignment_raw_file:
title: "Alignment raw file"
description: "Plots raw alignment rates to all pre-alignments and primary genome."
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
TSS_enrichment:
title: "TSS enrichment file"
description: "Plots TSS scores for each sample."
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
Library_complexity:
title: "Library complexity file"
description: "Plots each sample's library complexity on a single plot."
type: object
object_type: image
properties:
path:
type: string
thumbnail_path:
type: string
title:
type: string
required:
- path
- thumbnail_path
- title
consensus_peaks_file:
title: "consesus peak file"
description: "A set of consensus peaks across samples."
type: object
object_type: file
properties:
path:
type: string
title:
type: string
thumbnail_path:
type: string
required:
- path
- title
counts_table:
title: "Project peak coverage file"
description: "Project peak coverages: chr_start_end X sample"
type: object
object_type: file
properties:
path:
type: string
title:
type: string
thumbnail_path:
type: string
required:
- path
- title