-
Notifications
You must be signed in to change notification settings - Fork 12
/
wf-variantcall.cwl
270 lines (270 loc) · 6.17 KB
/
wf-variantcall.cwl
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
class: Workflow
cwlVersion: v1.0
hints: []
inputs:
- id: batch_rec
type:
items:
fields:
- name: description
type: string
- name: resources
type: string
- name: reference__fasta__base
type: File
- name: config__algorithm__variantcaller
type: string
- name: reference__snpeff__GRCh38_86
type: File
- name: config__algorithm__coverage_interval
type:
- string
- 'null'
- name: genome_resources__variation__encode_blacklist
type:
- 'null'
- string
- name: metadata__batch
type:
- 'null'
- string
- name: genome_resources__variation__lcr
type: File
- name: metadata__phenotype
type: string
- name: reference__twobit
type: File
- name: config__algorithm__validate
type: File
- name: config__algorithm__validate_regions
type: File
- name: genome_build
type: string
- name: vrn_file
type:
- 'null'
- string
- name: genome_resources__aliases__human
type:
- string
- 'null'
- boolean
- name: config__algorithm__tools_off
type:
items: string
type: array
- name: genome_resources__variation__dbsnp
type: File
- name: genome_resources__variation__polyx
type: File
- name: genome_resources__variation__cosmic
type:
- 'null'
- string
- name: reference__genome_context
type:
items: File
type: array
- name: analysis
type: string
- name: config__algorithm__tools_on
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: config__algorithm__effects
type: string
- name: config__algorithm__variant_regions
type:
- File
- 'null'
- name: genome_resources__aliases__ensembl
type: string
- name: config__algorithm__exclude_regions
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: reference__rtg
type: File
- name: genome_resources__aliases__snpeff
type: string
- name: align_bam
type:
- File
- 'null'
- name: regions__sample_callable
type:
- File
- 'null'
- name: config__algorithm__callable_regions
type: File
name: batch_rec
type: record
type: array
outputs:
- id: vc_rec
outputSource: compare_to_rm/vc_rec
type:
items:
fields:
- name: batch_samples
type:
- 'null'
- items: string
type: array
- name: validate__summary
type:
- File
- 'null'
- name: validate__tp
type:
- File
- 'null'
- name: validate__fp
type:
- File
- 'null'
- name: validate__fn
type:
- File
- 'null'
- name: description
type: string
- name: resources
type: string
- name: vrn_file
type: File
- name: reference__fasta__base
type: File
- name: config__algorithm__variantcaller
type: string
- name: config__algorithm__coverage_interval
type:
- string
- 'null'
- name: metadata__batch
type:
- 'null'
- string
- name: metadata__phenotype
type: string
- name: config__algorithm__validate
type: File
- name: config__algorithm__validate_regions
type: File
- name: genome_build
type: string
- name: genome_resources__aliases__human
type:
- string
- 'null'
- boolean
- name: config__algorithm__tools_off
type:
items: string
type: array
- name: reference__genome_context
type:
items: File
type: array
- name: analysis
type: string
- name: config__algorithm__tools_on
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: config__algorithm__effects
type: string
- name: config__algorithm__variant_regions
type:
- File
- 'null'
- name: genome_resources__aliases__ensembl
type: string
- name: config__algorithm__exclude_regions
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: genome_resources__aliases__snpeff
type: string
- name: regions__sample_callable
type:
- File
- 'null'
- name: config__algorithm__callable_regions
type: File
name: vc_rec
type: record
type: array
requirements:
- class: EnvVarRequirement
envDef:
- envName: MPLCONFIGDIR
envValue: .
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
steps:
- id: get_parallel_regions
in:
- id: batch_rec
source: batch_rec
out:
- id: region_block
run: steps/get_parallel_regions.cwl
- id: variantcall_batch_region
in:
- id: batch_rec
source: batch_rec
- id: region_block_toolinput
source: get_parallel_regions/region_block
out:
- id: vrn_file_region
- id: region_block
run: steps/variantcall_batch_region.cwl
scatter:
- region_block_toolinput
scatterMethod: dotproduct
- id: concat_batch_variantcalls
in:
- id: batch_rec
source: batch_rec
- id: region_block
source: variantcall_batch_region/region_block
- id: vrn_file_region
source: variantcall_batch_region/vrn_file_region
out:
- id: vrn_file
run: steps/concat_batch_variantcalls.cwl
- id: postprocess_variants
in:
- id: batch_rec
source: batch_rec
- id: vrn_file_toolinput
source: concat_batch_variantcalls/vrn_file
out:
- id: vrn_file
run: steps/postprocess_variants.cwl
- id: compare_to_rm
in:
- id: batch_rec
source: batch_rec
- id: vrn_file
source: postprocess_variants/vrn_file
out:
- id: vc_rec
run: steps/compare_to_rm.cwl