/
etl_http.cwl
335 lines (312 loc) · 7.98 KB
/
etl_http.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
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
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/amplicon_kit.yml
- $import: ../../tools/capture_kit.yml
- $import: ../../tools/readgroup.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
- id: bam_name
type: string
- id: gdc_token
type: File
- id: job_uuid
type: string
- id: amplicon_kit_set_uuid_list
type:
type: array
items: ../../tools/amplicon_kit.yml#amplicon_kit_set_uuid
- id: capture_kit_set_uuid_list
type:
type: array
items: ../../tools/capture_kit.yml#capture_kit_set_uuid
- id: readgroup_fastq_pe_uuid_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_pe_uuid
- id: readgroup_fastq_se_uuid_list
type:
type: array
items: ../../tools/readgroup.yml#readgroup_fastq_se_uuid
- id: readgroups_bam_uuid_list
type:
type: array
items: ../../tools/readgroup.yml#readgroups_bam_uuid
- id: known_snp_gdc_id
type: string
- id: known_snp_file_size
type: long
- id: known_snp_index_gdc_id
type: string
- id: known_snp_index_file_size
type: long
- id: reference_amb_gdc_id
type: string
- id: reference_amb_file_size
type: long
- id: reference_ann_gdc_id
type: string
- id: reference_ann_file_size
type: long
- id: reference_bwt_gdc_id
type: string
- id: reference_bwt_file_size
type: long
- id: reference_dict_gdc_id
type: string
- id: reference_dict_file_size
type: long
- id: reference_fa_gdc_id
type: string
- id: reference_fa_file_size
type: long
- id: reference_fai_gdc_id
type: string
- id: reference_fai_file_size
type: long
- id: reference_pac_gdc_id
type: string
- id: reference_pac_file_size
type: long
- id: reference_sa_gdc_id
type: string
- id: reference_sa_file_size
type: long
- id: run_markduplicates
type:
type: array
items: long
- id: thread_count
type: long
outputs:
- id: bam
type: File
outputSource: transform/output_bam
- id: sqlite
type: File
outputSource: transform/sqlite
steps:
- id: extract_readgroup_fastq_pe
run: extract_readgroup_fastq_pe_http.cwl
scatter: readgroup_fastq_pe_uuid
in:
- id: readgroup_fastq_pe_uuid
source: readgroup_fastq_pe_uuid_list
- id: gdc_token
source: gdc_token
out:
- id: output
- id: extract_readgroup_fastq_se
run: extract_readgroup_fastq_se_http.cwl
scatter: readgroup_fastq_se_uuid
in:
- id: readgroup_fastq_se_uuid
source: readgroup_fastq_se_uuid_list
- id: gdc_token
source: gdc_token
out:
- id: output
- id: extract_readgroups_bam
run: extract_readgroups_bam_http.cwl
scatter: readgroups_bam_uuid
in:
- id: readgroups_bam_uuid
source: readgroups_bam_uuid_list
- id: gdc_token
source: gdc_token
out:
- id: output
- id: extract_amplicon_kits
run: extract_amplicon_kit_http.cwl
scatter: amplicon_kit_set_uuid
in:
- id: amplicon_kit_set_uuid
source: amplicon_kit_set_uuid_list
- id: gdc_token
source: gdc_token
out:
- id: output
- id: extract_capture_kits
run: extract_capture_kit_http.cwl
scatter: capture_kit_set_uuid
in:
- id: capture_kit_set_uuid
source: capture_kit_set_uuid_list
- id: gdc_token
source: gdc_token
out:
- id: output
- id: extract_known_snp
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: known_snp_gdc_id
- id: file_size
source: known_snp_file_size
out:
- id: output
- id: extract_known_snp_index
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: known_snp_index_gdc_id
- id: file_size
source: known_snp_index_file_size
out:
- id: output
- id: extract_reference_amb
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_amb_gdc_id
- id: file_size
source: reference_amb_file_size
out:
- id: output
- id: extract_reference_ann
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_ann_gdc_id
- id: file_size
source: reference_ann_file_size
out:
- id: output
- id: extract_reference_bwt
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_bwt_gdc_id
- id: file_size
source: reference_bwt_file_size
out:
- id: output
- id: extract_reference_dict
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_dict_gdc_id
- id: file_size
source: reference_dict_file_size
out:
- id: output
- id: extract_reference_fa
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_fa_gdc_id
- id: file_size
source: reference_fa_file_size
out:
- id: output
- id: extract_reference_fai
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_fai_gdc_id
- id: file_size
source: reference_fai_file_size
out:
- id: output
- id: extract_reference_pac
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_pac_gdc_id
- id: file_size
source: reference_pac_file_size
out:
- id: output
- id: extract_reference_sa
run: ../../tools/gdc_get_object.cwl
in:
- id: gdc_token
source: gdc_token
- id: gdc_uuid
source: reference_sa_gdc_id
- id: file_size
source: reference_sa_file_size
out:
- id: output
- id: root_fasta_files
run: ../../tools/root_fasta_dnaseq.cwl
in:
- id: fasta
source: extract_reference_fa/output
- id: fasta_amb
source: extract_reference_amb/output
- id: fasta_ann
source: extract_reference_ann/output
- id: fasta_bwt
source: extract_reference_bwt/output
- id: fasta_dict
source: extract_reference_dict/output
- id: fasta_fai
source: extract_reference_fai/output
- id: fasta_pac
source: extract_reference_pac/output
- id: fasta_sa
source: extract_reference_sa/output
out:
- id: output
- id: root_known_snp_files
run: ../../tools/root_vcf.cwl
in:
- id: vcf
source: extract_known_snp/output
- id: vcf_index
source: extract_known_snp_index/output
out:
- id: output
- id: transform
run: transform.cwl
in:
- id: bam_name
source: bam_name
- id: job_uuid
source: job_uuid
- id: amplicon_kit_set_file_list
source: extract_amplicon_kits/output
- id: capture_kit_set_file_list
source: extract_capture_kits/output
- id: readgroup_fastq_pe_file_list
source: extract_readgroup_fastq_pe/output
- id: readgroup_fastq_se_file_list
source: extract_readgroup_fastq_se/output
- id: readgroups_bam_file_list
source: extract_readgroups_bam/output
- id: known_snp
source: root_known_snp_files/output
- id: reference_sequence
source: root_fasta_files/output
- id: run_markduplicates
source: run_markduplicates
- id: thread_count
source: thread_count
out:
- id: output_bam
- id: sqlite