-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathvegetation.wf_new_stagein.yaml
287 lines (287 loc) · 8 KB
/
vegetation.wf_new_stagein.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
$graph:
- class: Workflow
doc: Main stage manager
id: stage-manager
inputs:
aoi:
doc: Area of interest in WKT
id: aoi
label: Area of interest
type: string
input_reference:
doc: EO product for vegetation index
id: input_reference
label: EO product for vegetation index
type: string[]
input_reference2:
doc: EO product for vegetation index
id: input_reference2
label: EO product for vegetation index
type: string[]
job:
doc: the job doc
label: the job doc
type: string
outputfile:
doc: the outputfile doc
label: the outputfile doc
type: string
parameter_A:
doc: EO product for vegetation index
label: EO product for vegetation index
type: string[]
parameter_B:
doc: EO product for vegetation index
label: EO product for vegetation index
type: string[]
store_apikey:
doc: the store_apikey doc
label: the store_apikey doc
type: string
store_host:
doc: the store_host doc
label: the store_host doc
type: string
store_username:
doc: the store_username doc
label: the store_username doc
type: string
label: theStage
outputs:
wf_outputs:
outputSource:
- node_stage_out/wf_outputs_out
type:
items: Directory
type: array
requirements:
ScatterFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
steps:
node_stage_in:
in:
input_reference: input_reference
parameter_A: parameter_A
parameter_B: parameter_B
out:
- input_reference_out
run:
arguments:
- position: 1
prefix: -t
valueFrom: ./
baseCommand: stage-in
class: CommandLineTool
hints:
DockerRequirement:
dockerPull: eoepca/stage-in:0.2
id: stagein
inputs:
input_reference:
inputBinding:
position: 2
type: string
parameter_A:
doc: EO product for vegetation index
label: EO product for vegetation index
type: string[]
parameter_B:
doc: EO product for vegetation index
label: EO product for vegetation index
type: string[]
outputs:
input_reference_out:
outputBinding:
glob: .
type: Directory
requirements:
EnvVarRequirement:
envDef:
PATH: /opt/anaconda/envs/env_stagein/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ResourceRequirement: {}
scatter: input_reference
scatterMethod: dotproduct
node_stage_in_1:
in:
input_reference2: input_reference2
parameter_A: parameter_A
parameter_B: parameter_B
out:
- input_reference2_out
run:
arguments:
- position: 1
prefix: -t
valueFrom: ./
baseCommand: stage-in
class: CommandLineTool
hints:
DockerRequirement:
dockerPull: eoepca/stage-in:0.2
id: stagein
inputs:
input_reference2:
inputBinding:
position: 2
type: string
parameter_A:
doc: EO product for vegetation index
label: EO product for vegetation index
type: string[]
parameter_B:
doc: EO product for vegetation index
label: EO product for vegetation index
type: string[]
outputs:
input_reference2_out:
outputBinding:
glob: .
type: Directory
requirements:
EnvVarRequirement:
envDef:
PATH: /opt/anaconda/envs/env_stagein/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ResourceRequirement: {}
scatter: input_reference2
scatterMethod: dotproduct
node_stage_out:
in:
job: job
outputfile: outputfile
store_apikey: store_apikey
store_host: store_host
store_username: store_username
wf_outputs: on_stage/wf_outputs
out:
- wf_outputs_out
run:
baseCommand: stage-out
class: CommandLineTool
hints:
DockerRequirement:
dockerPull: eoepca/stage-out:0.2
inputs:
job:
doc: the job doc
inputBinding:
position: 1
prefix: --job
label: the job doc
type: string
outputfile:
doc: the outputfile doc
inputBinding:
position: 5
prefix: --outputfile
label: the outputfile doc
type: string
store_apikey:
doc: the store_apikey doc
inputBinding:
position: 4
prefix: --store-apikey
label: the store_apikey doc
type: string
store_host:
doc: the store_host doc
inputBinding:
position: 2
prefix: --store-host
label: the store_host doc
type: string
store_username:
doc: the store_username doc
inputBinding:
position: 3
prefix: --store-username
label: the store_username doc
type: string
wf_outputs:
inputBinding:
position: 6
type: Directory[]
outputs:
wf_outputs_out:
outputBinding:
glob: .
type: Directory[]
requirements:
EnvVarRequirement:
envDef:
PATH: /opt/anaconda/envs/env_stageout/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ResourceRequirement: {}
on_stage:
in:
aoi: aoi
input_reference: node_stage_in/input_reference_out
input_reference2: node_stage_in_1/input_reference2_out
out:
- wf_outputs
run: '#vegetation-index'
- baseCommand: vegetation-index
class: CommandLineTool
hints:
DockerRequirement:
dockerPull: eoepca/vegetation-index:0.2
id: clt
inputs:
inp1:
inputBinding:
position: 1
prefix: --input_reference
type: Directory
inp2:
inputBinding:
position: 2
prefix: --aoi
type: string
outputs:
results:
outputBinding:
glob: .
type: Directory
requirements:
EnvVarRequirement:
envDef:
PATH: /opt/anaconda/envs/env_vi/bin:/opt/anaconda/envs/env_vi/bin:/home/fbrito/.nvm/versions/node/v10.21.0/bin:/opt/anaconda/envs/notebook/bin:/opt/anaconda/bin:/usr/share/java/maven/bin:/opt/anaconda/bin:/opt/anaconda/envs/notebook/bin:/opt/anaconda/bin:/usr/share/java/maven/bin:/opt/anaconda/bin:/opt/anaconda/condabin:/opt/anaconda/envs/notebook/bin:/opt/anaconda/bin:/usr/lib64/qt-3.3/bin:/usr/share/java/maven/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/fbrito/.local/bin:/home/fbrito/bin:/home/fbrito/.local/bin:/home/fbrito/bin
PREFIX: /opt/anaconda/envs/env_vi
ResourceRequirement: {}
stderr: std.err
stdout: std.out
- class: Workflow
doc: Vegetation index processor, the greatest
id: vegetation-index
inputs:
aoi:
doc: Area of interest in WKT
label: Area of interest
type: string
input_reference:
doc: EO product for vegetation index
label: EO product for vegetation index
type: Directory[]
input_reference2:
doc: EO product for vegetation index
label: EO product for vegetation index
type: Directory[]
label: Vegetation index
outputs:
- id: wf_outputs
outputSource:
- node_1/results
type:
items: Directory
type: array
requirements:
- class: ScatterFeatureRequirement
steps:
node_1:
in:
inp1: input_reference
inp2: aoi
out:
- results
run: '#clt'
scatter: inp1
scatterMethod: dotproduct
cwlVersion: v1.0