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vegetation.wf.yaml
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vegetation.wf.yaml
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$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
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
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
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
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
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