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pipeline_v2.cwl
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pipeline_v2.cwl
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cwlVersion: v1.2
$namespaces:
s: https://schema.org/
ogc: http://www.opengis.net/def/media-type/ogc/1.0/
$graph:
- class: Workflow
id: openoil_pipeline
doc: Animation of an oil spill with openoil
inputs:
lat:
type: float
doc: The latitude of the study area
s:name: Input lat float
s:description: The latitude of the study area
s:keywords:
- lat
- float
lon:
type: float
doc: The longitude of the study area
s:name: Input lon float
s:description: The longitude of the study area
s:keywords:
- lon
- float
time:
type: string
doc: The start time of the simulation
s:name: Input time string
s:description: The start time of the simulation. Type dd-mm-yyyy
s:keywords:
- time
- string
# %d-%m-%Y %H:%M:%S
# https://strftime.org/
oiltype:
type: string
doc: The type of the oil to run the simulation
s:name: Input oiltype string
s:description: The type of the oil to run the simulation
s:keywords:
- oiltype
- string
duration:
type: int
doc: The simulation duration
s:name: Input duration int
s:description: The simulation duration
s:keywords:
- duration
- int
steps:
simulation:
run: '#openoil'
in:
lat: lat
lon: lon
time: time
oiltype: oiltype
duration: duration
out:
- simulation
- metadata
animation:
run: '#animation'
in:
file: simulation/simulation
out:
- animation
2stac:
run: '#2stac'
in:
result: animation/animation
metadata: simulation/metadata
out:
- results
outputs:
- id: wf_outputs
outputSource:
- 2stac/results
type:
Directory
# class metadata
s:name: openOil pipeline
s:description: Simulation and animation of oil spill
s:keywords:
- oil spill
- openoil
- opendrift
- animation
s:programmingLanguage: python
s:softwareVersion: 1.0.10
s:sourceOrganization:
- class: s:Organization
s:name: INESCTEC
s:url: https://inesctec.pt
- class: s:Organization
s:name: D.U.TH
s:url: https://env.duth.gr
s:author:
- class: s:Person
s:name: Georgios Sylaios
s:email: gsylaios@env.duth.gr
- class: s:Person
s:name: Nikolaos Kokkos
s:email: nikolaoskokkos@gmail.com
s:contributor:
- class: s:Person
s:name: Miguel Correia
s:email: miguel.r.correia@inesctec.pt
- class: CommandLineTool
baseCommand: openoil
id: openoil
arguments:
- --lat
- valueFrom: $( inputs.lat )
- --lon
- valueFrom: $( inputs.lon )
- --time
- valueFrom: $( inputs.time )
- --oiltype
- valueFrom: $( inputs.oiltype )
- --duration
- valueFrom: $( inputs.duration )
inputs:
lat:
type: float
doc: The latitude of the study area
s:name: Input lat float
s:description: The latitude of the study area
s:keywords:
- lat
- float
lon:
type: float
doc: The longitude of the study area
s:name: Input lon float
s:description: The longitude of the study area
s:keywords:
- lon
- float
time:
type: string
doc: The start time of the simulation
s:name: Input time string
s:description: The start time of the simulation. Type dd-mm-yyyy
s:keywords:
- time
- string
# %d-%m-%Y %H:%M:%S
# https://strftime.org/
oiltype:
type: string
doc: The type of the oil to run the simulation
s:name: Input oiltype string
s:description: The type of the oil to run the simulation
s:keywords:
- oiltype
- string
duration:
type: int
doc: The simulation duration
s:name: Input duration int
s:description: The simulation duration
s:keywords:
- duration
- int
outputs:
simulation:
format: ogc:netcdf
type: File
outputBinding:
glob: "result/simulation.nc"
s:fileFormat: "application/x-netcdf; format=CF-1.4"
metadata:
type: File
outputBinding:
glob: "result/metadata.json"
doc: metadata description
s:fileFormat: "application/json"
requirements:
NetworkAccess:
networkAccess: true
ResourceRequirement: {}
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: iliad-repository.inesctec.pt/openoil_simulation:1.0.11
s:name: openOil model
s:description: Simulation of oil spill
s:keywords:
- oil spill
- openoil
- opendrift
s:programmingLanguage: python
s:softwareVersion: 1.0.11
s:sourceOrganization:
- class: s:Organization
s:name: INESCTEC
s:url: https://inesctec.pt
- class: s:Organization
s:name: D.U.TH
s:url: https://env.duth.gr
s:author:
- class: s:Person
s:name: Georgios Sylaios
s:email: gsylaios@env.duth.gr
- class: s:Person
s:name: Nikolaos Kokkos
s:email: nikolaoskokkos@gmail.com
s:contributor:
- class: s:Person
s:name: Miguel Correia
s:email: miguel.r.correia@inesctec.pt
s:codeRepository: https://pipe-drive.inesctec.pt/cwl/openoil_attached/simulation.cwl
s:dateCreated: "2023-04-21"
- class: CommandLineTool
baseCommand: animation
id: animation
arguments:
- --file
- valueFrom: $( inputs.file )
inputs:
file:
type: File
doc: NetCDF file that contains the simulation
s:name: Input simulation File
s:description: NetCDF file that contains the simulation
s:keywords:
- simulation
- File
s:fileFormat: "application/x-netcdf; format=CF-1.4"
outputs:
animation:
type: File
doc: The animation from the openoil simulation
outputBinding:
glob: "result/animation.gif"
s:fileFormat: "image/gif"
requirements:
NetworkAccess:
networkAccess: true
# EnvVarRequirement:
# envDef:
# # PATH: /srv/conda/envs/openoil/bin:/srv/conda/bin:/srv/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
# HOME: /tmp
ResourceRequirement: {}
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: iliad-repository.inesctec.pt/openoil_animation:1.0.2
s:name: openOil animation
s:description: Animation of oil spill
s:keywords:
- oil spill
- openoil
- opendrift
s:programmingLanguage: python
s:softwareVersion: 1.0.2
s:sourceOrganization:
- class: s:Organization
s:name: INESCTEC
s:url: https://inesctec.pt
- class: s:Organization
s:name: D.U.TH
s:url: https://env.duth.gr
s:author:
- class: s:Person
s:name: Georgios Sylaios
s:email: gsylaios@env.duth.gr
- class: s:Person
s:name: Nikolaos Kokkos
s:email: nikolaoskokkos@gmail.com
s:contributor:
- class: s:Person
s:name: Miguel Correia
s:email: miguel.r.correia@inesctec.pt
s:codeRepository: https://pipe-drive.inesctec.pt/cwl/openoil_attached/animation.cwl
s:dateCreated: "2023-04-21"
- class: CommandLineTool
baseCommand: 2stac
id: 2stac
arguments:
- --result
- valueFrom: $( inputs.result )
- --metadata
- valueFrom: $( inputs.metadata )
inputs:
result:
type: File
doc: The resulting file of the previous model to insert in STAC
s:name: Input result file
s:description: The resulting file of the previous model to insert in STAC
s:keywords:
- result
- File
s:fileFormat: "*/*"
metadata:
type: File
doc: The resulting metadata of the previous model to insert in STAC
s:name: Input metadata file
s:description: The resulting metadata of the previous model to insert in STAC
s:keywords:
- metadata
- File
s:fileFormat: "application/json"
outputs:
results:
outputBinding:
glob: .
type: Directory
doc: STAC output
requirements:
EnvVarRequirement:
envDef:
PATH: /srv/conda/envs/model-env/bin:/srv/conda/bin:/srv/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ResourceRequirement: {}
InlineJavascriptRequirement: {}
DockerRequirement:
dockerPull: iliad-repository.inesctec.pt/2stac:1.0.0
s:name: 2Stac
s:description: Transform the result into a STAC
s:keywords:
- stac
- metadata
s:programmingLanguage: python
s:softwareVersion: 1.0.10
s:sourceOrganization:
- class: s:Organization
s:name: INESCTEC
s:url: https://inesctec.pt
- class: s:Organization
s:name: D.U.TH
s:url: https://env.duth.gr
s:author:
- class: s:Person
s:name: Georgios Sylaios
s:email: gsylaios@env.duth.gr
- class: s:Person
s:name: Nikolaos Kokkos
s:email: nikolaoskokkos@gmail.com
s:contributor:
- class: s:Person
s:name: Miguel Correia
s:email: miguel.r.correia@inesctec.pt
s:codeRepository: https://pipe-drive.inesctec.pt/cwl/openoil_attached/2stac.cwl
s:dateCreated: "2023-04-21"
s:softwareVersion: 1.0.10
s:name: openOil model
s:description: Simulation of oil spill