cwlVersion: v1.2 $namespaces: s: https://schema.org/ cwltool: http://commonwl.org/cwltool# $graph: - class: Workflow id: wp6tools_pipeline doc: wp6 workflow inputs: latitude: type: float label: Latitude doc: The latitude of the study area longitude: type: float label: Longitude doc: The longitude of the study area radius: type: float label: radius doc: The radius of the study area type: type: string url: type: string samples: type: string time: type: string minutes: type: string frames: type: string density: type: string output-format: type: string? default: stac template_file: type: string cesium_mappings: type: string unity_mappings: type: string endpoint: type: string? doc: S3 storage endpoint region: type: string? doc: S3 storage region access_key: type: string? doc: S3 storage access_key secret_key: type: string? doc: S3 storage secret_key session_token: type: string? doc: S3 storage region bucket: type: string? doc: S3 storage bucket base_path: type: string? doc: S3 storage final directory name default: "wp6tools_virtual_choreographies_pipeline" steps: # step_point2bbox: # run: 'https://pipe-drive.inesctec.pt/application-packages/tools/point2bbox/point2bbox_2_0_0.cwl#point2bbox' # in: # lat: latitude # lon: longitude # radius: radius # out: # - lon_min # - lon_max # - lat_min # - lat_max # step_bathymetry: # run: 'https://pipe-drive.inesctec.pt/application-packages/tools/bathymetry-forth/bathymetry_forth_2_0_0.cwl#bathymetry' # in: # lon_min: step_point2bbox/lon_min # lon_max: step_point2bbox/lon_max # lat_min: step_point2bbox/lat_min # lat_max: step_point2bbox/lat_max # out: # - result # - metadata step_generate_model: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/wp6tools-generate-model/wp6tools_generate_model_0_2_0.cwl#generate-model' in: type: type url: url latitude: latitude longitude: longitude radius: radius samples: samples time: time minutes: minutes out: - result step_extract_particles: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/wp6tools-extract-particles/wp6tools_extract_particles_0_2_0.cwl#extract-particles' in: input-file: step_generate_model/result output-format: default: "stac" projection-function: default: "none" projection-resolution: default: "none" latitude-variable: default: "lat" longitude-variable: default: "lon" time-variable: default: "time" out: - result step_crop_frames: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/wp6tools-crop-frames/wp6tools_crop_frames_0_2_0.cwl#crop-frames' in: particles: step_extract_particles/result frames: frames out: - result step_generate_contours: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/wp6tools-generate-contours/wp6tools_generate_contours_0_2_0.cwl#generate-contours' in: cropped: step_crop_frames/result density: density output-format: output-format out: - result dir2files: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/dir2files/dir2files_0_2_0.cwl#dir2files' in: input_dir: step_generate_contours/result out: - output_files json_append: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/json-append/json_append_wp6tools_pipeline_0_2_0.cwl#json_append_wp6tools_pipeline' in: files: dir2files/output_files out: - result step_virtual_choreographies_generator: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/virtual-choreographies-generator/virtual_choreographies_generator_0_2_0.cwl#virtual-choreographies-generator' in: dataset: json_append/result template_url: template_file out: - vc step_virtual_choreographies_unity_plugin: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/virtual-choreographies-unity-plugin/virtual_choreographies_unity_plugin_0_2_0.cwl#virtual-choreographies-unity-plugin' in: vc: step_virtual_choreographies_generator/vc mappings_url: unity_mappings out: - platform_choreography step_virtual_choreographies_cesium_plugin: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/virtual-choreographies-cesium-plugin/virtual_choreographies_cesium_plugin_0_2_0.cwl#virtual-choreographies-cesium-plugin' in: vc: step_virtual_choreographies_generator/vc mappings_url: cesium_mappings out: - platform_choreography step_metadata_2stact2: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/wp6tools-metadata-2stac2/wp6tools_metadata_2stac2_0_2_0.cwl#metadata-2stact2' in: latitude: latitude longitude: longitude radius: radius frames: frames time: time out: - result step_2stac2: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/2stac2/2stac2_wp6tools_pipeline_0_2_0.cwl#2stac2_wp6tools_pipeline' in: unity_choreography: step_virtual_choreographies_cesium_plugin/platform_choreography cesium_choreography: step_virtual_choreographies_unity_plugin/platform_choreography metadata: step_metadata_2stact2/result out: - stac_result step_2s3: run: 'https://pipe-drive.inesctec.pt/application-packages/tools/2s3/2s3_0_2_0.cwl#2s3' when: $(inputs.endpoint != null && inputs.endpoint != "") in: region: region endpoint: endpoint access_key: access_key secret_key: secret_key session_token: session_token bucket: bucket directory: step_2stac2/stac_result out: - base_path outputs: - id: wf_output_2stac2 outputSource: - step_2stac2/stac_result type: Directory # - id: wf_output_bathymetry # outputSource: # - step_bathymetry/result # type: # File hints: "cwltool:Secrets": secrets: [access_key,secret_key,session_token] requirements: InlineJavascriptRequirement: {} s:name: wp6tools_pipeline s:description: wp6 tools workflow to generate contours s:keywords: - oil spill - opendrift - choreographies - virtual choreographies - 2s3 - wp6 - tools s:softwareVersion: 0.2.0 s:sourceOrganization: class: s:Organization s:name: INESCTEC s:url: https://inesctec.pt s:address: class: s:PostalAddress s:addressCountry: PT s:author: class: s:Person s:name: Miguel Correia s:email: miguel.r.correia@inesctec.pt s:codeRepository: https://pipe-drive.inesctec.pt/application-packages/workflows/wp6tools-inesctec/wp6tools_inesctec_REF_0_2_0.cwl s:dateCreated: "2025-02-10T11:27:50Z"