{ "type":"FeatureCollection", "features":[ { "geometry":{ "coordinates":[ [ [ -180.0, -90.0 ], [ 180.0, -90.0 ], [ 180.0, 90.0 ], [ -180.0, 90.0 ], [ -180.0, -90.0 ] ] ], "type":"Polygon" }, "type":"Feature", "properties":{ "outputs":[ { "id":"pipeline_output", "type":"Directory" } ], "programming_language":"python", "keywords":[ "oil spill", "SAR", "Sentinel-1", "deep learning", "object detection" ], "inputs":[ { "doc":"Path to directory as a string where to find input files and where to store outputs", "id":"use_case_directory", "type":"string" }, { "doc":"Bounding box for image search", "id":"bbox", "type":"string?" }, { "doc":"Start date for data search", "id":"start_date", "type":"string?" }, { "doc":"Time interval (n of days) for data search", "id":"time_interval", "type":"int?" }, { "doc":"End date for data search", "id":"end_date", "type":"string?" }, { "doc":"Enable verbose logging", "id":"verbose", "type":"boolean?" }, { "doc":"Enable debug mode", "id":"debug", "type":"boolean?" }, { "id":"asf_username", "type":"string" }, { "id":"asf_password", "type":"string" }, { "default":"NO", "id":"cont_slick", "type":"string" }, { "default":"NO", "id":"sat", "type":"string" }, { "default":24.069118741783797, "id":"min_lon", "type":"float" }, { "default":24.990341065648366, "id":"max_lon", "type":"float" }, { "default":35.09663196120557, "id":"min_lat", "type":"float" }, { "default":35.990635331961315, "id":"max_lat", "type":"float" }, { "default":35.496, "id":"lat_point", "type":"float" }, { "default":-15.7433, "id":"lon_point", "type":"float" }, { "default":"2024-11-07T06:22:00Z", "id":"date_spill", "type":"string" }, { "id":"spill_dur", "type":"string" }, { "id":"spill_res", "type":"string" }, { "default":1.4, "id":"spill_tons", "type":"float" }, { "id":"username", "type":"string" }, { "id":"password", "type":"string" }, { "id":"ftp_server", "type":"string" }, { "id":"ftp_user", "type":"string" }, { "id":"ftp_password", "type":"string" }, { "id":"remote_dir", "type":"string" } ], "description":"Sentinel-1 Oil Spill Object Detection and Forecasting Pipeline using Deep Learning tecniques", "maintainer":null, "sdPublisher":[ { "name":"Application Package Registry", "class":"Organization", "url":"https://iliad-registry.inesctec.pt" } ], "temporal_coverage":"2014-01-01T00:00:00Z/", "contributor":null, "spatial_coverage":{ "geo":{ "box":"-90 -180 90 180" }, "class":"schema:GeoShape" }, "id":"oilspill_pipeline_medslik_146", "software_version":"1.0.0", "class":"Workflow", "latest":true, "identifier":"urn:apkg:workflow:forth:gr:oilspill_pipeline_medslik_146:1.0.0", "citation":"", "date_created":"2024-12-01", "author":[ { "name":"Sabrina Outmani", "email":"outmani@meeo.it" }, { "name":"Noemi Fazzini", "email":"fazzini@meeo.it" }, { "name":"Antonios Parasyris", "email":"antonisparasyris@iacm.forth.gr" } ], "sdDatePublished":"2025-06-11T14:23:15.877984Z", "url":"https://iliad-registry.inesctec.pt/collections/apkg/items/urn:apkg:workflow:forth:gr:oilspill_pipeline_medslik_146:1.0.0?f=cwl", "license":"https://opensource.org/licenses/MIT", "code_repository":null, "source_organization":[ { "address":{ "address_country":"IT" }, "name":"MEEO SRL", "url":"https://meeo.it/" }, { "address":{ "address_country":"GR" }, "name":"FORTH", "url":"https://www.forth.gr/" }, { "address":{ "address_country":"PT" }, "name":"INESCTEC", "url":"https://inesctec.pt" } ], "name":"Sentinel-1 Oil Spill Object Detection Pipeline 1-2-3-4 and Medslik Forecasting", "cwl":"cwlVersion: v1.2\n$namespaces:\n s: https://schema.org/\n cwltool: http://commonwl.org/cwltool\n$graph:\n- class: Workflow\n id: oilspill_pipeline_medslik_146\n doc: Oil Spill Detection and Analysis Pipeline 1-2-3-4, Medslik forecasting\n inputs:\n use_case_directory:\n doc: Path to directory as a string where to find input files and where to store\n outputs\n type: string\n bbox:\n doc: Bounding box for image search\n type: string?\n start_date:\n doc: Start date for data search\n type: string?\n time_interval:\n doc: Time interval (n of days) for data search\n type: int?\n end_date:\n doc: End date for data search\n type: string?\n verbose:\n doc: Enable verbose logging\n type: boolean?\n debug:\n doc: Enable debug mode\n type: boolean?\n asf_username:\n type: string\n asf_password:\n type: string\n cont_slick:\n type: string\n default: 'NO'\n sat:\n type: string\n default: 'NO'\n min_lon:\n type: float\n default: 24.069118741783797\n max_lon:\n type: float\n default: 24.990341065648366\n min_lat:\n type: float\n default: 35.09663196120557\n max_lat:\n type: float\n default: 35.990635331961315\n lat_point:\n type: float\n default: 35.496\n lon_point:\n type: float\n default: -15.7433\n date_spill:\n type: string\n default: '2024-11-07T06:22:00Z'\n spill_dur:\n type: string\n spill_res:\n type: string\n spill_tons:\n type: float\n default: 1.4\n username:\n type: string\n password:\n type: string\n ftp_server:\n type: string\n ftp_user:\n type: string\n ftp_password:\n type: string\n remote_dir:\n type: string\n steps:\n step_data_search:\n in:\n bbox: bbox\n use_case_directory: use_case_directory\n start_date: start_date\n time_interval: time_interval\n end_date: end_date\n verbose: verbose\n debug: debug\n asf_username: asf_username\n asf_password: asf_password\n run: '#datasearch_tool'\n out:\n - results\n - sentinel_list\n step_preprocessing:\n in:\n use_case_directory: step_data_search/results\n sentinel_list: step_data_search/sentinel_list\n verbose: verbose\n debug: debug\n run: '#preprocessing_tool'\n out:\n - results\n - db_list\n step_object_detection:\n in:\n use_case_directory: step_preprocessing/results\n db_list: step_preprocessing/db_list\n verbose: verbose\n debug: debug\n run: '#object_detection_tool'\n out:\n - results\n - png_output_path\n - csv_output_path\n step_segmentation:\n in:\n use_case_directory: step_object_detection/results\n sentinel_list: step_data_search/sentinel_list\n png_output_path: step_object_detection/png_output_path\n csv_output_path: step_object_detection/csv_output_path\n verbose: verbose\n debug: debug\n run: '#segmentation_tool'\n out:\n - results\n step_medslik:\n in:\n cont_slick: cont_slick\n sat: sat\n min_lon: min_lon\n max_lon: max_lon\n min_lat: min_lat\n max_lat: max_lat\n lat_point: lat_point\n lon_point: lon_point\n date_spill: date_spill\n spill_dur: spill_dur\n spill_res: spill_res\n spill_tons: spill_tons\n username: username\n password: password\n ftp_server: ftp_server\n ftp_password: ftp_password\n ftp_user: ftp_user\n remote_dir: remote_dir\n results: step_segmentation/results\n run: '#medslik_tool'\n out:\n - results\n outputs:\n pipeline_output:\n type: Directory\n outputSource: step_medslik/results\n s:name: Sentinel-1 Oil Spill Object Detection Pipeline 1-2-3-4 and Medslik Forecasting\n s:description: Sentinel-1 Oil Spill Object Detection and Forecasting Pipeline using\n Deep Learning tecniques\n s:keywords:\n - oil spill\n - SAR\n - Sentinel-1\n - deep learning\n - object detection\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n s:sourceOrganization:\n - class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: INESCTEC\n s:url: https://inesctec.pt\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:author:\n - class: s:Person\n s:email: outmani@meeo.it\n s:name: Sabrina Outmani\n - class: s:Person\n s:email: fazzini@meeo.it\n s:name: Noemi Fazzini\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n s:dateCreated: '2024-12-01'\n s:temporalCoverage: 2014-01-01T00:00:00Z/\n s:spatialCoverage:\n class: s:GeoShape\n s:box: -90 -180 90 180\n s:license: https://opensource.org/licenses/MIT\n s:citation: ''\n s:sdDatePublished: '2025-06-11T14:23:15.877984Z'\n s:sdPublisher:\n class: Organization\n name: Application Package Registry\n url: https://iliad-registry.inesctec.pt\n s:identifier: urn:apkg:workflow:forth:gr:oilspill_pipeline_medslik_146:1.0.0\n- class: CommandLineTool\n id: datasearch_tool\n baseCommand:\n - /srv/miniconda3/envs/oilspill001/bin/python\n - -m\n - oilspill001.main\n arguments:\n - valueFrom: $(inputs.bbox)\n prefix: --bbox\n - --use-case-directory\n - valueFrom: $(inputs.use_case_directory)\n - --start-date\n - valueFrom: $(inputs.start_date)\n - valueFrom: $(inputs.time_interval)\n prefix: --time-interval\n - valueFrom: $(inputs.end_date)\n prefix: --end-date\n - valueFrom: $(inputs.verbose)\n prefix: --verbose\n - valueFrom: $(inputs.debug)\n prefix: --debug\n - --asf-username\n - valueFrom: $(inputs.asf_username)\n - --asf-password\n - valueFrom: $(inputs.asf_password)\n inputs:\n bbox:\n type: string?\n doc: Bounding box for image search\n s:name: Bounding Box\n s:description: Optional bounding box to restrict the image search.\n use_case_directory:\n type: string\n doc: Directory where to find input files and store outputs\n s:name: Use Case Directory\n s:description: Directory to store input and output files.\n start_date:\n type: string?\n doc: Start date for data search\n s:name: Start Date\n s:description: The start date to search for data.\n time_interval:\n type: int?\n doc: Time interval (n of days) for data search\n s:name: Time Interval\n s:description: Number of days for the data search interval.\n end_date:\n type: string?\n doc: End date for data search\n s:name: End Date\n s:description: The end date for data search (optional).\n verbose:\n type: boolean?\n doc: Enable verbose logging\n s:name: Verbose Logging\n s:description: Flag to enable verbose logging.\n debug:\n type: boolean?\n doc: Enable debug mode\n s:name: Debug Mode\n s:description: Flag to enable debug mode for additional logging.\n asf_username:\n type: string\n doc: Username for ASF\n s:name: ASF Username\n s:description: Username for the ASF platform authentication.\n asf_password:\n type: string\n doc: Password for ASF\n s:name: ASF Password\n s:description: Password for the ASF platform authentication.\n outputs:\n results:\n type: Directory\n outputBinding:\n glob: $(inputs.use_case_directory)\n sentinel_list:\n type: File\n outputBinding:\n glob: $(inputs.use_case_directory)/raw_sentinel/sentinel_paths.txt\n requirements:\n - class: DockerRequirement\n dockerPull: registry.services.meeo.it/outmani/iliad_oil_spill_pilot/oilspill001:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: InlineJavascriptRequirement\n s:name: Sentinel-1 Oil Spill Detection Data Search\n s:description: ASF search for SAR images from Sentinel-1\n s:keywords:\n - oil spill\n - SAR\n - Sentinel-1\n - ASF\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n s:sourceOrganization:\n - class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: INESCTEC\n s:url: https://inesctec.pt\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:author:\n - class: s:Person\n s:name: Sabrina Outmani\n s:email: outmani@meeo.it\n - class: s:Person\n s:name: Noemi Fazzini\n s:email: fazzini@meeo.it\n s:dateCreated: '2024-12-01'\n s:temporalCoverage: 2014-01-01T00:00:00Z/\n s:spatialCoverage:\n class: s:GeoShape\n s:box: -90 -180 90 180\n s:codeRepository: null\n s:license: https://opensource.org/licenses/MIT\n s:citation: ''\n- class: CommandLineTool\n id: preprocessing_tool\n baseCommand:\n - /srv/miniconda3/envs/oilspill002/bin/python\n - -m\n - oilspill002.main\n arguments:\n - --use-case-directory\n - valueFrom: $(inputs.use_case_directory.path)\n - --sentinel-list\n - valueFrom: $(inputs.sentinel_list.path)\n - valueFrom: '${ return inputs.verbose ? ''--verbose'' : ''''; }\n\n '\n shellQuote: false\n - valueFrom: '${ return inputs.debug ? ''--debug'' : ''''; }\n\n '\n shellQuote: false\n inputs:\n use_case_directory:\n type: Directory\n doc: Directory where to find input files and store outputs\n s:name: Use Case Directory\n s:description: Directory to store input and output files.\n sentinel_list:\n type: File\n doc: .txt file containing sentinel data paths (output from application package\n 1) - sentinel_paths.txt\n s:name: Sentinel list file\n s:description: Text file containing sentinel data paths (output from application\n package 1) - sentinel_paths.txt\n verbose:\n type: boolean?\n doc: Enable verbose logging\n s:name: Verbose Logging\n s:description: Flag to enable verbose logging.\n debug:\n type: boolean?\n doc: Enable debug mode\n s:name: Debug Mode\n s:description: Flag to enable debug mode for additional logging.\n outputs:\n results:\n type: Directory\n outputBinding:\n glob: $(inputs.use_case_directory.path)\n db_list:\n type: File\n outputBinding:\n glob: $(inputs.use_case_directory.path)/intermediate_dir/db_paths.txt\n requirements:\n - class: InitialWorkDirRequirement\n listing:\n - entryname: $(inputs.use_case_directory.basename)\n entry: $(inputs.use_case_directory)\n writable: true\n - class: DockerRequirement\n dockerPull: registry.services.meeo.it/outmani/iliad_oil_spill_pilot/oilspill002:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: InlineJavascriptRequirement\n s:name: Sentinel-1 Oil Spill Detection Pipeline Preprocessing Tool\n s:description: Pre-processing of SAR images from Sentinel-1\n s:keywords:\n - oil spill\n - SAR\n - Sentinel-1\n - snappy\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n s:sourceOrganization:\n - class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: INESCTEC\n s:url: https://inesctec.pt\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:author:\n - class: s:Person\n s:email: outmani@meeo.it\n s:name: Sabrina Outmani\n - class: s:Person\n s:email: fazzini@meeo.it\n s:name: Noemi Fazzini\n s:dateCreated: '2024-12-01'\n s:temporalCoverage: 2014-01-01T00:00:00Z/\n s:spatialCoverage:\n class: s:GeoShape\n s:box: -90 -180 90 180\n s:license: https://opensource.org/licenses/MIT\n s:citation: ''\n- class: CommandLineTool\n id: object_detection_tool\n baseCommand:\n - /srv/miniconda3/envs/oilspill003/bin/python\n - -m\n - oilspill003.main\n arguments:\n - --use-case-directory\n - valueFrom: $(inputs.use_case_directory.path)\n - --db-list\n - valueFrom: $(inputs.db_list.path)\n - valueFrom: '${ return inputs.range ? ''--range'' : ''''; }\n\n '\n shellQuote: false\n - valueFrom: '${ return inputs.verbose ? ''--verbose'' : ''''; }\n\n '\n shellQuote: false\n - valueFrom: '${ return inputs.debug ? ''--debug'' : ''''; }\n\n '\n shellQuote: false\n inputs:\n use_case_directory:\n type: Directory\n doc: Directory where to find input files and store outputs\n s:name: Use Case Directory\n s:description: Directory to store input and output files.\n db_list:\n type: File\n doc: .txt file containing paths of preprocessed sentinel-1 images (output from\n application package 2) - db_paths.txt\n s:name: Db list file\n s:description: .txt file containing paths of preprocessed sentinel-1 images\n (output from application package 2) - db_paths.txt\n range:\n type: string?\n doc: optional range 0-100 for image contrast enhancement\n s:name: Range\n s:description: optional range 0-100 for image contrast enhancement\n verbose:\n type: boolean?\n doc: Enable verbose logging\n s:name: Verbose Logging\n s:description: Flag to enable verbose logging.\n debug:\n type: boolean?\n doc: Enable debug mode\n s:name: Debug Mode\n s:description: Flag to enable debug mode for additional logging.\n outputs:\n results:\n type: Directory\n outputBinding:\n glob: $(inputs.use_case_directory.path)\n png_output_path:\n type: File\n outputBinding:\n glob: $(inputs.use_case_directory.path)/intermediate_dir/png_paths.txt\n csv_output_path:\n type: File\n outputBinding:\n glob: $(inputs.use_case_directory.path)/intermediate_dir/csv_paths.txt\n requirements:\n - class: InitialWorkDirRequirement\n listing:\n - entryname: $(inputs.use_case_directory.basename)\n entry: $(inputs.use_case_directory)\n writable: true\n - class: DockerRequirement\n dockerPull: registry.services.meeo.it/outmani/iliad_oil_spill_pilot/oilspill003:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: InlineJavascriptRequirement\n s:name: Sentinel-1 Oil Spill Object Detection Pipeline\n s:description: Deep learning model designed for detecting oil spill signals globally\n from pre-processedSAR images from Sentinel-1.\n s:keywords:\n - oil spill\n - SAR\n - Sentinel-1\n - deep learning\n - object detection\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n s:sourceOrganization:\n - class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: INESCTEC\n s:url: https://inesctec.pt\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:author:\n - class: s:Person\n s:email: outmani@meeo.it\n s:name: Sabrina Outmani\n - class: s:Person\n s:email: fazzini@meeo.it\n s:name: Noemi Fazzini\n s:dateCreated: '2024-12-01'\n s:temporalCoverage: 2014-01-01T00:00:00Z/\n s:spatialCoverage:\n class: s:GeoShape\n s:box: -90 -180 90 180\n s:license: https://opensource.org/licenses/MIT\n s:citation: ''\n- class: CommandLineTool\n id: segmentation_tool\n baseCommand:\n - /srv/miniconda3/envs/oilspill004/bin/python\n - -m\n - oilspill004.main\n arguments:\n - --use-case-directory\n - valueFrom: $(inputs.use_case_directory.path)\n - --sentinel-list\n - valueFrom: $(inputs.sentinel_list.path)\n - --png-output-path\n - valueFrom: $(inputs.png_output_path.path)\n - --csv-output-path\n - valueFrom: $(inputs.csv_output_path.path)\n - valueFrom: '${ return inputs.delete ? ''--delete'' : ''''; }\n\n '\n shellQuote: false\n - valueFrom: '${ return inputs.verbose ? ''--verbose'' : ''''; }\n\n '\n shellQuote: false\n - valueFrom: '${ return inputs.debug ? ''--debug'' : ''''; }\n\n '\n shellQuote: false\n inputs:\n use_case_directory:\n type: Directory\n doc: Directory where to find input files and store outputs\n s:name: Use Case Directory\n s:description: Directory to store input and output files.\n sentinel_list:\n type: File\n doc: .txt file containing sentinel data paths (output from application package\n 1) - sentinel_paths.txt\n s:name: Sentinel list file\n s:description: Text file containing sentinel data paths (output from application\n package 1) - sentinel_paths.txt\n png_output_path:\n type: File\n doc: .txt file containing png data paths (output from application package 3)\n - png_paths.txt\n s:name: Png list file\n s:description: Text file containing sentinel data paths (output from application\n package 3) - png_paths.txt\n csv_output_path:\n type: File\n doc: .txt file containing csv data paths (output from application package 3)\n - csv_paths.txt\n s:name: Csv list file\n s:description: Text file containing sentinel data paths (output from application\n package 3) - csv_paths.txt\n delete:\n type: boolean?\n doc: Enable deletion of generated auxiliary files\n s:name: null\n s:description: Enable deletion of generated auxiliary files\n verbose:\n type: boolean?\n doc: Enable verbose logging\n s:name: Verbose Logging\n s:description: Flag to enable verbose logging.\n debug:\n type: boolean?\n doc: Enable debug mode\n s:name: Debug Mode\n s:description: Flag to enable debug mode for additional logging.\n outputs:\n results:\n type: Directory\n outputBinding:\n glob: $(runtime.outdir)\n requirements:\n - class: InitialWorkDirRequirement\n listing:\n - entryname: $(inputs.use_case_directory.basename)\n entry: $(inputs.use_case_directory)\n writable: true\n - class: DockerRequirement\n dockerPull: registry.services.meeo.it/outmani/iliad_oil_spill_pilot/oilspill004:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: InlineJavascriptRequirement\n s:name: Sentinel-1 Oil Spill Detection and Segmentation Pipeline\n s:description: Deep learning model for detection and segmentation oil spills in\n Sentinel-1 SAR images.\n s:keywords:\n - oil spill\n - SAR\n - Sentinel-1\n - deep learning\n - segmentation\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n s:sourceOrganization:\n - class: s:Organization\n s:name: MEEO SRL\n s:url: https://meeo.it/\n s:address:\n class: s:PostalAddress\n s:addressCountry: IT\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: INESCTEC\n s:url: https://inesctec.pt\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:author:\n - class: s:Person\n s:email: outmani@meeo.it\n s:name: Sabrina Outmani\n - class: s:Person\n s:email: fazzini@meeo.it\n s:name: Noemi Fazzini\n s:dateCreated: '2024-12-01'\n s:temporalCoverage: 2014-01-01T00:00:00Z/\n s:spatialCoverage:\n class: s:GeoShape\n s:box: -90 -180 90 180\n s:license: https://opensource.org/licenses/MIT\n s:citation: ''\n- class: CommandLineTool\n id: medslik_tool\n baseCommand:\n - /opt/miniconda3/envs/application/bin/python\n - /opt/MEDSLIK_GLO/RUN_medslik.py\n arguments:\n - --cont_slick\n - valueFrom: $(inputs.cont_slick)\n - --sat\n - valueFrom: $(inputs.sat)\n - --min_lon\n - valueFrom: $(inputs.min_lon)\n - --max_lon\n - valueFrom: $(inputs.max_lon)\n - --min_lat\n - valueFrom: $(inputs.min_lat)\n - --max_lat\n - valueFrom: $(inputs.max_lat)\n - --lat_point\n - valueFrom: $(inputs.lat_point)\n - --lon_point\n - valueFrom: $(inputs.lon_point)\n - valueFrom: $(inputs.date_spill)\n prefix: --date_spill\n - --spill_dur\n - valueFrom: $(inputs.spill_dur)\n - --spill_res\n - valueFrom: $(inputs.spill_res)\n - --spill_tons\n - valueFrom: $(inputs.spill_tons)\n - --username\n - valueFrom: $(inputs.username)\n - --password\n - valueFrom: $(inputs.password)\n - --ftp_server\n - valueFrom: $(inputs.ftp_server)\n - --ftp_user\n - valueFrom: $(inputs.ftp_user)\n - --ftp_password\n - valueFrom: $(inputs.ftp_password)\n - --remote_dir\n - valueFrom: $(inputs.remote_dir)\n inputs:\n cont_slick:\n type: string\n default: 'NO'\n sat:\n type: string\n default: 'NO'\n min_lon:\n type: float\n default: 24.069118741783797\n max_lon:\n type: float\n default: 24.990341065648366\n min_lat:\n type: float\n default: 35.09663196120557\n max_lat:\n type: float\n default: 35.990635331961315\n lat_point:\n type: float\n default: 35.496\n lon_point:\n type: float\n default: -15.7433\n date_spill:\n type: string?\n spill_dur:\n type: string\n spill_res:\n type: string\n spill_tons:\n type: float\n default: 1.4\n username:\n type: string\n password:\n type: string\n ftp_server:\n type: string\n ftp_user:\n type: string\n ftp_password:\n type: string\n remote_dir:\n type: string\n outputs:\n results:\n outputBinding:\n glob: $(runtime.outdir)/MEDSLIK_GLO/OUT/\n type: Directory\n doc: All results\n requirements:\n NetworkAccess:\n networkAccess: true\n ResourceRequirement: {}\n InlineJavascriptRequirement: {}\n DockerRequirement:\n dockerPull: antonisparasyris/iliad:medslik-4.0\n EnvVarRequirement:\n envDef:\n PATH: /opt/miniconda3/envs/application/bin:/opt/conda/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin\n hints:\n cwltool:Secrets:\n secrets:\n - username\n - password\n - ftp_server\n - ftp_password\n s:name: medslik\n s:softwareVersion: 0.1.0\n s:description: medslik\n s:keywords:\n - medslik\n - oil spill\n s:programmingLanguage: python\n s:producer:\n class: s:Organization\n s:name: FORTH\n s:url: https://forth.gr\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n s:sourceOrganization:\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n s:author:\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n s:mantainer:\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n s:contributor:\n - class: s:Person\n s:name: Miguel Correia\n s:email: miguel.r.correia@inesctec.pt\n s:codeRepository: null\n s:dateCreated: '2025-01-27T16:00:00Z'\n", "producer":[ { "address":{ "address_country":"GR" }, "name":"FORTH", "url":"https://www.forth.gr/" } ], "family":"urn:apkg:workflow:forth:gr:oilspill_pipeline_medslik_146" }, "id":"urn:apkg:workflow:forth:gr:oilspill_pipeline_medslik_146:1.0.0" }, { "geometry":{ "coordinates":[ [ [ -180.0, -90.0 ], [ 180.0, -90.0 ], [ 180.0, 90.0 ], [ -180.0, 90.0 ], [ -180.0, -90.0 ] ] ], "type":"Polygon" }, "type":"Feature", "properties":{ "outputs":[ { "id":"swan_output", "type":"Directory" } ], "programming_language":"python", "keywords":[ "swan", "Heraklion", "wave", "hidromod" ], "inputs":[ { "keywords":[ "string", "password" ], "doc":"Password for CMEMS Download", "id":"cmems_password", "type":"string" }, { "keywords":[ "string", "username" ], "doc":"Username for CMEMS Download", "id":"cmems_username", "type":"string" }, { "keywords":[ "int", "forecast" ], "doc":"forecast for the model", "id":"forecast", "type":"int" }, { "keywords":[ "int", "Hindcast" ], "doc":"Hindcast for the model", "id":"hindcast", "type":"int" }, { "keywords":[ "string", "password" ], "doc":"Password for WRF Download", "id":"wrf_ftpserver", "type":"string" }, { "keywords":[ "string", "username" ], "doc":"Username for WRF Download", "id":"wrf_password", "type":"string" }, { "keywords":[ "string", "username" ], "doc":"Username for WRF Download", "id":"wrf_username", "type":"string" } ], "description":"This 500m and 50m resolution SWAN wave model is designed specifically for the Heraklion Port area, spanning a geographical range from West: 25.0 to East: 25.3, and South: 35.32 to North: 35.57. It utilizes ocean boundary conditions derived from the CMEMS Mediterranean Sea Waves Analysis and Forecast model to ensure accurate wave dynamics within the Mediterranean context. Meteorological forcing is provided by the high-resolution ICON 7km dataset, offering detailed and reliable atmospheric inputs.", "maintainer":null, "sdPublisher":[ { "name":"Application Package Registry", "class":"Organization", "url":"https://iliad-registry.inesctec.pt" } ], "temporal_coverage":null, "contributor":[ { "name":"Jo\u00e3o Ribeiro", "email":"joao.ribeiro@hidromod.com" }, { "name":"Miguel Delgado", "email":"miguel.delgado@hidromod.com" }, { "name":"Vassiliki Metheniti", "email":"vasmeth@iacm.forth.gr" }, { "name":"Antonios Parasyris", "email":"antonisparasyris@iacm.forth.gr" } ], "spatial_coverage":{ "geo":{ "box":"-90 -180 90 180" }, "class":"schema:GeoShape" }, "id":"run_swan_creta", "software_version":"1.0.0", "class":"Workflow", "latest":true, "identifier":"urn:apkg:workflow:hidromod:pt:run_swan_creta:1.0.0", "citation":null, "date_created":null, "author":[ { "name":"Miguel Delgado", "email":"miguel.delgado@hidromod.com" }, { "name":"Jo\u00e3o Ribeiro", "email":"joao.ribeiro@hidromod.com" } ], "sdDatePublished":"2025-06-11T14:23:14.122317Z", "url":"https://iliad-registry.inesctec.pt/collections/apkg/items/urn:apkg:workflow:hidromod:pt:run_swan_creta:1.0.0?f=cwl", "license":null, "code_repository":null, "source_organization":[ { "address":{ "address_country":"PT" }, "name":"Hidromod", "url":"https://hidromod.com/" } ], "name":"Execution of SWAN wave model", "cwl":"$graph:\n- class: Workflow\n doc: Execution of SWAN wave model, designed specifically for the Heraklion Port\n area\n inputs:\n cmems_password:\n doc: Password for CMEMS Download\n type: string\n s:description: Password for CMEMS Download\n s:keywords:\n - string\n - password\n s:name: CMEMS Password\n cmems_username:\n doc: Username for CMEMS Download\n type: string\n s:description: Username for CMEMS Download\n s:keywords:\n - string\n - username\n s:name: CMEMS Username\n forecast:\n doc: forecast for the model\n type: int\n s:description: forecast for the model\n s:keywords:\n - int\n - forecast\n s:name: Hindcast\n hindcast:\n doc: Hindcast for the model\n type: int\n s:description: Hindcast for the model\n s:keywords:\n - int\n - Hindcast\n s:name: Hindcast\n wrf_ftpserver:\n doc: Password for WRF Download\n type: string\n s:description: FTP Server for WRF Download\n s:keywords:\n - string\n - password\n s:name: WRF Password\n wrf_password:\n doc: Username for WRF Download\n type: string\n s:description: Username for WRF Download\n s:keywords:\n - string\n - username\n s:name: WRF Username\n wrf_username:\n doc: Username for WRF Download\n type: string\n s:description: Username for WRF Download\n s:keywords:\n - string\n - username\n s:name: WRF Username\n outputs:\n swan_output:\n type: Directory\n outputSource: execution50m/swan_result\n steps:\n preparation:\n in:\n forecast: forecast\n hindcast: hindcast\n cmems_password: cmems_password\n cmems_username: cmems_username\n wrf_ftpserver: wrf_ftpserver\n wrf_username: wrf_username\n wrf_password: wrf_password\n run: '#preparation'\n out:\n - swan_preparation_directory\n execution500m:\n in:\n forecast: forecast\n hindcast: hindcast\n swan_preparation_directory: preparation/swan_preparation_directory\n run: '#execution500m'\n out:\n - swan_execution500m_directory\n execution50m:\n in:\n forecast: forecast\n hindcast: hindcast\n swan_directory: execution500m/swan_execution500m_directory\n run: '#execution50m'\n out:\n - swan_result\n id: run_swan_creta\n s:author:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n s:description: 'This 500m and 50m resolution SWAN wave model is designed specifically\n for the Heraklion Port area, spanning a geographical range from West: 25.0 to\n East: 25.3, and South: 35.32 to North: 35.57. It utilizes ocean boundary conditions\n derived from the CMEMS Mediterranean Sea Waves Analysis and Forecast model to\n ensure accurate wave dynamics within the Mediterranean context. Meteorological\n forcing is provided by the high-resolution ICON 7km dataset, offering detailed\n and reliable atmospheric inputs.'\n s:keywords:\n - swan\n - Heraklion\n - wave\n - hidromod\n s:name: Execution of SWAN wave model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:sdDatePublished: '2025-06-11T14:23:14.122317Z'\n s:sdPublisher:\n class: Organization\n name: Application Package Registry\n url: https://iliad-registry.inesctec.pt\n s:identifier: urn:apkg:workflow:hidromod:pt:run_swan_creta:1.0.0\n- class: CommandLineTool\n requirements:\n - class: InlineJavascriptRequirement\n - class: ShellCommandRequirement\n - class: DockerRequirement\n dockerPull: hidromodadmin/iliad_heraklion_500m_50m:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: LoadListingRequirement\n loadListing: deep_listing\n inputs:\n cmems_password:\n type: string\n cmems_username:\n type: string\n forecast:\n type: int\n hindcast:\n type: int\n wrf_ftpserver:\n type: string\n wrf_password:\n type: string\n wrf_username:\n type: string\n outputs:\n swan_preparation_directory:\n type: Directory\n outputBinding:\n glob: .\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: '\"/home/heraklionport_500m/prepare_swan.sh $(runtime.outdir) \\\n\n $(inputs.forecast) \\\n\n $(inputs.hindcast) \\\n\n ''$(inputs.cmems_password)'' \\\n\n ''$(inputs.cmems_username)'' \\\n\n ''$(inputs.wrf_ftpserver)'' \\\n\n ''$(inputs.wrf_username)'' \\\n\n ''$(inputs.wrf_password)''\"\n\n '\n shellQuote: false\n id: preparation\n s:author:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n s:description: Download and preparation of all the required files to execute SWAN\n s:keywords:\n - swan\n - Heraklion\n - wave\n - hidromod\n - preparation\n s:name: Preparation of SWAN wave Model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n- class: CommandLineTool\n requirements:\n - class: InitialWorkDirRequirement\n listing: '$(inputs.swan_preparation_directory.listing.map(function(item) { return\n {entry: item, writable: true}; }))'\n - class: InlineJavascriptRequirement\n - class: ShellCommandRequirement\n - class: DockerRequirement\n dockerPull: hidromodadmin/iliad_heraklion_500m_50m:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: LoadListingRequirement\n loadListing: deep_listing\n inputs:\n forecast:\n type: int\n hindcast:\n type: int\n swan_preparation_directory:\n type: Directory\n outputs:\n swan_execution500m_directory:\n type: Directory\n outputBinding:\n glob: .\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: '\"/home/heraklionport_500m/500m.sh $(runtime.outdir) $(inputs.forecast)\n $(inputs.hindcast)\"\n\n '\n shellQuote: false\n id: execution500m\n s:author:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n s:description: Execution of SWAN 500m wave model with data from the preparation\n s:keywords:\n - swan\n - Heraklion\n - wave\n - hidromod\n - execution\n s:name: Execution of SWAN wave Model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n- class: CommandLineTool\n requirements:\n - class: InitialWorkDirRequirement\n listing: '$(inputs.swan_directory.listing.map(function(item) { return {entry:\n item, writable: true}; }))'\n - class: InlineJavascriptRequirement\n - class: ShellCommandRequirement\n - class: DockerRequirement\n dockerPull: hidromodadmin/iliad_heraklion_500m_50m:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: LoadListingRequirement\n loadListing: deep_listing\n inputs:\n forecast:\n type: int\n hindcast:\n type: int\n swan_directory:\n type: Directory\n outputs:\n swan_result:\n type: Directory\n outputBinding:\n glob: $(\"results\")\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: '\"/home/heraklionport_500m/50m.sh $(runtime.outdir) $(inputs.forecast)\n $(inputs.hindcast)\"\n\n '\n shellQuote: false\n id: execution50m\n s:author:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n s:description: Execution of SWAN 50m wave model with data from the preparation and\n the execution of 500m\n s:keywords:\n - swan\n - Heraklion\n - wave\n - hidromod\n - execution\n s:name: Execution of SWAN wave Model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n$namespaces:\n ogc: http://www.opengis.net/def/media-type/ogc/1.0/\n s: https://schema.org/\ncwlVersion: v1.2\ns:description: 'This 500m and 50m resolution SWAN wave model is designed specifically\n for the Heraklion Port area, spanning a geographical range from West: 25.0 to East:\n 25.3, and South: 35.32 to North: 35.57. It utilizes ocean boundary conditions derived\n from the CMEMS Mediterranean Sea Waves Analysis and Forecast model to ensure accurate\n wave dynamics within the Mediterranean context. 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class: InitialWorkDirRequirement\n listing: '$(inputs.swan_preparation_directory.listing.map(function(item) { return\n {entry: item, writable: true}; }))'\n - class: InlineJavascriptRequirement\n - class: ShellCommandRequirement\n - class: DockerRequirement\n dockerPull: hidromodadmin/iliad_heraklion_500m_50m:1.0.0\n - class: NetworkAccess\n networkAccess: true\n - class: LoadListingRequirement\n loadListing: deep_listing\n inputs:\n forecast:\n type: int\n hindcast:\n type: int\n swan_preparation_directory:\n type: Directory\n outputs:\n swan_execution500m_directory:\n type: Directory\n outputBinding:\n glob: .\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: '\"/home/heraklionport_500m/500m.sh $(runtime.outdir) $(inputs.forecast)\n $(inputs.hindcast)\"\n\n '\n shellQuote: false\n id: execution500m\n s:author:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xC3\\xA3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:description: Execution of SWAN 500m wave model with data from the preparation\n s:keywords:\n - swan\n - Heraklion\n - wave\n - hidromod\n - execution\n s:name: Execution of SWAN wave Model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:sdDatePublished: '2025-06-11T14:23:15.203079Z'\n s:sdPublisher:\n class: Organization\n name: Application Package Registry\n url: https://iliad-registry.inesctec.pt\n s:identifier: urn:apkg:tool:hidromod:pt:execution500m:1.0.0\n", "producer":[ { "address":{ "address_country":"PT" }, "name":"Hidromod", "url":"https://hidromod.com/" } ], "family":"urn:apkg:tool:hidromod:pt:execution500m" }, "id":"urn:apkg:tool:hidromod:pt:execution500m:1.0.0" }, { "geometry":{ "coordinates":[ [ [ -180.0, -90.0 ], [ 180.0, -90.0 ], [ 180.0, 90.0 ], [ -180.0, 90.0 ], [ -180.0, -90.0 ] ] ], "type":"Polygon" }, "type":"Feature", "properties":{ "outputs":[ { "id":"visir_output", "type":"Directory" } ], "programming_language":"python", "keywords":[ "hidromod", "visir", "VISIR", "least CO2 emissions", "optimal ship routes", "least distance", "least time", "regional", "high resolution", "global", "FORTH", "CMRL" ], "Secrets":{ "secrets":[ "wrf_username", "wrf_password", "cmems_username", "cmems_password" ] }, "inputs":[ { "doc":"FTP Server for WRF Download", "id":"wrf_ftpserver", "type":"string" }, { "doc":"Password for WRF Download", "id":"wrf_password", "type":"string" }, { "doc":"Username for WRF Download", "id":"wrf_username", "type":"string" }, { "doc":"Remote dir path from root for WRF Download", "id":"wrf_remotedir", "type":"string" }, { "doc":"Vessel Type (sail or motor)", "id":"vessel_type", "type":"string" }, { "doc":"CMEMS Username", "id":"cmems_username", "type":"string" }, { "doc":"CMEMS Password", "id":"cmems_password", "type":"string" }, { "doc":"Departure Date (%Y-%m-%dT%H:%M:00Z)", "id":"departure_date", "type":"string" }, { "doc":"Starting Latitude", "id":"start_lat", "type":"float" }, { "doc":"Starting Longitude", "id":"start_lon", "type":"float" }, { "doc":"Ending Latitude", "id":"end_lat", "type":"float" }, { "doc":"Ending Longitude", "id":"end_lon", "type":"float" }, { "doc":"Max Draught", "id":"maxDraught", "type":"float" }, { "doc":"Optional Bathymetry File", "id":"bathymetry_file", "type":"File?" } ], "description":"Solving Dijkstra's optimization algorithm to find optimal ship routes that minimize CO2 emissions, trip time and distance. Using VISIR II software (https://zenodo.org/records/10960842 created by CMCC), that runs using forcing from either CMRL's (https://crl.iacm.forth.gr/en/) high resolution models in the southern Greece region forecasting atmospheric state (WRF 3km x 3km), hydrodynamics (NEMO 1km x 1km) and waves (Wavewatch III 1km x 1km), or the GFS/CMEMS lower resolution forecasts to be able to generalize to routes globally.", "maintainer":null, "sdPublisher":[ { "name":"Application Package Registry", "class":"Organization", "url":"https://iliad-registry.inesctec.pt" } ], "temporal_coverage":null, "contributor":[ { "name":"Vassiliki Metheniti", "email":"vasmeth@iacm.forth.gr" }, { "name":"Antonios Parasyris", "email":"antonisparasyris@iacm.forth.gr" }, { "name":"Jo\u00e3o Ribeiro", "email":"joao.ribeiro@hidromod.com" }, { "name":"Miguel Delgado", "email":"miguel.delgado@hidromod.com" } ], "spatial_coverage":{ "geo":{ "box":"-90 -180 90 180" }, "class":"schema:GeoShape" }, "id":"run_visir", "software_version":"1.0.0", "class":"Workflow", "latest":true, "identifier":"urn:apkg:workflow:forth:gr:run_visir:1.0.0", "citation":null, "date_created":null, "author":[ { "name":"Vassiliki Metheniti", "email":"vasmeth@iacm.forth.gr" }, { "name":"Antonios Parasyris", "email":"antonisparasyris@iacm.forth.gr" }, { "name":"Jo\u00e3o Ribeiro", "email":"joao.ribeiro@hidromod.com" }, { "name":"Miguel Delgado", "email":"miguel.delgado@hidromod.com" } ], "sdDatePublished":"2025-06-11T14:23:17.001124Z", "url":"https://iliad-registry.inesctec.pt/collections/apkg/items/urn:apkg:workflow:forth:gr:run_visir:1.0.0?f=cwl", "license":null, "code_repository":null, "source_organization":[ { "address":{ "address_country":"GR" }, "name":"FORTH", "url":"https://www.iacm.forth.gr/" }, { "address":{ "address_country":"GR" }, "name":"CMRL", "url":"https://crl.iacm.forth.gr/en/" }, { "address":{ "address_country":"PT" }, "name":"Hidromod", "url":"https://hidromod.com/" } ], "name":"Execution of VISIR model", "cwl":"$namespaces:\n s: https://schema.org/\n cwltool: http://commonwl.org/cwltool#\n$graph:\n- class: Workflow\n hints:\n cwltool:Secrets:\n secrets:\n - wrf_username\n - wrf_password\n - cmems_username\n - cmems_password\n inputs:\n wrf_ftpserver:\n doc: FTP Server for WRF Download\n type: string\n wrf_password:\n doc: Password for WRF Download\n type: string\n wrf_username:\n doc: Username for WRF Download\n type: string\n wrf_remotedir:\n doc: Remote dir path from root for WRF Download\n type: string\n vessel_type:\n type: string\n doc: Vessel Type (sail or motor)\n cmems_username:\n type: string\n doc: CMEMS Username\n cmems_password:\n type: string\n doc: CMEMS Password\n departure_date:\n type: string\n doc: Departure Date (%Y-%m-%dT%H:%M:00Z)\n start_lat:\n type: float\n doc: Starting Latitude\n start_lon:\n type: float\n doc: Starting Longitude\n end_lat:\n type: float\n doc: Ending Latitude\n end_lon:\n type: float\n doc: Ending Longitude\n maxDraught:\n type: float\n doc: Max Draught\n bathymetry_file:\n type: File?\n doc: Optional Bathymetry File\n outputs:\n visir_output:\n type: Directory\n outputSource: running/visir_output\n steps:\n running:\n in:\n wrf_ftpserver: wrf_ftpserver\n wrf_username: wrf_username\n wrf_password: wrf_password\n wrf_remotedir: wrf_remotedir\n vessel_type: vessel_type\n cmems_username: cmems_username\n cmems_password: cmems_password\n departure_date: departure_date\n start_lat: start_lat\n start_lon: start_lon\n end_lat: end_lat\n end_lon: end_lon\n maxDraught: maxDraught\n bathymetry_file: bathymetry_file\n run: '#running'\n out:\n - visir_output\n id: run_visir\n s:author:\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:contributor:\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:description: Solving Dijkstra's optimization algorithm to find optimal ship routes\n that minimize CO2 emissions, trip time and distance. Using VISIR II software (https://zenodo.org/records/10960842\n created by CMCC), that runs using forcing from either CMRL's (https://crl.iacm.forth.gr/en/)\n high resolution models in the southern Greece region forecasting atmospheric state\n (WRF 3km x 3km), hydrodynamics (NEMO 1km x 1km) and waves (Wavewatch III 1km x\n 1km), or the GFS/CMEMS lower resolution forecasts to be able to generalize to\n routes globally.\n s:keywords:\n - hidromod\n - visir\n - VISIR\n - least CO2 emissions\n - optimal ship routes\n - least distance\n - least time\n - regional\n - high resolution\n - global\n - FORTH\n - CMRL\n s:name: Execution of VISIR model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: FORTH\n s:url: https://www.iacm.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n s:sourceOrganization:\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.iacm.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: CMRL\n s:url: https://crl.iacm.forth.gr/en/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:sdDatePublished: '2025-06-11T14:23:17.001124Z'\n s:sdPublisher:\n class: Organization\n name: Application Package Registry\n url: https://iliad-registry.inesctec.pt\n s:identifier: urn:apkg:workflow:forth:gr:run_visir:1.0.0\n- class: CommandLineTool\n requirements:\n - class: InlineJavascriptRequirement\n - class: ShellCommandRequirement\n - class: DockerRequirement\n dockerPull: antonisparasyris/iliad:ship_routing\n - class: NetworkAccess\n networkAccess: true\n - class: LoadListingRequirement\n loadListing: deep_listing\n - class: InitialWorkDirRequirement\n listing:\n - entryname: /VISIR/__data/bathymetry/GEBCO_2024_sub_ice_topo.nc\n entry: $(inputs.bathymetry_file)\n hints:\n cwltool:Secrets:\n secrets:\n - wrf_username\n - wrf_password\n - cmems_username\n - cmems_password\n inputs:\n wrf_ftpserver:\n type: string\n wrf_password:\n type: string\n wrf_username:\n type: string\n wrf_remotedir:\n type: string\n vessel_type:\n type: string\n cmems_username:\n type: string\n cmems_password:\n type: string\n departure_date:\n type: string\n start_lat:\n type: float\n start_lon:\n type: float\n end_lat:\n type: float\n end_lon:\n type: float\n maxDraught:\n type: float?\n bathymetry_file:\n type: File?\n outputs:\n visir_output:\n type: Directory\n outputBinding:\n glob: ./OUTPUT\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: '\"/VISIR/run.sh ''$(inputs.wrf_ftpserver)'' ''$(inputs.wrf_username)''\n ''$(inputs.wrf_password)'' ''$(inputs.wrf_remotedir)'' \\\n\n ''$(inputs.vessel_type)'' ''$(inputs.cmems_username)'' ''$(inputs.cmems_password)''\n ''$(inputs.departure_date)'' $(inputs.start_lat) \\\n\n $(inputs.start_lon) $(inputs.end_lat) $(inputs.end_lon)$(inputs.maxDraught ?\n '' '' + inputs.maxDraught : '''')\"\n\n '\n shellQuote: false\n id: running\n s:author:\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:contributor:\n - class: s:Person\n s:email: vasmeth@iacm.forth.gr\n s:name: Vassiliki Metheniti\n - class: s:Person\n s:email: antonisparasyris@iacm.forth.gr\n s:name: Antonios Parasyris\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:description: Solving Dijkstra's optimization algorithm to find optimal ship routes\n that minimize CO2 emissions, trip time and distance. Using VISIR II software (https://zenodo.org/records/10960842\n created by CMCC), that runs using forcing from either CMRL's (https://crl.iacm.forth.gr/en/)\n high resolution models in the southern Greece region forecasting atmospheric state\n (WRF 3km x 3km), hydrodynamics (NEMO 1km x 1km) and waves (Wavewatch III 1km x\n 1km), or the GFS/CMEMS lower resolution forecasts to be able to generalize to\n routes globally.\n s:keywords:\n - hidromod\n - visir\n - VISIR\n - least CO2 emissions\n - optimal ship routes\n - least distance\n - least time\n - regional\n - high resolution\n - global\n s:name: Execution of VISIR model\n s:programmingLanguage: python\n s:softwareVersion: 1.0.0\n s:producer:\n class: s:Organization\n s:name: FORTH\n s:url: https://www.iacm.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n s:sourceOrganization:\n - class: s:Organization\n s:name: FORTH\n s:url: https://www.iacm.forth.gr/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: CMRL\n s:url: https://crl.iacm.forth.gr/en/\n s:address:\n class: s:PostalAddress\n s:addressCountry: GR\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\ncwlVersion: v1.2\n", "producer":[ { "address":{ "address_country":"GR" }, "name":"FORTH", "url":"https://www.iacm.forth.gr/" } ], "family":"urn:apkg:workflow:forth:gr:run_visir" }, "id":"urn:apkg:workflow:forth:gr:run_visir:1.0.0" }, { "geometry":{ "coordinates":[ [ [ 10.403, 35.503 ], [ 11.397, 35.503 ], [ 11.397, 36.497 ], [ 10.403, 36.497 ], [ 10.403, 35.503 ] ] ], "type":"Polygon" }, "type":"Feature", "properties":{ "outputs":[ { "id":"roms_output", "type":"Directory" } ], "programming_language":"python", "keywords":[ "roms", "tunisia" ], "inputs":[ { "doc":"forecast for the model", "id":"forecast", "type":"int" }, { "doc":"Hindcast for the model", "id":"hindcast", "type":"int" }, { "doc":"Password for Copernicus Download", "id":"roms_password", "type":"string" }, { "doc":"Username for Copernicus Download", "id":"roms_username", "type":"string" }, { "doc":"Simulation start date. If none is provided, today is used as reference", "id":"timenow", "type":"string" } ], "description":"Ocean Digital Twin in Tunisia uses ROMS for precise aquaculture forecasts, enhancing sustainability.", "maintainer":[ { "name":"Hidromod", "email":"iliad@hidromod.com" } ], "sdPublisher":[ { "name":"Application Package Registry", "class":"Organization", "url":"https://iliad-registry.inesctec.pt" } ], "temporal_coverage":null, "contributor":[ { "name":"Jo\u00e3o Ribeiro", "email":"joao.ribeiro@hidromod.com" }, { "name":"Miguel Delgado", "email":"miguel.delgado@hidromod.com" } ], "spatial_coverage":{ "geo":{ "box":"35.503 10.403 36.497 11.397" }, "class":"schema:GeoShape" }, "id":"download_metoceanographic_data", "software_version":"1.1.1", "class":"Workflow", "latest":true, "identifier":"urn:apkg:workflow:hidromod:pt:download_metoceanographic_data:1.1.1", "citation":null, "date_created":"2023-12-04", "author":[ { "name":"Miguel Delgado", "email":"miguel.delgado@hidromod.com" }, { "name":"Jo\u00e3o Ribeiro", "email":"joao.ribeiro@hidromod.com" } ], "sdDatePublished":"2025-06-11T14:23:18.414816Z", "url":"https://iliad-registry.inesctec.pt/collections/apkg/items/urn:apkg:workflow:hidromod:pt:download_metoceanographic_data:1.1.1?f=cwl", "license":"https://creativecommons.org/licenses/by/4.0/", "code_repository":null, "source_organization":[ { "address":{ "address_country":"PT" }, "name":"Hidromod", "url":"https://hidromod.com/" } ], "name":"ROMS Tunisia", "cwl":"$graph:\n- class: Workflow\n doc: Download of metoceanographic data\n inputs:\n forecast:\n doc: forecast for the model\n type: int\n hindcast:\n doc: Hindcast for the model\n type: int\n roms_password:\n doc: Password for Copernicus Download\n type: string\n roms_username:\n doc: Username for Copernicus Download\n type: string\n timenow:\n doc: Simulation start date. If none is provided, today is used as reference\n type: string\n outputs:\n roms_output:\n type: Directory\n outputSource: run_roms/roms_output\n steps:\n download_data:\n in:\n forecast: forecast\n hindcast: hindcast\n roms_password: roms_password\n roms_username: roms_username\n timenow: timenow\n run: '#download_data'\n out:\n - roms_directory\n run_roms:\n in:\n forecast: forecast\n hindcast: hindcast\n roms_directory: download_data/roms_directory\n timenow: timenow\n run: '#run_roms'\n out:\n - roms_output\n id: download_metoceanographic_data\n s:author:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:maintainer:\n - class: s:Organization\n s:email: iliad@hidromod.com\n s:name: Hidromod\n s:description: Ocean Digital Twin in Tunisia uses ROMS for precise aquaculture forecasts,\n enhancing sustainability.\n s:keywords:\n - roms\n - tunisia\n s:name: ROMS Tunisia\n s:programmingLanguage: python\n s:softwareVersion: 1.1.1\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:dateCreated: '2023-12-04'\n s:spatialCoverage:\n class: s:geo\n s:box: 35.503 10.403 36.497 11.397\n s:license: https://creativecommons.org/licenses/by/4.0/\n s:sdDatePublished: '2025-06-11T14:23:18.414816Z'\n s:sdPublisher:\n class: Organization\n name: Application Package Registry\n url: https://iliad-registry.inesctec.pt\n s:identifier: urn:apkg:workflow:hidromod:pt:download_metoceanographic_data:1.1.1\n- class: CommandLineTool\n requirements:\n - class: InlineJavascriptRequirement\n - class: ShellCommandRequirement\n - class: DockerRequirement\n dockerPull: hidromodadmin/iliad_roms_tunisia:1.1.1\n - class: NetworkAccess\n networkAccess: true\n - class: LoadListingRequirement\n loadListing: deep_listing\n inputs:\n forecast:\n type: int\n hindcast:\n type: int\n roms_password:\n type: string\n roms_username:\n type: string\n timenow:\n type: string\n outputs:\n roms_directory:\n type: Directory\n outputBinding:\n glob: $(\"roms\")\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: \"\\\"/move_struct.sh $(runtime.outdir)\\\"; python3 /model/RomsOP.py --type\\\n \\ preparation --forecast $(inputs.forecast) --hindcast $(inputs.hindcast) \\\\\\\n \\n --roms_password $(inputs.roms_password) --roms_username $(inputs.roms_username)\\\n \\ --timenow $(inputs.timenow);\\n\"\n shellQuote: false\n id: download_data\n s:author:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:maintainer:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:codeRepository: https://raw.githubusercontent.com/ILIAD-ocean-twin/application_package/main/ROMS_Tunisia/workflow.cwl\n s:description: Download a preparation of executable to be used when executing ROMS\n s:keywords:\n - roms\n - tunisia\n - preparation\n s:name: Preparation of ROMS Model\n s:programmingLanguage: python\n s:softwareVersion: 1.1.1\n s:producer:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:sourceOrganization:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:dateCreated: '2023-12-04'\n s:spatialCoverage:\n class: s:geo\n s:box: 35.503 10.403 36.497 11.397\n s:license: https://creativecommons.org/licenses/by/4.0/\n- class: CommandLineTool\n requirements:\n - class: InitialWorkDirRequirement\n listing:\n - entryname: roms\n writable: true\n entry: $(inputs.roms_directory)\n - class: DockerRequirement\n dockerPull: hidromodadmin/iliad_roms_tunisia:1.1.1\n - class: InlineJavascriptRequirement\n - class: NetworkAccess\n networkAccess: true\n inputs:\n forecast:\n type: int\n hindcast:\n type: int\n roms_directory:\n type: Directory\n timenow:\n type: string\n outputs:\n roms_output:\n type: Directory\n outputBinding:\n glob: roms/[0-9]*\n baseCommand:\n - /bin/bash\n - -c\n arguments:\n - valueFrom: 'python3 /model/RomsOP.py --type execution --forecast $(inputs.forecast)\n --hindcast $(inputs.hindcast) --timenow $(inputs.timenow);\n\n '\n shellQuote: false\n id: run_roms\n s:author:\n - class: s:Person\n s:email: joao.ribeiro@hidromod.com\n s:name: \"Jo\\xE3o Ribeiro\"\n s:contributor:\n - class: s:Person\n s:email: miguel.delgado@hidromod.com\n s:name: Miguel Delgado\n s:maintainer:\n - class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:codeRepository: https://raw.githubusercontent.com/ILIAD-ocean-twin/application_package/main/ROMS_Tunisia/workflow.cwl\n s:description: Execution of ROMS model with data from the preparation\n s:keywords:\n - roms\n - tunisia\n - execution\n s:name: Execution of ROMS Model\n s:programmingLanguage: python\n s:softwareVersion: 1.1.1\n s:publisher:\n class: s:Organization\n s:name: Hidromod\n s:url: https://hidromod.com/\n s:address:\n class: s:PostalAddress\n s:addressCountry: PT\n s:sourceOrganization:\n - 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