@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix ExpressionTool: .
cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputDirectory)" ;
cwl:loadListing "deep_listing"
] ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputDirectory)" ;
cwl:loadListing "deep_listing"
] ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputDirectory)" ;
cwl:loadListing "deep_listing"
] ;
sld:type cwl:Directory .
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "/download-data.sh" ) ;
cwl:baseCommand ( "/bin/bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/azimuth:main"
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] .
rdfs:label "Zenodo id for models collection" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:default "7580707" ;
sld:type xsd:string .
rdfs:label "Zenodo id for reference data collection" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:default "7587774" ;
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:Directory .
rdfs:label "Output directory for models and reference data" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:default "./frmatch" ;
sld:type xsd:string .
rdfs:label "Zenodo id for reference data collection" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:default "15750919" ;
sld:type xsd:string .
sld:type cwl:Directory .
sld:type [ sld:items cwl:Directory , cwl:File ;
sld:type sld:array
] .
cwl:source , , .
sld:type xsd:string .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "/download-data.sh" ) ;
cwl:baseCommand ( "/bin/bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/popv:main"
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
rdfs:label "Output directory for models and reference data" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:default "./popv" ;
sld:type xsd:string .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:out ;
cwl:run .
cwl:source .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.2" ;
ExpressionTool:expression "${\n var parts = inputs.outputDirectory.split('/');\n var listing = inputs.files;\n for (var i = parts.length - 1; i >= 0; --i) {\n listing = [{\n class: 'Directory',\n basename: parts[i],\n listing: listing\n }];\n }\n\n return { directory: listing[0] }\n}\n" ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "/download-data.sh" ) ;
cwl:baseCommand ( "/bin/bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/frmatch:main"
] .
rdfs:label "Organ mapping json file" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File , sld:null .
rdfs:label "Output directory for model data" ;
sld:default "./models" ;
sld:type xsd:string .
rdfs:label "Output directory for reference data" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:default "./azimuth" ;
sld:type xsd:string .