@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix EnvVarRequirement: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix InlineJavascriptRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix EnvironmentDef: .
@prefix cwl: .
@prefix ExpressionTool: .
cwl:inputBinding [ CommandLineBinding:prefix
"--ensemble-lookup" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ensemble-lookup" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ensemble-lookup" ] ;
sld:type cwl:File , sld:null .
rdfs:label "Organ id column in crosswalk table" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-organ-id-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-organ-id-column" ] ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:label "Gene expression column" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gene-expr-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gene-expr-column" ] ;
sld:type xsd:string , sld:null .
rdfs:label "Data to annotate in h5ad format" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
rdfs:label "Data to get gene expression for in h5ad format" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out , , ;
cwl:run ;
cwl:when "$(!!inputs.options)" .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/main.py" ) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/celltypist:main"
] .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/main.py" ) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/extract-summary:main"
] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] .
sld:type , sld:null .
rdfs:label "Data to annotate in h5ad format" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:Directory .
rdfs:label "Output match type column name" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--match-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--match-column" ] ;
sld:type xsd:string , sld:null .
cwl:source ;
cwl:valueFrom "$(inputs.options.celltypist || null)" .
rdfs:comment "Cell id column" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-id-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-id-column" ] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--unknown-labels-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--unknown-labels-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--unknown-labels-key" ] ;
sld:type xsd:string , sld:null .
sld:type , sld:null .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/main.py" ) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs , ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/gene-expression:main"
] .
cwl:inputBinding [ CommandLineBinding:prefix
"--ensemble-lookup" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ensemble-lookup" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-ontology-dir" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-ontology-dir" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-ontology-dir" ] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:when "$(!!inputs.matrix)" .
rdfs:label "Popv specific options" ;
sld:fields , , , , , , , , , , , ;
sld:type sld:record .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/main.py" ) ;
cwl:baseCommand ( "python" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ghcr.io/hubmapconsortium/hra-workflows/crosswalking:main"
] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] .
cwl:source ;
cwl:valueFrom "$(self.summarize || {})" .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Base jsonld context to add summary to." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--jsonld-context" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--jsonld-context" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"annotations.csv" ] ;
sld:type cwl:File .
rdfs:label "Gene expression options" ;
sld:fields , , , ;
sld:type sld:record .
cwl:outputSource , , ;
cwl:pickValue "first_non_null" ;
sld:type cwl:File .
sld:type [ sld:fields , , , , , , ;
sld:type sld:record
] .
cwl:outputBinding [ CommandOutputBinding:glob
"report.json" ] ;
sld:type cwl:File .
rdfs:label "Organ uberon id in format 'UBERON:1234'" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--organ" ] ;
sld:type xsd:string .
cwl:in , , ;
cwl:out , , ;
cwl:run ;
cwl:when "$(!!inputs.options)" .
sld:type .
cwl:outputBinding [ CommandOutputBinding:glob
"report.json" ] ;
sld:type cwl:File , sld:null .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"annotated_matrix.h5ad" ] ;
sld:type cwl:File .
rdfs:label "Celltypist specific options" ;
sld:fields , ;
sld:type sld:record .
sld:type .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"report.json" ] ;
sld:type cwl:File .
rdfs:label "Data layer to use" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-layers-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-layers-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-layers-key" ] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--query-batch-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-batch-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-batch-key" ] ;
sld:type xsd:string , sld:null .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types , , , , ,
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ;
InlineJavascriptRequirement:expressionLib
"var ALGORITHMS = [\"azimuth\", \"celltypist\", \"popv\"];\n\n/**\n * Finds the algorithm selected in the option object\n *\n * @param {object} obj Options\n * @returns {string} Name of algorithm or null if no match was found\n */\nfunction _find_algorithm(obj) {\n for (var index = 0; index < ALGORITHMS.length; ++index) {\n var name = ALGORITHMS[index];\n if (typeof obj[name] === \"object\") {\n return name;\n }\n }\n\n return null;\n}\n\n/**\n * Selects an output directory based on the provided options\n *\n * @param {object} obj Options\n * @returns The selected output directory\n */\nfunction selectOutputDirectory(obj) {\n return obj[\"directory\"] || _find_algorithm(obj) || \".\";\n}\n\n/**\n * Creates default summarize step options based on the provided options\n *\n * @param {object} obj Options\n * @returns Default summarize options\n */\nfunction getDefaultSummarizeOptions(obj) {\n return {\n annotationMethod: _find_algorithm(obj) || \"unknown\",\n };\n}\n"
] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
sld:type , sld:null .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"annotations.csv" ] ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
sld:type .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types , ,
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .
cwl:source .
cwl:in , ;
cwl:out , ;
cwl:run ;
cwl:when "$(!!inputs.matrix)" .
rdfs:label "Annotation column" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--annotation-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--annotation-column" ] ;
sld:type xsd:string , sld:null .
rdfs:label "Data to get crosswalking for in h5ad format" ;
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run [ a cwl:ExpressionTool ;
ExpressionTool:expression "${ return { report: inputs.reports[inputs.reports.length - 1] }; }\n" ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ]
] .
cwl:outputBinding [ CommandOutputBinding:glob
"annotated_matrix.h5ad" ] ;
sld:type cwl:File .
sld:type , sld:null .
rdfs:label "Number of top genes per cell type to save" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gene-expr-count" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gene-expr-count" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "Gene expression column" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gene-expr-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gene-expr-column" ] ;
sld:type xsd:string , sld:null .
cwl:in , ;
cwl:out , ;
cwl:run ;
cwl:when "$(!!inputs.matrix)" .
rdfs:label "Output clid column name" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--clid-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--clid-column" ] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-batch-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-batch-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-batch-key" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:Directory .
cwl:source ;
cwl:valueFrom "$(inputs.options.popv || null)" .
rdfs:label "Organ level column in crosswalk table" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-organ-level-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-organ-level-column" ] ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "Cell label column" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-label-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cell-label-column" ] ;
sld:type xsd:string , sld:null .
a cwl:ExpressionTool ;
ns1:original_cwlVersion "v1.2" ;
ExpressionTool:expression "${\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:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--query-labels-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-labels-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--query-labels-key" ] ;
sld:type xsd:string , sld:null .
cwl:source ;
cwl:valueFrom "$(self.geneExpression || {})" .
cwl:outputBinding [ CommandOutputBinding:glob
"annotations.csv" ] ;
sld:type cwl:File .
rdfs:label "Organ uberon id in format 'UBERON:1234'" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--organ" ] ;
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-labels-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-labels-key" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ref-labels-key" ] ;
sld:type xsd:string , sld:null .
rdfs:label "Organ uberon id in format 'UBERON:1234'" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--organ" ] ;
sld:type xsd:string .
cwl:source .
sld:type xsd:string .
rdfs:label "CL label column in crosswalk table" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-clid-label-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-clid-label-column" ] ;
sld:type xsd:string , sld:null .
cwl:loadContents true ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(inputs.options.azimuth || null)" .
sld:type xsd:string , sld:null .
sld:type , sld:null .
rdfs:label "Match type column in crosswalk table" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-match-column" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"--crosswalk-table-match-column" ] ;
sld:type xsd:string , sld:null .
cwl:source ;
cwl:valueFrom "$(self.directory || {})" .
rdfs:label "crosswalking options" ;
sld:fields , , , , , , , , , ;
sld:type sld:record .