ProcessRequirement Class
DockerRequirement Class
ProcessRequirementList
FileDefList(...) EnvironmentDefList(...) ProcessRequirementList(...)
... | element or list of the element. |
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a ProcessRequirement object or subclass object.
class
(character) The specific requirement type.
dockerPull
(character) Get a Docker image using docker pull
dockerLoad
(character) Specify a HTTP URL from which to download a Docker image using docker load.
dockerFile
(character) Supply the contents of a Dockerfile which will be build using docker build.
dockerImageId
(character) The image id that will be used for docker run. May be a human-readable image name or the image identifier hash. May be skipped if dockerPull is specified, in which case the dockerPull image id will be used.
dockerOutputDirectory
(character) Set the designated output directory to a specific location inside the Docker container.
Indicates that the workflow platform must support nested workflows in the run field of (WorkflowStep)(#workflowstep).
filename
(characterORExpression) The name of the file to create in the output directory.
fileContent
(characterORExpression) If the value is a string literal or an expression which evalutes to a string, a new file must be created with the string as the file contents. If the value is an expression that evaluates to a File object, this indicates the referenced file should be added to the designated output directory prior to executing the tool. Files added in this way may be read-only, and may be implemented through bind mounts or file system links in such a way as to avoid unecessary copying of the input file.
fileDef
(FileDefList) The list of files.
envName
(character) The environment variable name.
envValue
(characterORExpression) The environment variable value.
envDef
(EnvironmentDefList) The list of environment variables.
Indicates that the workflow platform must support the scatter and scatterMethod fields of (WorkflowStep)(#workflowstep).
id
(character) Used to identify the expression engine in the engine field of Expressions.
requirements
[ProcessRequirement]Requirements to run this expression engine, such as DockerRequirement for specifying a container with the engine.
engineCommand
[character] The command line to invoke the expression engine.
engineConfig
[character] Additional configuration or code fragments that will also be passed to the expression engine. The semantics of this field are defined by the underlying expression engine. Intended for uses such as providing function definitions that will be called from CWL expressions.
dkr <- DockerRequirement(dockerImageId = "testid") cfr <- CreateFileRequirement(fileDef = FileDefList(FileDef(filename = "hello.txt"))) sfr <- SubworkflowFeatureRequirement() evr <- EnvVarRequirement(envDef = EnvironmentDefList( EnvironmentDef(envName = "path", envValue = "testpath") )) safr <- ScatterFeatureRequirement() eer <- ExpressionEngineRequirement(id = "hello") ProcessRequirementList(dkr, cfr, sfr, evr, safr, eer)#> [[1]] #> class: DockerRequirement #> dockerImageId: testid #> #> [[2]] #> class: CreateFileRequirement #> fileDef: #> - filename: hello.txt #> fileContent: ~ #> #> [[3]] #> class: SubworkflowFeatureRequirement #> #> [[4]] #> class: EnvVarRequirement #> envDef: #> - envName: path #> envValue: testpath #> #> [[5]] #> class: ScatterFeatureRequirement #> #> [[6]] #> class: ExpressionEngineRequirement #> id: hello #> requirements: [] #>