ProcessRequirement: ProcessRequirement Class

In tengfei/rabix.R: R utilities for rabix.

Description

ProcessRequirement Class

ProcessRequirementList

Usage

FileDefList(...)

EnvironmentDefList(...)

ProcessRequirementList(...)

Arguments

...	element or list of the element.

Value

a ProcessRequirement object or subclass object.

ProcessRequirement

A process requirement declares a prerequisite that may or must be fufilled before executing a process. See Process.hints and Process.requirements. Process requirements are the primary mechanism for specifying extensions to the CWL core specification.

class

(character) The specific requirement type.

DockerRequirement Class

Indicates that a workflow component should be run in a Docker container, and specifies how to fetch or build the image.

If a CommandLineTool lists DockerRequirement under hints or requirements, it may (or must) be run in the specified Docker container. The platform must first acquire or install the correct Docker image, as described by DockerRequirement. The platform must execute the tool in the container using docker run with the appropriate Docker image and the tool command line. The workflow platform may provide input files and the designated output directory through the use of volume bind mounts. The platform may rewrite file paths in the input object to correspond to the Docker bind mounted locations. When running a tool contained in Docker, the workflow platform must not assume anything about the contents of the Docker container,such as the presence or absence of specific software, except to assume that the generated command line represents a valid command within the runtime environment of the container.

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.

SubworkflowFeatureRequirement Class

Indicates that the workflow platform must support nested workflows in the run field of (WorkflowStep)(#workflowstep).

FileDef Class

Define a file that must be placed by in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template.

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.

CreateFileRequirement Class

Define a list of files that must be created and placed by the workflow platform in the designated output directory prior to executing the command line tool. See FileDef for details.

fileDef

(FileDefList) The list of files.

EnvironmentDef Class

Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input.

envName

(character) The environment variable name.

envValue

(characterORExpression) The environment variable value.

EnvVarRequirement Class

Define a list of environment variables which will be set in the execution environment of the tool. See EnvironmentDef for details.

envDef

(EnvironmentDefList) The list of environment variables.

ScatterFeatureRequirement Class

Indicates that the workflow platform must support the scatter and scatterMethod fields of (WorkflowStep)(#workflowstep).

ExpressionEngineRequirement Class

Define an expression engine, as described in Expressions.

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.

Examples

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)

tengfei/rabix.R documentation built on May 31, 2019, 8:34 a.m.