requirements: requireDocker

In Rcwl: An R interface to the Common Workflow Language

Description

requireDocker

requireJS

requireSoftware

InitialWorkDirRequirement

Dirent class

Create manifest for configure files

SubworkflowFeatureRequirement

ScatterFeatureRequirement

MultipleInputFeatureRequirement

StepInputExpressionRequirement

Usage

requireDocker(
  docker = NULL,
  Load = NULL,
  File = NULL,
  Import = NULL,
  ImageId = NULL,
  OutputDir = NULL
)

requireJS(expressionLib = list())

requireSoftware(packages = list())

requireInitialWorkDir(listing = list())

Dirent(entryname = character(), entry, writable = FALSE)

requireManifest(inputID, sep = "\\n")

requireSubworkflow()

requireScatter()

requireMultipleInput()

requireStepInputExpression()

Arguments

docker	The docker pull address.
Load	dockerLoad
File	dockerFile
Import	dockerImport
ImageId	dockerImageId
OutputDir	dockerOutputDirectory
expressionLib	optional code
packages	The list of software to be configured.
listing	The list of files or directories.
entryname	The name of the file or subdirectory to create in the output directory.
entry	charactor or expression.
writable	boolean.
inputID	The input ID from corresponding 'InputParam'.
sep	The separator of the input files in the manifest config.

Details

https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent

Value

A DockerRequirement list

A InlineJavascriptRequirement list

A SoftwareRequirement list

A InitialWorkDirRequirement list

A SubworkflowFeatureRequirement list

A ScatterFeatureRequirement list

A MultipleInputFeatureRequirement list

A StepInputExpressionRequirement list

Examples

p1 <- InputParam(id = "ifiles", type = "File[]?", position = -1)
CAT = cwlParam(baseCommand = "cat",
requirements = list(requireDocker("alpine"), requireManifest("ifiles"), requireJS()),
arguments = list("ifiles"),
inputs = InputParamList(p1))

Rcwl documentation built on Nov. 8, 2020, 8:11 p.m.