cwl-requirements.RdrequireDocker: If a workflow component should be run in a Docker container, this function specifies how to fetch or build the image.
requireJS: Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation.
requireSoftware: A list of software packages that should be configured in the environment of the defined process.
InitialWorkDirRequirement: Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.
: Dirent: Define a file or subdirectory that must be placed 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.
Create manifest for configure files.
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() requireRscript(rscript)
| docker | Character. Specify a Docker image to retrieve using docker pull. |
|---|---|
| Load | Character. Specify a HTTP URL from which to download a Docker image using docker load. |
| File | Character. Supply the contents of a Dockerfile which will be built using docker build. |
| Import | Character. Provide HTTP URL to download and gunzip a Docker images using `docker import. |
| ImageId | 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 must be used. |
| OutputDir | Character. Set the designated output directory to a specific location inside the Docker container. |
| expressionLib | optional list. Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions. |
| packages | The list of software to be configured. |
| listing | The list of files or subdirectories that must be placed in the designated output directory prior to executing the command line tool. |
| entryname | Character or Expression. The name of the file or subdirectory to create in the output directory. The name of the file or subdirectory to create in the output directory. If entry is a File or Directory, the entryname field overrides the value of basename of the File or Directory object. Optional. |
| entry | Charactor or expression. Required. |
| writable | Logical. If true, the file or directory must be writable by the tool. Changes to the file or directory must be isolated and not visible by any other CommandLineTool process. Default is FALSE (files and directories are read-only). Optional. |
| inputID | The input ID from corresponding `InputParam`. |
| sep | The separator of the input files in the manifest config. |
| rscript | An R script to run. |
requireDocker: A list of docker requirement to fetch or build the image.
requireJS: A list of inline Javascript requirement.
requireSoftware: A list of software requirements.
requireInitialWorkDir: A list of initial work directory requirements.
Dirent: A list.
requireSubworkflow: A SubworkflowFeatureRequirement list.
rquireScatter: A ScatterFeatureRequirement list.
requireMultipleInput: A MultipleInputFeatureRequirement list.
requireStepInputExpression: A StepInputExpressionRequirement list.
A requirement list with Rscript as manifest entry.
More details about `requireDocker`, see: https://www.commonwl.org/v1.0/CommandLineTool.html#DockerRequirement
More details about `requireJS`, see: https://www.commonwl.org/v1.0/CommandLineTool.html#InlineJavascriptRequirement
More details about `requireSoftware`, see: https://www.commonwl.org/v1.0/CommandLineTool.html#SoftwareRequirement
More details about `requireInitialWorkDir`, See: https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
More details about `Dirent`, See:https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent
p1 <- InputParam(id = "ifiles", type = "File[]?", position = -1) CAT <- cwlProcess(baseCommand = "cat", requirements = list(requireDocker("alpine"), requireManifest("ifiles"), requireJS()), arguments = list("ifiles"), inputs = InputParamList(p1))