cwlStepParam: cwlStepParam

In Rcwl: An R interface to the Common Workflow Language

Description

A workflow steps paramter, which connect multiple command line steps into a workflow. More details: stepInParamList.

Usage

cwlStepParam(
  cwlVersion = "v1.0",
  cwlClass = "Workflow",
  requirements = list(),
  id = character(),
  label = character(),
  doc = list(),
  intent = list(),
  hints = list(),
  arguments = list(),
  extensions = list(),
  inputs = InputParamList(),
  outputs = OutputParamList(),
  steps = stepParamList()
)

Arguments

cwlVersion	CWL version
cwlClass	"Workflow".
requirements	Requirements that apply to either the runtime environment or the workflow engine.
id	The unique identifier for this process object.
label	A short, human-readable label of this object.
doc	A documentation string for this object.
intent	An identifier for the type of computational operation, of this Process.
hints	Any or a list for the workflow engine.
arguments	Command line bindings which are not directly associated with input parameters.
extensions	A list of extensions and metadata.
inputs	A object of 'InputParamList'.
outputs	A object of 'OutputParamList'.
steps	A list of 'stepParamList'.

Value

An object of class 'cwlStepParam'.

Examples

input1 <- InputParam(id = "sth")
echo1 <- cwlParam(baseCommand = "echo",
                  inputs = InputParamList(input1))
input2 <- InputParam(id = "sthout", type = "File")
echo2 <- cwlParam(baseCommand = "echo",
                  inputs = InputParamList(input2),
                  stdout = "out.txt")
i1 <- InputParam(id = "sth")
o1 <- OutputParam(id = "out", type = "File", outputSource = "echo2/output")
wf <- cwlStepParam(inputs = InputParamList(i1),
                   outputs = OutputParamList(o1))
s1 <- Step(id = "echo1", run = echo1, In = list(sth = "sth"))
s2 <- Step(id = "echo2", run = echo2, In = list(sthout = "echo1/output"))
wf <- wf + s1 + s2

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