cwlWorkflow: cwlWorkflow function

In hubentu/Rcwl: An R interface to the Common Workflow Language

cwlWorkflow function

Description

The constructor function for 'cwlWorkflow' object, which connects multiple command line steps into a workflow.

steps: Function to extract and assign workflow step slots.

Usage

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

## S4 method for signature 'cwlWorkflow,cwlStep'
e1 + e2

steps(cwl)

steps(cwl) <- value

Arguments

cwlVersion	CWL version
cwlClass	"Workflow".
requirements	Requirements that apply to either the runtime environment or the workflow engine.
id	A user-defined unique identifier for this workflow.
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	An object of 'InputParamList'.
outputs	An object of 'OutputParamList'.
steps	A list of 'cwlStepList'.
e1	A 'cwlWorkflow' object.
e2	A 'cwlStep' object.
cwl	A 'cwlWorkflow' object.
value	A list of 'cwlSteps' to assign.

Value

cwlWorkflow: An object of class 'cwlWorkflow'.

steps: A list of 'cwlStep' objects.

See Also

stepInParamList

Examples

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

hubentu/Rcwl documentation built on May 9, 2024, 2:14 a.m.