cwlWorkflow function

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

steps: Function to extract and assign workflow step slots.

cwlWorkflow(
  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 = cwlStepList()
)

# S4 method for 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