runCWL: run cwlParam

In Rcwl: An R interface to the Common Workflow Language

Description

Execute a cwlParam object with assigned inputs.

Usage

runCWL(
  cwl,
  prefix = tempfile(),
  cwlRunner = "cwltool",
  cwlTemp = NULL,
  outdir = ".",
  cwlArgs = character(),
  stdout = TRUE,
  stderr = TRUE,
  showLog = FALSE,
  docker = TRUE,
  ...
)

Arguments

cwl	A 'cwlParam' or 'cwlStepParam' object.
prefix	The prefix of 'cwl' and 'yml' file to write.
cwlRunner	The path to the 'cwltool' or 'cwl-runner'. If not exists, the cwltool package will be installed by 'reticulate'.
cwlTemp	Path to keep temporary files. If a directory path is given, the temporary files will be kept in the directory.
outdir	Output directory, default current directory.
cwlArgs	The arguments for 'cwltool' or 'cwl-runner'. For example, "–debug" can work with 'cwltool' to show debug information.
stdout	standard output from 'system2'.
stderr	standard error from 'system2'. By setting it to "", the detailed running logs will return directly.
showLog	Whether to show log details to standard out. i.e. stderr = "".
docker	Whether to use docker, or "sigularity" if use Singularity runtime to run container.
...	The other options from 'writeCWL' and 'system2'.

Value

A list of outputs from tools and logs from cwltool.

Examples

input1 <- InputParam(id = "sth")
echo <- cwlParam(baseCommand = "echo",
                 inputs = InputParamList(input1))
echo$sth <- "Hello World!"
## res <- runCWL(echo)

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