runCWL: run cwlProcess

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

run cwlProcess

Description

Execute a cwlProcess object with assigned inputs.

Usage

runCWL(
  cwl,
  cwlRunner = "cwltool",
  outdir = ".",
  cachedir = NULL,
  cwlTemp = NULL,
  cwlArgs = character(),
  stdout = TRUE,
  stderr = TRUE,
  showLog = FALSE,
  docker = TRUE,
  conda = FALSE,
  yml_prefix = deparse(substitute(cwl)),
  yml_outdir = tempfile(),
  ...
)

Arguments

cwl	A 'cwlProcess' or 'cwlWorkflow' object.
cwlRunner	The path to the 'cwltool' or 'cwl-runner'. If not exists, the cwltool package will be installed by 'reticulate'.
outdir	Output directory, default is current working directory.
cachedir	Directory to cache intermediate workflow outputs to avoid recomputing steps.
cwlTemp	File path to keep intermediate files. If a directory path is given, the intermediate files will be kept in the directory. Default is NULL to remove all intermediate files.
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.
conda	Whether to install packages using conda if 'SoftwareRequirement' is defined.
yml_prefix	The prefix of '.cwl' and '.yml' files that are to be internally executed.
yml_outdir	The output directory for the '.cwl' and '.yml' files.
...	The other options from 'writeCWL' and 'system2'.

Value

A list of outputs from tools and logs from cwltool.

Examples

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

hubentu/Rcwl documentation built on March 13, 2023, 11:13 p.m.