runCWL: run cwlProcess

View source: R/runCWL.R

runCWLR Documentation

run cwlProcess

Description

Execute a cwlProcess object with assigned inputs.

Usage

runCWL(
  cwl,
  outdir = ".",
  cwlRunner = "cwltool",
  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.

outdir

Output directory, default is current working directory.

cwlRunner

The path to the 'cwltool' or 'cwl-runner'. If not exists, the cwltool package will be installed by 'reticulate'.

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)

rworkflow/Rcwl documentation built on May 10, 2024, 6:21 a.m.