run cwlProcess

Execute a cwlProcess object with assigned inputs.

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