cwlLoad

To source Rcwl scripts

cwlLoad(
  rname,
  bfc = NULL,
  env = .GlobalEnv,
  cwlfile = NULL,
  dir = tempdir(),
  ...
)

Arguments

rname	The name or filepath of tool or pipeline to install (`rname` or `fpath` column from the `bfc` object returned from `cwlSearch`). It can also be a CWL url or a github repo.
bfc	The `BiocFileCache` object for the recipes returned from `cwlUpdate`. The default is NULL which automatically detect the "Rcwl" cache directory.
env	The R enviroment to export to. The default is `.GlobalEnv`.
cwlfile	For github repo input, The relative path of a CWL file inside of the github repo.
dir	For github repo input, the directory to clone the repo.
...	More options from git2r::clone.

Value

A `cwlProcess` object. For pipelines, the dependent tools will also loaded.

Details

Note to developers that the dependent Rcwl scripts should be included in the recipe with `@include` tag.

Examples

if (FALSE) {
tls <- cwlSearch("bwa")
tls$rname
bwa <- cwlLoad("tl_bwa")
bwa <- cwlLoad(tls$fpath[tls$rname == "tl_bwa"])  ## equivalent
bwa
}