cwlLoad: cwlLoad

In rworkflow/RcwlPipelines: Bioinformatics pipelines based on Rcwl

cwlLoad

Description

To source Rcwl scripts

Usage

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. 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.

Details

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

Value

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

Examples

## Not run: 
tls <- cwlSearch("bwa")
title(tls)
bwa <- cwlLoad("tl_bwa")
bwa <- cwlLoad(tls$fpath[tls$rname == "tl_bwa"])  ## equivalent
bwa

## End(Not run)

rworkflow/RcwlPipelines documentation built on Nov. 18, 2023, 8:51 p.m.