cwlLoad: cwlLoad

In RcwlPipelines: Bioinformatics pipelines based on Rcwl

Description

To source Rcwl scripts

Usage

cwlLoad(rname, bfc = NULL, env = .GlobalEnv)

Arguments

rname	The name or filepath of tool or pipeline to install ('rname' or 'fpath' column from the 'bfc' object returned from 'cwlSearch').
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'.

Details

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

Value

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

Examples

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

## End(Not run)

RcwlPipelines documentation built on March 7, 2021, 2 a.m.