wdltoolInputs: return inputs from wdltool

In seandavi/wdlRunR: Interact with the Broad Institute Cromwell workflow manager

Description

This little function just runs the command-line wdltool inputs on a wdl file and returns a data.frame of input names and input types.

Usage

wdltoolInputs(wdlfile, wdltoolJar = Sys.getenv("WDLTOOL_JAR",
  "wdltool.jar"))

Arguments

wdlfile	The filename of a WDL file from which to get inputs.
wdltoolJar	The filename of the wdltool jar file; if not specified, the environment variable WDLTOOL_JAR is consulted.

Value

a 2-column data.frame with the input name and the input type as the two columns.

Examples

version = '0.8'
tmpfile = file.path(tempdir(),'wdltool.jar')
fp = getWdltoolJar(wdltool_version = version,
                   destfile = tmpfile)
wdltoolInputs(system.file(package='wdlRunR','wdl/fastqc_task.wdl'))

seandavi/wdlRunR documentation built on Oct. 28, 2021, 12:42 a.m.