SYSargsList {systemPipeR}R Documentation

SYSargsList

Description

S4 class container for storing parameters of command-line- or R-based software. SYSargsList instances are constructed by the SYSargsList function.

Usage

SYSargsList(args = NULL, targets = NULL, wf_file = NULL, input_file = NULL, dir_path = ".", inputvars = NULL, step_index = "default", silent = FALSE, restartProject = TRUE, rm_targets_col = NULL, dependency = NULL)

Arguments

args

SYSargs2 object

targets

the path to targets file. The targets file can be either a simple tabular or yml file. Also, it is possible to assign NULL to run the pipeline without the 'targets' file. This can be useful for running specific workflows that do not require input files.

wf_file

name and path to CWL param file.

input_file

name and path to input file.

dir_path

full path to the directory with the CWL param and input files.

inputvars

variables list defined in the input file that matches the column names defined in the targets file.

step_index

character with the step index name.

silent

If set to TRUE, all messages returned by the function will be suppressed.

restartProject

restart previous workflow run.

rm_targets_col

targets file colunms to be removed.

dependency

step previous dependency.

Value

SYSargsList object

Author(s)

Daniela Cassol

See Also

showClass("SYSargsList")

Examples

dir_path <- system.file("extdata/cwl/example/", package="systemPipeR")
sal <- SYSargsList(wf_file="example.cwl", input_file="example_single.yml", dir_path = dir_path)
sal
cmdlist(sal)

[Package systemPipeR version 1.26.3 Index]