loadWorkflow: Constructs SYSargs2 object from CWL param and targets files

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

The constructor functions create an SYSargs2 S4 class object from three input files: a CWL param and input files, and one simple tabular or yml file, a targets file. The latter is optional for workflow steps lacking input files. TheCWL param provides all the parameters required for running command-line software, following the standard and specification defined on Common Workflow Language (CWL). The input file provides additional information for the command-line, allowing each sample level input/outfile operation uses its own SYSargs2 instance. In the targets file users could provide the paths to the initial sample input files (e.g. FASTQ) along with sample labels, and if appropriate biological replicate and contrast information for controlling differential abundance analyses.

Usage

loadWorkflow(targets = NULL, wf_file, input_file, dir_path = ".")

Arguments

targets	either the path to targets file or an object of SYSargs2 class. 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.

Value

SYSargs2 object

Author(s)

Daniela Cassol and Thomas Girke

See Also

renderWF showClass("SYSargs2")

Examples

## Construct SYSargs2 object from CWl param, CWL input, and targets files 
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
WF <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl", 
                  input_file="hisat2-mapping-se.yml", dir_path=dir_path)
WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
WF

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.