renderWF: Populate all the command-line in an 'SYSargs2' object
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

The SYSargs2 S4 class object is constructed from the loadWorkflow, which stores all the information and instructions needed for processing a set of input files with a specific command-line or a series of command-line within a workflow. The renderWF function populates all the command-line for each sample in each step of the particular workflow. Each sample level input/outfile operation uses its own SYSargs2 instance. The output of SYSargs2 define all the expected output files for each step in the workflow, which usually it is the sample input for the next step in an SYSargs2 instance. Between different instances, this connectivity is established by writing the subsetting output with the writeTargetsout function to a new targets file that serves as input to the next loadWorkflow and renderWF call. By chaining several SYSargs2 steps together one can construct complex workflows involving many sample-level input/output file operations with any combination of command-line or R-based software.

1	renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH_"))

`WF`	Object of class `SYSargs2`.
`inputvars`	variables list defined in the `input` file that matches the column names defined in the `targets` file.

SYSargs2 object

Daniela Cassol and Thomas Girke

showClass("SYSargs2") loadWorkflow writeTargetsout

## 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