renderWF {systemPipeR} | R Documentation

## Populate all the command-line in an `SYSargs2` object

### Description

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.

### Usage

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

### Arguments

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

### Value

`SYSargs2` object

### Author(s)

Daniela Cassol and Thomas Girke

### See Also

`showClass("SYSargs2")` `loadWorkflow` `writeTargetsout`

### 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", package="systemPipeR")
    WF <- loadWorkflow(targets=targets, wf_file="hisat2-se/hisat2-mapping-se.cwl",
                       input_file="hisat2-se/hisat2-mapping-se.yml",
                       dir_path=dir_path)
    WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH_", SampleName="_SampleName_"))
    WF

[Package systemPipeR version 1.18.2 Index]