loadWorkflow {systemPipeR} | R Documentation

## Constructs SYSargs2 object from CWL param and targets files

### 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. The`CWL 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

[Package systemPipeR version 1.21.6 Index]