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]