configWF {systemPipeR} | R Documentation

## Workflow Steps Selection

### Description

This function allows the user to control of which step of the workflow will be run and the generation of the new RMarkdown.

### Usage

    configWF(x = sysargslist, input_steps = "ALL", exclude_steps = NULL, silent = FALSE, ...)

### Arguments

`x` | object of class `SYSargsList`.
`input_steps` | a character vector of all steps desires to preserve on the output file. Default is `ALL`. It can be used the symbol ":" to select many steps in sequence, for example, input_steps=1:5.2, from step 1 to step 5.2. The symbol "." represents the substeps and symbol "," is used to separate selections. Jump from a major step to sub-step is supported, but if a major step is selected/excluded, all sub-steps of this major step will be selected/excluded. Repeatedly selected steps will only result in a unique step.It is recommended to put major steps in `input_steps`, like `1:4, 6:8, 10`; and unwanted sub-steps in `exclude_step`, like `1.1, 3.1.1-3.1.3, 6.5`. Reverse selecting is supported e.g. `10:1`.
`exclude_steps` | a character vector of all steps desires to remove on the output file.
`silent` | if set to TRUE, all messages returned by the function will be suppressed.
`...` | Additional arguments to pass on to `configWF()`.

### Author(s)

Daniela Cassol

### Examples

    ## Not run:
    library(systemPipeRdata)
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
    SYSconfig <- initProject(projPath="./", targets=targets, script=script, overwrite=TRUE, silent=TRUE)

    sysargslist <- configWF(x=sysargslist)

    ## End(Not run)

[Package systemPipeR version 1.22.0 Index]