SPRproject: Workflow Project Initiation

Description Usage Arguments Value Author(s) See Also Examples

View source: R/sysargslist_utilities.R

Description

Function to construct SYSargsList workflow control environment (S4 object). This function creates the directory structure, with it is not available on the fly to register all the parameters of the workflow. This function checks the project structure, which by default is:

The default structure of the project directories can be modified here.

Usage

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SPRproject(projPath = getwd(), data = "data", param = "param", results = "results",
                      logs.dir= ".SPRproject", sys.file=".SPRproject/SYSargsList.yml", 
                      envir = new.env(), restart = FALSE, load.envir = FALSE,
                      overwrite = FALSE, silent = FALSE)

Arguments

projPath

a character vector of a full project path name. Default is the current path.

data

a character vector of a data directory name. Default is data. This subdirectory in the project stores all the raw data, reference, and annotation files.

param

a character vector of a param directory name. Default is param. This subdirectory in the project stores all the parameter and configuration files.

results

a character vector of a results directory name. Default is results. This subdirectory in the project stores all the analysis results, including but not limited: alignment, variant, and peak files (BAM, VCF, BED); tabular result files; and image/plot files.

logs.dir

a character vector of a logs directory name. Default is .SPRproject.

sys.file

name and path of the SYSargsList file which will store all the project configuration information. Default is .SPRproject/SYSargsList.yml.

envir

the environment in which expr is to be evaluated. Default will create a new.env(). Another option is to use globalenv().

restart

if set to TRUE, existing SYSargsList save in the directory will be used to restart the workflow.

load.envir

after running the workflow, the environment can be saved on disk. This argument allows to load the environment and recover all the objects. This argument can be set as TRUE when restart = TRUE.

overwrite

if set to TRUE, existing logs files or directory of same name will be overwritten.

silent

if set to TRUE, all messages returned by the function will be suppressed.

Value

SPRproject will return a SYSargsList object.

Author(s)

Daniela Cassol

See Also

See also as SYSargsList-class.

Examples

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## Construct SYSargsList object from Rmd file
library(systemPipeRdata)
sal <- SPRproject(overwrite=TRUE)
sal

tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.