initWF: Workflow Project Initiation

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

Collection of functions to construct SYSargsList workflow control environment (S4 object). initWF function constructs SYSargsList S4 class objects from a script file. The latter is an RMarkdown file containing all the workflow steps. In the future, it will be accepting other formats, as Rscript and bash. This file is defined either by the sysconfig file or script argument. Internally, initWF function calls initProject function, which creates a storage folder for all the logs, and the output to stdout or stderr. This function also creates the SYSconfig.yml on the fly to register all the parameters of the workflow. This function checks the project structure, which by default is:

• SYSproject/

  • data/

  • param/

  • results/

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

Usage

initWF(sysconfig = NULL, subProj = FALSE, dir_str = "level0", dirName = "default", 
script, targets = NULL, silent = FALSE, overwrite = FALSE)

initProject(projPath = "./", data = "data", param = "param", results = "results", 
script = NULL, targets = NULL, subProj = FALSE, filename = "SYSconfig.yml", 
overwrite = FALSE, silent = FALSE)

SYSproject(projPath = "./", overwrite = FALSE, silent = FALSE, tempdir = FALSE)

Arguments

sysconfig	a character vector of a full sysconfig file path name. Default is NULL, which the function understand that the Rmd will be provide.
subProj	is set TRUE, the project will be initialized and a new directory will be generated, at the same level as the current project, maintaining the directory structure. It will create an empty results folder, coping the param from the current project, and creating a symbolic link for the data folder.
dir_str	if subProj is set TRUE, it will create a directory on the same level of the current location.Default is level0.
dirName	if subProj is set TRUE, the directory name can be defined here.
script	a character vector of a full script file path name. This file containing all the information to run all the steps on the workflow analysis. The current format accepted is Rmd.
targets	a character vector of a full sample annotation file path name. Default is NULL. 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.
silent	if set to TRUE, all messages returned by the function will be suppressed.
overwrite	if set to TRUE, existing files or directories of same name will be overwritten.
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.
filename	name and path of the output file which will store all the project configuration information. Default is SYSconfig.yml.
tempdir	if set to TRUE, the temporary directory for the workflow management files will be created.

Details

SYSproject function detects and creates the project directory to store all the flat files from the workflow management. If overwrite is TRUE, the previous folder will be deleted and replace for a new one. Also, the user can choose to store all this information on a temporary folder, setting tempdir = TRUE.

initProject function detects an existing project or creates a project structure on the path provide.

Value

SYSproject will return a character vector containing the path name. initProject will return a list containing all the information in the sysconfig file. initWF will return a SYSargsList object.

Author(s)

Daniela Cassol and Thomas Girke

See Also

See also as SYSargsList-class.

Examples

## Not run: 
## Construct SYSargsList object from Rmd file
library(systemPipeRdata)
script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- tempdir()
SYSconfig <- initProject(projPath=dir_path, targets=targets, script=script, overwrite = TRUE)
sysargslist <- initWF(sysconfig ="SYSconfig.yml")

## End(Not run)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.