genWorkenvir: Generate workflow templates

In tgirke/systemPipeRdata: systemPipeRdata: Workflow templates and sample data

Generate workflow templates

Description

Generates workflow templates for systemPipeR package. The template environemts contain a predifined directory structure along with run parameter files and sample data. The strucutre of the workflow templates and the sample data are described in all details in the Overview Vignette of the systemPipeR package.

Usage

genWorkenvir(workflow, mydirname=NULL, bam=FALSE)

Arguments

workflow	character string of workflow templates to be generated. Supported values can be checked with the ⁠\link{availableWF}()⁠ function.
mydirname	Specifies the name of the workflow directory. The default NULL uses the name of the chosen workflow. An error is issued if a directory of the same name and path exists already.
bam	If bam=TRUE pregenerated short read alignment (BAM) files will be included in the results directory of the workflow environment. Note, these BAM files have been generated with the HISAT2 aligner using the FASTQ files provided in the data directory. The default bam=FALSE omits this step meaning no BAM files will be copied into the results directory.

Details

Check the output of ⁠\link{availableWF}()⁠ to the current workflow templates available on systemPipeR Organization.

For an interactive() session, the readline() function provides the option choose between proceeding or not, through options: yes or no. For non-interactive use, if there is no package install, the option yes will be selected.

Value

Workflow directory containing sample data and parameter files along with the following subdirectories:

param/	stores parameter files
data/	stores input data
results/	stores output results

For more details, please consult the Overview Vignette (HTML) of the systemPipeR package (http://bioconductor.org/packages/systemPipeR).

Author(s)

Thomas Girke and Daniela Cassol

Examples

## Return location of sample data
samplepaths <- pathList()
## Not run: 
## Generate varseq workflow environment
genWorkenvir(workflow="varseq", mydirname=NULL)
setwd("varseq")

## End(Not run)

tgirke/systemPipeRdata documentation built on Oct. 24, 2024, 9:49 p.m.