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, ref="master", subdir=NULL, url=NULL, urlname=NULL)

Arguments

workflow	character string of workflow templates to be generated. Supported values can be checked with the ⁠\link{availableWF}()⁠ function. Workflow name containing a '/' are treated as GitHub repositories and installed using ⁠BiocManager::\link{install_github}()⁠. For Github workflow templates, the format systemPipeR/repo is required. See Details.
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.
ref	Desired GitHub reference for the branch name. Default to master branch.
subdir	subdirectory within GitHub repo that contains the R package, if it is required.
url	character string of a specifies the URL of a different version of the R Markdown workflow template or other file to download. The default NULL copies the current version available in the 'systemPipeRdata' or the workflow template on GitHub being selected.
urlname	character string with the name where the downloaded file is saved. This is argument is required when the url is provided.

Details

When installing GitHub Workflow Packages under systemPipeR Organization, it is requested to the remotes package function ⁠BiocManager::\link{install_github}()⁠ to build vignettes and also install all the dependencies, via dependencies=TRUE, build_vignettes=TRUE.

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

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, url=NULL, urlname=NULL)
setwd("varseq")

## List Workflow Templates from \code{systemPipeRdata} package and \code{systemPipeR} Organization 
availableWF(github = TRUE)
## Generate 'systemPipeR/systemPipeChIPseq' workflow environment 
genWorkenvir(workflow="systemPipeR/systemPipeChIPseq", mydirname=NULL, ref="master", subdir=NULL)
setwd("systemPipeChIPseq")

## Download a specific R Markdown file
genWorkenvir(workflow="systemPipeR/systemPipeRNAseq", mydirname="rnaseq", url = "https://raw.githubusercontent.com/systemPipeR/systemPipeRNAseq/cluster/vignettes/systemPipeRNAseq.Rmd", urlname = "rnaseq_V-cluster.Rmd")

## End(Not run)

tgirke/systemPipeRdata documentation built on Oct. 19, 2023, 9:20 p.m.