preprocessReads: Run custom read preprocessing functions

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

Run custom read preprocessing functions

Description

Applies custom read preprocessing functions to single-end or paired-end FASTQ files. The function uses the FastqStreamer function from the ShortRead package to stream through large files in a memory-efficient manner.

Usage

preprocessReads(args = NULL,
                FileName1 = NULL, FileName2 = NULL, 
                outfile1 = NULL, outfile2 = NULL, 
                Fct, batchsize = 100000, overwrite = TRUE, ...)

Arguments

args	Object of class SYSargs or SYSargs2.
FileName1	Path to input forward fastq file. Defaul is NULL.
FileName2	Path to input reverse fastq file. Defaul is NULL
outfile1	Path to output forward fastq file. Defaul is NULL
outfile2	Path to output reverse fastq file. Defaul is NULL
Fct	character string of custom read preprocessing function call where both the input and output needs to be an object of class ShortReadQ. The name of the input ShortReadQ object needs to be fq.
batchsize	Number of reads to process in each iteration by the internally used FastqStreamer function.
overwrite	If TRUE existing file will be overwritten.
...	To pass on additional arguments to the internally used writeFastq function.

Value

Writes to files in FASTQ format. Their names are specified by outpaths(args).

Author(s)

Thomas Girke

See Also

FastqStreamer

Examples

## Preprocessing of single-end reads
dir_path <- system.file("extdata/cwl/preprocessReads/trim-se", package="systemPipeR")
targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
trim <- loadWorkflow(targets=targetspath, wf_file="trim-se.cwl", input_file="trim-se.yml", dir_path=dir_path)
trim <- renderWF(trim, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
## Not run: 
preprocessReads(args=trim[1], Fct="trimLRPatterns(Rpattern='GCCCGGGTAA', subject=fq)", batchsize=100000, overwrite=TRUE, compress=TRUE)

## End(Not run)

## Preprocessing of paired-end reads
dir_path <- system.file("extdata/cwl/preprocessReads/trim-pe", package="systemPipeR")
targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
trim <- loadWorkflow(targets=targetspath, wf_file="trim-pe.cwl", input_file="trim-pe.yml", dir_path=dir_path)
trim <- renderWF(trim, inputvars=c(FileName1="_FASTQ_PATH1_", FileName2="_FASTQ_PATH2_", SampleName="_SampleName_"))
trim
## Not run: 
preprocessReads(args=trim[1], Fct="trimLRPatterns(Rpattern='GCCCGGGTAA', subject=fq)", batchsize=100000, overwrite=TRUE, compress=TRUE)

## End(Not run)

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.