Run custom read preprocessing functions

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.

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

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_"))
if (FALSE) {
preprocessReads(args=trim[1], Fct="trimLRPatterns(Rpattern='GCCCGGGTAA', subject=fq)", batchsize=100000, overwrite=TRUE, compress=TRUE)
}

## 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
#> Instance of 'SYSargs2':
#>    Slot names/accessors: 
#>       targets: 18 (M1A...V12B), targetsheader: 4 (lines)
#>       modules: 0
#>       wf: 0, clt: 1, yamlinput: 6 (inputs)
#>       input: 18, output: 18
#>       cmdlist: 18
#>    Sub Steps:
#>       1. trim-pe (rendered: TRUE)
#> 
#> 
if (FALSE) {
preprocessReads(args=trim[1], Fct="trimLRPatterns(Rpattern='GCCCGGGTAA', subject=fq)", batchsize=100000, overwrite=TRUE, compress=TRUE)
}