ctk_fastq2collapse: Wrapper function for ctk's fastq2collapse

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Wrapper function for ctk's fastq2collapse

Description

Wrapper function for ctk's fastq2collapse

Usage

ctk_fastq2collapse(
  filesToRun,
  outFile = file.path(dirname(fileToRun), paste("Collapsed_", basename(fileToRun), sep =
    "")),
  sb = "fastq2collapse.pl",
  perl = "perl",
  PATHTOPERLLIB = NULL,
  stderr = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_fastq2collapse_stderr.txt")),
  stdout = file.path(dirname(fileToRun), paste0(basename(fileToRun),
    "_ctk_fastq2collapse_stdout.txt")),
  useClipRConda = ifelse(is.null(getOption("CLIPflexR.condaEnv")), FALSE, TRUE),
  additional_Args = NULL,
  verbose = FALSE,
  writelog = T
)

Arguments

filesToRun	path to file to process (fastq).
outFile	output file (fastq).
sb	path to fastq2collapse.pl from CTK.
perl	path to PERL
PATHTOPERLLIB	path to PERL5LIB.
stderr	path to stdout file.
stdout	path to stdout file.
useClipRConda	use conda environment installed by Herper, TRUE (default) or FALSE.
additional_Args	additional arguments to be passed to system call.
verbose	print messages, TRUE or FALSE (default).
writelog	write stderr/stdout logs, TRUE (default) or FALSE.

Value

Path to collapsed fastq file.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile_FF <- ctk_fastqFilter(testFQ,qsFilter = "mean:0-29:20",verbose=TRUE)
FqFile <- decompress(FqFile_FF,overwrite=TRUE)
FqFile_clipped <- fastx_clipper(FqFile,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose=TRUE)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.