fastqc: Run FASTQC

In neurogenomics/EpiProcess: Preprocess epigenomic data for downstream analysis

Run FASTQC

Description

Run FASTQC on fastq files.

Usage

fastqc(
  files,
  outdir = file.path(tempdir(), "EpiPrepare_results", "fastqc"),
  dir = file.path(tempdir(), "fastqc_temp"),
  format = "fastq",
  threads = 1,
  background = FALSE,
  force_new = FALSE,
  return_all = FALSE,
  conda_env = "epiprepare",
  verbose = TRUE,
  ...
)

Arguments

files	Paths to files of the type specified in format.
outdir	Create all output files in the specified output directory. Please note that this directory must exist as the program will not create it. If this option is not set then the output file for each sequence file is created in the same directory as the sequence file which was processed.
dir	Selects a directory to be used for temporary files written when generating report images. Defaults to system temp directory if not specified.
format	Bypasses the normal sequence file format detection and forces the program to use the specified format. Valid formats are bam,sam,bam_mapped,sam_mapped and fastq.
threads	Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of memory so you shouldn't run more threads than your available memory will cope with, and not more than 6 threads on a 32 bit machine.
force_new	If FASTQ results for these files already exist, overwrite them (default: FALSE).
return_all	Return all FASTQ results located in the outdir, even if they are not from one of the files in this run (default: FALSE).
verbose	Print messages.
...	Additional string arguments to be passed to fastqc.
ex	Path to fastqc software executable.

neurogenomics/EpiProcess documentation built on March 19, 2022, 7:13 a.m.