run_fastq_screen: Run Fastq-Screen

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run Fastq-Screen

Description

Run the fastq-screen tool

Usage

run_fastq_screen(
  input = NULL,
  out.dir = NULL,
  aligner = "bwa",
  conf = NULL,
  top = NULL,
  threads = 2,
  parallel = FALSE,
  cores = 4,
  fastq_screen = NULL,
  execute = TRUE,
  version = FALSE
)

Arguments

input	Vector of the full names and paths of the fastq files, usually only the forward reads set, required
out.dir	Path to the directory to which to write the results. If NULL, which is the default, a directory named "fastq_screen" is created in the current working directory.
aligner	The name of the program to perform the mapping, default bwa. Valid mappers are "bwa", "bowtie" and "bowtie2". Default set to bwa
conf	The path to the configuration file, required
top	Create a temporary datset by selecting the number of reads followed by how many to skip e.g setting 'top' to 500000,1000000 will skip the first 1 million reads and map 500 thousand reads
threads	The number of threads to use. The default is 2.
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
fastq_screen	The path to the fastq_screen executable.
execute	Whether to execute the commands or not, default set to TRUE
version	Returns the version number

Value

A file with the FastqScreen commands

Examples

 ## Not run: 
path <- "raw_reads"
mate1 <- list.files(path = path, pattern = "*_R1_001.fastq.gz$", full.names = TRUE)

fastq_screen_cmds <- run_fastq_screen(input = mate1,
                                      out.dir = fastq.screen.dir,
                                      conf = "/export/jessie3/gmh5n/PipelineTest/fastq_screen.conf",
                                      top = "100000,5000",
                                      fastq_screen = "/software/fastq_screen_v0.13.0/fastq_screen")

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.