run_fastq_screen: Run Fastq-Screen

Description Usage Arguments Value Examples

View source: R/run_fastq_screen.R

Description

Run the fastq-screen tool

Usage

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run_fastq_screen(
  fq.files = NULL,
  out.dir = NULL,
  aligner = "bwa",
  conf = NULL,
  top = NULL,
  threads = 2,
  fastq_screen = NULL,
  version = FALSE
)

Arguments

fq.files

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.

fastq_screen

The path to the fastq_screen executable.

version

Returns the version number

Value

A file with the FastqScreen commands

Examples

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

fastq_screen_cmds <- run_fastq_screen(fq.files = 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 June 19, 2021, 1:08 p.m.