run_nanofilt: Run the NanoFilt program

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

Run the NanoFilt program

Description

Runs the NanoFilt tool, can be used to filter nanopore reads reads

Usage

run_nanofilt(
  input = NULL,
  sample_names = NULL,
  out_dir = NULL,
  min_length = NULL,
  parallel = FALSE,
  cores = 4,
  execute = FALSE,
  nanofilt = NULL,
  version = FALSE
)

Arguments

input	List of the paths to files containing to the nanopore reads, required
sample_names	List of sample names, required
out_dir	Name of the directory from the BWA output
min_length	Minimum length for the reads
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
nanofilt	Path to the NanoFilt program, required
version	Returns the version number

Value

A list with the NanoFilt commands

Examples

 ## Not run: 
path <- "/Path/To//NanoFilt"
input_files <- c("sample1.fastq", "sample2.fastq")
sample_names <- gsub(".fastq","",input_files)
out_directory <- "filtered_reads"
min_length <- 10000

run_nanofilt(input = input_files,
             sample_names = sample_names,
             out_dir = out_directory,
             min_length = min_length,
             nanofilt = path)

## End(Not run)

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