run_centrifuge: Run Centrifuge

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

Run Centrifuge

Description

Runs the Centrifuge tool

Usage

run_centrifuge(
  input1 = NULL,
  input2 = NULL,
  index = NULL,
  sample.name = NULL,
  out.dir = NULL,
  threads = 10,
  min_hit_length = 15,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  centrifuge = NULL,
  version = FALSE
)

Arguments

input1	List of the paths to files containing to the forward reads
input2	List of the paths to files containing to the reverse reads
index	Path to the reference metagenome index
sample.name	List of the sample names
out.dir	Name of the directory from the Centrifuge output
threads	Number of threads for Centrifuge to use, default set to 10
min_hit_length	minimum length of partial hits, default set to the minimum allowed of 15
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
centrifuge	Path to the Centrifuge program
version	Returns the version number

Value

A list with the Centrifuge commands

Examples

## Not run: 
path <- "/software/centrifuge-1.0.4/centrifuge"
in1 <- c("sample_1_1.fq","sample_2_1.fq")
in2 <- c("sample_1_2.fq","sample_2_2.fq")
sample_names <- c("sample_1","sample_2")
ref <- "/path/to/centrifuge/reference/index"

run_centrifuge(input1 = in1,
               input2 = in2,
               index = ref,
               sample.name = sample_names,
               out.dir = "test_dir",
               min_hit_length = 16,
               execute = FALSE,
               centrifuge = path)

## End(Not run)

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