run_minimap2: Run Minimap2

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

Run Minimap2

Description

Runs the Minimap2 tool, can be used for single end and paired end reads from Illumina, Oxford Nanopore and PacBio platforms

Usage

run_minimap2(
  input1 = NULL,
  input2 = NULL,
  index = NULL,
  genome = NULL,
  sample.name = NULL,
  out.dir = NULL,
  platform = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  minimap2 = NULL,
  version = FALSE
)

Arguments

input1	input1 List of the paths to files containing to the forward reads, required
input2	input2 List of the paths to files containing to the reverse reads, required for paired end sequence data
index	Path to the reference genome minimap index
genome	Path to the reference genome fasta
sample.name	List of the sample names, required
out.dir	Name of the directory from the Minimap2 alignments.
platform	Names of the sequencing platform used for the reads, choose either "ONT", "PacBio" or "Illumina"
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
minimap2	Path to the Minimap2 program, required
version	Returns the version number

Value

A list with the Minimap2 commands

Examples

## Not run: 
  # Set the variables
  minimap2 <- "/software/minimap2-v2.21/minimap2"
  out.dir <- "minmap2_alignments"
  input1 <- c("sample1_R1.fq", "sample2_R1.fq")
  input2 <- c("sample1_R2.fq", "sample2_R2.fq")
  sample.names <- c("sample1", "sample2")
  genome <- "reference.fa"
  index <- "reference.mmi"

  # Get the version number
  run_minimap2(minimap2 = minimap2,
               version = TRUE)

  # Alignment commands
  minimap_cmds <- run_minimap2(input1 = input,
                               sample.name = sample.names,
                               index = index,
                               out.dir = out.dir,
                               platform = "ONT",
                               parallel = TRUE,
                               cores = 2,
                               execute = FALSE,
                               minimap2 = minimap2)

  minimap_cmds

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Aug. 4, 2024, 3:18 a.m.