index_ref_bwa: Index reference genome

View source: R/bwa.R

index_ref_bwaR Documentation

Index reference genome

Description

This function indexes a reference genome using the bwa aligner

Usage

index_ref_bwa(
  bin_bwa = build_default_tool_binary_list()$bin_bwa,
  file = "",
  threads = 4,
  ram = 4,
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("refIndex"),
  task_name = "refIndex",
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_bwa

Path to bwa executable. Default path tools/bwa/bwa.

file

Path to the input file with the reference genome in FASTA format.

verbose

Enables progress messages. Default False.

executor_id

Task EXECUTOR ID. Default "refIndex"

task_name

Task name. Default "refIndex"

mode

REQUIRED Where to parallelize. Default local. Options "local","batch"

time

OPTIONAL If batch mode. Max run time per job. Default "48:0:0"

update_time

OPTIONAL If batch mode. Job update time in seconds. Default 60.

wait

OPTIONAL If batch mode wait for batch to finish. Default FALSE

output_dir

Path to the output directory.


TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.