trimming_skewer: Adapter sequence trimmer using skewer

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Adapter sequence trimmer using skewer

Description

Detects and removes adapter sequences from single and paired read data

Usage

trimming_skewer(
  bin_skewer = build_default_tool_binary_list()$bin_skewer,
  file_R1 = "",
  file_R2 = "",
  xadapt = "",
  yadapt = "",
  mean_quality = 0,
  min_length = 18,
  max_length = "",
  threads = 3,
  ram = 4,
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  output_name = "",
  mode = "local",
  executor_id = make_unique_id("trimmingSkewer"),
  task_name = "trimmingSkewer",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_skewer	Path to skewer executable. Default path tools/skewer/skewer.
file_R1	Path to the input file with the sequence.
file_R2	Optional Path to the input with the reverse read sequence.
xadapt	Optional Adapter sequence/file.
yadapt	Optional Adapter sequence/file.
mean_quality	The lowest mean quality value allowed before trimming. Default 0
min_length	Minimum length of reads allowed after trimming. Default 18
max_length	Maximum length of reads allowed after trimming. Default No limit.
threads	Number of CPU cores to use. Default 3.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Executor ID. Default "trimmingSkewer"
task_name	Name of the task. Default "trimmingSkewer"
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

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