preprocess_seq: Preprocess sequencing data

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

Preprocess sequencing data

Description

Preprocess sequencing data

Usage

preprocess_seq(
  sample_sheet = build_default_sample_sheet(),
  vars_list = build_default_variable_list(),
  config = suppressWarnings(build_default_config()),
  opts_list = build_default_option_list(),
  pmts_list = build_default_parameter_list(),
  steps_list = build_default_steps_list(),
  bin_list = build_default_binary_list(),
  ref_list = build_default_reference_list(),
  merge_level = "library",
  nest_ws = 1,
  nesting = "",
  executor_id = make_unique_id("preprocessSEQ"),
  task_name = "preprocessSEQ",
  output_dir = ".",
  ram = 1,
  header = TRUE,
  sep = "",
  threads = 1,
  mode = "local",
  batch_config = build_default_preprocess_config(),
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL,
  verbose = FALSE
)

Arguments

sample_sheet	Input sample sheet
config	Default tool configure
merge_level	Which level to merge samples
nest_ws	Nesting white-space separator
executor_id	Executor ID. Default "fastQC"
task_name	Name of the task. Default "fastQC"
output_dir	Path to the output directory.
ram	RAM memory for batched job. Default 4
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
hold	Job to hold on in batched mode.
verbose	Enables progress messages. Default False.
vars	Default variables

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