for_id: For each variable in sample sheet

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

For each variable in sample sheet

Description

Run through each variable in sample sheet and report information

Usage

for_id(
  seq_info,
  output_dir = ".",
  name = "",
  vars_list = build_default_variable_list(),
  pmts_list = build_default_parameter_list(),
  bin_list = build_default_binary_list(),
  ref_list = build_default_reference_list(),
  nesting = "",
  merge_level = "library",
  nest_ws = 1,
  print_tree = FALSE,
  executor_id = make_unique_id("loopVariables"),
  task_name = "loopVariables",
  ram = 1,
  threads = 1,
  mode = "local",
  batch_config = build_default_preprocess_config(),
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL,
  verbose = FALSE
)

Arguments

seq_info	Sample sequencing information
output_dir	Path to the output directory.
pmts_list	List with parameters
bin_list	List with binaries
ref_list	List with references
nesting	Starting nesting level
merge_level	Level to merge samples. Default library
nest_ws	Nesting ws to provide. Default 1
executor_id	Executor ID. Default "fastQC"
task_name	Name of the task. Default "fastQC"
ram	RAM memory for batched job. Default 4
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
batch_config	Batch method configuration
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.
var_list	List with variables

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