parallel_sample_bigBedToBed_ucsc: Parallel implementation of bigBedToBed function

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

Parallel implementation of bigBedToBed function

Description

This function takes a bigBed file and converts it to a bed file

Usage

parallel_sample_bigBedToBed_ucsc(
  bin_ucsc = build_default_tool_binary_list()$bin_ucsc$bigBedToBed,
  bigBeds = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("parSampleBigBedToBed"),
  task_name = "parSampleBigBedToBed",
  mode = "local",
  time = "48:0:0",
  threads = 4,
  ram = 4,
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_ucsc	Path to bigBedtoBed script. Default path tools/OtherToolsr/bigBedToBed.
bigBeds	Path to directory with BAM files to merge.
verbose	OPTIONAL Enables progress messages. Default False.#
executor_id	Task EXECUTOR ID. Default "mardupsGATK"
task_name	Task name. Default "mardupsGATK"
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
threads	Number of threads . Default 4
ram	RAM memory. Default 4
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	OPTIONAL Hold job until job is finished. Job ID.
header	Create column header. Default TRUE

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