parse_picard_metrics: Parse HS metrics and WGS metrics picard info

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

Parse HS metrics and WGS metrics picard info

Description

Parse HS metrics and WGS metrics picard info

Usage

parse_picard_metrics(
  summary = "",
  output_dir = ".",
  output_name = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 1,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("parsePicardMetrics"),
  task_name = "parsePicardMetrics",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

summary	Path to Picard summary file
output_dir	Path to the output directory.
output_name	File output name
verbose	Enables progress messages. Default False.
ram	RAM memory to use in GB. Default 4.
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	OPTIONAL HOld job until job is finished. Job ID.
executor	OPTIONAL Task executor name. Default "recalCovariates"
task	OPTIONAL Task name. Default "recalCovariates"

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