gather_BQSR_reports_gatk: Wrapper around gatk GatherBQSRReports 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

Wrapper around gatk GatherBQSRReports function

Description

This functions collects the Recalibration reports generated from scattered parallel_generate_BQSR output This function wraps around gatk GatherBQSRReports function. For more information about this function: https://gatk.broadinstitute.org/hc/en-us/articles/360036829851-GatherBQSRReports

Usage

gather_BQSR_reports_gatk(
  sif_gatk = build_default_sif_list()$sif_gatk,
  report = "",
  output_name = "Report",
  clean = FALSE,
  output_dir = ".",
  tmp_dir = ".",
  verbose = FALSE,
  executor_id = make_unique_id("gatherBQSR"),
  task_name = "gatherBQSR",
  batch_config = build_default_preprocess_config(),
  mode = "local",
  time = "48:0:0",
  threads = 4,
  ram = 4,
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sif_gatk	REQUIRED Path to gatk executable. Default tools/gatk/gatk.
report	REQUIRED Path to indivual reports.
output_name	OPTIONAL Name for the output report file.
clean	Clean input files. Default TRUE.
output_dir	OPTIONAL Path to the output directory.
tmp_dir	OPTIONAL Path to temporary directory.
verbose	OPTIONAL Enables progress messages. Default False.
executor_id	Task EXECUTOR ID. Default "gatherBQSR"
task_name	Task name. Default "gatherBQSR"
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 to split the work. Default 3
ram	OPTIONAL If batch mode. RAM memory in GB per job. Default 1
update_time	OPTIONAL If batch mode. Show job updates every update time. Default 60
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL HOld job until job is finished. Job ID.

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