gather_bam_files_picard: Wrapper around gatk GatherBamFiles 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 GatherBamFiles function

Description

This functions collects the Recalibration reports generated from scattered parallel_apply_BQSR output This function wraps around gatk GatherBamFiles function. For more information about this function: https://gatk.broadinstitute.org/hc/en-us/articles/360037055512-GatherBamFiles-Picard-

Usage

gather_bam_files_picard(
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bam = "",
  output_name = "File",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  clean = FALSE,
  executor_id = make_unique_id("gatherBAM"),
  task_name = "gatherBAM",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_picard	REQUIRED Path to picard executable. Default tools/picard/build/libs/picard.jar.
bam	REQUIRED Path to BAM file/s.
output_name	OPTIONAL Name for the output file name.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
threads	OPTIONAL Number of threads to split the work. Default 4
ram	OPTIONAL RAM memory to asing to each thread. Default 4
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
clean	Clean input files. Default TRUE.
executor_id	Task EXECUTOR ID. Default "gatherBAM"
task_name	Task name. Default "gatherBAM"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Show job updates every update time. Default 60
hold	OPTIONAL HOld job until job is finished. Job ID.
tmp_dir	OPTIONAL Path to the temporary directory.

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