concat_file_list: Concat multiple delimited files

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

Concat multiple delimited files

Description

This function functions calls Haplotypecaller across multiple regions in parallel. If a vector of normal samples are provided these will be processed in co-joint calling mode. To run in normal mode suppply a normal sample.

Usage

concat_file_list(
  files = "",
  sep = "\t",
  header = FALSE,
  name = FALSE,
  output_name = "concat",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 4,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("concat_files"),
  task_name = "concat_files",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

files	REQUIRED Files to concatenate
sep	OPTIONAL Delimiter separator
header	OPTIONAL Is header present
output_name	OPTIONAL Name for the output. If not given the name of the first tumour sample of the samples will be used.
output_dir	OPTIONAL Path to the output directory.
verbose	OPTIONAL Enables progress messages. Default False.
batch_config	REQUIRED Additional batch configuration if batch mode selected.
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"
executor_id	Task EXECUTOR ID. Default "recalCovariates"
task_name	Task name. Default "recalCovariates"
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.
filter	OPTIONAL Filter variants. Default TRUE

Details

//TODO validate co-joint calling mode

For more information read: https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller

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