multisample_clonet_trento: Process multiple tumour samples using CLONET

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

Process multiple tumour samples using CLONET

Description

This function identifies a set of BAM files as tumour and normal and processes them using the CLONET pipeline in parallel If sample sheet is provided data has to be supplied in the following format: patient_id tumour normal version

Usage

multisample_clonet_trento(
  sample_sheet = NA,
  bam_dir = "",
  normal_id = "",
  patient_id = "",
  version = "V3",
  tc = NULL,
  ploidy = NULL,
  tmp_dir = ".",
  header = TRUE,
  sep = "",
  threads = 3,
  ram = 4,
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("multi_clonet"),
  task_name = "multi_clonet",
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

sample_sheet	Path to sample sheet or data.frame.
bam_dir	Path to bam directory. Only if sample sheet is not provided.
normal_id	Normal sample identifier. Only if sample sheet is not provided.
patient_id	Patient id. Only if sample sheet is not provided.
tc	Pre-computed tumour content. Default NULL.
ploidy	Pre-computed ploidy. Default NULL.
tmp_dir	Path to temporary file directory.
threads	Number of CPU cores to use. Default 3.
ram	RAM memory for batched job. Default 4
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
executor_id	Executor ID. Default "preprocess_trento"
task_name	Name of the task. Default "preprocess_trento"
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
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	Job to hold on in batched mode.

Details

Header can be ommitted if data is given in the order above and header argument is set to FALSE. Sample sheet separator can be set using the sep argument.

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