clonet_trento: Process a pair of tumour-normal 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 a pair of tumour-normal samples using CLONET

Description

This function takes a pair of tumour and normal BAMS and applies the CLONET pipeline

Usage

clonet_trento(
  sif_clonet = build_default_sif_list()$sif_clonet$V3,
  version = "V3",
  tumour = "",
  normal = "",
  patient_id = "",
  tc = NULL,
  ploidy = NULL,
  tmp_dir = ".",
  threads = 3,
  ram = 4,
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("clonet"),
  task_name = "clonet",
  mode = "local",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

version	PCF Select panel version to use
tumour	Path to tumour BAM file
normal	Path to normal BAM file
patient_id	Patient id.
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 "clonet"
task_name	Name of the task. Default "clonet"
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.
sif_path	Path to singularity image file

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