new_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

new_clonet_trento(
  sif_clonet = build_default_sif_list()$sif_clonet$V3,
  version = "V3",
  tumour = NULL,
  normal = NULL,
  patient_id = NULL,
  tc = NULL,
  ploidy = 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.
sif_path	Path to singularity image file
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Executor ID. Default "clonet"
task_name	Name of the task. Default "clonet"
threads	Number of CPU cores to use. Default 3.
ram	RAM memory for batched job. Default 4
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
output_dir	Path to the output directory.
tmp_dir	Path to temporary file directory.
verbose	Enables progress messages. Default False.
hold	Job to hold on in batched mode.

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