parallel_samples_call_ascat: Analyze in parallel multiple pair of tumour-normal samples...

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

Analyze in parallel multiple pair of tumour-normal samples using ASCAT

Description

\\ TO DO FIX PARALLELIZATION IN LOCAL. Seems to be issues with running multiple files

Usage

parallel_samples_call_ascat(
  bin_allele_counter = build_default_tool_binary_list()$bin_allele_counter,
  tumour = NULL,
  normal = NULL,
  patient_id = NULL,
  ref_dataset = "battenberg",
  gender = "XY",
  genome_version = "HG19",
  panel_version = "V3",
  output_dir = ".",
  gamma = 1,
  penalty = 25,
  verbose = FALSE,
  ascat_ref = build_default_reference_list(),
  batch_config = build_default_preprocess_config(),
  threads = 8,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("parPrepareASCAT"),
  task_name = "parPrepareASCAT",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_allele_counter	REQUIRED Path to allele_counter binary.
tumour	REQUIRED Path to tumour BAM file.
normal	REQUIRED Path to normal BAM file.
patient_id	REQUIRED Path to normal BAM file.
ref_dataset	OPTIONAL Reference dataset for panel allele and loci selection. Default battenberg
gender	OPTIONAL Sample gender. Default XY.
genome_version	OPTIONAL Genome reference version. Default HG19.
panel_version	OPTIONAL PCF Select panel version. Default V3.
output_dir	OPTIONAL Path to the output directory.
gamma	OPTIONAL Gamma parameter. Default 1.
penalty	OPTIONAL Penalty parameter. Default 25.
verbose	OPTIONAL Enables progress messages. Default False.
ascat_ref	OPTIONAL List with default references.
batch_config	OPTIONAL List with default references.
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.

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