circ_quant_rna: Quantify circRNA expression using ciriQuant

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

Quantify circRNA expression using ciriQuant

Description

Wrapper for CIRIquant tool.

Usage

circ_quant_rna(
  bin_ciri_quant = build_default_tool_binary_list()$bin_ciri_quant,
  file_R1 = "",
  file_R2 = "",
  ciri_input = "",
  output_dir = ".",
  config = "database/yaml/config/yaml",
  output_name = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("circRNAquant"),
  task_name = "circRNAquant",
  mode = "local",
  threads = 3,
  ram = 4,
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_ciri_quant	Path to enviroment containing CIRIquant.
file_R1	Path to the input file with the sequence.
file_R2	Path to the input with the reverse read sequence.
ciri_input	Optional Path to CIRI2 output file.
output_dir	Path to the output directory.
config	Path to yaml config file.
output_name	File output name
verbose	Enables progress messages. Default False.
executor_id	Executor ID. Default "fastQC"
task_name	Name of the task. Default "fastQC"
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
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
hold	Job to hold on in batched mode.

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