circ_rna: Generate a quality control (QC) report from a fastaqc file

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

Generate a quality control (QC) report from a fastaqc file

Description

This function takes a set of sequence files (fastq,SAM,BAM...) and returns a report in HTML format.

Usage

circ_rna(
  bin_ciri = build_default_tool_binary_list()$bin_ciri,
  file_R1 = "",
  file_R2 = "",
  output_dir = ".",
  ref_genome = "database/Homo_sapiens_GRCh38.fa",
  db_annot = "database/human_gencode_vch38.gtf",
  output_name = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  executor_id = make_unique_id("circRNA"),
  task_name = "circRNA",
  mode = "local",
  threads = 3,
  ram = 4,
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_ciri	Path to fastQC executable. Default path tools/CIRI/CIRI_Full_v2.1.1.jar.
file_R1	Path to the input file with the sequence.
file_R2	Optional Path to the input with the reverse read sequence.
output_dir	Path to the output directory.
ref_genome	Path to reference genome
db_annot	Path to annotation GTF 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.