rnaseq_summary_metrics_bam_picard: Generate BAM Summary for RNAseq data

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 BAM Summary for RNAseq data

Description

Generate BAM Summary for RNAseq data

Usage

rnaseq_summary_metrics_bam_picard(
  bin_picard = build_default_tool_binary_list()$bin_picard,
  bam = "",
  output_dir = ".",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  tmp_dir = ".",
  threads = 1,
  ram = 4,
  ri = "",
  ref_flat = "",
  mode = "local",
  executor_id = make_unique_id("RNAsummaryMetrics"),
  task_name = "RNAsummaryMetrics",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bam	Path to the input file with the sequence.
output_dir	Path to the output directory.
verbose	Enables progress messages. Default False.
tmp_dir	Path to TMP directory. Default .
ram	RAM memory to use in GB. Default 4.
ri	Ribosomal interval for RNAseq data. Interval format.
ref_flat	Path to flat refrence. Interval format.
executor_id	OPTIONAL Task executor name. Default "recalCovariates"
task_name	OPTIONAL 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.
bin_samtools	Path to picard executable. Default path tools/picard/build/libs/picard.jar.

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