summary_metrics_bam_picard: Generate BAM General Summary Metrics

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 General Summary Metrics

Description

Generate BAM General Summary Metrics

Usage

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 = 3,
  ram = 4,
  mode = "local",
  executor_id = make_unique_id("summaryMetrics"),
  task_name = "summaryMetrics",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_picard	Path to picard executable. Default tools/picard/build/libs/picard.jar.
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.
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.
executor	OPTIONAL Task executor name. Default "recalCovariates"
task	OPTIONAL Task name. Default "recalCovariates"

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