star_align_fastq_core: Title

In jrboyd/ssvRecipes: Recipes using seqsetvis

Title

Description

Title

Usage

star_align_fastq_core(
  FASTQ_VAR,
  fastq_paths,
  index_path = HG38_STAR_INDEX,
  gtf_path = HG38_v28_GTF_URL,
  star_path = STAR_PATH,
  cache_path = "~/.cache",
  n_cores = 8,
  hold_jids = NA,
  out_path = file.path(getwd(), "alignment"),
  output_prefix = NULL,
  do_submit = TRUE
)

Arguments

FASTQ_VAR	readFilesIn arg to supply STAR
fastq_paths	paths to fastq files
index_path	path to star index
gtf_path	path (local or url) to gtf
star_path	path to star executable
cache_path	cache location
n_cores	number of threads to use
hold_jids	job ids to hold for, default NA is none.
out_path	directory to output to
output_prefix	custom output directory per fastq_paths. default is basename of fastq_paths
do_submit	if FALSE, qsub is skipped but submit scripts remain. Default is TRUE.

Value

list length 2 of output dirs and job ids

jrboyd/ssvRecipes documentation built on May 22, 2022, 7:07 a.m.