star_align_fastq_core: Title

View source: R/functions_RNAseq_counts.R

star_align_fastq_coreR Documentation

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.