subFastQC: Submit a cluster job to fastQC a directory

In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions

Description

Submit a cluster job to fastQC a directory

Usage

subFastQC(fastqDir, fastqPattern = "*.gz", outDir = "pre",
  projName = "Sandbox", noSub = F,
  projDir = file.path("/scratch/pschofield/Projects", projName),
  fastQCDir = file.path("/scratch/pschofield/Projects", projName,
  "fastqc"), jobName = paste0("fastQC_", projName),
  fastqcMod = "apps/fastqc/0.11.3/linux-x86_64", nproc = 16,
  mem = "48gb", makeCVS = T)

Arguments

fastqDir	input directory
fastqPattern	pattern for fastq file names unix wildcards not re
outDir	subdirectory of project fastqc directory
projName	project name will build output path
noSub	debug flag
fastQCDir	output root directory
jobName	name for job script
fastqcMod	fastQC module to load
makeCVS	make cvs file with listing details

PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.