subFastQC: Submit a cluster job to fastQC a directory

Description Usage Arguments

View source: R/subFastQC.R

Description

Submit a cluster job to fastQC a directory

Usage

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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 Nov. 11, 2018, 5:15 a.m.