tmp/fastqcParser.R

In msubirana/DNAseqPipeline: What the Package Does (One Line, Title Case)

#load package
devtools::load_all('/gpfs42/robbyfs/scratch/lab_lpasquali/msubirana/marc/repos/DNAseqPipeline')

#parse arguments
args <- base::commandArgs(trailingOnly = TRUE)

#define variables
file <- args[1]
out_dir <- args[2]
threads <- parallel::detectCores()


#realign BAMs using DNAseqPipeline::realignBwa
fastqc(file=file,
       out_dir=out_dir,
       threads=threads)