tmp/realignBwaParser.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
bam <- args[1]
ref <- args[2]
out_dir <- args[3]
threads <- parallel::detectCores()


#realign BAMs using DNAseqPipeline::realignBwa
realignBwa(bam=bam,
           ref=ref,
           out_dir=out_dir,
           threads=threads)