tmp/bwaAlignment.R

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

library(devtools)
devtools::load_all('/imppc/labs/lplab/share/marc/repos/ergWgsTools')
ref <- '/imppc/labs/lplab/share/marc/refgen/hg38/hg38.fa'
threads <- parallel::detectCores()

args <- commandArgs(trailingOnly = TRUE)

fastq <- args[1]
out_path <- args[2]


bwaAlignment(fastq = fastq,
             ref = ref,
             out_path = out_path,
             threads = threads)