mapping_walt.slrm

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --time=40:00:00
#SBATCH --mem=64G
#SBATCH --job-name="walt"
#SBATCH -o walt_%A.out # Standard output
#SBATCH -e walt_%A.err # Standard error

#############################################
# input variables:
#   R1: Read-1 file
#   R2: Read-2 file
#   INDEX: genome index
#   MAPPED_DIR: mapped reads directory
#############################################

# Sets up the prefix naming for output files 
MAPPED=`basename $R1 |awk '{split($0, a, "_R1"); print a[1]}'`

# Runs the WALT mapping algorithm for bisulfite sequencing libraries
# Allows 6 mismatches
# Run accross 8 threads
# Output is sam file type
walt -m 6 -t 8 -i ${INDEX} -1 ${R1} -2 ${R2} -o ${MAPPED_DIR}/${MAPPED}.sam