add bowtie2 wrapper

[JRWallace]

#SBATCH -t 16:00:00
#SBATCH -n 64
#SBATCH --mem=128G
#SBATCH -J hg19_map
#SBATCH --mem=64GB
#SBATCH --mail-type=ALL
#SBATCH --mail-user=joselynn_wallace@brown.edu
source /gpfs/runtime/cbc_conda/bin/activate_cbc_conda
for sample in `ls /gpfs/data/cbc/cut_run/cleaned/fastq/*1.fq.gz`
do
fastq_dir="/gpfs/data/cbc/cut_run/cleaned/fastq"
align_dir="/gpfs/data/cbc/cut_run/cleaned/alignments"
base=$(basename $sample "1.fq.gz")
bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700 -p 8 -x /gpfs/data/cbc/cut_run/cleaned/bowtie2_index/hg19 -1 ${fastq_dir}/${base}1.fq.gz -2 ${fastq_dir}/${base}2.fq.gz -S ${align_dir}/${base}bowtie2.sam
done```