add batch script and BWA example folder to novice material

novice/exercises/batch_job.sh

+#!/bin/bash
+
+srun ./hpc_example -t 30 -m 200
+

novice/exercises/bwa/bwa_batch.sh

+#!/bin/bash
+#SBATCH -J bwa
+#SBATCH --time=00-00:06:00
+#SBATCH --mem=4000M
+#SBATCH --nodes=1
+#SBATCH --tmp=1G
+#SBATCH --gres=tmp:1G
+#SBATCH --output=bwa.out
+#SBATCH --open-mode=append
+
+## load required modules
+module load SAMtools BWA
+
+## copy data to /tmp and change directory to /tmp
+cp /g/its/home/pecar/benchmarks/msmith_bwa/Ecoli_genome.fa.gz $TMPDIR
+cp /g/its/home/pecar/benchmarks/msmith_bwa/reads_*.fq.gz $TMPDIR 
+cd $TMPDIR
+
+## create an index
+bwa index -p ecoli Ecoli_genome.fa.gz 
+
+## perform alignment
+bwa mem -t $SLURM_CPUS_PER_TASK ecoli reads_1.fq.gz reads_2.fq.gz > aligned.sam
+
+## create a compressed BAM file
+samtools view -b aligned.sam > aligned.bam
+
+## copy results back to where job was submitted from
+cp aligned.bam $SLURM_SUBMIT_DIR/