#!/bin/bash
#run alignment script

#loop through samples
cat sampleInfo | while read read1 read2 sampleID parentsample nothing;
do
#change into sample directory
cd /scratch/cmp1g20/RMS_resistance_data/LUCILES_DATA/RAW_DATA/"$sampleID"
#copy alignment script
cp /scratch/cmp1g20/RMS_resistance_data/LUCILES_DATA/alignment_summary.sh .
#submit alignment script
sbatch ./alignment_summary.sh
cd ../../
done

