cleanup.sh

#!/bin/bash

# Script to clean up big repetitive files and zip fastqs. Run after you are 
# sure the pipeline ran successfully.  Run from top directory (HIC001 e.g.).
total=`ls -l aligned/merged_sort.txt | awk '{print $5}'`
total2=`ls -l aligned/merged_nodups.txt aligned/dups.txt aligned/opt_dups.txt | awk '{sum = sum + $5}END{print sum}'`
if [ $total -eq $total2 ]; then rm aligned/merged_sort.txt; rm -r splits; else echo "Problem: The sum of merged_nodups and the dups files is not the same size as merged_sort.txt"; fi
#bzip2 fastq/*.fastq