#!/bin/bash

cd “#{jobs_dir}/../” echo “#{script_name} is starting at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs” if [ ! -s “#{bqsr_file}” ]; then

echo "Error: missing recalfile #{bqsr_file}"
exit 100

fi

rm core.* 2> /dev/null

#{print_reads_params.join(“s”)} \

#{print_reads_params['params'].join(" \\\n  ")} \\
#{run_local}

EXITSTATUS=$?

# throw error if < 1024 bytes if [ $(stat –printf=“%s” “#{output}”) -le 1024 ] then

exit 100

fi echo “#{script_name} is finished at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs”

exit $EXITSTATUS