#!/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