#!/bin/bash

cd “#{jobs_dir}/../” echo “#{script_name} is starting at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs” rm core.* 2> /dev/null

# Check BAM EOF BAM_28=$(tail -c 28 #{input}|xxd -p) if [ “#{magic28}” != “$BAM_28” ] then

echo "Error with BAM EOF"
exit 100

fi

#{base_recalibrator_params.join(“s”)} \

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

EXITSTATUS=$?

force error when missing recalFile. Would prevent continutation of pipeline if [ ! -s #{output} ] then

echo "Missing #{output}"
exit 100

fi

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

exit $EXITSTATUS