#!/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