#!/bin/bash
cd “#{jobs_dir}/../” echo “#{script_name} is starting at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs” echo #{mem_params.join(“s”)} #{mem_params.join(“ \n ”)} \
#{run_local}
force error when missing/empty sam . Would prevent continutation of pipeline if [ ! -s #{output} ] then
echo "Missing SAM:#{output} file!" exit 100
fi
# check STDOUT has correct termination string HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep “ Processed”)
if [ -n “$HASENDING” ] then
OK=1
else
#echo " empty variable" echo "Error: Improper stdout termination" echo $EXITSTATUS echo "bwa (mem) has likely crashed. Exiting" exit 100
fi echo “#{script_name} is finished at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs”