#!/bin/bash
cd “#{jobs_dir}/../” echo “#{script_name} is starting at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs” #{samp_options.join(“ \n ”)} \
#{run_local}
# check file size less than 1MB
if [ $(stat –printf=“%s” “#{output}”) -le 1024000 ] then
echo "Error with output." exit 100
fi
check STDOUT has correct termination string HASENDING=$(tail -5 #{jobs_dir}/#{script_name}.err | grep “ sequences have been processed.”)
if [ -n “$HASENDING” ] then
echo "OUTPUT ok."
else
#echo " empty variable" echo "Improper stdout termination" exit 100
fi
check for correct number of sequences processed, based on fastq records
PROCESSED=$(tail -5 #{jobs_dir}/#{script_name}.err | grep “ sequences have been processed.” | grep -o “[0-9]\+”)
echo “checking stdout file: ” #{jobs_dir}/#{script_name}.err echo “bwa processed” $PROCESSED echo “#{script_name} is finished at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs”