#!/bin/bash

cd “#{jobs_dir}/../” echo “#{script_name} is starting at $(date +%Y%m%d%H%M%S)” >> “#{jobs_dir}/finished_jobs” echo #{aln_params_for_r1.join(“s”)} #{aln_params_for_r1.join(“ \n ”)} \

#{run_local}

force error when missing/empty sai . Would prevent continutation of pipeline if [ ! -s “#{output}” ] then

echo "Missing SAI:#{output} file!"
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

OK=1

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

if [[ “#{input}” =~ gz$ ]] then

LINESFASTQ1=$(gunzip -c "#{input}" | wc -l)

else # non gz files

LINESFASTQ1=$(wc -l "#{input}" | cut -d" " -f1 )

fi

echo "Fastq1 number lines:= " $LINESFASTQ1
SEQLINES=$[ $LINESFASTQ1 / 4 ]
echo "Estimated Minimum Sequences:= " $SEQLINES
if (( "$PROCESSED" >= "$SEQLINES" ))
  then
    echo "Complete."
  else
    echo "Error, incorrect number of processed sequences"
    exit 100
fi

#################################################################### # PAIR 2 # run and check pair 2 # # ####################################################################

#{aln_params_for_r2.join(“ \n ”)} \

#{run_local}

force error when missing/empty sai . Would prevent continutation of pipeline if [ ! -s “#{output2}” ] then

echo "Missing SAI:#{output2} file!"
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

OK=1

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

if [[ “#{input2}” =~ gz$ ]] then

LINESFASTQ2=$(gunzip -c "#{input2}" | wc -l)

else # non gz files

LINESFASTQ2=$(wc -l "#{input2}" | cut -d" " -f1 )

fi

echo "Fastq2 number lines:= " $LINESFASTQ2
SEQLINES=$[ $LINESFASTQ2 / 4 ]
echo "Estimated Minimum Sequences:= " $SEQLINES
if (( "$PROCESSED" >= "$SEQLINES" ))
  then
    echo "Complete."
  else
    echo "Error, incorrect number of processed sequences"
    exit 100
fi

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