#!/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”