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Update setu.sh #1

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Update setu.sh #1

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15 changes: 12 additions & 3 deletions setu.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,9 @@ reads=${READS}
out=${OUTDIR}
force=${FORCE}

#Set time
start_time="$(date +%s)"

#Lower case and upper case in bash var1=TesT; var2=tEst; echo ${var1,,} ${var2,,}; echo ${var1^^} ${var2^^}
#shopt -s nocasematch

Expand All @@ -53,8 +56,8 @@ then
if [[ $force == 'on' ]] ; then rm -rf mkdir $out; mkdir $out; else mkdir $out ; fi
source ./scriptBase/pe.sh
#Move all to OUTFILE
mv ASM_CORONA_PE logfile ragout_spades finished_Assembly $out
mv *.{bam,sam,out,fastq,stats,fq,bai,pdf,txt,cov,h5} $out
mv spades trimlog ragout final_output assembly_stats $out
mv *.{bam,sam,fastq,stats,fq,pdf,txt,cov} $out

#PE end here
elif [[ ${mode,,} == long ]]
Expand Down Expand Up @@ -82,5 +85,11 @@ else
echo "Did you forgot to provide the mode info"
fi

stop_time="$(expr "$(date +%s)" - $start_time)"
echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
echo "Setu completed successfully!"
printf "Total runtime: %.0f hours " "$(printf "$(expr $stop_time / 3600)")"
printf "%.0f minutes " "$(printf "$(expr $stop_time / 60 % 60)")"
printf "%.0f seconds\n" "$(printf "$(expr $stop_time % 60)")"
echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"

echo "setu DONE ..."