Shell Programming and Scripting

additional() {
    printf "\n\n"
    printf "Are there additional files to be analyzed?  Y/N "; read match_choice

    case "$match_choice" in
        [yY]) menu; break;;
        [nN]) move; printf "Select folders are being copied to MedexPatients on medex as well as to the import folders "; break;;
    esac
}

move() {
# move specific folders to MedexPatients on medex CIFS share
mkdir -p /home/cmccabe/medex/MedexPatients/$filename
rsync -av --exclude='/home/cmccabe/Desktop/NGS/API/$filename/bedtools' --exclude='/home/cmccabe/Desktop/NGS/API/$filename/torrent' --exclude='/home/cmccabe/Desktop/NGS/API/$filename/igv' /home/cmccabe/Desktop/NGS/API/$filename/bam /home/cmccabe/Desktop/NGS/API/$filename/fastqc /home/cmccabe/Desktop/NGS/API/$filename/lowcoverage /home/cmccabe/Desktop/NGS/API/$filename/panel /home/cmccabe/Desktop/NGS/API/$filename/picard /home/cmccabe/Desktop/NGS/API/$filename/vcf /home/cmccabe/Desktop/NGS/API/$filename/*.txt /home/cmccabe/Desktop/NGS/API/$filename/*.pdf /home/cmccabe/Desktop/NGS/API/$filename/*.log /home/cmccabe/medex/MedexPatients/$filename

# move to GenePerecent on CIFS share medex
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/panel/20x/percent/*.txt /home/cmccabe/medex/GenePercent

# move to LowCoverage
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/lowcoverage/20x/*.txt /home/cmccabe/medex/LowCoverage

# move to MedexVariants
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/vcf/panel/annovar/*.txt /home/cmccabe/medex/MedexVariants

# move to Quality Metrics
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/pdf/*.txt /home/cmccabe/medex/QualityMetrics

echo "analysis complete with new folder created and files moved to medex, the folder will now be sent to archive : $(backup)"
}

backup() {
# move folder to backup
printf "\n The directory will be moved to backup "; mv -v /home/cmccabe/Desktop/NGS/API/$filename /media/cmccabe/"My Book Western Digital"/ClinicalRuns; run ;;
}