set -xv  # add error checking
dir=/home/cmccabe/folder  # define directory as dir
# Find oldest directory
find "$dir" -maxdepth 1 -mindepth 1 -type d -printf '%T+\t%P\0' | sort -z |  #s earch dir for only folders by time and sort
while read -r -d $'\t' time && read -r -d '' filename  # read each folder into $filename and grab oldest
do  # start loop
 printf "The oldest folder is $filename, created on $time\n"  # print message with oldest folder
folder="$(echo $filename|cut -d'_' -f8-)" # split on _ and print  # create $folder variable with parse output
echo "The folder is" "$folder"  # confirm parse message --- user_S5-0271-96-v5.6 --- is an example
# Find matching pdf
pdf=$(awk -v FL="$filename" '  # store oldest folder and $FL
         FNR == 1 {filenum++}  # start loop
         filenum==1 && index($0, FL) { # look at only 1 folder and index
              match($0, "_0*([0-9]+)/") # match substring _user in each folder name
              FNUM=substr($0,RSTART+1,RLENGTH-2) # extract contents and store as $FNUM --- user_S5-0271-96-v5.6 --- is an example  
          }filenum==2 && $0 ~ FNUM".pdf$"') # print $FNUM for pdf
   break  # end loop
done  # end processing
echo "The matching pdf is" $pdf  # confirm pdf match
# copy pdf to folder
if [[ "$pdf" = "$folder" ]] # only execute file--->folder value match
      then  # perform action on match
   cp $dir/*$pdf.pdf $dir/*$folder  # copy pdf to matching folder
fi  # end 
done # processing complete

cmccabe@Satellite-M645:~$ set -xv
cmccabe@Satellite-M645:~$ dir=/home/cmccabe/folder
dir=/home/cmccabe/folder
+ dir=/home/cmccabe/folder
cmccabe@Satellite-M645:~$ # Find oldest directory
# Find oldest directory
cmccabe@Satellite-M645:~$ find "$dir" -maxdepth 1 -mindepth 1 -type d -printf '%T+\t%P\0' | sort -z |
find "$dir" -maxdepth 1 -mindepth 1 -type d -printf '%T+\t%P\0' | sort -z |
> while read -r -d $'\t' time && read -r -d '' filename
while read -r -d $'\t' time && read -r -d '' filename
> do
do
>  printf "The oldest folder is $filename, created on $time\n"
 printf "The oldest folder is $filename, created on $time\n"
> folder="$(echo $filename|cut -d'_' -f8-)" # split on _ and print
folder="$(echo $filename|cut -d'_' -f8-)" # split on _ and print
> echo "The folder is" "$folder"
echo "The folder is" "$folder"
> # Find matching pdf
# Find matching pdf
> pdf=$(awk -v FL="$filename" '
pdf=$(awk -v FL="$filename" '
>          FNR == 1 {filenum++}
         FNR == 1 {filenum++}
>          filenum==1 && index($0, FL) { 
         filenum==1 && index($0, FL) { 
>               match($0, "_0*([0-9]+)/")
              match($0, "_0*([0-9]+)/")
>               FNUM=substr($0,RSTART+1,RLENGTH-2)
              FNUM=substr($0,RSTART+1,RLENGTH-2)
>               gsub(/^0+/,"", FNUM)
              gsub(/^0+/,"", FNUM)
>           }filenum==2 && $0 ~ FNUM".pdf$"')
          }filenum==2 && $0 ~ FNUM".pdf$"')
>    break
   break
> done
done
+ sort -z
+ find /home/cmccabe/folder -maxdepth 1 -mindepth 1 -type d -printf '%T+\t%P\0'
+ read -r -d '	' time
+ read -r -d '' filename
+ printf 'The oldest folder is R_2019_01_30_14_24_53_user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions, created on 2019-03-01+11:32:47.3690364740\n'
The oldest folder is R_2019_01_30_14_24_53_user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions, created on 2019-03-01+11:32:47.3690364740
echo $filename|cut -d'_' -f8-
++ echo R_2019_01_30_14_24_53_user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
++ cut -d_ -f8-
+ folder=user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
+ echo 'The folder is' user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
The folder is user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions
awk -v FL="$filename" '
         FNR == 1 {filenum++}
         filenum==1 && index($0, FL) { 
              match($0, "_0*([0-9]+)/")
              FNUM=substr($0,RSTART+1,RLENGTH-2)
              gsub(/^0+/,"", FNUM)
          }filenum==2 && $0 ~ FNUM".pdf$"'
++ awk -v FL=R_2019_01_30_14_24_53_user_S5-0271-96-v5.6_Oncomine_Childhood_Cancer_Research_DNA_and_Fusions '
         FNR == 1 {filenum++}
         filenum==1 && index($0, FL) { 
              match($0, "_0*([0-9]+)/")
              FNUM=substr($0,RSTART+1,RLENGTH-2)
              gsub(/^0+/,"", FNUM)
          }filenum==2 && $0 ~ FNUM".pdf$"'
+ pdf=
+ break
cmccabe@Satellite-M645:~$ echo "The matching pdf is" $pdf
echo "The matching pdf is" $pdf
+ echo 'The matching pdf is'
The matching pdf is