I have a directory that is in the below order (the --- is not part of the directory tree, only there to help illustrate:

Code:

DATE      --- main level
Folder1   --- level under DATE
plugin_out  --- level under Folder1
variantCaller_out.40   --- level under plugin_out
001,002,003  --- level under variantCaller_out.40

The bash below reads each line in out.txt and uses that in a below. So for this example a would be /home/cmccabe/nfs/exportedReports/Folder1. What I am having trouble with is the vcf.gz being searched for is two more levels down (last level in the above). /home/cmccabe/nfs/exportedReports/plugin_out/variantCaller_out.40/001. The level right before that /home/cmccabe/nfs/exportedReports/plugin_out/variantCaller_out.40 is consistent unitil the ., then the numbers varies. So in this example variantCaller_out.40 the portion in bold will change. The last level has 3 folders 001, 002, 003 that the vcf.gz can be found in.

I guess what I am trying to do is search for each vcf.gzin

Code:

/home/cmccabe/nfs/exportedReports/Folder1/plugin_out/variantCaller*/{001,002,003}

Bash

Code:

a=/home/cmccabe/nfs/exportedReports;DEST="/home/cmccabe/Desktop/NGS/API/$DATE";
while read line; do find $a/$line -name "*vcf.gz" -exec cp {} $DEST \;
done < out.txt

contents of out.txt

Code:

Folder1

within Folder1

Code:

plugin_out

next level Folder1/plugin_out

Code:

variantCaller_out.40

next level Folder1/plugin_out/variantCaller_out.40

Code:

001
002
003

Currently I am getting syntax errors. Thank you .