Entering edit mode
23 months ago
Thermite21
•
0
Hi, I've written a bash script for running QUAST on 125 contig files. Code is below:
for prefix in $(ls /my/path/*output/Contigs.fa)
do
python ~/anaconda3/bin/metaquast.py -t 16 -r ~/path to reference/ -o ${prefix%.*)_quast ${prefix}
done
I'd like for the output to be named on the basis of the sample name since this way the output results in creation of the results in the same way I've provided the path. It'd be ideal for the process to stop at output portion ( meaning the name of each genome sample). Any help is appreciated.
