I have multiple .GFF files, each in a single directory per annotated whole genome, that I wish to copy into a single directory so that I can perform a core genome alignment.
However the following code does not seem to work:
for pathname in "~/ST_0075/annotations/*/*.gff"; do cp "$pathname" ~/ST_0075/alignment; done
The directory structure is the following:
Home -ST_0075 ---Annotations -----Sample_001 ----------001.gff
The goal is to copy from multiple Sample_XXX subdirectories within
Annotations the XXX.gff files into another directory named