BUD Algorithm Contig Carry over

[glickmac]

I have not implemented a method to remove empty fa files (generated by the contig_extend script) from the next iteration of the Bud Algorithm. This should reduce the time for the subsequent iterations.

Brainstorming ideas to do this:

1. a bash script to retain .fa files > than 0 bytes then filter contigs in combined file by names of files left

2. A script that creates a list of empty file names and filters contig keys in a dictionary format.

[glickmac]

Currently the workflow just outputs the .fa files from contig_extend into a directory (extended_contigs) and uses the assembled contigs in the next loop iteration