-w not working

[s-j-mc]

Hello,

Firstly, thank you for creating this tool!

I just wanted to point out that the -w options apprears to not work as intended. I expected the frags and msa folders to be inside the run1/Ashure/ folder I have created, but instead these are output to the directory where I run the python script from.

Command:
ashure.py run -fq run1/raw_data/virus.fastq.gz -db run1/viruses.fasta -w run1/Ashure/ -o1 run1/Ashure/ashure_consensus.csv -r fgs,msa,cons,clst

Thanks,
Sam