Workflow to extract all 16S and genome annotations from PATRIC

Workflow to map FASTQ against a DMND database with FAMLI

Delay polling frequency

New feature - Load data from SRA as well as S3

Make sure to pass a trailing slash for the folder name

Import re

Make job names safe for AWS Batch

Parameterize the folder that the map_viruses results are placed in

Fix invoking command syntax for FAMLI

Update docker image with FAMLI

Update image for integrating assemblies

Add resources and fix batch job name prefix

I think that this check was redundant

Pass in assembly memory / vcpu params

Task and method to run VirFinder on de novo assembled contigs